title: R6EO771M2

city: Oslo

first: Jerome

last: Ruzzin

address: Sognsvannveien 9

department: Dept. of Molecular Medicine, Section of Biochemistry

country: Norway

institute: University of Oslo

description: Library name: 27-24726-R6EO771M2

data_processing:
RNA-seq reads were filtered to remove low-quality reads by fastp . Filtered reads were aligned to the mouse genome  with STAR (v2.7.10a)  using the Gencode annotation (gencode.vM21)
Transcript abundance was estimated using featureCounts in Subread v2.0.1. DESeq2 , as implemented in SARTools , was used to normalize the raw counts, apply exploratory analysis.
Assembly: GRCm38vM21
Supplementary files format and content: raw read count
Supplementary files format and content: txt

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, #11995-065, Gibco) supplemented with 10% Fetal Bovine Serum (#10091148, Invitrogen) and 1% penicillin-streptomycin (Pen/Strep; #15140-122, Gibco) at 37°C

extract_protocol:
total RNA was extracted using the RNeasy Mini Kit (74106, Qiagen) according to the manufacturer's instructions
mRNA was prepared for sequencing from total RNA samples using TruSeq Stranded mRNA library kit from Illumina

value: Breast cancer

value: WT

value: co-cultured with MLg


title: ChIP_Rx_U2OSMYCtetOn_RNAPIIS2_DMSO_R1

status: Public on Feb 06 2026

type: SRA

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

country: Germany

institute: University of Wuerzburg

description: Library name: ChIP_Rx_U2OSMYCtetOn_RNAPIIS2_DMSO_R1

library_source: genomic

data_processing:
ChIP-Rx samples were mapped separately to the human GRCh38 genome and to the murine GRCm39 genome using Bowtie2 with -N 1 parameters. Subsequently, aligned reads were spike-normalized by dividing the number of mapped reads aligned to GRCh38 by the number of reads mapped to GRCm39 for each sample and multiplying this ratio with the smallest number of reads aligned to GRCm39 for any sample.
GRCh38
bedgraph files for each condition and replicate.

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
To crosslink cells following treatment, 1% v/v formaldehyde was added to the cell culture medium and incubated 5 min rotating at RT. 125 mM glycine were added to stop the reaction and incubated for 5 min rotating at RT. Cells were then harvested in ice-cold PBS containing protease and phosphatase inhibitors (Sigma Aldrich). Cells were centrifuged (1,500 rpm, 20 min, 4°C) and the pellet was resuspended in ChIP lysis buffer I (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40). For spike-normalization, 10% murine NIH3T3 cells were added based on the cell number. After 20 min incubation on ice, nuclei were pelleted by centrifugation (1,500 rpm, 20 min, 4°C) and subsequently lysed by incubation in ChIP lysis buffer II (10 mM Tris pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) for 10 min on ice. The chromatin was fragmented using the Covaris Focused Ultrasonicator M220 (50 min; cycles/burst, 200; peak power, 75; duty factor, 10), and the required fragment size of 150-300 bp was validated by agarose gel electrophoresis. The fragmented chromatin was collected by centrifugation (14,000 rpm, 20 min, 4°C). For each IP, 100 µl of each Protein A and Protein G-coupled Dynabeads (Thermo Fisher Sientific) were pre-incubated overnight with 15 µg antibody in the presence of 5 mg/mL BSA at 4°C. Subsequently, beads were added to the chromatin and incubated overnight at 4°C on a rotating wheel. Immunoprecipitated protein-chromatin complexes were washed 3 times each with ice-cold ChIP wash buffer I (20 mM Tris pH 8.1, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), ChIP wash buffer II (20 mM Tris pH 8.1, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), ChIP wash buffer III (10 mM Tris pH 8.1, 250 mM LiCl, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate; including a 5 min incubation at 4°C), and once with ice-cold TE buffer. Protein-chromatin complexes were eluted twice by incubating in 150 µl elution buffer 100 mM NaHCO3, 1% SDS) for 15 min at RT. To remove potential RNA contaminations, IP and input samples were treated with RNase A for 1 h at 37°C. Samples were de-crosslinked by incubation at 65°C shaking overnight, and then treated with Proteinase K for 2 h at 45°C to degrade the protein. The amount of DNA was quantified using Quant-iT PicoGreen dsDNA assay (Thermo Fisher Scientific)
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s instructions.

treatment_protocol: Treatment as indicated

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

tag: treatment

value: doxycycline (1 µg/ml, 24 h); DMSO


title: GEM-X Flex Gene Expression, pool of 4 samples (Pool 1)

city: San Francisco

first: Ayushi

last: Agrawal

state: CA

address: 1650 Owens St

country: USA

institute: Gladstone Institutes

description:
Library name: GEM_Well_1
10X Genomics GEM-X Flex gene expression single-nucleus RNA-sequencing

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were performed using the 10x Genomics Cell Ranger v9.0.1 multi pipeline (https://www.10xgenomics.com/support/software/cell-ranger/latest). FASTQ files were aligned to the 10x Genomics pre-built GRCm39 reference (refdata-gex-GRCm39-2024-A) using the Chromium mouse transcriptome probe set v1.1.1. The create-bam option was set to false to skip BAM file generation. Sample demultiplexing was performed for each GEM well based on feature barcode oligos defined in the corresponding configuration files. The per-well config files (GEM_Well_1_config.csv, GEM_Well_2_config.csv, GEM_Well_3_config.csv, GEM_Well_4_config.csv) are provided in the processed data files. Filtered gene expression count matrices were generated and used for downstream analysis using the Seurat R package (https://satijalab.org/seurat/).
Assembly: Mouse GRCm39 (10x Genomics pre-built reference refdata-gex-GRCm39-2024-A was used and is available at https://www.10xgenomics.com/support/software/cell-ranger/downloads#reference-downloads)
Supplementary files format and content: Filtered feature-barcode count matrix in the Hierarchical Data Format (HDF5 or H5) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices)
Supplementary files format and content: Quality control summary metrics from Cell Ranger multi in comma-separated values (CSV) format
Supplementary files format and content: Configuration file in CSV format used for sample demultiplexing within a given GEM well

molecule: nuclear RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Mice were housed at room temperature and humidity (approximately 20 °C and 50% humidity) with a 12h:12h light: dark cycle. Mice were fed a chow diet (PicoLab 5058).  All experiments in animals were approved by the Institutional Animal Care and Use Committee at UCSF/Gladstone Institutes. Mice were genotyped by polymerase chain reaction (PCR) followed by MwoI restrcition digestion from a tail clipping.

extract_protocol:
Nuclei were isolated from frozen mouse hemi brains using Dounce homogenization (10 strokes of Pestle A, 20 strokes of Pestle B) in 1 mL of cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.5 mM spermidine, 0.15 mM spermine, 1% Triton) containing RNase inhibitor in a 2 mL Dounce, followed by preparation of an Iodixanol gradient (25%, 30%, 40% Iodixanol layers) and density gradient centrifugation in a swinging bucket centrifuge. Nuclei appeared as a band between the 30% and 40% Iodixanol layers after centrifugation. Nuclei were washed, counted, and centrifuged at 350 rcf. After removing the supernatant the nuclei pellet was resuspended in Fixation Buffer B containing 4% Formaldehyde from the 10x Genomics GEM-X Flex Sample Preparation Kit v2. Nuclei samples were fixed overnight at 4 degrees C before addition of Additive C reagent and being quenched with Quenching Buffer B provided with the Sample Preparation Kit.
GEM-X Flex Gene Expression libraries were prepared using the 10x Genomics User Guide CG000787 (GEM-X Flex Reagent Kit for Multiplexed Samples). 300,000 fixed nuclei per mouse sample was used for the GEM-X Flex probe hybridization step. Probe hybridization was conducted using the GEM-X Flex Mouse Transcriptome Probe Kit, 16 Samples. After overnight probe hybridization 4 separate pools containing 4 samples each were generated for a total of 16 samples. Each pool was run across 1 GEM (Gel Bead in Emulsion) reaction for a total of 4 GEM reactions. After GEM generation and barcoding, GEMs were recovered and the resulting material underwent Pre-Amplification and SPRI bead cleanup. For each pool of 4 samples, we generated 1 GEM-X Flex Gene Expression library for a total of 4 libraries. During the final library construction PCR step each library was uniquely indexed using the 10x Genomics Dual Index Plate TS Set A. After the final library construction PCR and SPRI bead size selection, the final GEM-X Flex Gene Expression libraries underwent BioAnalyzer QC (Agilent High Sensitivity DNA Kit). All libraries contain the standard Illumina paired-end constructs that start and end with P5 and P7 sequences. Read 1 encodes the 16 bp GEM barcode and the 12 bp UMI. Read 2 encodes the ligated probe insert, a constant sequence, and the 8 bp Probe Barcode sequence that identifies the mouse probe set used in the hybridization step.

treatment_protocol: At p0, mice were randomly assigned treatment of daily 3uL/g intraperitoneal with either phosphate buffered saline vehicle or 750 mg/kg Nicotinamide Riboside for 5 days until collection.  Before collection, mice were perfused with PBS, and the left hemi-brains (excluding the olfactory bulb) were collected from both Control and NAXD KO mice (n = 4 per genotype per treatment group).

value: Brain


title: R7EO771M1

description: Library name: 28-24727-R7EO771M1

library_source: transcriptomic

molecule: total RNA


city: New York

first: Zihan

last: Xu

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
Library name: PerturbFate pooled screen Tri-omics New RNA-67
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

library_source: other

data_processing:
For PerturbFate Dual-omics libraries, BCL files were demultiplexed into FASTQ files using P7 PCR barcodes. Each FASTQ file contained all RNA and ATAC reads from the same indexing PCR well. During barcode extraction, reads from the oligo-dT/randomN RNA and ATAC modalities were split into separate files based on modality-specific adapter sequence matching. Read1 matching the "TG" sequence at the 41–42 nt position was classified as transcriptome data. Oligo-dT-originated RNA reads required at least 10 consecutive T bases at positions 51–60 nt, while randomN-originated RNA reads did not exhibit this pattern. ATAC read pairs were identified by the Tn5 ME sequence at the 41–50 nt position of Read1.
For the PerturbFate Dual-omics RNA reads, cell barcodes and UMI sequences from Read1 were appended to the headers of each Read2 FASTQ file, and only Read2 was used for subsequent steps. Poly(A) sequences, adapter sequences, and low-quality bases were trimmed from Read2 of oligo-dT reads, while 14 additional bases (potential priming hexamer and UMI sequences) were removed from randomN reads using Trim_Galore (0.6.7). After this step, oligo-dT and randomN reads were combined for further processing. STAR (2.7.9a) was used to map reads to the hg38 reference genome (GRCh38.p13, GENCODE). Reads with a mapping score ≥30 were selected using SAMtools (1.13). Single-cell deduplication was performed based on UMI sequences and alignment locations, and retained reads were split into SAM files per cell. Finally, single-cell gene-to-cell raw count matrices were constructed by assigning reads to genes.
For the PerturbFate Dual-omics ATAC reads, cell barcodes from RNA Read1 were appended to the headers of both ATAC Read1 and Read2 FASTQ files. Adapter sequences were removed in paired-end mode using Trim_Galore (0.6.7). STAR (2.7.9a) was used to map read pairs to the hg38 reference genome (GRCh38.p13, GENCODE). Picard (2.27.4) was used to remove PCR duplicates, and TSV files containing genomic locations and full cell barcodes were generated for SnapATAC2 (2.6.1)
sgRNA reads were matched against constant sequences in Read1 and Read2, allowing a maximum of one mismatch. For each filtered read pair, the cell barcode, sgRNA sequence, and UMI were extracted from designed positions. Extracted sgRNA sequences with at most one mismatch from the sgRNA library were corrected. UMI sequences were used for deduplication by collapsing identical UMIs for each individual sgRNA under a unique cell barcode. Cells with sgRNA UMI counts exceeding 5 were retained, and the sgRNA × cell count matrix was constructed.
For PerturbFate Tri-omics, most computational steps were the same as described above, with minor modifications. In this protocol, nascent and pre-existing transcriptomes from the same cell were amplified separately using distinct P7 PCR barcodes and processed as separate cells (two groups of reads with distinct cell barcodes). These were matched after single-cell gene-to-cell raw count matrices were generated. Additionally, because ATAC DNA underwent secondary tagmentation, the pipeline was modified to process single-end Read1 of ATAC fragments for chromatin accessibility quantification. The sgRNA library from the same cell was amplified from both nascent and pre-existing transcriptome PCR wells but shared a unique cell barcode for matching, achieved by adding the same barcoded sgRNA inner P7-U6 primer to paired nascent and pre-existing transcriptome PCR wells.
Assembly: hg38
Supplementary files format and content: RDS file contains a sparse matrix that can be read into R
Supplementary files format and content: csv file include meta data of cells
Supplementary files format and content: h5ad file include an anndata object containing a peak x count matrix with cell meta data

molecule: other

source_name: A375 cell line

growth_protocol: A375-dCas9-BFP-KRAB cells were transduced with a sgRNA library at a low MOI and BFP+ GFP+ double positive cells were sorted out. Cells were cultured for additional 6 days with either DMSO or 1uM Vemurafenib treatment.

extract_protocol:
After trypsinization, cells in each 6cm dish were collected into a 15ml falcon tube and kept on ice. Cells were spun down at 300xg for 5 minutes (4 °C) and washed once in 3ml ice-cold PBS. Every 1M cells were fixed with 1ml ice-cold 1% FA in PBS for 10 minutes on ice. For every 1mL cell suspension, 20μL of 10% Triton X-100 (0.2% final) was added to the tube to permeabilize cells for 3 min on ice. Spin down tubes at 500g for 3 min at 4 ̊C and quickly aspirate the supernatant. Cells are resuspended in 500uL of PBSI, and mix with 500uL 100 mM Tris-HCl pH8 with 5 μL of 10% Triton-X100. Spin down tubes at 500g for 5 min at 4 ̊C.
Fixed cells underwent Tn5 tagmentation in bulk, reverse transcription in bulk, two rounds of indexing ligation, and finally indexing PCR. SgRNA libraries were further separated and enriched by another round of PCR. A step-by-step experimental protocol of PerturbFate library preparation is included in the supplementary material of the publication.

treatment_protocol: On day6, before the end of the screen, 2.5ml of the original media from each plate was mixed with 2.5uL of 200mM 5EU dissolved in DMSO and was put back for nascent RNA metabolic labeling. After 1 hour of treatment, cells were harvested for PerturbFate profiling.

value: A375 cell line

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-72
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-68
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-66
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: Mouse embryos, E2.5, KO, H3K9ac

city: Barcelona

first: Agustín

middle: Sánchez

last: Belmonte

state: Barcelona

address: Nazaret 115 -117

department: Systems Oncology Program

country: Spain

institute: Vall d ́Hebron Institute of Oncology (VHIO)

description: embryos were collected in the indicated stage and dissagregated for epigenetic analysis

data_processing:
Quality control was performed using fastqc.
Paired-end reads were aligned against mm10 genome using Bowtie2 (version 2.4.2) with the following parameters “-local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”. Then we excluded reads that fail in the alignment using samtools (version 1.11) and duplicated reads with GATK (version 4.1.9).
Bam files were converted to bigwig using bamCoverage from deeptools (version 3.5.1).
Assembly: GRCh38
Supplementary files format and content: bigwig

source_name: Mouse embryos

growth_protocol: Embryos were directly isolated from the female donors prior to epigenetic analysis

extract_protocol:
E2.5 blastocysts, zona pellucida was removed passing the embryos by mouth pipetting through three consecutive drops of Tyrode’s acidic solution pH 2.5 (Sigma T1788). After careful examination under the microscope for disintegration of the pellucida, tyrode’s solution was immediately neutralized with a double volume of PBS pH 7.4 (Gibco #10010023), and embryos were placed into 20 μL of dissociation buffer composed of TrypLE™ Express Enzyme (Gibco # 12604013) / Accutase (Gibco # A1110501) in a 1:1 ratio, in a low binding 200 μL microcentrifuge tube. To avoid attachment of the embryos to the pulled crystal capillaries, capillaries were coated with 1% BSA in PBS beforehand. Blastocysts were incubated for 20 minutes in dissociation buffer at 37ºC, pipetted up and down gently 60 times with 20 μL low binding pipette tips, incubated 10 additional minutes at 37ºC and pipetted up and down again gently 40 times to disaggregate the last ICM cell clumps. After dissociation, the resulting cell suspension was neutralized with 40uL of 1% cell culture grade BSA (Sigma # A8806). In the case of 8-cell and morula stage embryos, pellucida was removed as abovementioned and embryos were placed in 20 μL of Accutase (Gibco # A1110501) for 20 min at 37ºC. After incubation, embryos were pipetted up and down 50 times until complete disaggregation and neutralized by the addition of 40 μL of 1% cell culture grade BSA (Sigma # A8806) to avoid the formation of clumps after dissociation.  Then, cell suspensions were immediately placed on ice until processing for scRNA-seq
DNA samples were processed through subsequent enzymatic treatments for end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" (NEB #E7645). Adapter-ligated libraries were completed by a PCR of 21 cycles of amplification, with 63º T(ann/ext) for 10s, and extracted with a (single) double-sided SPRI size selection.
Ultra-low input CUT&RUN

treatment_protocol: In the KI condition, female donors were fed with doxycicline diet from the presence of plug to the isolation stage (E2.5)

value: Mouse embryos

value: Blastocyst cells

value: miR203 KO


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-69
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: glycine3

city: Chongqing

first: feng

last: wang

address: #10 Changjiang Branch Road

department: Department of Cardiology, Daping Hospital

country: China

institute: The Third Military Medical University

description:
Library name: sample 6
FPKM.G3

data_processing:
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: We aligned reads of all samples to the rat reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions
Supplementary files format and content: count and FPKM values for each sample

organism: Rattus norvegicus

source_name: heart

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: heart

value: primary rat cardiomyocytes


title: R7MLgE1

description: Library name: 24-24723-R7MLgE1

source_name: MLg

value: MLg

value: Lung fibroblasts

value: co-cultured with EO771


title: Mouse embryos, E2.5, WT, H3K9ac

value: miR203 WT


title: ChIP_Rx_U2OSMYCtetOn_RNAPII_DMSO_R1

description: Library name: ChIP_Rx_U2OSMYCtetOn_RNAPII_DMSO_R1

value: Bone

value: Osteosarcoma cell line


title: glycine2

description:
Library name: sample 5
FPKM.G2


title: glycine1

description:
Library name: sample 4
FPKM.G1


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-65
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: ChIP_Rx_U2OSMYCtetOn_RNAPIIS2_CBL_R1

description: Library name: ChIP_Rx_U2OSMYCtetOn_RNAPIIS2_CBL_R1

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h); CBL0137 (5 µM, 2 h)


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-64
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line


title: ChIP_Rx_U2OSMYCtetOn_RNAPII_PlaB_R1

description: Library name: ChIP_Rx_U2OSMYCtetOn_RNAPII_PlaB_R1

value: doxycycline (1 µg/ml, 24 h); PlaB (1 µM, 4 h)


title: R6MLgE2

description: Library name: 23-24722-R6MLgE2

value: WT


title: R6EO771M1

description: Library name: 25-24724-R6EO771M1

value: Breast cancer

value: co-cultured with MLg


title: PBS3

description:
Library name: sample 3
FPKM.C3


title: R5MLgE1

description: Library name: 21-24720-R5MLgE1


title: ChIP_Rx_U2OSMYCtetOn_RNAPII_CBL_R1

description: Library name: ChIP_Rx_U2OSMYCtetOn_RNAPII_CBL_R1


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-63
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: R6MLgE1

description: Library name: 22-24721-R6MLgE1


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-61
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: PBS1

description:
Library name: sample 1
FPKM.C1

value: heart

value: primary rat cardiomyocytes


title: IMR90_D28_5

city: Rochester

first: David

last: Monroe

address: 200 1st St SW

institute: Mayo Clinic

description: Library name: sample_16

data_processing:
The European Galaxy server (UseGalaxy.eu)
HISAT2 (v 2.0.5.2) of individual unpaired reads; aligned to mus musculus (mm10 FULL)
FeatureCounts (Galaxy Version 1.4.6.p5)
Assembly: Homo sapien h38
Supplementary files format and content: FeatureCounts outputs tabular file containing counted reads per gene per row

source_name: cultured cells

growth_protocol: IMR-90 human fibroblasts were obtained from the American Type Culture Collection (ATCC), cultured in Eagle’s Minimum Essential Medium supplemented with 10% (v/v) fetal bovine serum, and 1x antibiotic/antimycotic, and maintained in a 370C incubator with 5% CO2.

extract_protocol:
Purification of RNA was performed with RNeasy Mini Columns (QIAGEN, Valencia, CA) with RNase-free DNase solution (QIAGEN) applied to degrade contaminating genomic DNA. RNA quantity was assessed with Nanodrop spectrophotometry (ThermoFisher).
RNA libraries for RNA-seq were prepared using Illumina RNA Prep Kit following manufacturers protocols

treatment_protocol: For the senescence induction experiments, IMR-90 cells were grown to 80% confluence in 6-well dishes and treated with 20 µM etoposide (Sigma-Aldrich, St. Louis, MO) for 48 hours. As a control, untreated cells (Week 0) were collected (n=5) and the etoposide removed from the remaining cells and allowed to grow until harvested for the subsequent timepoints at Weeks 1 and 4 (n=6 each).

value: fibroblast

value: Etoposide


title: IMR90_D28_6

description: Library name: sample_17


title: R6EO771C1

description: Library name: 19-24718-R6EO771C1

value: co-cultured with C2C12


title: R3EO771C1

description: Library name: 20-24719-R3EO771C1


title: PBS2

description:
Library name: sample 2
FPKM.C2


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-62
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: R5EO771M1

description: Library name: 26-24725-R5EO771M1


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-58
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-60
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-59
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: CONTROL_4

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

description: Library name: CTRL_4

data_processing:
Sequence reads were validated for quality with FastQC (v0.11.9), and adapter contamination removed with fastp with options -q 30 -l 50 (v0.21.0; Chen et al., 2018).
Reads were aligned to the reference transcriptome (TAIR10.51) with the STAR aligner (v2.7.9; (Dobin et al., 2013).
Aligned reads were quantified with RSEM (v1.3.1; Li & Dewey, 2011)
Assembly: TAIR10.51
Supplementary files format and content: Quantified reads per gene, .tsv format

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Protoplast culture

growth_protocol: Plants were grown at 22 °C on 1 % agar plates containing 0.5 x Murashige and Skoog (MS) medium (Duchefa Biochem.) in long day conditions (16 hours light, 8 hours dark) following stratification for three days at 4 °C.

extract_protocol:
Roots of six day old seedlings or A. thaliana Col-0 were cut 0.5 - 0.7 cm from their tip and a total of 180 mg of root tissue was collected.
Single cell ATAC-seq libraries were produced from freshly isolated nuclei in accordance with the 10X Genomics Chromium Single Cell ATAC-seq kit protocol (v 1.1 protocol, Rev D), targeting ~14-15,000 nuclei per reaction. The adapter-ligated libraries were amplified using nine PCR cycles.

value: Protoplast culture


title: IMR90_D28_3

description: Library name: sample_14


title: R5EO771C2

description: Library name: 18-24717-R5EO771C2


title: CONTROL_2

description: Library name: CTRL_2


title: CONTROL_3

description: Library name: CTRL_3


title: IMR90_D28_2

description: Library name: sample_13


title: ChIP_Rx_U2OSMYCtetOn_input_pool_R1

description: Library name: ChIP_Rx_U2OSMYCtetOn_input_pool_R1

value: Bone

value: Osteosarcoma cell line

value: merged of conditions


title: R5C2C12E2

description: Library name: 15-24714-R5C2C12E2

value: Myotubes

value: co-cultured with EO771


title: IMR90_D28_4

description: Library name: sample_15


title: CONTROL_1

description: Library name: CTRL_1


title: IMR90_D7_6

description: Library name: sample_11


title: GATA4_ox_4

description: Library name: GATA4_4


title: R6C2C12E1

description: Library name: 16-24715-R6C2C12E1

value: WT


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-56
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-54
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-57
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: IMR90_D28_1

description: Library name: sample_12


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-55
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: IMR90_D7_5

description: Library name: sample_10


title: R5EO771C1

description: Library name: 17-24716-R5EO771C1

value: Breast cancer


title: GATA4_ox_3

description: Library name: GATA4_3


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-52
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: Melanoma


title: R5C2C12E1

description: Library name: 14-24713-R5C2C12E1


title: IMR90_D7_3

description: Library name: sample_8


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-50
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: BRAF V600E


title: R3C2C12E1

description: Library name: 13-24712-R3C2C12E1


title: IMR90_D7_4

description: Library name: sample_9


title: GATA4_ox_2

description: Library name: GATA4_2


title: IMR90_D7_1

description: Library name: sample_6


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-53
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: DMSO or Vemurafenib


title: R6EO771P2

description: Library name: 12-24711-R6EO771P2

value: not co-cultured


title: IMR90_D0_6

description: Library name: sample_5

value: untreated


title: GATA4_ox_1

description: Library name: GATA4_1


title: GATA2_ox_2

description: Library name: GATA2_2


title: grf6 grf8, dehydrated (4h), rep 3

city: Changchun

first: Liangliang

last: Li

address: 4888 Shengbei Street, Kuancheng District

department: Northeast Institute of Geography and Agroecology

institute: Chinese Academy of Sciences

description: Library name: grf6 grf8-4 h-3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments. Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables (gene expression) into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Assembly: tair_TAIR10
Supplementary files format and content: The txt files include the AGI code, count and FPKM for each sample.

source_name: Rosette leaves

growth_protocol: 12-day-old wild-type (WT) and grf6 grf8 mutant plants were transferred from 1/2 Murashige and Skoog (MS) plates to soil and grown for 12 additional day.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired. A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X).And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000.

treatment_protocol: The rosette leaves of 24-day-old wild-type (WT) and grf6 grf8 mutant plants were harvested after dehydration for 0, 2, and 4 h, and then frozen in liquid nitrogen immediately.

value: Rosette leaves

value: grf6 grf8 mutant

value: dehydration (4 h)


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-48
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: grf6 grf8, dehydrated (4h), rep 4

description: Library name: grf6 grf8-4 h-4


title: R6MLgP1

description: Library name: 7-24706-R6MLgP1

value: MLg

value: Lung fibroblasts


title: R5EO771P1

description: Library name: 11-24710-R5EO771P1


title: R6MLgP2

description: Library name: 8-24707-R6MLgP2


title: GATA2_ox_4

description: Library name: GATA2_4

value: Protoplast culture


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-49
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: IMR90_D7_2

description: Library name: sample_7

value: fibroblast

value: Etoposide


title: R3EO771P2

description: Library name: 10-24709-R3EO771P2


title: IMR90_D0_4

description: Library name: sample_3


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-46
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-51
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: IMR90_D0_3

description: Library name: sample_2


title: GATA2_ox_1

description: Library name: GATA2_1


title: R3EO771P1

description: Library name: 9-24708-R3EO771P1


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-47
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: IMR90_D0_5

description: Library name: sample_4


title: R3MLgP2

description: Library name: 5-24704-R3MLgP2


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-45
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: R5MLgP2

description: Library name: 6-24705-R5MLgP2


title: R5C2C12P1

description: Library name: 4-24703-R5C2C12P1

value: Myotubes


title: IMR90_D0_1

description: Library name: sample_1


title: grf6 grf8, dehydrated (4h), rep 2

description: Library name: grf6 grf8-4 h-2


title: R3C2C12P2

description: Library name: 3-24702-R3C2C12P2

value: WT


title: grf6 grf8, dehydrated (2h), rep 4

description: Library name: grf6 grf8-2 h-4

value: dehydration (2 h)


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_PlaB_MYC_IP_R1

data_processing:
For seCLIP experiments, the analysis was performed according to the Skipper workflow (Boyle et al 2023). Fastq files of CLIP and input samples were normalized to sequencing depth using seqtk. Per condition, the same input subsampled using different random seeds was provided. For samples spiked with cDNA, reads mapping to the DNA spike-in were identified using STAR (Dobin et al. 2013). Accordingly, fastq files were normalized according to the number of reads mapping to the spike-in in each sample. Multiplexed eCLIPs were demultiplexed using UMItools (Smith et al. 2017) and used without further normalization. Subsequently, samples were trimmed utilizing skewer (Jiang et al. 2014) and extracts unimolecular identifiers (UMIs) using fastp (Chen et al 2018) and aligned to the human genome version GRCh38 for all MYC seCLIP and eCLIP experiments or to the murine genome version GRCm38 for TLR3 seCLIPs using STAR (Dobin et al. 2013). PCR duplicates were removed by using UMItools (Smith et al. 2017). To identify genomic regions with enriched signal in the CLIP over the SMI input, the automated Skipper analysis pipeline was used 46. The GENCODE version 38 gene annotations were obtained from gencodegenes.org. Transcripts were filtered based on total RNA-seq data in K562 cells with a minimum expression level of one transcript per million. A custom parse_gff.R script (Boyle et al 2023) was used to define RNA feature and transcript types (CDS_START ‘Start codon’, CDS_STOP ‘Stop codon’, CDS ‘CDS’ (of protein coding genes), UTR5 ‘5’ UTR’, UTR3 ‘3’ UTR’, EXON_SMALL ‘ncRNA’ (including snoRNA, snRNA, scaRNA, scRNA, miRNA, vault_RNA, rRNA, rRNA_pseudogene, Mt_rRNA, Mt_tRNA, ribozyme, sRNA, misc_RNA), INTRON ‘Intron’, EXON_LNCRNA ‘lncRNA’ (including lncRNA, processed_transcript), EXON_MRNA ‘Other’ (including Immunoglobulin (Ig) variable chain and T-cell receptor (TcR) genes, retaind_intron, non_stop_decay, protein_cidubg_LoF, nonsense_mediated_decay, TEC), PSEUDO ‘Pseudogene’ (including inactivated immunoglobulin genes, pseudogene, polymorphic_pseudogene, translated_pseudogene, translated_unprocessed_pseudogene, pseudogene, transcribed_unprocessed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, unitary_pseudogene, processed_pseudogene, unprocessed_pseudogene), PRIMIRNA ‘pri-miRNA’, SS3_ADJ ‘3’ splice site adj. (100 bp intronic region downstream of the 3’ splice site), SS3_ADJ ‘5’ splice site adj. (100 bp intronic region upstream of the 5’ splice site), SSB_ADJ ‘Branch point prox. (500 bp intronic region centered around the branch point), SS3_PROX ‘3’ splice site prox. (500 bp intronic region downstream of the 3’ splice site), SS5_PROX ‘5’ splice site prox. (500 bp intronic region upstream of the 5’ splice site), SSB_PROX ‘Branch point prox. (500 bp intronic region centered around the branch point)). Each feature was tiled into evenly spaced windows of maximum 100 nucleotides in length and then tested for enrichment in immunoprecipitated over SMI samples using a beta-binomial distribution that accounts for overdispersion in read counts and GC bias. For the analysis of TLR3 seCLIPs by Skipper, statistical thresholds calculated from the fit of the beta-binomial distribution were derived from the automated Skipper pipeline (only windows passing a 20% false discovery rate in both replicates of each experiment were considered enriched), while for MYC seCLIP experiments the statistical thresholds were customized. Within individual replicates, windows that passed a p value threshold p<0.05 were considered enriched windows. Of these, windows that were identified in both replicates and passed a 20% FDR in at least one of the replicates were designated as reproducibly enriched windows. Windows that were called in more than 17% of all K562 and HepG2 ENCODE eCLIP samples were blacklisted and removed. For calling TLR3 reproducible enriched windows in the TLR3-IPs, reproducible enriched windows identified in IgG and NXL controls were blacklisted additionally. Reproducible windows were fine mapped by centering them around the local maximum of binding enrichment per window and adjusted to a fixed size of 75 nt. For RNA motif identification the HOMER script findMotifsGenome.pl (http://homer.ucsd.edu/homer/) was run with the following options: -preparsedDir <directory> -size given -rna -nofacts -S 20 -len 5,6,7,8,9 -nlen 1 -bg <background windows>. A random RNA background was specified by selecting random 75 nt windows belonging to the same RNA feature group. To visualize similarities in binding characteristics to different RNA transcript types in a t-SNE plot, performed MYC seCLIP data was pooled with ENCODE reference RBP eCLIP data, and plotted together in a two-dimensional space using the Rtsne package (https://lvdmaaten.github.io/tsne/). Several random seeds were tested to confirm a reproducible association of the queried protein with a certain feature type. Enrichment odds ratios (ORs), represented by the enrichment of observed CLIP enrichment over a baseline CLIP enrichment per RNA feature type, were calculated based on the call_enriched_windows.R script (Boyle et al 2023). For metagenes and heatmaps, log2FCs of CLIP/input were determined based on deduplicated bam files using bamCompare and plotted using deeptools (Ramirez et al. 2014) using the –sortUsingSamples and --averageTypeSummaryPlot mean options. Intersections between different sets of reproducible enriched windows were generated and visualized using intervene (Khan et al. 2014). Publicly available ENCODE eCLIP and control datasets were downloaded and log2 ratios of CLIP over SMIs were calculated using bamCompare and plotted over called windows of interest using deeptools (Ramirez et al. 2014).
Assembly: GRCh38 (MYC seCLIPs/eCLIPs) or GRCm38 (TLR3 seCLIPs)
Supplementary files format and content: bedgraph files

extract_protocol:
seCLIP (single-end enhanced cross-linking and immunoprecipitation) sequencing was performed as described in Van Nostrand et al. and Blue et al. All seCLIP experiments were conducted in duplicates with one pooled size-matched inputs per condition. Per IP sample, 30-40 million cells were crosslinked with UV-C light (254 nm, 2 min, 400 mJ/ cm2). Not UV-crosslinked cells were used as negative control. Cells were lysed in seCLIP lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% (vol/vol) Igepal CA-630, 0.1% (vol/vol) SDS and 0.5% (wt/vol) sodium deoxycholate) supplemented with a protease inhibitor cocktail (Sigma-Aldrich) and 440 U/ml murine RNase inhibitor (NEB), and 10% of crosslinked murine NIH 3T3 cells were added to each sample as spike-in. Samples were sonicated using the M220 Focused-ultrasonicator (Covaris) for 3 min. Next, samples were treated with 40 U RNase I (Thermo Fisher Scientific) and 10 U Turbo DNase for 5 min at 37  °C shaking at 1200 rpm. After centrifugation at 15,000 g for 10 min at 4 °C, supernatants were added to pre-coupled protein A/G Dynabeads (62.5 µl each per IP) to the antibody of interest (10 µg per sample) and incubated rotating at 4 °C overnight. 2% v/v of the lysate (20 µl) including beads were taken as SMInput, both for the RNA gel and for the diagnostic western blot. The remaining lysate was magnetically separated and washed 2 times with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1% (vol/vol) Igepal CA-630, 1 mM EDTA, 0.1% (vol/vol) SDS and 0.5% (wt/vol) sodium deoxycholate), followed by a transition wash which was conducted by adding 500 µl of high-salt wash buffer, mixing and then adding 500 µl of wash buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, 0.2% (vol/vol) Tween-20 and 5 mM NaCl). Three more washes with wash buffer were conducted, before the immunoprecipitated RNA was dephosphorylated on-beads using the FastAP and PNK enzymes. Therefore, 1X FastAP buffer (Thermo Fisher Scientific), 80 U murine RNase inhibitor (NEB), 4 U Turbo DNase (NEB) and 3 U FastAP enzyme (Thermo Fisher Scientific) were added in a total volume of 50 µl and incubated for 20 min at 37 °C shaking at 1,200 rpm. Without removing the phosphorylation mix, 150 µl PNK master mix (1x PNK7 buffer (700 mM Tris-HCl pH 7, 100 mM MgCl2), 40 U PNK4 enzyme) were added and incubated for another 20 min at 37 °C (shaking at 1,200 rpm). Samples were then washed with 200 µl seCLIP high-salt wash buffer once, followed by a transition wash and three further washings with seCLIP wash buffer. 10% of the IP samples were saved for biotin-labeling to visualize the RNA cross-linked to the protein of interest. To the remaining RNA, InvRiL19 RNA adapters (IDT) were ligated by incubating the samples with 25 µl 3’RNA linker mix (1.2x RNA ligase buffer (no DTT), 1.2 µM ATP, 3.6% DMSO, 0.024% v/v Tween-20, 18% w/v PEG 8000, 0.8 U murine RNase inhibitor (NEB), 72 U T4 RNA ligase high-concentration enzyme) rotating at RT for 75 min. Beads were then washed as follows: 1x wash buffer, transition wash to high-salt wash buffer, 1x high-salt wash buffer, transition wash to wash buffer, 3x wash buffer. After the final wash, 20% per IP sample was kept for the diagnostic western blot. To all IP and SMInput samples, NuPAGE LDS buffer (Thermo Fisher Scientific) containing DTT (98 mM, freshly prepared) was added before samples were incubated at 70 °C for 10 min. After magnetically separating the beads from the lysates, RNA-protein complexes were separated by gel electrophoresis using 8% Bis-Tris gels, and transferred onto nitrocellulose or methanol-activated PVDF membranes for the RNA gels and western blots, respectively. The diagnostic western blot was used as a guide to cut out the region of the membrane starting from the observed size of the protein of interest and extending until the maximal expected size of the RNA-protein complexes (but at least ~75 kDa larger). Membrane pieces were then sliced into ~2 mm x 2 mm squares and transferred into a fresh tube. To digest the protein, membranes were incubated with 24 U proteinase K (Roth) in PKS buffer for 20 min at 37 °C followed by an incubation at 50 °C for another 20 min. RNA was extracted using the RNA Clean and Concentrator-5 kit (Zymo) following the manufacturer’s instructions, and RNA was eluted in 10 µl H2O. Next, SMInput samples were dephosphorylated by incubating each SMInput RNA sample with 20 µl of dephosphorylation master mix (1x FastAP buffer (Thermo Fisher Scientific), 40 U murine RNase inhibitor (NEB), 2 U FastAP enzyme (Thermo Fisher Scientific) incubating at 37 °C for 20 min shaking at 1,200 rpm, followed by another 20 min incubation at 37 °C (1,200 rpm) in PNK master mix (1.05x PNK7 buffer, 5.26 mM DTT, 2 U Turbo DNase (NEB), 40 U T4 PNK enzyme). RNA was purified using the Clean & Concentrator 5 kit (Zymo) as described before. To append the SMInput RNA with 3’ RNA adapters, 1.5 µl 100% DMSO and 0.5 µl InvRil19 adapter were added per sample and incubated at 65 °C for 2 min. 13.5 µl of SMInput RNA ligation master mix (0.976x RNA ligase buffer (NEB), 0.976 mM ATP, 2.93% DMSO, 0.02% v/v Tween-20, 14.63 w/v PEG 8000, 12 U murine RNase inhibitor, 36 U T4 RNA ligase high-concentration enzyme) were added and samples were incubated at RT for 60 min on a rotating wheel. To purify the RNA, 15 µl MyOne Silane Dynabeads per sample were washed ones with RLT buffer (Qiagen), resuspended in RLTW buffer (RLT + 0.025% v/v Tween-20) and added to the RNA. An equal volume of 100% EtOH was added and samples were incubated at RT for 10 min, before samples were washed three times with 80% v/v EtOH. After the final wash, beads were tried and subsequently eluted in 9.5 µl of TT elution buffer (10 mM Tris-HCl pH 7.4, 0.1 mM EDTA, 0.01% (vol/vol) Tween-20). All IP and SMInput samples were next reverse transcribed using the SuperScript III enzyme. For that, 1 µl of 5 µM InvAR17 RT primer  and 1 µl of 10 mM dNTPs were added per RNA sample and incubated for 2 min at 65 °C. 10 µl of reverse transcription master mix (1x first strand buffer (Invitrogen), 5 mM DTT, 8 U murine RNase inhibitor (NEB), 120 U Superscript III enzyme (Invitrogen)) were added to each sample and incubated at 55 °C for 20 min. 2.5 µl ExoSAP-IT (Thermo Fisher Scientific) were used to remove unincorporated dNTPs and RT primers (37 °C, 15 min) before 1 µl of 0.5 M EDTA was added. To remove RNA stands, 3 µl of 1 M sodium hydroxide were added and incubated at 70 °C for 10 min. 3 µl of 1 M hydrochloric acid were added to neutralize the sodium hydroxide. RNAs were again purified using MyOne Silane beads as described earlier. After drying, 2.5 µl of 5’ adapter master mix (4.66 µM InvRand3Tr3 adapter and 7.77% DMSO in TT elution buffer) were directly added to the beads and incubated at 70 °C for 2 min before 7.8 µl of ligation master mix (0.097% RNA ligase buffer (NEB), 1.94 mM DTT, 0.97 mM ATP, 0.019% v/v Tween-20, 17.48% PEG 8000, 30 U T4 RNA ligase high-concentration enzyme (NEB), 5’ deadenylase enzyme (NEB)) and incubated at RT overnight. RNA was subsequently purified using MyONE silane beads as described earlier. To estimate the number of cycles required for the final PCR, qPCRs were conducted. For multiplexing of eCLIPs, each RNA adapters containing unique barcodes (RNA_A01, RNA_B06, RNA_C01, RNA_D08, RNA_X1A, RNA_X1B) based on 44 were ligated to the RNA after immunoprecipitation. At least one third of each sample was mixed and further processed as a pool. SMI were separately run through the gel and barcoded RNA adapters were ligated after RNA isolation from the nitrocellulose membranes. As for the IP samples, inputs were merged to a pool and processed together. For total input samples, 20 µl of lysate were taken before the immunoprecipitation. Using the eCLIP adapter strategy 44, the in-line barcode on read 1 was later used to demultiplex the samples bioinformatically. Samples labeled with * contain 10% murine spike-in (NIH 3T3) that has not been used for further analysis.
cDNA libraries were amplified using a three-step, six cycle amplification followed by a two-step amplification bringing each sample to its calculated number of cycles. The final libraries were either purified using an agarose gel-based strategy cutting out gel pieces corresponding to 175-300 bp in size and purifying the DNA using the Qiagen MiniElute gel extraction kit following the manufacturer’s instructions. Alternatively, samples were cleaned using a two-sided selection with SPRI beads (0.7x right-sided, followed by a 1x left-sided selection). The quality and quantity of the libraries were assessed using the Fragment Analyzer (Agilent). To account for different cycle number used during final PCR amplification (e.g. for IgG controls), a DNA spike-in containing adaptors for the Illumina index primers used in the final PCR was generated and equal amounts were added to the immunoprecipitation samples prior to the final PCR for indicated experiments, resulting in different relative ratios of CLIP:DNA spike-in in the final libraries as observed upon measurement using the fragment analyzer.

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h), PlaB (1 µM, 4 h)


title: grf6 grf8, dehydrated (2h), rep 3

description: Library name: grf6 grf8-2 h-3


title: grf6 grf8, dehydrated (2h), rep 2

description: Library name: grf6 grf8-2 h-2


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-43
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

value: BRAF V600E

value: DMSO or Vemurafenib


title: grf6 grf8, dehydrated (4h), rep 1

description: Library name: grf6 grf8-4 h-1

value: Rosette leaves

value: grf6 grf8 mutant

value: dehydration (4 h)


title: R3C2C12P1

description: Library name: 2-24701-R3C2C12P1

value: not co-cultured


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-44
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: grf6 grf8, dehydrated (2h), rep 1

description: Library name: grf6 grf8-2 h-1


title: R2C2C12P1

description: Library name: 1-24700-R2C2C12P1


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-42
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_PlaB_MYC_IP_R2


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_DMSO_MYC_IP_R2

value: doxycycline (1 µg/ml, 24 h)


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-41
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-40
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: PS19 CK2α'(+/-) rep 4

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
Library name: PSHET724_3
column name in subread_counts.txt: PSHET724_3

data_processing:
Raw, paried reads were processed via CHURP pipelien (https://github.com/msi-ris/CHURP) using default setting.
The cleaned gene count table per sample was analyzed with R (v4.4.2) package DESeq2 (v1.46.0) to identify differentially expressed genes.
R package gprofiler2 (v0.2.3) and clusterProfiler (v4.14.6) was used for pathway enrichment. Various R packages, including pheatmap and ggplot2, were used to generate visualization plots.
Assembly: GRCm39 plus human gene MAPT
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: subread_counts.txt

source_name: Hippocampus

extract_protocol:
Hippocampus samples were dissected, flash frozen liquid nitrogen, and RNA was harvested and extracted using Qiagen RNeasy Mini kit. QC was conducted by Novogene using agilent 5400.
Novogene conducted library construction. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Hippocampus

tag: age

tag: Sex

value: F

tag: strain

value: C57Bl/6 x B6C3H


title: PS19 CK2α'(+/-) rep 3

description:
Library name: PSHET719_4
column name in subread_counts.txt: PSHET719_4

value: M


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_PlaB_Input

value: Bone


title: grf6 grf8, dehydrated (0h), rep 4

description: Library name: grf6 grf8-0 h-4

value: dehydration (0 h)


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_DMSO_Input

value: Osteosarcoma cell line

value: MYC-Tet-On


title: grf6 grf8, dehydrated (0h), rep 3

description: Library name: grf6 grf8-0 h-3


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_DMSO_MYC_IP_R1


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-38
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-37
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: Melanoma


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-39
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: BRAF V600E


title: grf6 grf8, dehydrated (0h), rep 1

description: Library name: grf6 grf8-0 h-1


title: grf6 grf8, dehydrated (0h), rep 2

description: Library name: grf6 grf8-0 h-2


title: PS19 CK2α'(+/-) rep 1

description:
Library name: PSHET720_3
column name in subread_counts.txt: PSHET720_3


title: PS19 CK2α'(+/-) rep 2

description:
Library name: PSHET595_6
column name in subread_counts.txt: PSHET595_6


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_pool_IgG_IP_R1

value: merge


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-36
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: DMSO or Vemurafenib


title: WT, dehydrated (4h), rep 4

description: Library name: WT-4 h-4

value: Rosette leaves

value: WT


title: CK2α'(+/-) rep 5

description:
Library name: HET736_3
column name in subread_counts.txt: HET736_3


title: CK2α'(+/-) rep 4

description:
Library name: HET735_4
column name in subread_counts.txt: HET735_4


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_pool_IgG_Input


title: eCLIP_U2OSMYCtetOn_splicing_inhibition_pool_IgG_IP_R2


title: eCLIP_U2OSMYCtetOn_siEXOSC5_MYC_IP_R2

value: doxycycline (1 µg/ml, 24 h), 48 h siEXOSC5


title: CK2α'(+/-) rep 3

description:
Library name: HET568_6
column name in subread_counts.txt: HET568_6


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-35
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: WT, dehydrated (4h), rep 2

description: Library name: WT-4 h-2

value: dehydration (4 h)


title: CK2α'(+/-) rep 2

description:
Library name: HET566_5
column name in subread_counts.txt: HET566_5

value: Hippocampus


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-34
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: eCLIP_U2OSMYCtetOn_siEXOSC5_MYC_IP_R1


title: CK2α'(+/-) rep 1

description:
Library name: HET361_3
column name in subread_counts.txt: HET361_3


title: WT, dehydrated (4h), rep 3

description: Library name: WT-4 h-3


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-33
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: WT, dehydrated (2h), rep 4

description: Library name: WT-2 h-4

value: dehydration (2 h)


title: High PS19 rep 3

description:
Library name: PS726_1
column name in subread_counts.txt: PS726_1

value: High PS19

value: C57Bl/6 x B6C3H


title: WT, dehydrated (4h), rep 1

description: Library name: WT-4 h-1


title: eCLIP_U2OSMYCtetOn_siEXOSC5_Input

value: Bone


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-31
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: eCLIP_U2OSMYCtetOn_siMYC_MYC_IP_R2

value: doxycycline (1 µg/ml, 24 h), 48 h siMYC


title: eCLIP_U2OSMYCtetOn_siMYC_MYC_IP_R1

value: Osteosarcoma cell line


title: WT, dehydrated (2h), rep 2

description: Library name: WT-2 h-2


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-32
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: eCLIP_U2OSMYCtetOn_siMYC_Input

value: MYC-Tet-On


title: High PS19 rep 2

description:
Library name: PS795_5
column name in subread_counts.txt: PS795_5

value: M


title: WT, dehydrated (2h), rep 3

description: Library name: WT-2 h-3


title: High PS19 rep 1

description:
Library name: PS800_4
column name in subread_counts.txt: PS800_4

value: F


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-29
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

value: BRAF V600E


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-28
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: DMSO or Vemurafenib


title: eCLIP_U2OSMYCtetOn_siNTC_MYC_IP_R1

value: doxycycline (1 µg/ml, 24 h), 48 h siNTC


title: WT, dehydrated (0h), rep 4

description: Library name: WT-0 h-4

value: Rosette leaves

value: WT

value: dehydration (0 h)


title: WT, dehydrated (0h), rep 3

description: Library name: WT-0 h-3


title: Low PS19 rep 3

description:
Library name: PS723_6
column name in subread_counts.txt: PS723_6

value: Hippocampus

value: Low PS19


title: eCLIP_U2OSMYCtetOn_siNTC_Input


title: Low PS19 rep 4

description:
Library name: PS737_1
column name in subread_counts.txt: PS737_1

value: C57Bl/6 x B6C3H


title: WT, dehydrated (0h), rep 1

description: Library name: WT-0 h-1


title: WT, dehydrated (0h), rep 2

description: Library name: WT-0 h-2


title: Low PS19 rep 2

description:
Library name: PS593_1
column name in subread_counts.txt: PS593_1


title: eCLIP_U2OSMYCtetOn_pool_IgG_IP_R2

value: Bone

value: merge


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-27
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: WT, dehydrated (2h), rep 1

description: Library name: WT-2 h-1

value: dehydration (2 h)


title: eCLIP_U2OSMYCtetOn_pool_IgG_IP_R1

value: Osteosarcoma cell line

value: MYC-Tet-On


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-30
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-26
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: Low PS19 rep 1

description:
Library name: PS359_5
column name in subread_counts.txt: PS359_5

value: M


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-25
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line


title: CD4i_R2L48_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description: Library name: CD4i_R2L48_GEX_lib

data_processing:
Raw data from pooled samples were processed by Cell Ranger v9.0.1 using the 2024-A probe set reference. UMI counts were demultiplexed back to each individual donor and stimulation condition using the barcodes in the sample_name: sample_probe_barcode metadata column.
raw_matrix_genome_annotation:Chromium Human Transcriptome Probe Set v1.1.0: 2024-A , raw_matrix_value_units:UMI, raw_matrix_assays: scRNA-seq, CRISPR interference, raw_matrix_feature_keys:gene symbol for scRNA-seq, guide_id for CRISPR interference guides, raw_matrix_background_barcodes_included:False
Assembly: GRCh38
Supplementary files format and content: h5, count matrix: scRNA-seq and crispr guide UMI

source_name: blood

extract_protocol:
Naive human CD4+ T cells were isolated isolated with the EasySep Human Naive CD4+ T Cell Isolation Kit (catalog no. #19555, STEMCELL Technologies) according to the manufacturer’s protocol from PBMC-enriched leukapheresis products (Leukopaks, STEMCELL Technologies, catalog no. 70500) from healthy donors, after institutional review board–approved informed written consent (STEMCELL Technologies). After isolation (day 0), 30 million naive human CD4+ T cells were seeded at 1 x 106 cells/ml in X-VIVO 15 (Lonza Bioscience, catalog no. 04–418Q) supplemented with 5% fetal calf serum (FCS) (cXVIVO) and 200 IU/ml of recombinant human IL-2 (Amerisource Bergen, catalog no. 10101641). Cells were activated using ImmunoCult human CD3/CD28/CD2 T cell activator (10990, STEMCELL Technologies) at 25 µl/ml. The next morning, cells were transduced with 2% v/v concentrated ZIM3KRAB-dCas9-BlastR lentivirus. In the afternoon, cells were transduced with 0.1% v/v [multiplicity of infection (MOI) ~ 0.2] genome-scale sgRNA library lentivirus. At day 3, cells were centrifuged and resuspended with above medium supplemented with 200 IU/mL IL-2. Blasticidin and puromycin were added to 10 µg/mL and 2 µg/mL final concentrations, respectively. At day 5, cells were counted and diluted to 5 x 105 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 10 µg/mL blasticidin. Recombinant human IL-7 (R&D Systems, catalog no. 207-IL) was also added to a final concentration of 5 ng/mL. At day 7, cells were counted and diluted to 7.5 x 105 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin. At both day 8 and day 10, cells were centrifuged and resuspended at 5 x 105 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 5 ng/mL IL-7. At day 12 morning, cells were centrifuged and resuspended at 1 x 106 cells/ml with cXVIVO supplemented with 200 IU/mL IL-2 and split into three populations. The first population (Rest) was kept at a resting state without restimulation and harvested in the afternoon after 8 hours. The second population (Stim8hr) was restimulated by adding 12.5 µL/ml ImmunoCult human CD3/CD28/CD2 T cell activator and harvested in the afternoon after 8 hours. The third population (Stim48hr) was restimulated by adding 12.5 µL/ml ImmunoCult human CD3/CD28/CD2 T cell activator and harvested after 48 hours.
GEM-X Flex Sample Preparation v2 Kit (10x genomics, catalog no. 1000781) per the manufacturer’s instructions

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

tag: donor ethnicity

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

tag: genetic perturbation_strategy

value: CRISPR interference

tag: crispr system_type

value: constitutive

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-24
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: eCLIP_U2OSMYCtetOn_siNTC_MYC_IP_R2

tag: tissue

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h), 48 h siNTC


title: eCLIP_U2OSMYCtetOn_pool_IgG_Input

value: merge


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-23
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: WT rep 3

description:
Library name: WT592_2
column name in subread_counts.txt: WT592_2

value: Hippocampus

value: Control, wild type

tag: age

tag: Sex

value: M

tag: strain

value: C57Bl/6 x B6C3H


title: CD4i_R2L47_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L47_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

value: formaldehyde fixed -80C

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive


title: seCLIP_U2OSMYCtetOn_DOX_MYC_IP_R2_CBL0137

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

tag: treatment

value: doxycycline (1 µg/ml, 24 h), CBL0137 (5 µM, 2 h)


title: WT rep 2

description:
Library name: WT716_6
column name in subread_counts.txt: WT716_6

value: Hippocampus

value: Control, wild type

tag: age

tag: Sex

value: F

tag: strain

value: C57Bl/6 x B6C3H


title: CD4i_R2L46_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L46_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: sample preservation_method

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: WT rep 4

description:
Library name: WT748_3
column name in subread_counts.txt: WT748_3

tag: tissue

tag: genotype

tag: age

tag: Sex

value: M


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-21
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: seCLIP_U2OSMYCtetOn_DOX_MYC_IP_R1_CBL0137

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h), CBL0137 (5 µM, 2 h)


title: BcBKO

city: Hangzhou

first: Zhuoying

last: Yang

address: Yuhangtang Road

institute: Zhejiang University

description: Library name: Sample 2

data_processing:
The raw fastq files were subjected to processing using Cell Ranger 3.1.0 software, employing default mapping parameters. The reads were mapped to the mm10-2.1.0 genome. Subsequently, the CellRanger 'aggr' command was employed to normalize the sequencing depth across various samples, with a mean reads per cell exceeded 46,810 after normalization. The filtered expression matrix with cell barcodes and gene names was loaded with the ‘Read10X’ function of the Seurat (v.4.0.0) R package. First, single cells with the number of detected genes (nFeature_RNA) above 500 and detected mitochondria percentage (percent.mt) less than 5% were retained to exclude apoptotic or dead cells. Next, doublet or multiplet cells were determined with DoubletFinder (v.2.0.3). We used the dataset integration function of Seurat to exclude individual heterogeneities. The Seurat (v.4.0.0) package was used for follow-up dimension reduction and clustering.
Assembly: mm10-2.1.0
Supplementary files format and content: matrix files

source_name: islet

extract_protocol:
mouse islets were dispersed into single cells by digestion with TrypLE™ Express Enzyme (12604013; Gibco) first.  Each group of islets was pooled from at least three mice.
Single-cell libraries were prepared using Single Cell 3 Library & Gel Bead Kit v.3, following the guidelines provided by 10X Genomics. Cell counts  were assessed by a hemocytometer (Luna-FL, Logos Biosystems), with cell concentration adjusted to 1,000 cells per microliter. Approximately 16,000 cells were added into each channel of a 10X loading chip, with around 10,000 individual cells captured. Then, the captured cells were lysed, and the isolated RNA was barcoded through reverse transcription within individual 1140 gel beads in the emulsion. Subsequently,  the cDNA was subjected to amplification for library construction. The quality of cDNA and the cDNA libraries was assessed using Agilent 2100. In the end, these libraries were sequenced using an Illumina Hiseq X Ten platform, specifically facilitated by Annoroad Gene Technology.

value: islet

value: BcBKO


title: CD4i_R2L45_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L45_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

tag: anticoagulant

value: ACDA

tag: source

tag: description donor_sex

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

value: formaldehyde fixed -80C

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-20
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

value: DMSO or Vemurafenib


title: seCLIP_U2OSMYCtetOn_DOX_MYC_IP_R1_DMSO

tag: tissue

value: Bone

tag: cell type

value: Osteosarcoma cell line

value: MYC-Tet-On

tag: treatment

value: doxycycline (1 µg/ml, 24 h)


title: CD4i_R2L44_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L44_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

value: no, no, no, no

tag: donor blood_type

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: sample preservation_method

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

value: CD4-positive, alpha-beta T cell

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: library protocol

value: 10x Gene Expression Flex

tag: sample probe_barcode


title: WT rep 1

description:
Library name: WT798_3
column name in subread_counts.txt: WT798_3

value: Hippocampus

value: Control, wild type

tag: age

tag: Sex

value: F

tag: strain

value: C57Bl/6 x B6C3H


title: flox/flox

description: Library name: Sample 1

tag: tissue

value: islet

tag: genotype

value: flox/flox


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-18
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: seCLIP_U2OSMYCtetOn_DOX_IgG_IP

value: Bone

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h), CBL0137 (5 µM, 2 h)


title: TLAB, 8 dpf, rep 4

city: Greenwood

first: Heather

last: Flanagan-Steet

state: South Carolina

address: 113 Gregor Mendel Cir.

department: J.C. Self Research Institute

institute: Greenwood Genetic Center

description:
Library name: WT-4
GalnsWT.4

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36. The trimmed reads were mapped to the  Danio rerio GRCz10.89 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
From the resulting BAM files, unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
The gene hit counts table was used for downstream differential expression analysis.
Assembly: GRCz10.89
Supplementary files format and content: csv text file contains raw gene hit counts for each sample

organism: Danio rerio

source_name: whole animal

growth_protocol: Animals were maintained following standard zebrafish husbandry protocols. The galns mutant line (sa31602) was generated by the Sanger Center Tilling Screen and ultimately acquired from the Zebrafish International Resources Center (ZIRC). Gene specific primers were used to amplify a region surrounding the galns c.539+1G>A (Accession:NM_001080641) mutation, and galns+/m were identified by high resolution melt analysis of genomic DNA (gDNA). Heterozygous animals were outcrossed with the hybrid wild type strain (TLAB) 5 generations prior to experimental analyses.

extract_protocol:
Embryos were genotyped and collected at 8 dpf. Each sample for sequencing was comprised of 15 larvae, collected in 0.5 mL TRIzol reagent (Thermo), and snap frozen on dry ice. Frozen samples were shipped on dry ice to Azenta Life Sciences to complete RNA extraction, library extraction, and sequencing.
Libraries for RNA-seq were generated by Azenta Life Sciences. In short, mRNA was selected through poly-A enrichment, fragmented, and randomly primed. First and second strand cDNA synthesis was performed, followed by end repair, 5' phosphorylation, and dA-tailing. Finally, adapters were ligated and enriched via PCR prior to sequencing.

value: whole animal

value: WT

tag: time

value: 8 dpf


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-22
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: CD4i_R2L43_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L43_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

tag: donor blood_type

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: description donor_sex

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

tag: suspension type

value: cell

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: 10x Gene Expression Flex


title: TLAB, 8 dpf, rep 3

description:
Library name: WT-3
GalnsWT.3

tag: tissue

value: whole animal

tag: genotype

value: WT

tag: time

value: 8 dpf


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-17
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

tag: cell line

value: A375 cell line

tag: cell type

value: Melanoma

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


title: CD4i_R2L41_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L41_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

value: cell

value: adult stage

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: CD4i_R2L42_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L42_GEX_lib

tag: tissue

tag: donor blood_type

tag: anticoagulant

tag: source

tag: description donor_sex

tag: suspension type

tag: donor dev_stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: normal

tag: sample preservation_method

value: formaldehyde fixed -80C

value: pooled:D1 - Hispanic or Latin American, D2 - African American, D3 - African American, D4 - Asian

value: CRISPR interference

value: constitutive

value: CD4-positive, alpha-beta T cell

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

value: 10x Gene Expression Flex


title: seCLIP_U2OSMYCtetOn_DOX_Input_DMSO

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

tag: genotype

value: MYC-Tet-On

tag: treatment

value: doxycycline (1 µg/ml, 24 h)


title: seCLIP_U2O2MYCtetOn_MYC_IP_R2_DOX


title: seCLIP_U2OSMYCtetOn_DOX_Input_CBL0137

value: doxycycline (1 µg/ml, 24 h), CBL0137 (5 µM, 2 h)


title: TLAB, 8 dpf, rep 2

description:
Library name: WT-2
GalnsWT.2

value: whole animal

value: WT

tag: time

value: 8 dpf


title: CD4i_R2L39_GEX:scRNA-seq CRISPR interference screen of CD4+, ⍺β T cells, 4 pooled donors, 24 hr stim

description: Library name: CD4i_R2L39_GEX_lib

value: blood

value: CD4-positive, alpha-beta T cells

value: pooled:[ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator, IL2]

tag: experimental perturbation

value: 48 hr stimulation

tag: donor ids

tag: donor age

value: pooled:D1 - 29 years, D2 - 22 years, D3 - 23 years, D4 - 34 years

tag: donor weight

tag: donor height

tag: donor smoker

value: no, no, no, no

value: ACDA

value: STEMCELL technologies

value: pooled:D1 - female, D2 - female, D3 - female, D4 - male

value: cell

value: adult stage

value: TRUE

tag: donor ethnicity

tag: genetic perturbation_strategy

tag: crispr system_type

tag: suspension enriched_cell_types

tag: suspension depletion_factors

tag: library protocol

tag: sample probe_barcode


title: seCLIP_U2OSMYCtetOn_DOX_MYC_IP_R2_DMSO

tag: tissue

value: Bone

tag: cell line

tag: cell type

value: Osteosarcoma cell line

value: MYC-Tet-On

value: doxycycline (1 µg/ml, 24 h)


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-19
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad

value: A375 cell line

value: Melanoma

tag: genotype

value: BRAF V600E

tag: treatment

value: DMSO or Vemurafenib


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-16
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad


title: TLAB, 8 dpf, rep 1

description:
Library name: WT-1
GalnsWT.1

value: whole animal

value: WT

tag: time

value: 8 dpf


description:
Library name: PerturbFate pooled screen Tri-omics New RNA-15
PerturbFate Tri-omics single-cell library containing Nascent RNA modality
Tri_omics_RNA_cell_metadata.csv
LabeledRNA_gene_count_matrix.RDS
UnlabeledRNA_gene_count_matrix.RDS
Tri_omics_sgRNA_count_matrix.RDS
Tri_omics_ATAC_cell_metadata.csv
Tri_omics_ATAC_peak_count_matrix.h5ad