title: REH treated scRNA-seq Parse Biosciences Evercode, Rep2

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

description: Parse Biosciences Evercode whole transcriptome V1 mini kit library

data_processing:
ParseBiosciences-Pipeline v0.9.6p using a GRCh38 reference provided by 10x Genomics (refdata-gex-GRCh38-2020-A).
supplementary files format and content: ParseBiosciences-Pipeline v0.9.6p output files: DGE.mtx, cell_metadata.csv, all_genes.csv
Assembly: GRCh38

source_name: B cell precursor leukemia

growth_protocol: The human pre-B ALL cell line Reh (DSMZ, ACC 22), was cultured in RPMI-1640 (Sigma, R0883) medium supplemented with 2 mM L-Glutamine (Sigma, G7513), 100 U/ Penicillin and 100µg/mL Streptomycin (Sigma, P0781), and 10% heat-inactivated fetal bovine serum (HIFBS) (Sigma F9665)). The cell line was cultured at 37 ℃ in humidified air 95% with 5% CO2. Cell culture was split twice per week, the first two splits after thawing the cell line had an additional 10% HIFBS in the cell culture media to increase cell growth.

extract_protocol:
The cells recovered from each treatment condition (range 616k-1720k) were fixed according to the manufacturer’s protocol (Parse Biosciences) including 0.5% BSA in the fixation solution. After the fixation the cell concentration was measured for each suspension before being stored at -80°C. For barcoding, cell suspensions with equal number of cells from each treatment condition were thawed and split to two wells of the first barcoding plate of an Evercode whole transcriptome V1 mini kit (Parse Biosciences). Prior to library generation the pooled barcoded cell suspension concentration was evaluated by trypan blue (EVE cell counter) and propidium iodide label (Cellometer K2). Barcoding and sequencing library generation were performed according to the manufacturer’s protocol, generating two sub-libraries, the input cell concentration of the first sub-library (P1) was determined by trypan blue and the second sub-library (P2) was determined by propidium iodide label. The two final sequencing sub-libraries were evaluated on a TapeStation (Agilent) and quantitative real time PCR (qPCR) before being pooled together at equimolar concentrations.
The cells were harvested in phosphate buffered saline (PBS) and transferred to 15 ml polypropylene tubes. The PBS was pre-warmed to 37°C before cell harvest cell, then tubes kept at room temperature. The cells were spun at 200 g for 10 min, re-suspended in 2.0 ml PBS and the concentration and viability were evaluated for each treatment condition by AO-DAPI stain analyzed on a NucleoCounter-3000 (Chemometec).

treatment_protocol: Reh cells were added to a six-well plate 0.16 * 106 cells/well, 3 mL cell culture media per well. Two six-well plates were seeded on the day of the cell culture split and anticancer drugs were added to five individual wells per plate and the last well was a vehicle control for dimethyl sulfoxide (DMSO). The chosen concentrations and drugs were the following: 5 µM 5-azacytidine (A2385, Sigma), 10 µM dexamethasone (D1756, Sigma), 10 µM imatinib (I-5508, LC Lab), 1 µM XRP44X (X3129, Sigma-Aldrich), 0.56 µM fludarabine (S1391, Selleckchem) and in the control well 0.9 % (v/v) DMSO (D5879, Honeywell). The cells were harvested after a 72h incubation (37 ℃, humidity 95% with 5% CO2).

value: B cell precursor leukemia

tag: isolate

value: ACC 22 (REH)

tag: biomaterial provider

value: DSMZ

value: REH

value: 5µM 5-Azacytidine, 10µM Dexamethasone, 1µM XRP44X, 10µM Imatinib, 0.56µM Fludarabine, 0.9% DMSO, incubated for 72h (de-multiplexed by Parse Biosciences Evercode whole transcriptome V1 mini kit barcodes)

tag: tags


title: Twin9_FT4_low

status: Public on Jan 04 2024

type: genomic

city: Yamadaoka,Suitashi

first: Yuya

last: Arakawa

state: Osaka

department: Graduate school of Medicine

country: Japan

institute: Osaka university

description: peripheral blood sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Bead Chip

scan_protocol: Arrays were imaged using Illumina iScan System and iScan Control Software

data_processing: GenomeStudio

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using NucleoSpin® Blood L Kit according to standard instructions

tag: gender

value: Male

tag: sample type

value: whole blood

tag: disease state

value: normal


title: REH treated scRNA-seq Parse Biosciences Evercode, Rep1

type: SRA

library_source: transcriptomic single cell

molecule: polyA RNA

tag: tissue

tag: cell line

tag: treatment


title: Twin13_FT4_high

description: peripheral blood sample

value: Female


title: Twin8_FT4_low

description: peripheral blood sample


title: Twin9_FT4_high

description: peripheral blood sample


title: REH treated scRNA-seq 10X Fixed RNA Profiling, Pool1

description: 10X Fixed RNA Profiling three barcode set library, Probe-set: Chromium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv

data_processing:
Cellranger v7.0.1 multi, using a GRCh38 reference provided by 10x Genomics (refdata-gex-GRCh38-2020-A)
supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Assembly: GRCh38

extract_protocol:
For the 10x Chromium RNA profiling cells from each treatment condition were fixed with formaldehyde and additive according to the manufacturer’s protocol (10x Genomics). Fixation was performed at +4°C overnight. After buffer exchange, the fixed cells were stored at -80°C until processing. A four barcode (BC) set kit was used for subsequent barcoding of the six different samples, i.e., three BC sets were combined to each one 10x reaction. The post hybridization washes were done individually for each barcoded sample, according to the provided protocol from the manufacturer. Cell counting was performed using propidium iodide labeling (Cellometer K2). An equal number of cells from each sample was combined for a total of two reactions (lanes) in a Chromium iX instrument. The two libraries were generated according to the manufacturer’s protocols. The libraries were evaluated on a TapeStation (Agilent) and qPCR before being pooled together at equimolar concentrations.
The cells were harvested in phosphate buffered saline (PBS) and transferred to 15 ml polypropylene tubes. The PBS was pre-warmed to 37°C before cell harvest cell, then tubes kept at room temperature. The cells were spun at 200 g for 10 min, re-suspended in 2.0 ml PBS and the concentration and viability were evaluated for each treatment condition by AO-DAPI stain analyzed on a NucleoCounter-3000 (Chemometec).

value: 5µM 5-Azacytidine, 10µM Dexamethasone, 1µM XRP44X, incubated for 72h (de-multiplexed by 10X Fixed RNA Profiling barcodes)


title: Twin10_FT4_high

description: peripheral blood sample


title: SIDS_3_run_1

city: Boston

first: Benjamin

last: Okaty

state: MA

address: 77 Avenue Louis Pasteur

country: USA

institute: Harvard Medical School

description: 10X genomics

data_processing:
The CellRanger pipeline was used for transcript mapping (specifically to a pre-mRNA reference assembly as many nuclear transcripts are unspliced) and single-nuclei de-multiplexing.
Gene counts were analyzed using Seurat. First, Seurat objects for each sequenced sample were instantiated, merged together to form a single object, and then jointly re-normalized. In order to define discrete transcriptomically-defined clusters in our data (representing cell types and cell states), a heuristic parameter search was performed by systematically varying cluster resolution and examining the relationship between: (1) the number of Louvain clusters identified, (2) the extent to which these clusters parcellate clusters “visible” in the 2-D UMAP embedding, (3) and the number of significantly differentially expressed genes identified for each cluster. The initial iteration of this analysis identified two clusters that appeared to reflect “multiplets” (based on absence of unique marker genes and mixtures of marker genes from other clusters), that were excluded from further analysis (resulting in a total of 25,113 nuclei that passed our quality control thresholds), and the repeated process identified a total of 27 clusters (supplementary file: combined_SeuratObject_27_clusters.rds). Cases showed similar overall distributions of cell types, supporting consistent anatomy among cases.
While nuclei from the three non-inflammatory SIDS cases were largely intermingled in UMAP space, a subset of clusters were composed entirely of HPeV3+ SIDS nuclei, most notably clusters corresponding to vascular cells, microglia, astrocytes, and myelinating oligodendrocytes. Neighboring clusters corresponding to the same cell types (based on expression of established marker genes) were composed exclusively of nuclei from the three non-inflammatory SIDS cases, suggesting that HPeV3+ specific clusters may represent different cell-states, rather than distinct cell types. In order to calculate cell-type specific differential gene expression between HPeV3+ and non inflammatory SIDS cases, data were first “integrated” as described in Stuart, et al. 2018, to identify common cell types. Data integration resulted in 24 rather than 27 clusters, as HPev3+ specific clusters became intermingled with non-inflammatory SIDS (supplementary file: integrated_SeuratObject_24_clusters.rds).
Assembly: GRCh38-1.2.0
Supplementary files format and content: "filtered_feature_bc_matrix" suffix files are in h5 format, or Hierarchical Data Format, a binary format that more efficiently compresses and accesses large data sets than text formats. These files contain barcodes, features, and feature counts.
Supplementary files format and content: Processed supplementary files are in rds format, or R data serialization format, and contain the Seurat objects on which analysis was performed and figures generated in our associated publication.

molecule: nuclear RNA

source_name: medullary brainstem

extract_protocol:
Approximately 150-300μm of fresh frozen (non-fixed) brainstem tissue was cryosectioned at the level of the obex + 2mm (as identified by human brainstem atlas landmarks, consistent with our previous studies), a region containing both the raphe obscurus and raphe palladus, where 5-HT neuron cell bodies reside, as well as other nuclei implicated in cardiorespiratory regulation. Tissue sections were transferred to a 1.5ml Eppendorf tube on dry ice. Tissue was then homogenized and nuclei extracted using the Nuclei Isolation Kit:Nuclei EZ prep. Harvested nuclei were then incubated in NucBlue live cell stain for 20 minutes at room temperature, sorted on the On-Chip microfluidic sorter to eliminate tissue debris and other contaminants, and then quantified using a hemacytometer. Note: for two sample runs – SIDS2_run_1 and HPeV3_SIDS_run_1 – nuclei were additionally stained with NeuN, and NeuN positive and negative nuclei were separately sorted and sequenced (in an attempt to enrich for neuronal nuclei in the NeuN positive condition; library name suffixes indicate NeuN positive or negative condition). For all other sample runs, only NucBlue staining was performed.
Harvested nuclei were gently centrifuged and suspended to an appropriate concentration (~700-1200 nuclei/μl) and processed through the 10X Genomics Chromium Single Cell 3’ v3 protocol followed by Illumina NextSeq 500 sequencing.

value: medullary brainstem

tag: group

value: non-inflammatory SIDS


title: Twin12_FT4_low

description: peripheral blood sample


title: HPeV3_SIDS_run_2

description: 10X genomics

value: HPeV3+ SIDS case


title: SIDS_2_run_2

description: 10X genomics


title: Tumor tissue 3612

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
The long-read transcripts were assembled using SPADES from a python script
Single-cell transcriptome long reads were aligned to human reference genome hg38 by long-read aligner Minimap2
LOOPseq long-reads were analyzed by the tool SQANTI on full and trimmed dataset
Assembly: hg38
Supplementary files format and content: TXT for long-read annotation

molecule: total RNA

source_name: liver

extract_protocol:
HCC samples and benign liver samples were freshly dissected from a patient who underwent liver transplantation. The procurement procedure was approved by the institution review board of University of Pittsburgh. The procedure was compliant with all regulations related to the protocol. The dissected tissues were minced by scalpel and digested with collagenase/protease solution (VitaCyte, 007-1010) until the tissue was fully digested. The digestion time for each preparation was in a range 45-60 min. The digested tissue was removed and immediately cooled with ice-cold Leibovitz's L-15 Medium (Invitrogen, 11415114) supplemented with 10% fetal bovine serum (Sigma, F4135). The single-cell suspension was verified under the microscope. The number of live cells was estimated by trypan blue staining using a hemacytometer.
Follow pipelines for 10x Genomic single-cell and unique molecular index (UMI) barcoding, and LOOP UMI distribution and library construction
10X scRNA-seq + LOOP

value: liver

tag: cell type

value: HCC tumor


title: SIDS_1_run_1

description: 10X genomics


title: REH treated scRNA-seq 10X Fixed RNA Profiling, Pool2

value: 10µM Imatinib, 0.56µM Fludarabine, 0.9% DMSO, incubated for 72h (de-multiplexed by 10X Fixed RNA Profiling barcodes)


title: EAEIP, 3

city: SASKATOON

first: Michael

middle: C

last: Levin

state: Saskatchewan

address: 701 Queen St, CMSNRC (Cameco Multiple Sclerosis Neuroscience Research Centre)

country: Canada

institute: University of Saskatchewan

data_processing:
Adapter Trimming: Sequencing reads were extracted from each run and adapter trimmed using bcl2fastq (version 2.19.0.316; Illumina) with the following settings: “--use-bases-mask Y*,I8Y*,Y* --minimum-trimmed-read-length 0 --mask-short-adapter reads 0”. Residual sequencing adapters and low-quality bases were trimmed using fastp with default settings except for “-f 5 -Y 0 -g” and the adapter sequences specified by PerkinElmer for use with the NEXTFlex v3 kit.
Contig Assembly: Adapter-trimmed reads were assembled into contigs using rnaSPAdes (from SPAdes, version 3.15.3) with default settings.
Alignment: Contigs were aligned to the GRCm38 mouse reference genome using minimap2 (version 2.17) in spliced alignment mode to identify regions corresponding to putative hnRNP A1 RNA binding sites.
Site Selection: Sites identified in the animal-matched input samples, or the treatment-matched pooled IgG sample, were considered to be background signal and were depleted from the set of sites for each immunoprecipitation sample using bedtools subtract (version 2.29.2) with default settings. Overlapping and book-ended sites were combined using bedtools merge with default settings for each sample to generate a total hnRNP A1 footprint at each site.
Assembly: Mus musculus GRCm38
Supplementary files format and content: Files in .bed format indicating locations on GRCm36 genome. Output of Site Selection data processing step, indicating hnRNP A1 RNA binding footprint in that animal. Each file corresponds to a single animal.

organism: Mus musculus

source_name: spinal cord

growth_protocol: All animal experiments were performed in accordance with the University of Saskatchewan’s Animal Research Ethics Board under Animal Use Protocol AUP20170104. Mice were housed five to a cage under pathogen-free conditions on a 12h/12h light:dark cycle with ad libitum access to standard rodent chow and water. Adult female C57BL/6N mice (10 weeks) were purchased from Charles River Laboratories.

extract_protocol:
After dissecting the spinal column from the euthanized mouse, the spinal cord was hydraulically extruded through the cervical opening with sterile, RNase-free PBS. The cord was then diced into <1 cubic mm fragments in a petri dish with 5mL ice cold RNase-free PBS and UV crosslinked with two doses of 400mJ 254nm UV light, with swirling in between doses. Fragments were then collected into a 15mL conical tube in RNase-free PBS. Tissue was lysed in iCLIP lysis buffer [Van Nostrand et al (2016). Nature Methods, 13(6), 508–514. https://doi.org/10.1038/nmeth.3810] with protease and RNase inhibitors, then 2mg protein was immunoprecipitated with anti-hnRNP A1 antibody clone 9H10 in the presence of RNaseI overnight at 4degC,  using magnetic protein A/G beads. In parallel, equal amounts of naive samples were pooled to a total of 2mg, and equal amounts of EAE samples were pooled to a total of 2mg, and these pools were each immunoprecipitated in the presence of RNaseI with anti-IgG2a (clone GC198) as negative controls. Samples were washed after immunoprecipitation, RNA was end-healed (described below in library preparation), and then RNA was liberated from the crosslinked protein by treatment with Proteinase K. RNA was eluted using phenol-chloroform-isoamyl alcohol (25:24:1), then purified using the Zymo RNA Clean & Concentrator kit. Input samples were collected prior to immunoprecipitation, and RNA was extracted using the same Proteinase K,  phenol-chloroform-isoamyl alcohol, and Zymo kit process.
RNA was end-healed while still complexed with hnRNP A1/antibody/beads, but after immunoprecipitation and washing, using polynucleotide kinase (PNK) in two stages. First, at pH 6.5 in the absence of ATP to repair the 2’,3’-cyclic phosphate end of the RNA left by RNase I, and then at a pH of 7.6 supplemented with 1mM ATP to repair the 5’-hydroxyl end of the RNA left by RNaseI. Enzymes and buffers were washed away again prior to purification. Input samples were also end-healed as described. After purification, samples were prepared using the NEXTFlex Small RNA Sequencing Kit v3 according to the manufacturer’s protocol, with the recommended “No Size Selection Protocol” modification for bead cleanup, and using PAGE Size-selection and Cleanup to extract library DNA between 150-170nt in length. Sequencing libraries were quantified using a Qubit 4.0 fluorometer and Qubit 1x dsDNA HS assay. The library fragment length distributions were determined using a TapeStation 4150 instrument with High Sensitivity D1000 ScreenTape and reagents. The barcoded libraries were pooled equimolar and 76 bp paired-end reads generated on a NextSeq 550 instrument.

treatment_protocol: EAE was induced through active immunization with reagents purchased from Hooke Laboratories (cat. no. EK-2110). At 12 weeks of age, mice were subcutaneously immunized with 0.1 mL emulsion of MOG(35-55) in complete Freund’s adjuvant between both the shoulder blades and hind limbs. On days 0 and 1, mice also received 100 ng of pertussis toxin diluted in PBS intraperitoneally. Following induction, mice were evaluated daily for the appearance of clinical signs. Mice were assigned clinical scores based on disease severity according to the scoring scale established by Hooke Laboratories. Mice were sacrificed at 15 days post-clinical onset with an overdose of Euthanyl for spinal cord extraction.

tag: vendor

value: Charles River laboratories

tag: strain

tag: genotype

value: wild-type

value: spinal cord

tag: Sex

value: female

tag: rip antibody

value: anti-hnRNP A1 (clone 9H10)

value: anti-hnRNP A1 immunoprecipitation

value: EAE

tag: mouse identifier

tag: eae clinical_score


title: Tumor tissue 3611


title: REH treated scRNA-seq MULTI-seq

description: MULTI-seq, VD-3266-GE-REH-003: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript, VD-3266-BC-REH-003:  read1 file contains cell barcode and UMI; read2 file contains treatment tag

data_processing:
Cellranger v7.0.1 using a GRCh38 reference provided by 10x Genomics (refdata-gex-GRCh38-2020-A). LMO sequences were treated as Custom library.
supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Assembly: GRCh38

extract_protocol:
A volume equivalent to 500 000 of cells recovered from each treatment condition was transferred to six 15 ml tubes and PBS was added to obtain a total volume of 5 ml. Cells were collected by centrifugation 200 g for 10 min and transferred to a loBind 1.5 ml Eppendorf tube. Lipid modified oligos (LMO, Sigma) were used for barcode labeling as previously described (McGinnis et al., 2019). The processing was performed in six parallel tubes and wash steps and volumes were optimized to minimize the time of handling and cell loss. The final resuspension of the cells was made with PBS supplemented with 1% BSA and 0.5 U/µl RNase inhibitor was in a low volume (100 µl/sample) for a quick sorting. The samples were pooled and dead cells immediately removed by incubating with DAPI for 5 minutes followed by negative selection with a gentle sorting (Milteny MACS Quant Tyto). The purified cell suspension pool cell concentration and viability was evaluated by AO-DAPI (NucleoCounter-3000).  The cell suspension pool was immediately processed on one lane of a Chromium next GEM Single cell 3’ gene expression v3.1 dual index kit (10x Genomics) according to the manufacturer’s protocol. In the first step of cDNA purification the fraction of short cDNA, containing the barcode libraries, was saved for generating a barcode library according to the multi-seq protocol. The libraries were evaluated on a TapeStation (Agilent) and qPCR before being pooled with the aim of acquiring 50k and 5k reads per cell for the gene expression and barcode libraries, respectively.
The cells were harvested in phosphate buffered saline (PBS) and transferred to 15 ml polypropylene tubes. The PBS was pre-warmed to 37°C before cell harvest cell, then tubes kept at room temperature. The cells were spun at 200 g for 10 min, re-suspended in 2.0 ml PBS and the concentration and viability were evaluated for each treatment condition by AO-DAPI stain analyzed on a NucleoCounter-3000 (Chemometec).

value: B cell precursor leukemia

tag: isolate

value: ACC 22 (REH)

tag: biomaterial provider

value: DSMZ

value: REH

value: 5µM 5-Azacytidine, 10µM Dexamethasone, 1µM XRP44X, 10µM Imatinib, 0.56µM Fludarabine, 0.9% DMSO, incubated for 72h (de-multiplexed by MULTI-seq barcodes)


title: Twin8_FT4_high

description: peripheral blood sample

tag: gender

value: Female

value: whole blood

value: normal


title: Tumor tissue 3610

value: liver

value: HCC tumor


title: Twin7_FT4_high

description: peripheral blood sample

tag: sample type


title: Twin7_FT4_low

description: peripheral blood sample

tag: disease state


title: HPeV3_SIDS_run_1_neun_neg

description: 10X genomics

tag: tissue

value: medullary brainstem

value: HPeV3+ SIDS case


title: Twin6_FT4_low

description: peripheral blood sample


title: Twin10_FT4_low

description: peripheral blood sample


title: Twin6_FT4_high

description: peripheral blood sample


title: Tumor tissue 3608


title: FKH_Dnase

city: Nottingham

first: Sophie

middle: G

last: Kellaway

department: School of Medicine

country: United Kingdom

institute: University of Nottingham

library_source: genomic

data_processing:
Sequencing reads were processed with Trimmomatic v0.32 to remove sequencing adaptors and low-quality sequences, then aligned to hg38 with Bowtie2 v2.2.3 using the setting –very-sensitive-local. PCR duplicates were removed using the MarkDuplicates function in Picard 2.10.5. Peaks were called using MACS2 2.1.1 using the options -q 0.0005 -B –trackline –nomodel –shift 100 –extsize 200. Distal peaks were defined as being at least 1500 bp from the nearest transcription start site as annotated by Homer v4.11.
Assembly: hg38
Supplementary files format and content: bedgraph file containing read pileup from MACS2

source_name: AML cell line

growth_protocol: Cells were obtained from DSMZ and routinely cultured in RPMI 1640 with 10% FBS

extract_protocol:
DNaseI digestions were performed as previously described.1 Briefly, cells were permeabilised and digested with DNaseI (Worthington) for 3 minutes at 22°C, and the reactions were terminated by addition of SDS to 0.5%. DNA fragments between 250 and 350 bp were selected
DNaseI-seq libraries were prepared using the KAPA hyper prep kit

value: AML cell line


title: small RNAs associated with AGO2 in mouse embryonic stem cells, biological replicate 3

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

description:
small RNAs bound by AGO2
RIP_FA2_C

data_processing:
Basecalls performed using CASAVA version 1.4
For small RNAseq, sequenced reads were trimmed for adapter sequence using cutadapt. The resulting reads with a length between 17 and 30nt were retained for mapping by HISAT2 (v2.1.0).
Assembly: mm10
Supplementary files format and content: csv files containing the counts (in counts per million reads) for each sample

source_name: mouse embryonic stem cells (mESCs)

growth_protocol: All the mESCs used in this study were cultured on 0.5% gelatin-coated tissue culture plates in the 2i + Lif medium (DMEM/F-12, 2% FBS, 2mM L-Glutamine, 0.1mM MEM NEAA, 1% Penicillin-Streptomycin, 0.1 mM β-mercaptoethanol and 1000 U/mL mLIF, 1 x N2N27, 3 uM CHIR99021 and 1 uM PD0325901).

extract_protocol:
AGO1 and AGO2 were immunoprecipitated from the mESCs, and then RNA were isolated from the immunoprecipitated AGO1 and AGO2 via Trizol reagent.
small RNA-seq library was prepared using the CleanTag kit (Trilink)

value: mESCs

tag: genetic background

tag: antibody

value: FLAG-M2 (Sigma)


title: SIDS_2_run_1_neun_neg

description: 10X genomics

tag: group

value: non-inflammatory SIDS


title: small RNAs associated with AGO2 in mouse embryonic stem cells, biological replicate 2

description:
small RNAs bound by AGO2
RIP_FA2_B

tag: cell type


title: Twin5_FT4_low

description: peripheral blood sample


title: Tumor tissue 3361


title: Tumor tissue 3355


title: t69-FLT3_Dnase

data_processing: Sequencing reads were processed with Trimmomatic v0.32 to remove sequencing adaptors and low-quality sequences, then aligned to hg38 with Bowtie2 v2.2.3 using the setting –very-sensitive-local. PCR duplicates were removed using the MarkDuplicates function in Picard 2.10.5. Peaks were called using MACS2 2.1.1 using the options -q 0.0005 -B –trackline –nomodel –shift 100 –extsize 200. Distal peaks were defined as being at least 1500 bp from the nearest transcription start site as annotated by Homer v4.11.

source_name: CD34+ sorted AML blasts

growth_protocol: Human peripheral blood (sample labelled t(6;9)) or bone marrow (sample labelled t(6;9)/FLT3) was obtained with the required ethical approval from the NHS National Research Ethics Committee, with informed consent from patients from the Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, UK. Sample t(6;9)/FLT3 had mutations in CHK2 T367fs, ETV6 Q150X, FLT3 D835H, NRAS G12D and ZRS2 K106X alongside the translocation. Sample t(6;9) had mutations in TET2 L34F (VUS) and EZH2 D185H alongside the translocation. Mononuclear cells were purified on the day the sample was received by density centrifugation using Lymphoprep (Stemcell Technologies) and sorted for CD34 using MACS.

value: CD34+ sorted AML blasts


title: small RNAs associated with AGO2 in mouse embryonic stem cells, biological replicate 1

description:
small RNAs bound by AGO2
RIP_FA2_A


title: Twin5_FT4_high

description: peripheral blood sample


title: t69_Dnase


title: Benign tissue 3718

value: benign tissue


title: t69-FLT3_RNA

data_processing: Raw paired-end sequencing reads were processed with Trimmomatic v0.32 to remove sequencing adaptors and low-quality sequences, then aligned to hg38 with Hisat2 2.1.0 with default parameters. Gene expression values were calculated as fragments per kilobase of transcript per million mapped reads (FPKM) using Stringtie 1.3.3.

extract_protocol:
RNA was extracted using Trizol.
Sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero Human/Mouse/Rat


title: small RNAs associated with AGO1 in mouse embryonic stem cells, biological replicate 3

description:
small RNAs bound by AGO1
RIP_FA1_C


title: small RNAs associated with AGO1 in mouse embryonic stem cells, biological replicate 2

description:
small RNAs bound by AGO1
RIP_FA1_B


title: HPeV3_SIDS_run_1_neun_pos

description: 10X genomics


title: Twin4_FT4_low

description: peripheral blood sample


title: Twin4_FT4_high

description: peripheral blood sample


title: Benign tissue 3717


title: Benign tissue 3716


title: Spinal cord + Complete Freund's Adjuvant (CFA)_HTO

city: Stanford

first: Marius

middle: Marc-Daniel

last: Mader

state: CA

address: 265 Campus Drive

institute: Stanford University

description: 10x Genomics with cell hashing for 4 biological replicates

data_processing:
The Cell Ranger (v.6.1.2) analysis pipelines were utilized to align reads to the mm10 reference genome as well as GFP, and count barcodes/UMIs. Specifically, cell demultiplexing by assigning hashtag antibody oligo tags to cell-associated barcodes was performed with the Cell Ranger multi pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spinal cord

extract_protocol:
Single-nuclei preparation was performed as previously described (Hahn et al., 2022) with the following modifications. The thoracolumbar section of spinal cords were first mechanically dissociated with an ice-cold razor blade in a petri dish with 1ml EZ Prep lysis buffer (Sigma, NUC-101) on ice. Transfer of tissue suspension into a 2ml glass dounce tissue grinder tube (Sigma, D8938). Petri dish was rinsed off with another 1ml EZ buffer, which was added to the grinder tube. Suspension was homogenized by hand 25 times with pestle A followed by 25 times with pestle B while incorporating a 180-degree twist. Tissue homogenate was transferred to a fresh 15ml tube on ice. The grinder tube was rinsed with 2 ml fresh lysis buffer, which was added to the 15ml tube for a total volume of 4 ml. Samples were incubated on ice for 5 minutes. Nuclei were centrifuged at 500 x g for 5 minutes at 4°C, supernatant was removed, and the pellet resuspended with 4 ml EZ lysis buffer and incubated on ice for 5 minutes. Centrifugation at 500 x g for 5 minutes at 4°C was repeated. After removing the supernatant, the pellet was resuspended with 4 ml chilled PBS and filtered through a 35-um cell strainer into a 5 ml round bottom FACS tube (Corning, 352235). Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out leaving behind the nuclei pellet. The pellet was resuspended in 100µl FC block buffer (BD Biosciences, 553141, 1:50 in FACS buffer) and 1ul recombinant RNase inhibitor (Takara, 2313B) incubated on ice for 5min. FACS buffer consisted of PBS (Gibco, 10010049) containing 1% BSA (Thermo Fisher, BP9700100)). To 50µl of the cell suspension, we added 150µl FACS buffer with 2µl Olig2-Alexa Fluor488 (Sigma, MABN50A4), 1ul NeuN-AlexaFluor647 (Abcam, ab190565), 1.5ul RNase inhibitor, and Anti-Nuclear Pore Complex Protein Hashtag antibodies (1 µl; TotalSeq™-A0451, -A0452, -A0453, and -A0455, Biolegend, 682205, 682207, 682209, and 682213).. After 30min incubation covered from light and shaking on ice, 3ml FACS buffer were added. Following centrifugation at 300 x g for 10 minutes at 4°C with break 3, supernatant was gently poured out. The pellet was resuspended in 700µl FACS buffer with 3.5ul recombinant RNase inhibitor and Hoechst dye (Thermo Fisher, H3570, 1:2000) and incubated 4min on ice covered from light. Single nuclei were sorted on a MA900 Multi-Application Cell Sorter (Sony Biotechnology) gating for NeuN negative nuclei. 100,000 single nuclei per sample were collected into 1.5 ml DNA lo-bind tubes (Eppendorf, 022431021) containing 1 ml buffer mix with 800ul PBS, 200ul UltraPure BSA (Thermo Fisher, AM2618), and 5ul RNase inhibitor. If libraries were representing two animals, samples were pooled by collecting identical numbers (2x 50,000) of nuclei into the same sample tube. Collected nuclei were centrifuged at 400 x g for 5 minutes at 4°C with break 2. Supernatant was removed leaving 40µl suspended nuclei. Nuclei were counted using a hemacytometer (Sigma, Z359629-1EA) and assessed for concentration and quality.
Reagents of the Chromium Single Cell 3’ GEM & Gel Bead Kit v3.1 (10X Genomics, 1000121) were thawed and prepared according to the manufacturer’s protocol. Nuclei and master mix solution was adjusted to target 10,000 nuclei per sample and loaded on a standard Chromium Controller (10X Genomics, 1000204) according to manufacturer protocols with the addition of HTO additive primer at cDNA amplification. We applied 11 PCR cycles to generate cDNA. Immediately after cDNA amplification, HTO-derived cDNA and mRNA-derived cDNA were separated via SPRI bead size selection. Library construction was conducted using Chromium Single Cell 3’ Library Construction Kit v3 (10X Genomics, 1000121). We chose 13 PCR cycles for library generation. The HTO-derived cDNA was processed according to New York Genome Center Cell Hashing Protocol (https://citeseq.files.wordpress.com/2019/02/cell_hashing_protocol_190213.pdf) with 13 PCR cycles. Libraries were pooled at a proportion of 20% HTO-derived cDNA to 80% mRNA-derived cDNA. All reaction and quality control steps were carried out according to the manufacturer’s protocol and with recommended reagents, consumables, and instruments. Quality control of cDNA and libraries was conducted using a Bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility.
10X Nuc-seq, v3.1 chemistry, + Hashtag oligo library

value: Spinal cord

tag: treatment

value: Complete Freund's Adjuvant (CFA) injection

tag: molecule subtype

value: single-nuclei RNA


title: small RNAs associated with AGO1 in mouse embryonic stem cells, biological replicate 1

description:
small RNAs bound by AGO1
RIP_FA1_A


title: PBMC, scGlycan-seq

city: Tsukuba

first: Hiroaki

last: Tateno

state: Ibaraki

address: Tsukuba Central 2, 1-1-1 Umezono

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: 10x Genomics

library_source: other

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: PBMC

extract_protocol:
Panc04.03 and hTERT-HPNE were detached from culture dish using TrypLE (ThermoFischer) followed by washing and counting of the cell. PBMC were thawed in water bath followed by washing with warm RPMI-1640 media containg 10% FBS and counting.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 5` Gel Bead Kit v2 protocol, 10x Genomics). DNA-barcoded lectin reacted cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA and DNA-barcodes were amplified, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA and DNA-barcode was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction using Dual Index Plate TN Set A and Dual Index Plate TT Set A for cDNA and DNA-barcode respectively.

tag: cell line

value: PBMC

value: Peripheral blood mononuclear cells

tag: antibodies/tags

value: IgG1, k isotype Ctrl/TotalSeq-C0090; Mouse IgG1


title: Twin3_FT4_low

description: peripheral blood sample

value: Male

value: whole blood

value: normal


title: t69_RNA


title: Benign tissue 3715

value: liver


title: Twin3_FT4_high

description: peripheral blood sample


title: Benign tissue 3317


title: hTERT-HPNE, scGlycan-seq

description: 10x Genomics

source_name: hTERT-HPNE

value: hTERT-HPNE

value: normal pancreatic ducts cell


title: Twin2_FT4_low

description: peripheral blood sample


title: Spinal cord + phosphate-buffered saline (PBS)_HTO

tag: Sex

value: Female

tag: strain

value: Phosphate-buffered saline (PBS) injection


title: Twin2_FT4_high

description: peripheral blood sample


title: Spinal cord + Complete Freund's Adjuvant (CFA)_GEX


title: HEK293, 6h induction, replicate 3

city: Leicester

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

data_processing:
Adapters were trimmed with Cutadapt version 1.18
STAR version 2.7.3a was used to remove remaining rRNA reads and to map the remaining reads to the human genome
DESeq2 version 1.30.1 was used to obtain the list of differentially expressed genes
FPKM-normalized bigwig files were created with deepTools2 version 3.4.2 (39) bamCoverage tool with the parameters -bs 10 -p max – normalizeUsing RPKM
Assembly: hg38
Supplementary files format and content: bigwig files: genome-coverage files for all samples

growth_protocol: HEK293T cells were maintained in high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 5 mM glutamine at 37°C with 5% CO2

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep Plus kit
Unstranded poly(A)+ libraries were prepared by Novogene (UK)

treatment_protocol: HEK293T cells stably expressing inducible iRhom2-1-374 were treated with 100 ng/ml of doxycycline for 0h, 3h, and 6h

value: epithelial-like

tag: genotype

value: inducible iRhom2-1-374 fragment integrated

value: doxycycline

tag: time point


title: hTERT-HPNE, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files


title: PBMC, scRNA-seq

description: 10x Genomics


title: Benign tissue 3362

value: benign tissue


title: Twin1_FT4_low

description: peripheral blood sample


title: Spinal cord + phosphate-buffered saline (PBS)_GEX

value: Spinal cord


title: Panc04.03, scRNA-seq

description: 10x Genomics

value: Pancreatic ductal adrenocarcinoma cells


title: HEK293, 6h induction, replicate 1


title: HFSCs-treated4

city: Cleveland

first: Luyang

last: Xiong

state: OH

address: 9500 Euclid Ave

department: Lerner Research Institute

institute: Cleveland Clinic Foundation

data_processing:
Raw demultiplexed fastq paired end read files were trimmed of adapters and filtered using the program skewer to throw out any with an average phred quality score of less than 30 or a length of less than 36
Trimmed reads were then aligned using the HISAT2  aligner to the Mouse NCBI reference genome assembly version GRCm38 and sorted using SAMtools
Aligned reads were counted and assigned to gene meta-features using the program featureCounts as part of the Subread package
These count files were imported into the R programming language and were assessed for quality control, normalized and analyzed using an in-house pipeline utilizing the limma-trend method for differential gene expression testing and the GSVA library for gene set variation analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count_matrix.xlsx contains raw counts of all genes.

source_name: murine hair follicle stem cells

extract_protocol:
Clipped mouse dorsal skin was harvested and fat tissue was removed by gentle scalpel scrapping. Skin samples were then floated on 0.25% trypsin solution for 2 hours at 37℃ or overnight at 4℃. Then epidermis was detached from the dermis by gentle scalpel scraping and minced to prepare primary keratinocytes single-cell suspension, which was then filtered through a 70-µm cell strainer. Hair follicle stem cells were FACS-sorted based on expression of CD34 and CD49f.
Libraries were generated using the Nextera XT DNA Library Prep kit (Illumina).

tag: marker

value: CD34+CD49f+ HFSCs

value: treated


title: Panc04.03, scGlycan-seq

description: 10x Genomics

value: IgG1, k isotype Ctrl/TotalSeq-C0090; Mouse IgG1


title: Twin1_FT4_high

description: peripheral blood sample

tag: gender

value: Male


title: MS3

description:
rRNA-depleted total RNA
R2100163

data_processing:
Adapter Trimming: Reads were extracted and adapter trimmed using bcl2fastq (version 2.19.0.316; Illumina), and additional quality trimming was performed using fastp with default settings except for “-f 5 -Y 0 -g”.
Alignment: Trimmed reads were aligned to the GRCh38.p12 human reference genome (GENCODE Release 30) using STAR (version 2.5.1b) with default settings.
Deduplication: Aligned reads were deduplicated using NuDup (version 2.3.3; Tecan Genomics) with default settings.
Expression: Gene-level expression was quantified using htseq-count from the HTSeq package (version 0.11.3).
Assembly: GRCh38.p12 human reference genome (GENCODE Release 30)
Supplementary files format and content: Comma-separated value (.csv) file of number of reads mapped to each ENSEMBL GENE ID, in matrix format.

source_name: brain

extract_protocol:
Regions of interest in human grey matter were defined by immunostaining for hnRNP A1 to confirm grey matter regions with hnRNP A1 mislocalization in MS tissue, and grey matter regions with normal hnRNP A1 localization in control tissue, and the same region from an adjacent tissue section was dissected with a razor blade. RNA was extracted from each section (n=1 section per patient sample) using the Arcturus PicoPure extraction kit and its manufacturer's protocol.
10 ng of input RNA was used for library preparation using the Ovation SoLo RNA-Seq Library Preparation Kit (Tecan Genomics 0500-32) per the manufacturer’s instructions, which included an rRNA depletion step using the AnyDeplete Human Probe Mix. Libraries were quantified using a Qubit 4.0 Fluorometer and Qubit 1X dsDNA HS assay before being run on a TapeStation 4150 to assess library quality. Barcoded libraries were pooled equimolar and run on a NextSeq550 generating 75-bp paired-end reads.

value: female

tag: age

value: grey matter (cortex)

tag: patient status

value: Primary Progressive MS


title: HFSCs-treated3


title: HEK293, 3h induction, replicate 3


title: HEK293, 3h induction, replicate 2


title: MS2

description:
rRNA-depleted total RNA
R2100162

tag: tissue

value: Secondary Progressive MS


title: HFSCs-treated2


title: HFSCs-treated1


title: cisplatin-ip ABCB5+ #25

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

data_processing:
Trimming with preprocessReads from the systemPipeR package in R (Parameter: cutoff=20, low_quality_rate=0.4, batchsize=100000)
Aligment:tophat v2.1.1 bowtie v2.2.9 Parameter: -g 1 --segment-length 25 -i 30 -I 3000 Genome RN6
Read Counts: summarizeOverlaps from the GenomicsAlignments package in R Parameter: mode=Union, ignore.strand=TRUE, inter.feature=FALSE, singleEnd=TRUE
RPKM Normalization with the returnRPKM function from systemPipeR package in R
Assembly: rn6
Supplementary files format and content: RPKM values generated with returnRPKM function from systemPipeR in R, raw counts generated with summarizeOverlaps from GenomicsAlignments in R

organism: Rattus norvegicus

source_name: kidney

growth_protocol: Male Sprague Dawley (SD) rats (250g) were purchased from Janvier Labs (Le Genest Saint Isle, France). Experiment started after 2 weeks of acclimatization. The animals had free access to pelleted standard rat chow (rat/mouse maintenance V1534-0001, Ssniff, Soest, Germany) and water in a temperature- and humidity- controlled facility (22°C, 55+/-5% rel. Hum.) with 12h light/12h dark cycle.

extract_protocol:
fresh left kidney was collected and snap frozen
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: Rats were treated with a single intraperioteneal dose of cisplatin (7mg/kgBW). 15 days after animals were sacrificed and the left kidney was collected from gene expression profiling

value: kidney

value: Sprague Dawley (SD)

value: male


title: HEK293, 3h induction, replicate 1

value: epithelial-like


title: MS1

description:
rRNA-depleted total RNA
R2100157

value: Progressive MS


title: HFSCs-control3

value: untreated


title: cisplatin-iv ABCB5+ #26


title: HEK293, 0h induction, replicate 3

value: inducible iRhom2-1-374 fragment integrated


title: cisplatin-ip ABCB5+ #28


title: HEK293, 0h induction, replicate 1


title: HEK293, 0h induction, replicate 2


title: cisplatin-iv ABCB5+ #5


title: C2

description:
rRNA-depleted total RNA
R2100164

value: healthy control


title: HFSCs-control2


title: HEK293, 6h induction, replicate 2

value: doxycycline


title: C1

description:
rRNA-depleted total RNA
R2100154


title: cisplatin-iv ABCB5+ #8


title: HFSCs-control1

value: CD34+CD49f+ HFSCs


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_BORIS cells_Treated with WashOff DOX

status: Public on Jan 03 2024

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

data_processing:
ChIP-seq, ATAC-seq, CAGE-seq data: single-end or paired-end reads were aligned either to the UCSC hg19 (human samples) or UCSC mm9 (mouse samples) genome using Bowtie version 2 under default parameters.
RNA-seq data: FASTQ files were either mapped to the UCSC mouse (build mm9) or human ((build hg19) reference genomes using STAR with default settings. Normalized gene counts and differentially expressed genes (DEG) were obtained with the R package DESeq2.
For ChIP-seq and ATAC-seq data, output BAM files were converted into bdg track files using MACS2
For CAGE-seq, ChIP-seq, ATAC-seq data, output BAM files were converted into bigwig files using bamCoverage option in deepTools 3.5.0 in order to display normilized coverage throughout the genome (in RPKM).
ChIP-seq and ATAC-seq peaks were called using Model-based Analysis for ChIP-seq (MACS2) using default parameters.
CAGE-seq clusters were called using MACS2  with parameters (--nomodel --shift -1)
bdg files were generated using  MACS2  with default settings.
Assembly: hg19 (for human) amd mm9 (for mouse)
Supplementary files format and content: bdg, xlsx (differentially expressed genes (DEG) were obtained with the R package DESeq2), bigwig (BAM files normilized using bamCoverage option in deepTools 3.5.0 (in RPKM))

growth_protocol: DMEM (NIH3T3, 293T, MDA-MB-435, MCF7 cells), RPMI (K562, CH12cells), 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2. Stable NIH3T3, MDA-MB-435 and MCF7 clones were maintained under 150 mkg/ml of Hygromycin B.

extract_protocol:
ChIP-seq protocol: 2x10^6 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol:NIH3T3 cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
RNA-seq protocol:The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-seq library were prepared using TruSeq RNA Library Prep Kit (Illumina, Inc., USA)
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
CAGE-seq libraries were prepared by DNAFORM (Yokohama, Kanagawa, Japan).

treatment_protocol: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days. After Dox treatment, the media was replaced with regular media (without dox). The cells were allowed to grow for additional 5 days (washing off Dox).

value: Mouse immortalized embryonic fibroblast cell line

tag: chip antibody

value: H2A.Z (Abcam, catalog # ab4174)

value: WashOff DOX

value: NIH3T3 stably transfected with dox-inducible pBIGi BORIS-expressing plasmid (pBIG_BORIS)


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_BORIS cells_Treated with no DOX

treatment_protocol: The cells were cultured in the absence of doxycycline (noDox), under regular culturing conditions.

value: no DOX


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_EV cells_Treated with DOX

treatment_protocol: The cells were cultured in the presence of doxycycline (Dox) concentration (1 μg/mL) for 5 days, with the refreshment of dox every two days.

value: DOX

value: NIH3T3 stably transfected with dox-inducible pBIGi_EV (Empty Vector (luciferase) expressing plasmid (pBIG_EV)


title: CAGE-seq in NIH3T3+BORIS cells 3

extract_protocol:
ChIP-seq protocol: 2x106 asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1×phosphate buffered saline (PBS), and resuspended in chromatin immunoprecipitation (ChIP) lysis buffer (150 mM NaCl, 1 % Triton X-100, 0.1 % SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to 200–600 bp and immunoprecipitated with 5 μg of antibody. Immunoprecipitated DNA was purified with QIAquick columns (ZymaResearch).
ATAC-seq protocol:NIH3T3 cells (5 × 104) were pelleted by centrifugation and resuspended in 50 µL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630), gently pipetting up and down 10 times. Nuclei were pelleted by centrifugation at 2500g for 10 min at 4°C and resuspended in 25 µL of 2x TD Buffer (Illumina Cat #FC-121-1030), containing 8 µL of Tn5 Transposes (Illumina Cat #FC-121-1030) and 17 µL of nuclease free water. The rection was incubated for 30 min at 37°C. Tagmented DNA was purified by using a Zymo Research DNA Clean & Concentrator™-5 - Capped Columns.
RNA-seq protocol:The RNA sequencing library preparation and sequencing procedures were carried out according to Illumina protocols. Briefly, poly(A)-mRNA was purified from 5 μg of RNA with streptavidin-coated magnetic beads. After chemical fragmentation, mRNA fragments were reverse-transcribed and converted into double-stranded cDNA. Following end repair and A-tailing, paired-end adaptors were ligated to the ends of the DNA fragments. The ligated products were amplified with 18 cycles of PCR followed by purification using AMPure beads (Beckman Coulter). The enriched libraries were diluted to a final concentration of 5 nM.
ChIP-seq libraries were prepared using TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA) or NEBNext UltraII DNA Library Prep Kit for Illumina (BioLabs, catalog # E7645S).  Libraries were amplified using 15 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
RNA-seq library were prepared using TruSeq RNA Library Prep Kit (Illumina, Inc., USA)
ATAC-seq libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs). The libraries were size-selected  by adding 1.8X volume Agencourt AMPure XP beads (Beckman, 63881).
CAGE-seq libraries were prepared by DNAFORM (Yokohama, Kanagawa, Japan).

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#3

value: NIH3T3 stably expressing BORIS


title: ChIP-seq with H2AZ Abs in NIH3T3+pBIGi_BORIS cells_Treated with DOX


title: cisplatin-ip ABCB5+ #7

value: kidney

value: Sprague Dawley (SD)

value: male


title: CAGE-seq in NIH3T3+BORIS cells 4

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#4


title: CAGE-seq in NIH3T3+BORIS cells 2

value: Stable ectopic expression of BORIS from CpG-free plasmid (InvivoGen) - Clone#2


title: HFSCs-control4

value: untreated


title: RNA-seq in NIH3T3+EV cells

value: Stable ectopic expression of a control plasmid (empty vector, EV), expressing beta-galactosidase (CpG-free plasmid (InvivoGen))

value: NIH3T3 stably expressing EV (Empty Vector)


title: RNA-seq in NIH3T3+BORIS cells 3

value: Mouse immortalized embryonic fibroblast cell line


title: RNA-seq in NIH3T3+BORIS cells 2


title: C3

description:
rRNA-depleted total RNA
R2100156

value: grey matter (cortex)

value: healthy control


title: Input for NIH3T3+EV cells


title: CAGE-seq in NIH3T3+EV cells


title: ChIP-seq with BORIS Abs in NIH3T3+BORIS cells 4

value: BORIS custom-made mouse monoclonal (characterized in  PMID:21659515)


title: ChIP-seq with BORIS Abs in NIH3T3+BORIS cells 2


title: ChIP-seq with BORIS Abs in NIH3T3+EV cells


title: ChIP-seq with CTCF Abs in NIH3T3+BORIS cells 3

value: CTCF custom-made mouse monoclonal (characterized in PMID:15731119)


title: ChIP-seq with BORIS Abs in NIH3T3+BORIS cells 3


title: ChIP-seq with CTCF Abs in NIH3T3+EV cells


title: ChIP-seq with CTCF Abs in NIH3T3+BORIS cells 4


title: ChIP-seq with CTCF Abs in NIH3T3+BORIS cells 2


title: mRNA eIF2A∆+SM replicate 2

first: Swati

last: Gaikwad

address: Building 6, Room 233

department: Section on Nutrient Control Of Gene Expression

institute: National Institutes of Health

description: DESeq2 eIF2Adelta+SM vs eIF2Adelta.xlsx and DESeq2 eIF2Adelta+SM vs WT+SM.xlsx

data_processing:
For ribo-seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. Subsequently, rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq samples, the same protocol mentioned above for ribo-seq analysis was followed.
Translational efficiency change analysis was performed with R DESeq2 package.
Assembly: sacCer3
Supplementary files format and content: The DESeq2 files to represent fold-change and raw reads that were used as input for the fold-change analysis

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Yeast cells were generally grown to an OD600 of 0.5-0.6 in synthetic complete medium lacking isoleucine and valine (SC-Ilv) at 30°C.

extract_protocol: For RNA-seq library preparation, total RNA was extracted and purified from aliquots of the same snapped-frozen cells described above using hot phenol-chloroform extraction. Five µg of total RNA was randomly fragmented by mixing with 2× alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH ≈ 9.3). After incubation for 20 min at 95ºC, fragmentation reactions were mixed with ice-cold stop solution (300 mM NaOAc pH 5.5, 30 µg GlycoBlue (Invitrogen; AM9516)). RNA was precipitated by adding one part of isopropanol followed by the standard protocol of precipitation. Fragment size selection, library generation, and sequencing were carried out using the same protocol described above for RPF library preparation, except the Ribo-Zero Gold rRNA Removal Kit (Illumina; MRZ11124C), was employed to remove rRNA after linker-ligation.

treatment_protocol: Cells were treated with the antimetabolite Sulfometuron methyl (SM) at 1 µg/mL for 25 before harvesting.

value: yeast cell

value: F2247 (MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 ygr054w{delta}::kanMX4)

value: SM


title: mRNA WT+SM replicate 2

description: DESeq2 WT+SM vs WT.xlsx and DESeq2 eIF2Adelta+SM vs WT+SM.xlsx

value: WT

value: BY4742 (MAT{alpha} his3{delta}1 leu2{delta}0 lys{delta}2 ura3{delta}0)


title: mRNA WT+SM replicate 1


title: mRNA eIF2A∆ replicate 2

description: DESeq2 eIF2Adelta vs WT.xlsx and DESeq2 eIF2Adelta+SM vs eIF2Adelta.xlsx

growth_protocol: Yeast cells were generally grown to an OD600 of 0.5-0.6 in synthetic complete medium at 30°C.

treatment_protocol: No additional treatment

value: control


title: mRNA eIF2A∆ replicate 1


title: RNA-seq in NIH3T3+BORIS cells 4

value: NIH3T3 stably expressing BORIS


title: OIR_p17_S8

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Sequencing data was analyzed on the Galaxy web platform (usegalaxy.eu). Quality control was performed with FastQC (Galaxy Version 0.73, http://www. bioinformatics.babraham.ac.uk/projects/fastqc/, last access on 22nd January 2022).
Reads were mapped to the human or mouse reference genome (Gencode M28) with RNA STAR (Galaxy Version 2.7.8a, default parameters).
The BAM files for each sample from each lane were combined in one BAM file per sample using Merge BAM files (Galaxy Version 1.2.0).
Reads mapped to the human or mouse reference genome were counted by featureCounts (Galaxy Version 2.0.1, default parameters).
The output of featureCounts was imported to RStudio (version 1.4.1103, R Version 4.0.3). Gene symbols and gene types were determined based on Ensembl (Release 105, download: 28.01.2022). Genes with 0 reads in all samples were removed from further analysis. Principal component analysis (PCA) was applied to check for potential outlier and batch effects.
Normalized reads and differential gene expression were calculated using the R package DESeq2 (version 1.34) with default parameters (Benjamini-Hochberg adjusted p-values). Transcripts with log2 fold change (log2FC) >2 or <-2 and adjusted p-value <0.05 were considered as differentially expressed genes (DEG).
Assembly: Gencode M28
Supplementary files format and content: csv, normalized reads (DESeq2)

source_name: retina

extract_protocol:
The fellow eye of these mice as well as both eyes pooled for other animals from that litter were processed for retinal extraction straight after intracardiac PBS perfusion and enucleation. Instead of mounting them on a template, however, they were stored in RNAlater for up to 6 days and shipped at 2-8°C to the RNA sequencing provider. Samples containing one and two retinae showed similar quality and quantity of extracted RNA. Total RNA was extracted from mouse retina stabilized in RNAlater buffer according to the “Purification of total RNA from animal and human tissue” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany) and was performed by the Genomics Core Facility “KFB - Center of Excellence for Fluorescent Bioanalytics” (University of Regensburg, Regensburg, Germany; www.kfb-regensburg.de). In brief, after centrifugation for 5 minutes at 5,000 x g and removing the RNAlater, the tissue was disrupted and homogenized in 350 µl RLT buffer containing 1% beta-mercaptoethanol with Precellys CK14 ceramic beads (1 cycle of 15 seconds at 5,500 rpm) using a Precellys 24 Homogenisator (Bertin Corp., Rockville, MD, USA). Next, the sample was centrifuged for 2 minutes at full speed and 350 µl of the cleared supernatant was transferred to a new tube. One volume of 70 % ethanol was added and the samples were applied to a RNeasy MinElute spin column followed by an on-column DNase digestion and several wash steps. Finally, total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip reagent set (Agilent, Palo Alto, CA, USA).
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from approximately 1 ng total-RNA. Double stranded cDNA was amplified by long distance (LD) PCR (11 cycles) and purified via magnetic bead clean-up. Library preparation was carried out as described in the Illumina Nextera XT Sample Preparation Guide (Illumina, Inc., San Diego, CA, USA). Thereby, 150 pg of input cDNA were tagmented (tagged and fragmented) by the Nextera XT transposome. The products were purified and amplified via a limited-cycle PCR program to generate multiplexed sequencing libraries. For the PCR step, 1:5 dilutions of the unique dual indexing (i7 and I5) adapters were used. The libraries were quantified using the KAPA Library Quantification Kit - Illumina/ABI Prism User Guide (Roche Sequencing Solutions, Inc., Pleasanton, CA, USA). Equimolar amounts of each library were sequenced on an Illumina NextSeq 2000 instrument controlled by the NextSeq 2000 Control Software (NCS) v1.2.0.36376, using one 50 cycles P3 Flow Cell with the dual index, single-read (SR) run parameters. Image analysis and base calling were done by the Real Time Analysis Software (RTA) v3.7.17. The resulting .cbcl files were converted into .fastq files with the bcl2fastq v2.20 software.

value: retina

value: OIR p17


title: mRNA eIF2A∆+SM replicate 1


title: Ribo eIF2A∆+SM replicate 2

data_processing:
For ribo-seq samples, Fastq records are trimmed with fastxtoolkit (version 0.0.14) to remove adapters sequences. Subsequently, rRNA sequence was removed with Bowtie2 (version 2-2.3.5.1) then mapped to yeast genome (sacCer3) with tophat (version 2.1.1). Perfect reads were extracted with samtools (version 1.9) for downstream analysis. Normalized wiggle files and reads counts are generated with RiboSeq tools (https://github.com/hzhanghenry/RiboProR). For RNA-seq samples, the same protocol mentioned above for ribo-seq analysis was followed.
Translational efficiency change analysis was performed with R DESeq2 package.
Assembly: sacCer3
Supplementary files format and content: The DESeq2 files to represent fold-change and raw reads that were used as input for the fold-change analysis
Library strategy: Ribo-seq

extract_protocol:
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in "eIF1A residues implicated in cancer stabilize translation preinitiation complexes and favor suboptimal initiation sites in yeast" Martin Marcos et al. (2017) eLife 6:e31250
Ribosome-protected RNA 25-34 nt


title: mRNA WT replicate 2

description: DESeq2 eIF2Adelta vs WT.xlsx and DESeq2 WT+SM vs WT.xlsx


title: OIR_p17_S7


title: Ribo WT+SM replicate 2


title: Ribo eIF2A∆+SM replicate 1


title: mRNA WT replicate 1


title: OIR_p17_S6


title: Ribo eIF2A∆ replicate 2


title: Ribo WT+SM replicate 1


title: OIR_p17_S4


title: Ribo eIF2A∆ replicate 1


title: OIR_p17_S5


title: Ribo WT replicate 2


title: OIR_p17_S2


title: OIR_p17_S3


title: Ribo WT replicate 1


title: T7-assisted reporter mapping library for synHEK3 reporters in a population derived from 500 clones K562 wild-type Rep1

city: Seattle

first: Xiaoyi

last: Li

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

institute: University of Washington

description: T7-assisted reporter mapping library

data_processing:
T7-assisted reporter mapping: Sequencing reads were first demultiplexed using the bcl2fastq software. Under the current library design and sequencing scheme, Read1 started from genomic sequence and extended into the integrated synHEK3 construct, while Read2 contained reporter barcode information. Therefore, 1) for each sequencing read pair, the 16-bp reporter barcode was extracted from Read 2 and attached to the read name of Read 1. 2) Read1 was trimmed using cutadapt (v4.1) with following parameters: --cores=4 --discard-untrimmed -e 0.2 -m 10 -O 8 -a CCCTAGAAAGATAGTCTGCGTAAAATTGACGCATG. The adapter corresponded to the 3’ITR of piggyBac transposon. Since parameter “--discard-untrimmed” was used, only reads spanning insertion junctions were kept and trimmed. 3) Trimmed sequences were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). The “-Y” option was used to enable soft clipping for supplementary alignments. 4) Reads uniquely (without XA:Z tag) and contiguously mapped near putative piggyBac landing pads (TTAA motifs) were kept using samtools (v1.9) and a custom script. 5) Aligned reads were converted to BED format using the sam2bed function in bedops (v2.4.35). Reads aligned to standard chromosomes were kept. 6) Insertion points were calculated for all reads based on strand of alignment. And reads were sorted by the insertion coordinates. 7) The first 8-bp of reads were used as UMIs. A custom script was used to collapse reads at a per-location, per-barcode, per UMI basis. A barcode-location-UMI count table was generated. 8) synHEK3 barcodes <3 Levenshtein Distance at each location were collapsed and barcodes with > 3 UMIs were kept. 9) The count table was converted to a GenomicRanges object in R. Coordinates of the last 4 base pairs of aligned reads were designated as genomic locations of the inserted synHEK3 reporters. 10) “Landing pads” of the mapped synHEK3 reporters were retrieved using the getSeq() function in the BSgenome package. Reporters that didn’t have a TTAA sequence (which could be due to PCR error, mapping error, or the use of non-canonical landing pads) were removed. 11) SynHEK3 barcodes mapped to more than one location were removed.
SynHEK3 amplicon sequencing library: Sequencing reads from the Illumina NextSeq platforms were first demultiplexed using the bcl2fastq software. The 16-bp reporter barcodes were extracted from read and attached to its read name. Sequences around the CRISPR cut site were extracted for all reads. A barcode-editing outcome table was generated. For prime editing experiments, a custom script was used to align sequences to a reference sequence and count mutation frequency for every barcode. For Cas9 mutagenesis analysis, all sequences were aggregated and editing outcomes (alleles) with the highest number of counts were selected. These most frequent alleles were then aligned to reference sequences using needleall with the following parameters: -gapopen 20 -gapextend 0.5 -endopen 20. A custom script was used to annotate the mutational events.
Amplicon sequencing of endogenous genes: Sequencing reads were demultiplexed using the bcl2fastq software (Illumina). A custom script was used to determine frequencies of the introduced substitutions.
Assembly: GRCh38
Supplementary files format and content: CRISPRa_K562_new.csv contains editing efficiencies in the CRISPRa experiments in K562 cells
Supplementary files format and content: CRISPRa_WTC11_new.csv contains editing efficiencies in the CRISPRa experiments in WTC11 cells
Supplementary files format and content: PE2max_endogenous_121_K562.csv contains editing efficiencies of the 121 epegRNAs in K562 cells
Supplementary files format and content: PE_IL2RB_libraries.csv contains corrected editing efficiencies of epegRNA pools targeting IL2RB (with and without CRISPR activation of IL2RB)
Supplementary files format and content: T7-WT-Pool1.csv contains mapped locations, editing outcomes, and chromatin scores of synHEK3 reporters in wild-type K562 cells
Supplementary files format and content: T7-WT-Pool2.csv contains mapped locations, editing outcomes, and chromatin scores of synHEK3 reporters in wild-type K562 cells

growth_protocol: K562 cells (CCL-243) were purchased from ATCC and maintained in RPMI 1640 medium (Gibco) supplied with 10% FBS (Hyclone) and penicillin/streptomycin (Gibco, 100 U/ mL). The DHFR-dCas9-VPH (VP48-P65-HSF1) WTC11 (human iPSCs) line was generated by the Martin Kampmann lab (Tian et al. 2021). Cells were maintained on Geltrex (Gibco) coated plates in the mTeSR Plus medium (STEMCELL Technologies) supplied with 10 uM Y-27632 (Stemgent). 20 uM trimethoprim was added to culture for stabilization of dCas9-VPH. All cells were kept in a humidified incubator at 37 oC, 5% CO2.

extract_protocol:
K562 and WTC11 cells were lysed in a lysis buffer [100 mM Tris-HCl pH8.0, 0.05% SDS and 0.04 mg/mL proteinase K(Thermo Scientific)], and incubated at 50 oC 60 min and 80 oC 30 min.
T7-assisted reporter mapping: gDNA of K562 cells was purified using the DNeasy Blood & Tissue Kit (QIAGEN) and in vitro transcribed with the HiScribe T7 High Yield RNA Synthesis Kit (New England Biolabs). Briefly, each reaction (20 uL) contained 0.3~1 ug gDNA, NTPs (10 mM each) and 2 ul T7 RNA Polymerase Mix. The reaction mixture was incubated at 37 oC for 16 hours. Then, gDNA was digested with 2.5 uL DNase (Qiagen) in a 100 uL reaction at room temperature for 30 min. RNA was extracted with TRIzol LS Reagent (Invitrogen), and aqueous phase was precipitated with 1 volume of isopropanol and 5 ug Glycogen (Invitrogen) at -80 oC for 1 hour. RNA pellet was collected by centrifugation at 21,000 x g at 4 oC for 1 hour. The pellet was washed with 80% ice-cold ethanol and resuspended in 11.5 uL nuclease-free water. For reverse transcription, RNA was incubated with 0.5 uL 100 uM RT primer p6 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNN-3’) and 1 uL 10 mM dNTP at 65 oC for 5 min and cooled on ice. Then, 4 uL 5X RT buffer, 1 uL 100 mM DTT, 1 uL RNaseOUT (40 U/uL) and 1 uL SuperScript IV RT (200 U/uL, Invitrogen) were added and the reaction mixture was incubated at 23 oC for 10 min, 50  oC for 15 min and 80 oC for 10 min. cDNA library was amplified with KAPA2G Robust HotStart polymerase, using primers p7 (5’- GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGAAAGGAAGCCCTGCTTCCTCCAGAGGG-3’, 0.5 uM) and p8 (5’- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, 16~18 cycles; and 72 oC 1 min. The PCR product was subjected to double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The resulting product ranged from 200 to 1000 bp. To prepare Illumina sequencing libraries, 5-10 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles. The final PCR product underwent another round of double-sided size selection (0.5X, 0.9X) and cleaned up with AMPure XP beads. The library was sequenced on an Illumina MiSeq in paired-end mode (Read 1: 254 bp; Read2: 55bp). Amplicon sequencing of synHEK3 reporters: 100~250 ng gDNA or cell lysates were amplified using KAPA2G Robust HotStart ReadyMix with primers p9 (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCTACCCCGACCACATGAAGCAGC-3’, 0.5 uM) and p10 (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNGACCATGTCATCGCGCTTCTCGT-3’, 0.5 uM). PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 68-N oC 15 s, 72 oC 30 s, for 9 cycles (N was cycle number); 95 oC 15 s, 65 oC 15 s, 72 oC 30 s, for 11 cycles; and 72 oC 1 min. To ensure enough coverage and accurate measurement of editing efficiencies, for the K562 synHEK3 pool, we pooled products from at least 16 PCR reactions. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.  Other amplicon sequencing: Cell lysates or plasmids were directly used for PCR with the KAPA2G Robust HotStart ReadyMix with primers (0.5 uM each) designed for the endogenous targets. PCR reaction was performed as follows: 95 oC 3 min; 95 oC 15 s, 66-N oC 15 s, 72 oC 40 s, for 8 cycles (N was cycle number); 95 oC 15 s, 60 oC 15 s, 72 oC 40 s, for 11 cycles; and 72 oC 1 min. The PCR product was purified with AMPure XP beads. 5 ng PCR product was re-amplified with the Nextera P5 and TruSeq P7 library index primers for 5 cycles.
Amplicon sequencing

treatment_protocol: Transfections of K562 cells were performed using a Lonza Bioscience 4D-Nucleofector system and the SF Cell Line 4D-Nucleofector X kits (Lonza). For single nucleocuvettes (100 uL), 1-2 x 106 cells were transfected with up to 4 ug DNA. For 96-well Nucleocuvette plates (20 uL), 2 x 105 ~ 5 x 105 cells were transfected with up to 2 ug DNA. Program code was FF-120. CRISPRa experiments (K562): On Day 0, 4 x 105 K562 dCas9-VP64 cells were transfected with PB-CMV-MCP-XTEN80-p65-Rta-3xNLS-P2A-T2A-mPlum (600 ng) and paired pU6-Sp-gRNA-2XMS2 (200 ng each) plasmids targeting the same promoter. On Day 2, 4 x 105 cells from the previous transfection were transfected with pCMV-PEmax (Addgene: 174820) or PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast (800 ng) and the pU6-Sp-pegRNA plasmids (400 ng). All transfections were performed using the SF Cell Line 96-well Nucleofector Kit (Lonza) with program FF-120. Cells transfected with PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast were selected with 2 ug/mL Puromycin 24 hours after transfection for 2 days. Cells were lysed at Day 5 or 6 for gDNA collection. CRISPRa experiments (WTC11): On Day 0, 2 x 105 the DHFR-dCas9-VPH WTC11 cells were transfected with PB-CMV-MCP-XTEN80-p65-Rta-3xNLS-P2A-T2A-mPlum (2100 ng) and paired pU6-Sp-gRNA-2XMS2 (700 ng each) plasmids targeting the same promoter. 20 uM Trimethoprim was added to induce dCas9-VPH. On Day 3, 2 x 105 cells from the previous transfection were transfected with PB-UCOE-EF1a-PE2max-P2A-mCherry-PGK-Blast (2000 ng) and the pU6-Sp-pegRNA plasmids (1000 ng). All transfections were performed using the P3 Prime Cell 96-well Nucleofector Kit (Lonza) with program CB-150. Cells were continued to be treated with 20 uM Trimethoprim and were selected with 2 ug/mL Puromycin 24 hours after transfection for 1 day. Cells were lysed at Day 5 or 6 for gDNA collection.

value: lymphoblast

value: wild-type


title: OIR_p14_S6

value: OIR p14


title: T7-assisted reporter mapping library for synHEK3 reporters in a population derived from 500 clones K562 wild-type Rep2

description: T7-assisted reporter mapping library


title: OIR_p14_S5


title: OIR_p14_S3


title: nOIR_p17_S6

value: Control p17


title: OIR_p14_S2


title: OIR_p14_S1


title: nOIR_p17_S2


title: nOIR_p17_S3


title: nOIR_p17_S5


title: nOIR_p17_S1


title: nOIR_p14_S7

value: Control p14


title: OIR_p14_S4


title: nOIR_p14_S6


title: nOIR_p14_S5


title: nOIR_p14_S4


title: OIR_p17_S1


title: nOIR_p14_S3


title: nOIR_p17_S4


title: nOIR_p14_S2


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_516]

type: RNA

city: Leuven

first: Deniz

last: Oner

address: Gaston Geenslaan

country: Belgium

institute: KU Leuven

description: Gene expression data of infants from RESCEU case-control cohort

hyb_protocol: After fragmentation, denaturation and end-labeling the targets are hybridized on the single GO Screen plate, according to manufacturer’s instructions (Thermo Fisher; GeneChip Pico Reagent Kit).

scan_protocol: Single sample cartridge arrays were stained on a GeneChip Fluidics Station 450 and scanned on a GeneChip scanner 3000 7G while array plates were stained and imaged on the GeneTitan Multi-Channel Instrument.

data_processing:
Microarray data were preprocessed using R, Bioconductor package 40,41. Robust Multi-Array Average (RMA) function was used to normalize the raw data 42. Outliers were removed from the downstream data analysis based on visual guidance on principal component (PC) spectral map and sample clustering (Pearson correlation with complete linkage).
The clinical data necessary for batch correction (site of sample collection) is accessible by request only from the submitting party.

label: biotin

source_name: whole blood

label_protocol: First strand cDNA was synthesized with a combination of a Poly-dT and random primers containing a 5′-adaptor sequence. A 3’-adaptor was added to the single stranded cDNA followed by low-cycle PCR amplification. The cDNA was used as a template for in vitro transcription (IVT) that produces amplified amounts of antisense mRNA, (cRNA). The cRNA was then used as input for a second round of cDNA synthesis, producing double stranded cDNA.

extract_protocol: The whole blood samples were collected in Paxgene tubes (PAXgene® Blood RNA Tube, BD) and stored at –80 °C until the processing. The RNA was extracted using QIAsymphony PAXgene Blood RNA Kit (QIAGEN) according to the manufacturer’s instructions. After the quality control, the RNA was further processed for Clariom™ GOScreen microarray (Thermo Fisher).

value: whole blood

tag: gender / sex

value: Male

tag: age in days

tag: age group

tag: visit

value: RSV visit

tag: disease classification at rsv visit based on resvinet score

value: 4 - Severe


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_402]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_515]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_518]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_401]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_396]


title: nOIR_p14_S1

tag: treatment


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_529rr]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_400]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_284]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_394]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_318]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_100]


title: ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Rep2

description: ATAC seq library

data_processing:
For RNA-seq, sequencing reads were demultiplexed using the bcl2fastq software (Illumina),  aligned to the GRCh38 reference genome, and counted against all Ensembl genes using STAR (2.7.6a). Raw counts were analyzed with DESeq2.
For ATAC seq, sequencing reads were demultiplexed using the bcl2fastq software (Illumina), and processed using the ENCODE ATAC-seq pipeline. Filtered peaks were sorted and merged across samples using bedops (v2.4.35) and were used to generate a peak count table using featureCounts (v2.0.2). Raw counts were analyzed with DESeq2.
Assembly: GRCh38
Supplementary files format and content: ATAC_HLTF.csv contains a count table of merged ATAC peaks across all samples
Supplementary files format and content: RNAseq_HLTF_HLTF2367_vs_control.csv contains a gene count table of the batch 1 RNA seq samples
Supplementary files format and content: RNAseq_HLTF_HLTF2623_vs_control.csv contains a gene count table of the batch 2 RNA seq samples

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

extract_protocol:
Total RNAs were purified from cells using TRIzol LS Reagent (Invitrogen) following manufacturer’s instructions, treated with DNase (QIAGEN or Invitrogen) and cleaned up using RNeasy Mini kit (QIAGEN). For ATAC-seq, 1 x 105 cells were collected, washed with PBS, and pelleted by centrifugation at 500 xg, 4 oC for 5 min. Cells were then lysed with 50 uL lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) on ice for 3 min and neutralize with 250 uL RSB buffer with Tween-20 (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20).
For RNA-seq, 1 ug total RNA (RNA integrity >= 9.9) were used for stranded mRNA library preparation using the Illumina TruSeq® Stranded mRNA Library Prep kit. The RNA libraries were indexed using the Illumina TruSeq RNA UD Indexes. For ATAC-seq, 1 x 105 cells were collected, washed with PBS, and pelleted by centrifugation at 500 xg, 4 oC for 5 min. Cells were then lysed with 50 uL lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) on ice for 3 min and neutralize with 250 uL RSB buffer with Tween-20 (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). Nuclei were counted on a hemocytometer and 5 x 104 nuclei underwent tagmentation. For tagmentation, per 50 uL contained 25 uL 2x TD Buffer, 8.25 uL PBS, 0.5 uL 1% Digitonin, 0.5 uL 10% Tween-20, 2.5 uL Tn5 enzyme (Illumina, 2.5 uM) and 13.25 uL water. The reaction was incubated at 37oC for 30 min. DNA was purified using the Clean and Concentrate kit (Zymo) and eluted in 10 uL EB Buffer (QIAGEN). All or half of the eluted DNA was used for qPCR. In each reaction, 10 uL tagmented DNA was mixed with 25 uL 2x NEBNext High-Fidelity 2X PCR Master Mix (NEB), 2.5 uL i5 primer, 2.5 uL i7 primer, 0.25 uL 100X SYBR Green (Invitrogen) and 9.75 uL water. The qPCR reaction was performed as follows: 72oC 5 min, 98 oC 30 s; 98 oC 10 s, 63 oC 30 s, 72 oC 1 min. The reaction was stopped after 7 cycles. Libraries were pooled, purified with AMPure XP beads, and sequenced on an Illumina NextSeq 2000 sequencer.

treatment_protocol: Before harvesting, cells were kept on 1 ug/mL Doxycycline for 5 days for induction of shRNA expression.

tag: cell line

tag: cell type

value: PE2(+); rtTA(+); LT3-shRNA

value: Doxycycline 1 ug/mL for 5 days


title: RNA seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Batch2 Rep2

description: RNA seq library


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_222]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_058]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_055]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_062]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_040rr]


title: RNA seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Batch1 Rep2

description: RNA seq library


title: RNA seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Batch2 Rep3

description: RNA seq library


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_203]


title: ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Rep1

description: ATAC seq library


title: RNA seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Batch1 Rep1

description: RNA seq library


title: ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2367) targeting HLTF Rep2

description: ATAC seq library


title: RNA seq library of K562 cells expressing control shRNA Batch2 Rep3

description: RNA seq library


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_031]


title: RNA seq library of K562 cells expressing control shRNA Batch2 Rep2

description: RNA seq library


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_544]

value: 3 - Moderate


title: RNA seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Batch2 Rep1

description: RNA seq library


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_037]


title: RNA seq library of K562 cells expressing control shRNA Batch1 Rep2

description: RNA seq library


title: ATAC seq library of K562 cells expressing shRNA(HLTF_6596_2623) targeting HLTF Rep1

description: ATAC seq library


title: RNA seq library of K562 cells expressing control shRNA Batch2 Rep1

description: RNA seq library


title: RNA seq library of K562 cells expressing control shRNA Batch1 Rep1

description: RNA seq library


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_491]


title: ATAC seq library of K562 cells expressing control shRNA Rep2

description: ATAC seq library


title: ATAC seq library of K562 cells expressing control shRNA Rep1

description: ATAC seq library


title: Plasmid sequencing of epegRNA targeting endogenous loci Pool2 (Rep2)

description: Amplicon sequencing of plasmid pool


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_095]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_330]


title: Plasmid sequencing of epegRNA targeting endogenous loci Pool2 (Rep1)

description: Amplicon sequencing of plasmid pool


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_540]


title: Plasmid sequencing of epegRNA targeting endogenous loci Pool1 (Rep2)

description: Amplicon sequencing of plasmid pool


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_064]


title: Plasmid sequencing of epegRNA targeting endogenous loci Pool1 (Rep1)

description: Amplicon sequencing of plasmid pool


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_316]


title: Prime editing of 121 endogenous sites (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_033]

value: 2 - Mild


title: Prime editing of 121 endogenous sites (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon9 after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes

value: K562 CRISPRa IL2RB


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_296]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_054]


title: Prime editing of IL2RB Exon9 after activation of CDKL5 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes

value: K562 CRISPRa CDKL5


title: Prime editing of IL2RB Exon9 after activation of CDKL5 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_492]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_537rr]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_499]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_475]


title: Amplicon of unedited IL2RB for sequencing error correction Exon9

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_467]


title: RSV visit, RSV-infected, hospitalized with mechanical ventilation (severe disease) [A4398_382]


title: Prime editing of IL2RB Exon9 after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_459]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_450]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_460]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_458]


title: Prime editing of IL2RB Exon8 after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon8 after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_416]


title: Amplicon of unedited IL2RB for sequencing error correction Exon8

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon5 after activation of CDKL5 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_471]


title: Prime editing of IL2RB Exon8 after activation of CDKL5 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon5 after activation of CDKL5 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_398]


title: Prime editing of IL2RB Exon5 after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_346]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_322]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_397]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_288]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_304]


title: Amplicon of unedited IL2RB for sequencing error correction Exon5

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon4 after activation of CDKL5 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon8 after activation of CDKL5 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon4 after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_279]


title: Prime editing of IL2RB Exon4 after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon2 after activation of CDKL5 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_255]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_233]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_229]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_228]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_209]


title: Amplicon of unedited IL2RB for sequencing error correction Exon2

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_199]


title: Amplicon of unedited IL2RB for sequencing error correction Exon4

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_160rr]


title: Prime editing of IL2RB Exon10 after activation of CDKL5 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon5 after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon2 after activation of CDKL5 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon10 after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_243]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_207]


title: Prime editing of IL2RB Exon2 after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_211]


title: Prime editing of IL2RB Exon10 after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon4 after activation of CDKL5 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_155]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_156]


title: Prime editing of IL2RB Exon2 after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_231]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_144]


title: Prime editing of IL2RB Exon10 after activation of CDKL5 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon1 after activation of IL2RB in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Amplicon of unedited IL2RB for sequencing error correction Exon10

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon1 after activation of CDKL5 in K562 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_153]


title: Prime editing of IL2RB Exon1 after activation of CDKL5 in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_151]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_034]


title: Amplicon of unedited IL2RB for sequencing error correction Exon1 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of IL2RB Exon1 after activation of IL2RB in K562 (Rep1)

description: Amplicon sequencing of engogenous genes


title: Amplicon of unedited IL2RB for sequencing error correction Exon1 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_116]


title: Prime editing of WNT3A after activation of WNT3A in WTC11 (Rep2)

description: Amplicon sequencing of engogenous genes

value: hiPSC

value: NGN2; DHFR-dCas9-VPH

value: WTC11 CRISPRa WNT3A


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_390]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_154]


title: Prime editing of CXCR4 after activation of CREB3L3 in WTC11 (Rep1)

description: Amplicon sequencing of engogenous genes

value: WTC11 CRISPRa CREB3L3


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_415]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_272]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_302]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_157]


title: Prime editing of CXCR4 after activation of CXCR4 in WTC11 (Rep2)

description: Amplicon sequencing of engogenous genes

value: WTC11 CRISPRa CXCR4


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_266]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_340]


title: Prime editing of WNT3A after activation of WNT3A in WTC11 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_149]


title: Prime editing of CXCR4 after activation of CREB3L3 in WTC11 (Rep2)

description: Amplicon sequencing of engogenous genes


title: Prime editing of WNT3A after activation of CXCR4 in WTC11 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_063]


title: Prime editing of EGFR after activation of EGFR in WTC11 (Rep1)

description: Amplicon sequencing of engogenous genes

value: WTC11 CRISPRa EGFR


title: Prime editing of WNT3A after activation of CXCR4 in WTC11 (Rep2)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4397_1061]


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_038rr]


title: Prime editing of EGFR after activation of CREB3L3 in WTC11 (Rep1)

description: Amplicon sequencing of engogenous genes


title: RSV visit, RSV-infected, hospitalized without mechanical ventilation (moderate disease) [A4398_012]


title: Prime editing of WNT3A in wild-type K562 cells  (Rep1)

description: Amplicon sequencing of engogenous genes

value: lymphoblast

value: wild-type