title: PW_052_IC_rep1

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

institute: Emory University

data_processing:
The data pre-processing tool, fastp, was used to perform quality control and adapter trimming. Results were filtered by quality. The software program Hierarchical Indexing for Spliced Alignment of Transcripts 2 (HISAT2) was used to map RNA sequencing reads prior to building the index using the human reference genome grch38. Indices were used to map sequential reads to the human genome. FeatureCounts were applied to generate a matrix of row counts of each of the genes in all the samples.
Assembly: human reference genome grch38
Supplementary files format and content: txt, counts

source_name: blood

growth_protocol: Blood was collected by venipuncture into an ethylenediaminetetraacetic acid (EDTA) vacutainer tube and centrifuged at 400XG to separate cells from platelet-rich plasma. After initial separation, plasma was centrifuged at 3000XG for 10 minutes at 4C to remove any remaining red blood cells or platelets prior to being frozen at -80C. Pelleted blood cells were resuspended in sterile phosphate buffered saline (PBS; Thermo Fisher Scientific, Waltham, MA) with 2.5 mM EDTA up to the original whole blood volume. Neutrophils were purified by negative selection from PBS-EDTA washed whole blood using the EasySep Direct Human Neutrophil Isolation kit (StemCell Technologies, Cambridge, MA) according to the manufacturer’s protocol. There was >99% neutrophil purity based on cytospin staining with Diff-Quik.

extract_protocol:
RNA was isolated from blood neutrophils after overnight culture with poly(I:C) using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara Bio, San Jose, CA). RNA was quantified using a NanoDrop Fluorospectrometer (Thermo Fisher). RNA was quality assessed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA) in the Emory Integrated Genomics Core. cDNA was generated using the SMART-Seq® v4 Ultra® low Input RNA Kit (Takara Bio).
The final RNA-seq library was generated using the Nextera XT kit (Illumina, San Diego, CA).
RNA-seq libraries were sequenced on the Novaseq 6000 with a sequencing depth of 30M paired-end 100 base pair reads per sample.

treatment_protocol: Two million neutrophils were resuspended in Roswell Park Memorial Institute (RPMI) medium (Thermo Fisher) without serum and cultured overnight at 37°C and 5% CO2 in a humidified incubator with 740 ng/ml low molecular weight lyoVec poly(I:C) (InvivoGen, San Diego, CA) resuspended in endotoxin-free water. After centrifugation at 400ΧG, neutrophil pellets were saved in RNAlater (Thermo Fisher) and frozen at -80°C.

value: blood

value: primary human cell

value: Neutrophil

value: Not sensitized, male

value: poly(I:C) stimulation


title: PW_055_IC_rep1

status: Public on Jan 29 2024

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: PW_055_IC_rep2


title: PW_052_IC_rep2


title: PW_051_IC_rep2

value: Not sensitized, female


title: PW_056_IC_rep2


title: PW_051_IC_rep1


title: PW_048_IC_rep1


title: PW_056_IC_rep1


title: PW_048_IC_rep2


title: PW_047_IC_rep2


title: PW_047_IC_rep1


title: PW_027_IC_rep2

value: Sensitized, male


title: PW_045_IC_rep1


title: PW_029_IC_rep1


title: PW_042_IC_rep2


title: PW_029_IC_rep2


title: PW_042_IC_rep1


title: PW_023_IC_rep2


title: PW_026_IC_rep1


title: PW_027_IC_rep1


title: PW_025_IC_rep1


title: PW_023_IC_rep1


title: PW_021_IC_rep2


title: PW_013_IC_rep2


title: Naïve_Br_CD11b_replicate2

city: Seattle

first: Michael

last: Gerner

state: WA

address: 750 Republican St

department: Immunology

institute: University of Washington

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads.  The FASTQs were aligned to the GRCm38 mouse reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count.  QC and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCm38
Supplementary files format and content: 210408-P408-1_RawGeneCounts
Supplementary files format and content: 210408-P408-1_NormGeneCounts

organism: Mus musculus

source_name: Br

extract_protocol:
Cells were sorted on an Aria III (BD Biosciences) directly into reaction buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA/
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies).  Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer (Illumina) with paired-end 59-base reads, using NextSeq P2 sequencing kits (Illumina) with a target depth of 5 million reads per sample.

treatment_protocol: Mice were injected with 50µg papain and 10µg EaGFP in the ear or forepaw and draining LNs were harvested 48 hours later.

value: Br

value: MHC2-hi CD11c-int CD11b+ CD301b-

tag: mouse genotype

value: Naive


title: PW_013_IC_rep1


title: PW_026_IC_rep2


title: PW_021_IC_rep1


title: Papain_Au_TN_replicate2

source_name: Au

value: Au

value: MHC2-hi CD11c-int CD11b- CD301b-

value: Papain 48h


title: PW_012_IC_rep1


title: PW_045_IC_rep2


title: PW_011_IC_rep1


title: PW_009_IC_rep2

value: Sensitized, female


title: PW_009_IC_rep1


title: PW_008_IC_rep2


title: PW_007_IC_rep2


title: PW_008_IC_rep1


title: PW_012_IC_rep2


title: PW_006_IC_rep1


title: genomic DNA from MPNST; case 1

type: genomic

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: Final integrated diagnosis of High-grade undifferentiated spindle cell sarcoma

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan

data_processing: RStudio (R package ChAMP v2.26.0)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: MPNST; case 1

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from FFPE samples using Resnova MagPurix FFPE DNA Extraction Kit according to standard instructions

tag: gender

value: M

tag: sample type

value: DNA extracted from FFPE tissue

tag: study group


city: Beijing

first: Wenqing

last: Liu

email: puyulwq@163.com, liuwq21@gamils.com

address: No. 5 Summer Palace Road, Haidian District, Beijing

country: China

institute: Peking University

description: detect tRNA-W-CCA-4 expression level in wildtype HEK293T cells treated with tRNA-R-TCT-1 overexpression

library_source: other

data_processing:
Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.6) for quality control and adapter trimming. The key parameters were: --illumina --length 60 -e 0.3. The first 10-nucleotide random barcode at the 5’ end was removed by umi_tools (version 1.0.0).
Cleaned reads were mapped to the tRNA reference (hg38, NCBI Refseq) using bwa mem(0.7.17-r1188) with default parameters. A maximum of 3 mismatches were allowed for the mapped reads.
The tRNA counts were quantified by HTSeq(version 1.14), and tRNAs with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The tRNA expression level was quantified by FPKM.
Assembly: GRCh38
Supplementary files format and content: Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.6) for quality control and adapter trimming. The key parameters were: --illumina --length 60 -e 0.3. The first 10-nucleotide random barcode at the 5’ end was removed by umi_tools (version 1.0.0). Cleaned reads were mapped to the tRNA reference (hg38, NCBI Refseq) using bwa mem(0.7.17-r1188) with default parameters. A maximum of 3 mismatches were allowed for the mapped reads. The tRNA counts were quantified by HTSeq(version 1.14), and tRNAs with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The tRNA expression level was quantified by FPKM.

molecule: other

source_name: Epithelial

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
total RNA was extracted from cells using TRIzol reagent (Life Technologies)
RNA libraries were prepared using modified eCLIP library construction, NEBNext Small RNA library kits (NEB) and SMARTer Stranded Total RNA-Seq kits (v3) - Pico Input mammalian (Takara) Library Prep Kit following manufacturer's protocols.

treatment_protocol: For transfection, 2.5 x 105 of HEK293T cells were seeded on 24-well plates (Corning), and all transfections were conducted when cells reached approximately 80% confluency after 20-24h. The plasmids were extracted using EndoFree Mini Plasmid Kit II (TIANGEN BIOTECH, DP118), and were transfected into cells by Lipofectamine LTX reagent (Invitrogen) supplemented with PLUS reagent (Invitrogen) according to the manufacturer’s instructions.

value: Epithelial

value: human embryonic kidney 293 cells

value: WT

value: W-CCA-4-1, HEK293T, tRNA-W-CCA-4 overexpressed, rep 1


value: W-CCA-4-2, HEK293T, tRNA-W-CCA-4 overexpressed, rep 2


title: PW_007_IC_rep1

value: blood

value: primary human cell

value: Neutrophil

value: poly(I:C) stimulation


title: PW_005_IC_rep2

value: Sensitized, male


description: detect tRNA-R-TCT-1 expression level in wildtype HEK293T cells treated with tRNA-R-TCT-1 overexpression

value: R-TCT-1-2, HEK293T, tRNA-R-TCT-1 overexpressed, rep 2


title: HEK293T, untreated, rep 2

description: detect tRNA expression level in untreated wildtype HEK293T cells

value: CTRL-2, HEK293T, untreated, rep 2


description: detect tRNA-W-CCA-2 expression level in wildtype HEK293T cells treated with tRNA-R-TCT-1 overexpression

value: W-CCA-2-1, HEK293T, tRNA-W-CCA-2 overexpressed, rep 1


description: detect tRNA-R-TCG-4 expression level in wildtype HEK293T cells treated with tRNA-R-TCG-4 overexpression

value: R-TCG-4-1, HEK293T, tRNA-R-TCG-4 overexpressed, rep 1


description: detect tRNA-R-TCT-4 expression level in wildtype HEK293T cells treated with tRNA-R-TCT-1 overexpression

value: R-TCT-4-1, HEK293T, tRNA-R-TCT-4 overexpressed, rep 1


title: PW_011_IC_rep2

value: Not sensitized, male


title: HEK293T, untreated, rep 1

value: CTRL-1, HEK293T, untreated, rep 1


title: 16HBE, untreated, rep 1

description:
detect modification level of specific TGA sites in R553X in untreated 16HBE
targetseq-CFTRandmIDUA.xlsx

data_processing:
First, sequencing reads with the same unique molecular identifier (UMI) were grouped and UMI groups with less than 3 reads were discarded.
Then, PCR duplicates were removed by retaining the most consensus sequence in each UMI group.
Adapter sequences were further trimmed from deduplicated reads with Trim_galore software (version0.6.7) with default parameters.
The 10-nucleotide UMIs were removed by umi_tools (version 1.0.0).
The cleaned reads were mapped to the targeted sequences using PRAISE-tool and the deletion rate of target sites was calculated.
Assembly: GRCh38
Supplementary files format and content: First, sequencing reads with the same unique molecular identifier (UMI) were grouped and UMI groups with less than 3 reads were discarded. Then, PCR duplicates were removed by retaining the most consensus sequence in each UMI group. Adapter sequences were further trimmed from deduplicated reads with Trim_galore software (version0.6.7) with default parameters. The 10-nucleotide UMIs were removed by umi_tools (version 1.0.0). The cleaned reads were mapped to the targeted sequences using PRAISE-tool and the deletion rate of target sites was calculated.

growth_protocol: MEF cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. 16HBEge cells were grown under 5% CO2 at 37°C in MEM medium (Corning) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).

treatment_protocol: RESTART v3 expressing AAVs were packaged in PackGene Company. 16HBE cells were seeded at a density of 1x105 in 24-well plate (Corning). 24 hours after seeding, 16HBE cells (CFTR-R553X) were transduced by AAV2 at multiplicities of infection 1 x 105. The cell medium was changed 24 hours after transduction. A group of 16HBEge cells was treated with 100 µg/mL G418. 5 days after transduction and 18 hours after G418 treatment, whole cell patch clamp experiments were performed. Besides, MEFs were seeded into 100 mm culture dishes at a density of 1.5 x 105 cells and were transduced by AAVDJ at multiplicities of infection of 5 x 106, 24 hours after seeding. The cell medium was changed 48 hours after transduction, and cells were collected after 7 days.

value: Epithelial

value: human bronchial epithelial cell line


title: 16HBE, RESTART v3-treated, rep 2

description:
detect modification level of specific TGA sites in R553X with RESTART v3 treatment
targetseq-CFTRandmIDUA.xlsx


description: detect tRNA-R-TCG-1 expression level in wildtype HEK293T cells treated with tRNA-R-TCG-1 overexpression

value: human embryonic kidney 293 cells

value: WT

value: R-TCG-1-2, HEK293T, tRNA-R-TCG-1 overexpressed, rep 2


value: R-TCT-4-2, HEK293T, tRNA-R-TCT-4 overexpressed, rep 2


title: 16HBE, RESTART v3-treated, rep 1


value: R-TCG-4-2, HEK293T, tRNA-R-TCG-4 overexpressed, rep 2


title: PW_005_IC_rep1

value: blood

value: primary human cell

value: Neutrophil


title: PW_006_IC_rep2

value: poly(I:C) stimulation


title: 16HBE, 18S, rep 2

description:
detect modification level of 18S specific sites in wildtype HEK293T cells
targetseq-CFTRandmIDUA.xlsx


title: 16HBE, 18S, rep 1


title: teratoma scMultiome [ATAC] rep2

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

description:
scMultiome [ATAC]
teratoma_rep2_filtered_feature_bc_matrix.h5
teratoma_AGGR_filtered_feature_bc_matrix.h5
teratoma_AGGR_atac_fragments.tsv.gz
teratoma_AGGR_atac_fragments.tsv.gz.tbi

library_source: genomic

data_processing:
Cell Ranger ARC pipeline (version 2.0.0) was used to analyze snMultiome-Seq data (scRNA-Seq + scATAC-Seq) using default settings. File formats: Filtered Feature Barcode Matrix (filtered_feature_bc_matrix.h5): It includes gene and peak features in rows  and columns limited to barcodes identified as cells from the CellRanger Output. ATAC Fragments (atac_fragments.tsv.gz): This file contains count and barcode data for each ATAC fragment from the CellRanger Output. GEX Molecule Information (gex_molecule_info.h5): This hdf5 format file provides count and barcode details for each GEX molecule observed in the experiment generated from the CellRanger Output. GEX barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files are also provided. Post-sequencing, data from the three replicates were aggregated using ‘cellranger aggr’.
Assembly: hg38
Supplementary files format and content: barcodes, features, matrix, hdf5, ATAC fragments, ATAC fragments index, aggregated (hdf5, ATAC fragments, barcodes, features, matrix)
Library strategy: Multiome

source_name: teratoma generated from H1 hESCs

growth_protocol: H1 hESCs were cultured on Matrigel-coated plates in serum-free E8 media at 37oC with 5% CO2 and passaged using EDTA. hESCs were dissociated using EDTA, and 1 million hESCs were injected subcutaneously into SCID-beige mice. Following a period of three to four weeks, mice were euthanized, and teratomas were cleaned and flash frozen.

extract_protocol: scMultiome libraries (ATAC + GEX) were prepared by using the 10x Genomics Single Cell Multiome ATAC + Gene Expression kit, in accordance with the guidelines provided by the manufacturer

value: H1 hESC

value: teratoma


value: W-CCA-2-2, HEK293T, tRNA-W-CCA-2 overexpressed, rep 2


value: R-TCT-1-1, HEK293T, tRNA-R-TCT-1 overexpressed, rep 1


title: teratoma scMultiome [ATAC] rep3

description:
scMultiome [ATAC]
teratoma_rep3_filtered_feature_bc_matrix.h5
teratoma_AGGR_filtered_feature_bc_matrix.h5
teratoma_AGGR_atac_fragments.tsv.gz
teratoma_AGGR_atac_fragments.tsv.gz.tbi


title: teratoma scMultiome [GEX] rep3

description:
scMultiome [GEX]
teratoma_rep3_filtered_feature_bc_matrix.h5
teratoma_AGGR_filtered_feature_bc_matrix.h5
teratoma_AGGR_barcodes.tsv.gz
teratoma_AGGR_features.tsv.gz
teratoma_AGGR_matrix.mtx.gz


title: teratoma scMultiome [GEX] rep2

description:
scMultiome [GEX]
teratoma_rep2_filtered_feature_bc_matrix.h5
teratoma_AGGR_filtered_feature_bc_matrix.h5
teratoma_AGGR_barcodes.tsv.gz
teratoma_AGGR_features.tsv.gz
teratoma_AGGR_matrix.mtx.gz


title: mRNA-12_V2D0

city: Hamburg

first: Marylyn

middle: M.

last: Addo

address: Martinistraße 52

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.422 and quality control was performed using fastqc and BioBloom Species check.
Transcripts were mapped to the human genome using the pseudo-alignment software kallisto (0.46.1).
Supplementary files format and content: Homo_sapiens.GRCh38
Supplementary files format and content: comma separated values (csv) file with raw counts for each sample

source_name: Whole blood

extract_protocol:
RNA was isolated from PAXgene blood RNA tubes using Qiagen's BloodRNA Kit following manufacturer's protocol.
Library prepararation was performed using the TruSeq stranded mRNA library prep assay, according to manufacturer’s protocol.

value: Whole blood

tag: participant id

tag: vaccination

tag: time point

value: Pre

tag: v1 vaccine_type

tag: v2 vaccine_type

tag: v3 vaccine_type

tag: Sex

value: Male

tag: batch id


title: mRNA-12_V3D1

tag: tissue


title: mRNA-12_V2D1


title: mRNA-10_V2D0

value: Female


title: mRNA-08_V3D1


title: teratoma scMultiome [GEX] rep1

description:
scMultiome [GEX]
teratoma_rep1_filtered_feature_bc_matrix.h5
teratoma_AGGR_filtered_feature_bc_matrix.h5
teratoma_AGGR_barcodes.tsv.gz
teratoma_AGGR_features.tsv.gz
teratoma_AGGR_matrix.mtx.gz

tag: cell line


value: Epithelial

tag: cell type

value: human embryonic kidney 293 cells

value: R-TCG-1-1, HEK293T, tRNA-R-TCG-1 overexpressed, rep 1


title: mRNA-12_V3D0


title: mRNA-10_V2D1


title: mRNA-08_V2D1


title: mRNA-07_V3D1


title: mRNA-08_V3D0


title: mRNA-07_V3D0


title: mRNA-08_V2D0


title: mRNA-07_V2D1


title: mRNA-06_V2D1


title: mRNA-07_V2D0


title: mRNA-06_V2D0


title: Naïve_Br_CD301b_replicate2

value: Br

value: MHC2-hi CD11c-int CD11b+ CD301b+

value: Naive


title: mRNA-05_V2D1


title: teratoma scMultiome [ATAC] rep1

description:
scMultiome [ATAC]
teratoma_rep1_filtered_feature_bc_matrix.h5
teratoma_AGGR_filtered_feature_bc_matrix.h5
teratoma_AGGR_atac_fragments.tsv.gz
teratoma_AGGR_atac_fragments.tsv.gz.tbi


title: mRNA-03_V3D1


title: mRNA-03_V3D0


title: mRNA-05_V2D0


title: mRNA-02_V3D1


title: mRNA-01_V2D1


title: mRNA-02_V3D0


title: Naïve_Au_TN_replicate3

value: Au

value: MHC2-hi CD11c-int CD11b- CD301b-


title: mRNA-01_V2D0


title: ChAd-07_V2D1

value: ChAdOx


title: ChAd-07_V3D1


title: ChAd-08_V2D0


title: ChAd-05_V3D1


title: ChAd-07_V3D0


title: ChAd-06_V2D0


title: ChAd-06_V2D1


title: ChAd-07_V2D0


title: ChAd-05_V3D0


title: ChAd-04_V2D0


title: ChAd-04_V2D1


title: ChAd-03_V3D1


title: ChAd-03_V3D0


title: ChAd-05_V2D1


title: ChAd-03_V2D1


title: ChAd-02_V2D0


title: ChAd-03_V2D0


title: mRNA-01_V3D1


title: ChAd-02_V2D1


title: mRNA-01_V3D0


title: ChAd-01_V3D0


title: ChAd-01_V2D1


title: ChAd-01_V3D1


title: ChAd-01_V2D0


title: ChAd-08_V2D1


title: 2wk iPSC derived neuron, patient line FF2, FRDA unedited, replicate 2 batch 1 [2-wk-FF2-unedited_-2]

city: Austin

first: Anna

last: Warden

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description:
raw_counts.txt
raw_TPM.txt

data_processing:
FASTQ files from sequencing experiments were mapped to hg38. RNA-seq files were mapped using the alignment tool STAR (v2.7.10b).
Raw RNA-sequencing files were evaluated for quality control using FastQC (v0.12.0).
Gene expression raw counts was quantified by HOMER’s ‘analyzeRepeats’
Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Quantified read counts were normalized and analyzed using DESeq2 (v1.12.3) to determine differential expression between groups, within the R statistical computing environment (v4.2.2)
Assembly: hg38
Supplementary files format and content: tab-delimited text file inclues raw counts for each Sample
Supplementary files format and content: tab-delimited text file inclues raw TPM for each Sample

source_name: iPSC-dervied neurons

extract_protocol:
To perform the mRNA sequencing, total RNA was isolated using the RNeasy Tissue kit (Qiagen, Hilden, Germany, cat. 74104) according to the manufacturer’s instructions. RNA was assessed for quality using an Agilent Tapestation 4200, and 50 ng of RNA with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries
RNA sequencing libraries using the Illumina Stranded mRNA Prep (Illumina) following manufacturer’s instructions

value: iPSC-dervied neurons

value: reprogrammed patient line FF2

value: neuron

tag: genotype

value: FRDA

value: Unedited FRDA lines


title: 2wk iPSC derived neuron, patient line FF2, FRDA edited, replicate 1 batch  [2-wk-FF2-edited_-1]

description:
raw_counts.txt
raw_TPM.txt

value: Edited

tag: treatment

value: CRISPR corrected FRDA lines


title: ChAd-05_V2D0

value: Whole blood

value: Pre

value: Female


title: 2wk iPSC derived neuron, patient line FF1, FRDA edited, replicate 2 batch 1 [2wk-FF-1_-2]

description:
raw_counts.txt
raw_TPM.txt

value: reprogrammed patient line FF1


title: 2wk iPSC derived neuron, patient line FF2, FRDA unedited, replicate 1 batch 1 [2-wk-FF2-unedited_-1]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line FF2, FRDA edited, replicate 2 batch 1 [2-wk-FF2-edited_-2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 223, FRDA unedited, replicate 1 batch 1 [2wk-223_unedited-1]

description:
raw_counts.txt
raw_TPM.txt

value: reprogrammed patient line 225


title: 2wk iPSC derived neuron, patient line FF2, FRDA unedited, replicate 2 batch 2 [2-wk-FF2-unedited_-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line FF1, FRDA edited, replicate 1 batch 1 [2wk-FF-1_-1]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 223, FRDA edited, replicate 2 batch 1 [2wk-223_edited-2]

description:
raw_counts.txt
raw_TPM.txt

value: reprogrammed patient line 224


title: 2wk iPSC derived neuron, patient line 223, FRDA edited, replicate 1 batch 1 [2wk-223_edited-1]

description:
raw_counts.txt
raw_TPM.txt

value: reprogrammed patient line 223


title: 2wk iPSC derived neuron, patient line E35, FRDA edited, replicate 2 batch 1 [2wk-_E35-2]

description:
raw_counts.txt
raw_TPM.txt

value: reprogrammed patient line E35


title: 2wk iPSC derived neuron, patient line FF2, FRDA unedited, replicate 1 batch 2 [2-wk-FF2-unedited_-1b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line FF2, FRDA edited, replicate 2 batch 2 [2-wk-FF2-edited_-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line FF2, FRDA edited, replicate 1 batch 2 [2-wk-FF2-edited_-1b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line FF1, FRDA edited, replicate 2 batch 2 [2wk-FF-1_-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line FF1, FRDA edited, replicate 1 batch 2 [2wk-FF-1_-1b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line E35, FRDA edited, replicate 1 batch 2 [2wk-_E35-1b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line E35, FRDA edited, replicate 2 batch 2 [2wk-_E35-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 850, FRDA unedited, replicate 1 batch 2 [2wk-850-_UE-1b2]

description:
raw_counts.txt
raw_TPM.txt

value: reprogrammed patient line 850


title: 2wk iPSC derived neuron, patient line 850, FRDA edited, replicate 1 batch 2 [2wk-850-_Edt-1b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 850, FRDA edited, replicate 2 batch 2 [2wk-850-_Edt-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 223, FRDA unedited, replicate 2 batch 2 [2wk-223_unedited-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 850, FRDA unedited, replicate 2 batch 2 [2wk-850-_UE-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 223, FRDA unedited, replicate 2 batch 1 [2wk-223_unedited-2]

description:
raw_counts.txt
raw_TPM.txt

value: reprogrammed patient line 226


title: 2wk iPSC derived neuron, patient line E35, FRDA edited, replicate 1 batch 1 [2wk-_E35-1]

description:
raw_counts.txt
raw_TPM.txt

value: iPSC-dervied neurons


title: 2wk iPSC derived neuron, patient line 223, FRDA edited, replicate 2 batch 2 [2wk-223_edited-2b2]

description:
raw_counts.txt
raw_TPM.txt


title: 2wk iPSC derived neuron, patient line 223, FRDA edited, replicate 1 batch 2 [2wk-223_edited-1b2]

description:
raw_counts.txt
raw_TPM.txt


title: SNU-4837

city: Davis

first: Sarah

middle: S

last: Wang

state: CA

address: 1 Shields Ave

institute: University of California, Davis

data_processing:
Assembly: hg38
The CpG_Me pipeline (https://github.com/ben-laufer/CpG_Me) was used to perform all data processing steps.
Trim Galore was used to trim adapters and methylation bias.
FastQ Screen was used to screen for sample contamination.
Bismark was used align to the reference genome, remove PCR duplicates, calculate coverage, extract CpG methylation, and generate genome-wide cytosine reports (CpG count matrices).
Picard Tools was used to calculate insert size metrics.
MultiQC was used for quality control.
Supplementary files format and content: Bismark CpG methylation bedgraph files

source_name: pancreatic ductal adenocarcinoma patient-derived organoid

growth_protocol: Patient-derived organoids were grown to 70-90% confluency in a 50ul dome of 100% Matrigel with human organoid culture media [DMEM F12 Advanced (Invitrogen), 10 mM HEPES pH 7.2-7.5 (Invitrogen), 1X GlutaMax (Invitrogen), 1X Penicillin/Streptomycin (Invitrogen), 500 nM A83-01 (Tocris), 50 ng/mL hEGF (Invitrogen), 100 ng/mL hFGF-10 (Peprotech), 10 nM hGastrin I (Sigma), 100 ng/mL mNoggin (Peprotech), 1.25 mM N-aceylcysteine (Sigma), 10 mM Nicotinamide (Sigma), 100 ug/mL Primocin (InvivoGen), 1 uM PGE2 (Tocris), 1X B27 Supplement (Invitrogen), 10% R-spondin-conditioned media, 50% Afamin/Wnt3A conditioned media], in 4-6 wells of a 24-well plate.

extract_protocol:
Media was removed from Matrigel domes, and 4-6 wells of organoids were harvested in 1 mL of Cell Recovery Solution (Corning). DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit per manufacturer's instructions.
Swift BioSciences Accel-NGS Methyl-Seq DNA Library Kit
Whole genome bisulfite sequencing (WGBS)

value: male

tag: tumor stage

value: tumor (locally advanced)


title: SNU-4779

value: pancreatic ductal adenocarcinoma patient-derived organoid

value: female

value: tumor (metastatic)


title: SNU-4863

value: tumor (borderline)


title: SNU-5177


title: SNU-4482

value: tumor (resectable)


title: SNU-4893


title: SNU-4894


title: SNU-4871


title: SNU-4461


title: SNU-4457


title: SNU-4425


title: SNU-4378


title: SNU-4874


title: SNU-4557


title: SNU-4340


title: SNU-4354


title: 2wk iPSC derived neuron, patient line 223, FRDA unedited, replicate 1 batch 2 [2wk-223_unedited-1b2]

description:
raw_counts.txt
raw_TPM.txt

value: neuron

value: FRDA

value: Unedited FRDA lines


title: SNU-4243


title: SNU-4242


title: SNU-4305


title: SNU-4158


title: SNU-4206


title: SNU-4208


title: SNU-4192


title: SNU-4525


title: SNU-3947


title: SNU-4365


title: hN1

source_name: normal pancreatic ductal patient-derived organoid

value: normal


title: SNU-3898


title: hN4

value: normal pancreatic ductal patient-derived organoid


title: hN9


title: SNU-3912


title: hN18


title: SNU-3926


title: PW_025_IC_rep2

value: blood

value: primary human cell

value: Neutrophil

value: Not sensitized, female

value: poly(I:C) stimulation


title: SLX-22979.SITTB3.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0040

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: BSN +/- differentiated cells

library_source: transcriptomic single cell

data_processing:
Cellranger Version 6.0.1
Sequence reads were mapped to the human genome GRCh38
UMI and gene-level counts were performed against Ensembl gene model V100.
Assembly: GRCh38
Supplementary files format and content: Per cell gene count tables in HDF5

growth_protocol: The KOLF2.1J human-induced pluripotent stem cell line and its derivatives were maintained on Geltrex (Thermo Fisher Scientific A1413202) coated plates in supplemented StemFlex media (Thermo Fisher Scientific A3349401) with daily medium changes. For passaging, the cells were washed with PBS and treated with TrypLE Express (Gibco, 12604021) at 37℃ for 3 min. The cells were re-suspended in StemFlex media supplemented with 10 μM ROCK Inhibitor Y-27632 dihydrochloride (Stemcell Technologies, 72304). ROCK inhibitor was removed the following day with growth medium without the Y-27632. Unless otherwise stated, cells were split at a 1:5 ratio. The absence of mycoplasma was confirmed using an EZ-PCR Mycoplasma Test Kit (Biological Industries, 20-700-20) following the manufacturer's instructions.

extract_protocol:
On day 36, cells were dissociated using TrypLE™ and papain mixture, pelleted, and nuclei were isolated following a 10x Genomics protocol for single nucleus RNA Sequencing (NucSeq) as previously reported.
Sequencing libraries for single-nuclei suspension samples were generated using 10X Genomics Chromium Single-Cell 3′ Reagent kits (Pleasanton, CA, USA, version 3.1) according to the manufacturer’s menu. Briefly, nuclear suspensions were loaded onto the chromium chip along with gel beads, partitioning oil, and master mix to generate GEMs containing free RNA. RNA from lysed nuclei was reverse transcribed and cDNA was PCR amplified for 19 cycles. The amplified cDNA was used to generate a barcoded 3′ library according to the manufacturer's protocol, and paired-end sequencing was performed using an Illumina NovaSeq 6000 (San Diego, CA, USA, read 1: 28 bp and read 2: 91 bp). Library preparation and sequencing was performed by the Genomics Core, Cancer Research UK Cambridge Institute.
10X Single nucleus RNA-Seq

treatment_protocol: Gene edited BSN p.L400Wfs*114 heterozygous and WT clones were differentiated into hypothalamic-like neurons as previously described63,64. Briefly, cells were cultured overnight on 10cm plate Geltrex coated plates (9.5 x105 cells/well for 6-well plates) in StemflexTM with 10 μM ROCK inhibitor. Next day, neuroectoderm differentiation was initiated by dual SMAD inhibition using XAV939 (Stemgent 04-1946), LDN 193289 (Stemgent 04-0074) and SB 431542 (Sigma Aldrich S4317) and Wnt signaling inhibition using XAV939 (Stemgent 04-1946) in an in-house neural differentiation N2B27 medium64. From day 2 to day 7, cells were directed ‘towards ventral diencephalon’ with Sonic hedgehog activation, by the addition of Smoothened agonist SAG (1μM Thermo Fisher Scientific 56-666) and purmorphamine (PMC, 1 μM Thermo Fisher Scientific 54-022), with SMAD and Wnt inhibition molecules gradually replaced with N2 B27 medium changed every 2 days. At Day 8, the cells were switched into N2B27 with 5 μM DAPT (Sigma Aldrich D5942) to exit cell cycle. On Day 14, the cells were harvested with TrypLETM supplemented with papain (Worthington LK003176) and re-plated onto laminin–coated 6-well plates at a density of 3x106 cells per well in the presence of maturation medium containing brain-derived neurotrophic factor BDNF (10ng/ml, Sigma) containing N2B27. On day 16 media was changed to Synaptojuice 1 (N2B27, 10ng/ml BDNF, 2 μM PD0332991 (Sigma Aldrich, PZ0199), 5 μM DAPT, 370 μM CaCl2 (Sigma Aldrich, 21115), 1 μM LM22A4 (Tocris, 4607), 2 μM CHIR99021 (Cell Guidance Systems, SM13), 300 μM GABA (Tocris, 0344), 10 μM NKH447 (Sigma Aldrich, N3290)). Cells were maintained in Synaptojuice 1 for a week before being changed to Synaptojuice 2 (N2B27, 10ng/ml BDNF, 2 μM, 370 μM CaCl2 1 μM LM22A4, 2 μM CHIR99021). Cells were then maintained in Synaptojuice 2 until day 36, with media renewal every second day throughout the differentiation and maturation period.

value: iPSC-derived neurons

value: BSN+/-

value: Differentiated hypothalamic neurons

tag: library id

tag: 10x barcode

tag: flowcell

tag: clone


title: SLX-22979.SITTE2.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0006

description: BSN +/- differentiated cells


title: SNU-3997

value: pancreatic ductal adenocarcinoma patient-derived organoid

value: male


title: SLX-22979.SITTA3.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0006

description: BSN +/- differentiated cells


title: SLX-21198.SITTH1.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0006

description: BSN +/- differentiated cells


title: SLX-21198.SITTB1.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0006

description: BSN +/- differentiated cells


title: SLX-22979.SITTF3.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0040

description: BSN +/- differentiated cells


title: SLX-22979.SITTF2.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0040

description: BSN +/- differentiated cells


title: SLX-21198.SITTA1.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0006

description: BSN +/- differentiated cells


title: LN-3.3x-B

type: RNA

first: K

middle: Dane

last: Wittrup

state: Massachusetts

department: Koch Institute for Integrative Cancer Research

institute: Massachusetts Institute of Technology

description: Nanostring Canine IO nCounter panel (XT-CIO-12)

hyb_protocol: Hybridization of RNA to the Canine IO nCounter panel probe set (Nanostring) was performed according to manufacturer's instructions for 23 hours at 65C. Hybridized RNA was loaded into the analysis cartridge using Nanostring PrepStation.

scan_protocol: Scanning of analysis cartridge was performed on Nanostring Digital Analyzer under maximum resolution.

data_processing: Nanostring nSolver software was used to process count data, beginning with batch correction between cartridge scans using a panel standard control. Background thresholding was performed using the mean of 8 negative control probes. Normalization was performed in nSolver prior to analysis of differential gene expression and pathway analysis between cohorts.

molecule: polyA RNA

organism: Canis lupus familiaris

source_name: Lymph node metastasis

growth_protocol: n/a - client-owned dogs with malignant melanoma

extract_protocol: RNA was extracted from FFPE tissue scrolls (10um) using Qiagen FFPE RNEasy kit following manufacturer's protocol. Samples were QC'd for concentration and fragment analysis on Bioanalyzer (Agilent) prior to hybridization to the nCounter panel probe set.

treatment_protocol: Dogs with malignant melanoma were enrolled into four treatment cohorts to examine the safety and efficacy of different doses of intratumoral collagen-binding cytokines IL-2 and IL-12 after a single 9Gy dose of radiation therapy. Tissue from primary and metastatic tumors was collected from patients upon progression and euthanasia to examine modes of resistance to this combination therapy.

tag: melanoma

value: Oral malignant melanoma

value: IV

tag: age

tag: weight

value: 9Gy RT + Intratumoral IL-2 and IL-12

tag: dose level

value: 3.3x dose level (57.4 ug/kg IL-2; 6.86 ug/kg IL-12)

tag: survival


title: Tumor-3.3x-C

source_name: Tumor

value: III


title: Tumor-3.3x-B


title: LN-5x-A

value: 5x dose level (87 ug/kg IL-2; 10.4 ug/kg IL-12)


title: Tumor-5x-B


title: Lung-3.3x-B

source_name: Lung metastasis


title: Lung-3.3x-C


title: Lung-5x-B


title: Lung-5x-A


title: SLX-22979.SITTH3.WT.Differentiated hypothalamic neurons.Clone.FLD0122

description: BSN WT differentiated cells

value: WT


title: SLX-22979.SITTH2.WT.Differentiated hypothalamic neurons.Clone.FLD0122

description: BSN WT differentiated cells


title: SLX-22979.SITTD3.WT.Differentiated hypothalamic neurons.Clone.FLD0122

description: BSN WT differentiated cells


title: SLX-22979.SITTE3.BSN+/-.Differentiated hypothalamic neurons.Clone.FLD0006

description: BSN +/- differentiated cells


title: SLX-21197.SITTF10.WT.Differentiated hypothalamic neurons.Clone.FLD0122

description: BSN WT differentiated cells


title: Tumor-5x-A


title: Tumor-2x-B

value: II

value: 2x dose level (34.8 ug/kg IL-2; 4.16 ug/kg IL-12)


title: Tumor-3.3x-A


title: Lung-3.3x-A


title: iPSC-derived dopamine neurons, normal control, co-cultured with astrocytes, 3D (chip) format

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: 10x Genomics

data_processing:
Sample demultiplexing was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core.  Raw data were delivered as multiple gzipped fastq files.
Demultiplexed fastq files were run via CellRanger v6.1.2 using the "cellranger count" command with the "--include-introns" option using the precompiled CellRanger human reference sequence “v2020-A” provided on the 10x Genomics website.
CellRanger output “filtered_feature_bc_matrix files” (barcodes.tsv.gz, features.tsv.gz & matrix.mtx.gz) were loaded into R (v4.2.1) via Rstudio (v2022.07.1, Build 554) and combined into one matrix file per sample with genes as rows (with both gene symbol and Ensmbl ID) and cells (nuclei) as columns. Each matrix file was then processed by summing all Ensmbl IDs with the same gene symbol to the gene symbol level via standard R matrix processing functions.
Assembly: hg38
Supplementary files format and content: Comma separated count matricies with gene symbols as rows and cell ID as columns

molecule: nuclear RNA

source_name: frozen cell pellet

extract_protocol:
All steps were performed on ice.  Wide-bore Rainin LTS pipette tips were used exclusively throughout. Frozen cell pellets were thawed on ice, resuspended in cold homogenization buffer (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, 320 mM Sucrose, 0.1 mM EDTA, 0.1% NP40, RNAse inhibitors, and Protease inhibitors), and transferred to a 2 ml glass dounce.  The tissue was manually lysed with 50 strokes each of the "A" and "B" pestles.  Homogenate was filtered using 70 um Flowmi pipette tip filters and gently mixed 1:1 with a 50% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, and 50% Iodixanol).  A centrifugation gradient was set up using 600 ul 40% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, 0.2 ug/ul OrangeG, and 40% Iodixanol), 600 ul 29% Iodixanol solution (5mM MgCl2, 3mM Mg(Ac)2, 10mM Tris pH7.8, 0.017 mM PMSF, 0.17 mM b-mercaptoethanol, RNAse inhibitors, Protease inhibitors, 160 mM Sucrose, and 29% Iodixanol) and 800 ul of the 50% Iodixanol + Sample mixture (25% Iodixanol final concentration).  This was centrifuged at 3000 x g for 1 hour with the breaks disengaged.  Any debris on the top surface was removed, and 200 ul of the thin cloudy layer containing the nuclei was extracted, mixed with 1.8 ml PBS + 1% BSA solution, and centrifuged at 500 x g for 10 minutes with breaks engaged.  1.8 ml supernatant was removed and the remaining 200 ul plus nuclei pellet was resuspended in 1.8 ml PBS + 1% BSA solution.  The nuclei suspension was counted via hemocytometer and checked for nucleus quality.  A portion of this suspension was then diluted to achieve the correct nuclei concentration for the 10x Chromium NextGEM 3' protocol with a target of ~4,000 nuclei per sample.
Standard 10x protocol found in "Chromium NextGEM Single Cell 3' Reagent Kits v3.1 User Guide, Rev D" (single index)

value: frozen cell pellet

value: iPSC-derived dopamine neurons

value: normal control

value: Sciencell Catalog #1850 Human Astrocytes-midbrain

value: Astrocytes


title: SLX-21197.SITTA11.WT.Differentiated hypothalamic neurons.Clone.FLD0122

description: BSN WT differentiated cells

value: iPSC-derived neurons

value: Differentiated hypothalamic neurons


title: Lung-2x-A


title: Tumor-2x-A


title: LN-1x-A

value: Periocular melanoma

value: 1x dose level (17.4 ug/kg IL-2; 2.08 ug/kg IL-12)


title: HEK293T,RESTART v3-TGA-RNA,rep 2

description: detect global RNA expression level in wildtype HEK293T cells with RESTART v3-TGA treatment

data_processing:
Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.7) for quality control and adapter trimming. The key parameters were: -q 20 --phred33 --stringency 3 --length 20. Trimmed reads were down-sampled to 30Mb using seqtk. The key parameters were: seqtk sample -s 100 30000000.
Then the cleaned reads were mapped to the human genome (hg38, NCBI Refseq) using STAR (version 2.7.10b) with default parameters. Mapped reads were filtered by samtools (version 1.14). The key parameters were: samtools view -f 3 -F 256.
The gene counts were quantified by HTSeq (version 1.14),  and genes with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The gene expression level was quantified by FPKM.
Assembly: GRCh38
Supplementary files format and content: Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.7) for quality control and adapter trimming. The key parameters were: -q 20 --phred33 --stringency 3 --length 20. Trimmed reads were down-sampled to 30Mb using seqtk. The key parameters were: seqtk sample -s 100 30000000. Then the cleaned reads were mapped to the human genome (hg38, NCBI Refseq) using STAR (version 2.7.10b) with default parameters. Mapped reads were filtered by samtools (version 1.14). The key parameters were: samtools view -f 3 -F 256. The gene counts were quantified by HTSeq (version 1.14),  and genes with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The gene expression level was quantified by FPKM.

value: Epithelial

value: human embryonic kidney 293 cells


title: HEK293T,gctrl-TGA-RNA,rep 1

description: detect global RNA expression level in wildtype HEK293T cells with gctrl-TGA treatment


title: LN-3.3x-A

value: Oral malignant melanoma

value: 9Gy RT + Intratumoral IL-2 and IL-12

value: 3.3x dose level (57.4 ug/kg IL-2; 6.86 ug/kg IL-12)


title: HEK293T,gctrl-TGA-RNA,rep 2

value: WT


title: Tumor-1x-A

value: III


title: HEK293T,RESTART v3-TGA-RNA,rep 1


title: HEK293T,gctrl-TAG-RNA,rep 1

description: detect global RNA expression level in wildtype HEK293T cells with gctrl-TAG treatment


title: HEK293T,RESTART v3-TAG-RNA,rep 2

description: detect global RNA expression level in wildtype HEK293T cells with RESTART v3-TAG treatment


title: HEK293T,gctrl-TAG-RNA,rep 2


title: SLX-21197.SITTB11.WT.Differentiated hypothalamic neurons.Clone.FLD0122

description: BSN WT differentiated cells


title: HEK293T,RESTART v3-TAA-RNA,rep 2

description: detect global RNA expression level in wildtype HEK293T cells with RESTART v3-TAA treatment


title: HEK293T,RESTART v3-TAA-RNA,rep 1


title: HEK293T,gctrl-TAA-RNA,rep 2

description: detect global RNA expression level in wildtype HEK293T cells with gctrl-TAA treatment


title: U251, TRIM, 6Gy, 24h

city: RAMAT GAN

first: Garima

last: Chaturvedi

state: TEL AVIV

address: mAX VEANNA WEB, STREET 1

department: The Mina and Everard Goodman Faculty of Life Sciences

country: Israel

institute: Bar-Ilan University

data_processing:
Reads were sorted, according to their barcodes, to different fastq files for each bait and condition and aligned to the human (hg19) genome using BOWTIE
Reads were then counted for each HindIII site.
For domain detection, the number of reads on each HindIII site was counted in sliding windows of 50Kb with 25Kb steps.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes bedgraph for each sample
Library strategy: 4C-seq

growth_protocol: U251 cells were cultured in Dulbecco's modified Eagle's medium (DMEM; Sigma-Aldrich Inc., St. Louis, MO) treatments of the rest of the cells supplemented with 10% FBS, 3.2% nonessential amino acids (NEEA), 4 mmol/L l-Glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin on six 14cm plates.

extract_protocol:
The 4C (chromosome conformation capture) technique was carried out as previously described in Schwartz M et. al., 2015.
The cross-linked chromatin was subjected to overnight digestion with an excess amount of HindIII enzyme (New England Biolabs). Subsequently, the DNA ends were ligated under diluted conditions that promote the formation of junctions between cross-linked DNA fragments. The ligated junctions were then circularized through digestion with DpnII (Thermo Scientific). Chromosomal interactions with the target regions, known as baits, were amplified using inverse PCR primers (Supplementary Table S3) and Platinum Taq DNA Polymerase (LifeTechnologies). The Illumina Hi-seq 2000 platform was used to sequence 4C-seq libraries.

treatment_protocol: A total of 20x10^6 cells were exposed to IR doses of 1Gy and 6Gy, while 18.5x10^6 cells were maintained as the control group. Cells were harvested at 6 or 24 hours post-irradiation. Untreated cells were harvested 24 hours after the irradiation.

value: human glioblastoma cell line

value: Irradiation

tag: dose

tag: time

tag: bait

value: TRIM


title: U251, PRSS35, 6Gy, 24h

tag: cell line


title: U251, TRIM, 6Gy, 6h

tag: cell type


title: U251, TRIM, 1Gy, 24h

tag: genotype


title: U251, TRIM, 0h

tag: treatment

value: control


title: U251, PRSS35, 6Gy, 6h


title: SNU-5345

tag: tissue

value: pancreatic ductal adenocarcinoma patient-derived organoid

tag: Sex

value: male

tag: tumor stage

value: tumor (metastatic)


title: HEK293T,gctrl-TAA-RNA,rep 1


title: LN-2x-A

value: IV

value: 2x dose level (34.8 ug/kg IL-2; 4.16 ug/kg IL-12)


title: U251, PRSS35, 1Gy, 24h


title: PINK1 KO T cells

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: PINK KO mouse, CD4 T cells

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

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

value: spleen

value: PINK KO mouse

value: CD4 T


title: U251, PRSS35, 1Gy, 6h


title: HEK293T,RESTART v3-TGA-tRNA,rep 1

description: detect tRNA expression level in wildtype HEK293T cells with RESTART v3-TGA treatment

value: Epithelial

value: human embryonic kidney 293 cells


title: iPSC-derived dopamine neurons, normal control, co-cultured with astrocytes, 2D (plate) format

description: 10x Genomics

value: frozen cell pellet

value: iPSC-derived dopamine neurons

value: normal control

value: Sciencell Catalog #1850 Human Astrocytes-midbrain

value: Astrocytes


title: HEK293T,gctrl-TGA-tRNA,rep 2

description: detect tRNA expression level in wildtype HEK293T cells with gctrl-TGA treatment

value: WT


title: U251, PRSS35, 0h

value: human glioblastoma cell line

value: Irradiation

value: control


title: U251, TRIM, 1Gy, 6h

value: TRIM


title: HEK293T,gctrl-TGA-tRNA,rep 1


title: HEK293T,RESTART v3-TAG-tRNA,rep 1

description: detect tRNA expression level in wildtype HEK293T cells with RESTART v3-TAG treatment


title: HEK293T,gctrl-TAG-tRNA,rep 2

description: detect tRNA expression level in wildtype HEK293T cells with gctrl-TAG treatment


title: U251, PPIB, 1Gy, 24h

value: PPIB


title: U251, PPIB, 0h


title: U251, PPIB, 6Gy, 6h


title: U251, PPIB, 1Gy, 6h


title: HEK293T,RESTART v3-TAA-tRNA,rep 2

description: detect tRNA expression level in wildtype HEK293T cells with RESTART v3-TAA treatment


title: U251, PPIB, 6Gy, 24h


title: B6 KO T Cells

label: biotin-labeled with TdT (terminal deoxynucleotidyl transferase)

source_name: C54BL/6 WT mouse, CD4 T cells

value: C54BL/6 mouse


title: HEK293T,RESTART v3-TAA-tRNA,rep 1


title: HEK293T,gctrl-TAG-tRNA,rep 1


title: U251, HCRTR, 6Gy, 24h

value: HCRTR


title: U251, HCRTR, 6Gy, 6h


title: HEK293T,gctrl-TAA-tRNA,rep 2

description: detect tRNA expression level in wildtype HEK293T cells with gctrl-TAA treatment


title: U251, HCRTR, 1Gy, 24h


title: U251, HCRTR, 1Gy, 6h


title: HEK293T,18S,rep1

description: detect modification level of 18S specific sites in wildtype HEK293T cells


title: HEK293T,gctrl-TAA-tRNA,rep 1


title: U251, HCRTR, 0h


title: U251, BTG, 6Gy 24h

value: BTG


title: HEK293T,RESTART v3-target TAA,rep 2

description: detect modification level of specific TAA sites in wildtype HEK293T cells with RESTART v3 treatment


title: HEK293T,RESTART v3-target TAA,rep 1


title: U251, BTG, 1Gy 24h


title: HEK293T,RESTART v3-TAG-tRNA,rep 2


title: U251, BTG, 6Gy, 6h


title: HEK293T,RESTART v2-target TAA,rep 1

description: detect modification level of specific TAA sites in wildtype HEK293T cells with RESTART v2 treatment


title: U251, BTG, 1Gy, 6h


title: U251, BTG, 0h


title: U251, 6Gy I, 24h

data_processing:
The alignment was done using TopHat
Read count on transcripts was done using HTSeq
An expression and differential analysis were done using edgeR
Genes with FDR < 0.05 and logFC greater than |0.5| were considered differentially expressed
Functional enrichment was done using IPA (Qiagen
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes RPKM value for each sample

extract_protocol:
Total RNA was isolated from cells using an RNA purification kit (GeneAll) as directed by the manufacturer.
Messenger RNA (mRNA) was enriched from 1 μg of total RNA by Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), following the manufacturer's protocol. The NEBNext Ultra RNA Library Prep Kit (New England Biolabs) was used to create cDNA libraries in accordance with the manufacturer's instructions.


title: U251, 6Gy III, 24h


title: U251, 6Gy II, 24h


title: HEK293T,RESTART v3-target TAG,rep 1

description: detect modification level of specific TAG sites in wildtype HEK293T cells with RESTART v3 treatment


title: HEK293T,RESTART v1-target TAA,rep 1

description: detect modification level of specific TAA sites in wildtype HEK293T cells with RESTART v1 treatment


title: HEK293T,RESTART v3-target TAG,rep 2


title: HEK293T,RESTART v2-target TAG,rep 1

description: detect modification level of specific TAG sites in wildtype HEK293T cells with RESTART v2 treatment


title: U251, 6Gy III, 6h


title: U251, 6Gy I, 6h


title: U251, 6Gy II, 6h


title: U251, 1Gy III, 24h


title: HEK293T,RESTART v1-target TAG,rep 2

description: detect modification level of specific TAG sites in wildtype HEK293T cells with RESTART v1 treatment


title: HEK293T,RESTART v1-target TAG,rep 1


title: HEK293T,RESTART v3-target TGA,rep 2

description: detect modification level of specific TGA sites in wildtype HEK293T cells with RESTART v3 treatment


title: U251, 1Gy II, 24h


title: U251, 1Gy I, 24h


title: HEK293T,RESTART v3-target TGA,rep 1


title: HEK293T,RESTART v2-target TGA,rep 2

description: detect modification level of specific TGA sites in wildtype HEK293T cells with RESTART v2 treatment


title: U251, 1Gy III, 6h


title: HEK293T,RESTART v2-target TAA,rep 2


title: U251, 1Gy II, 6h


title: HEK293T,RESTART v2-target TGA,rep 1


title: U251, 1Gy I, 6h


title: HEK293T,RESTART v1-target TAA,rep 2


title: HEK293T,RESTART v1-target TGA,rep 2

description: detect modification level of specific TGA sites in wildtype HEK293T cells with RESTART v1 treatment


title: U251, control III, 0h


title: HEK293T,RESTART v2-target TAG,rep 2


title: U251, control I, 0h


title: HEK293T,RESTART v1-target TGA,rep 1


title: WISC_3101

city: Madison

first: James

middle: E

last: Gern

state: WI

address: K4/918 CSC, 600 Highland Ave

department: Pediatrics

institute: University of Wisconsin-Madison

description: nasopharyngeal swab from two-year-old child

data_processing:
Initial processing: Basecalling was performed with CASAVA and samples were demultiplexed with bcl2fastq.
Trimming: We removed Illumina adapter sequences and trimmed read ends to a minimum quality score of 20 using the skewer utility (PMID:24925680).
Expression quantification: Trimmed read pairs were provided to kallisto v0.46.1 (PMID:27043002) to quantify transcript-level expression values using a pre-built index built from Ensembl v96 GRCh38 (https://github.com/pachterlab/kallisto-transcriptome-indices/releases). We summarized the estimated counts values to the gene level using tximport (PMID:26925227).
Exploratory data analysis: Clustering and PCA analysis identified variation associated with whether the sample was collected in 2018. We adjusted for this in downstream analysis.
Assembly: GRCh38 v96
Supplementary files format and content: all_samples_gene_counts.tsv.gz: A compressed, single TSV file that gives the gene-level counts estimated by kallisto and summarized to the gene level using tximport. Column names correspond to sample titles.

source_name: nasopharyngeal cells and secretions

extract_protocol:
Coordinators obtained nasal cells and secretions by inserting a swab (#516CS01, Copan Inc., Murrieta, CA) into the nasopharynx, rotating it three times, and then immediately immersing it in a cell lysis buffer (RLT buffer, Qiagen, Ann Arbor MI) to preserved the RNA. The tube containing the swab tip was vortexed, kept at 4C overnight, and cryopreserved at -80C pending RNA extraction (RNeasy Micro Kit, Qiagen).
RNA (1 ng) was fragmented, and cDNA was synthesized using random hexamers (SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian reagents, Takara Inc). Next, we added Illumina-compatible indexed adapters and enzymatically depleted host rRNA. A second round of amplification was used to generate the final sequence library.

value: nasopharyngeal cells and secretions

value: 2 years

tag: farm status

value: F

tag: num respiratory_illnesses_by_2yrs

value: 2:Med (6-9 illnesses)

tag: collected 2018


title: WISC_3091

source_name: nasopharyngeal epithelial cells and secretions

tag: age

value: M


title: WISC_3061

value: nasopharyngeal epithelial cells and secretions

value: 3:High (10+ illnesses)


title: wild type, biological replicate 4

city: New York

last: Podlesny-Drabiniok

state: NY

address: 1425 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads QC FastQC v0.11.8
Adapter trimming Cutadapt v2.6
Alignment to the mouse genome STAR v2.5.3a
Assembly: mm10
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

source_name: brain

growth_protocol: Female Bhlhe40–/–Bhlhe41–/– (double knock-out, DKO) or wildtype (C57BL/6J or Rosa26Stop-YFP)

extract_protocol:
Rneasy Mini column (Qiagen)
TruSeq RNA Sample Prep Kit v2

treatment_protocol: no treatment

value: brain

value: female

value: microglia

value: no treatment


title: Bhlhe40/41-DKO, biological replicate 3

value: DKO


title: wild type, biological replicate 3

value: WT


title: Bhlhe40/41-DKO, biological replicate 2


title: wild type, biological replicate 5


title: Bhlhe40/41-DKO, biological replicate 4


title: WISC_3071


title: WISC_2991


title: S662D.Fast.4

city: San Francisco

first: Louis

last: Ptacek

institute: University of California San Francisco

data_processing:
fastq files were aligned to mm10 genome using STAR (2.7.10b) indexer with default options
Reads from aligned files were assigned to genes using Subread::featurecounts (v2.0.1) with options -J, -M, -p, -g
Assembly: mm10
Supplementary files format and content: output of Subreads::featurecounts by gene. Reads per gene per library

source_name: hypothalamus

extract_protocol:
Hypothalamus from coordinates: 0 to -3 mm anteroposterior, 1.5 to -1.5 mm mediolateral, 4 to 7 mm dorsoventral were dissected. Extraction was performed with Zymo total RNA columns.
polyA containing transcripts were enriched and library prepped by Novogene. Libraries were sequenced to ~20 million, paired-end, 150 bp reads.

treatment_protocol: Mice were fed ad libitum or fasted from ZT0 to ZT16.

value: hypothalamus

value: Male

tag: strain

value: 16 hour Fast

tag: timepoint


title: S662D.Fast.5


title: S662D.Fast.3


title: wild type, biological replicate 2


title: S662D.Fast.2


title: Bhlhe40/41-DKO, biological replicate 1


title: VML+Vehicle

city: Ann Arbor

first: Carlos

middle: Andres

last: Aguilar

address: 2200 Bonisteel Blvd

department: Biomedical Engineering

institute: University of Michigan

data_processing:
10x CellRanger v7.0.0 software’s mkfastq and multi command were run with default parameters except expect-cells = 8000 to produce HD5 matrices
Seurat V4.2 was used to filter ( genes expressed in less than 200 cells or cells expressing less than three genes were removed) and merge HD5 files.
Linear dimensional reduction was performed followed by FindNeighbors and RunUMAP.
Clustering was performed using the Louvain unsupervised clustering algorithm (resolution = 0.1). Seurat’s FindAllMarkers function was used to annotate cell types.
MAST was used to determine differential gene expression between treatments.
Assembly: mm39
Supplementary files format and content: raw count matrix.h5

source_name: TA muscle

growth_protocol: Bilateral 2mm biopsy punch defects were administered to the tibialis anterior muscles of young mice, then treated with maresin 1 or vehicle on days 1, 3, and 5 post injury. At 7 days post injury, mice were humanely euthanized, TAs extracted, pooled according to treatment.

extract_protocol:
TA muscles were pooled from three mice according to treatment, then digested into single-cell suspensions as described in manuscript.
cDNAs were prepared using the single-cell 3′ protocol as per the manufacturer’s instructions and sequenced on a NovaSeq 6000 (Illumina) with 26 bases for read1 and 98 × 8 bases for read2.

value: TA muscle

value: VML+vehicle


title: VML+Maresin 1

value: VML+maresin


title: WISC_2931

value: 2 years

value: F

value: 1:Low (0-5 illnesses)


title: S662D.Fast.1


title: U251, control II, 0h

value: human glioblastoma cell line

value: Irradiation

value: control


title: wild type, biological replicate 1

value: brain

value: female


title: Bhlhe40/41-DKO, biological replicate 5

value: microglia

value: no treatment


title: WISC_2921

value: nasopharyngeal epithelial cells and secretions

value: 3:High (10+ illnesses)


title: T4_4OHT_A

city: Montreal

first: Marlene

last: Oeffinger

state: Quebec

address: 110 Ave Pins Ouest

department: Center for Genetic and Neurological Diseases,

country: Canada

institute: IRCM

data_processing:
The overall quality of data (mapped reads, Gini index) was first assessed using MAGeCK. The sgRNA read count files were calculated using the raw fastq files for each experiment using the MAGeCK ‘count’ function on Galaxy Australia.
Assembly: TKOv3 sgRNA library
Supplementary files format and content: MAGeCK sgRNA read counts
Library strategy: sgRNA-seq

source_name: Eye; Pigmented epithelium; Retina

growth_protocol: Cells were cultured at 37C in 5 % CO2 in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 1 % PenStrep and 10 % fetal bovine serum (FBS, Wisent)

extract_protocol:
Total genomic DNA was purified using the Wizard Genomic DNA Purification Kit (Promega)
The libraries were prepared with a two-step PCR to (1) enrich guide-RNA regions in the genome and (2) amplify guide-RNAs with Illumina TruSeq adapters with i5 and i7 indices. PCR 1 was performed on 140 µg to 200 µg of genomic DNA (42 PCR reactions per sample, 25 cycles of amplification) using the LCV2 forward and reverse primers. All PCR products of the same sample were pooled, purified with KAPA Ampure beads (1X) and size-selected with KAPA Ampure beads (L:1 / R:0.5). PCR 2 was performed using i5 Forward and i7 Reverse primers (10 cycles) and purified with KAPA Ampure beads (1.2X). Size selection (range 100 bp-190 bp) was done with a Pippin Prep 2% agarose cassette followed by a purification with KAPA Ampure beads (1.2X).

treatment_protocol: Cells were treated with 100 nM Shield-1 (medchemexpress) and 100 nM 4-hydroxytamoxifen (4-OHT, medchemexpress) or DMSO for 1 hr at 37C 1 day after plating, washed twice with PBS, and replenished with fresh media.

value: Eye; Pigmented epithelium; Retina

value: Epithelial-like

value: p53-/-, DD-HA-ER-I-PpoI

value: Shield-1 + 4-OHT


title: T4_4OHT_B


title: S662D.AL.5

value: hypothalamus

value: Male

value: Ad Libitum Fed


title: T4_CTL_A

value: DMSO


title: WISC_2831

value: 2 years

value: F

value: 1:Low (0-5 illnesses)


title: T2_4OHT_B


title: T2_CTL_B


title: WISC_2781

value: 2:Med (6-9 illnesses)


title: WISC_2721


title: S662D.AL.1


title: T2_CTL_A


title: S662D.AL.3


title: T0_2

value: Untreated


title: WISC_2631


title: WISC_2761

value: M


title: S662D.AL.4


title: HEK293T,RESTART v3-TAG-RNA,rep 1

description: detect global RNA expression level in wildtype HEK293T cells with RESTART v3-TAG treatment

source_name: Epithelial

value: Epithelial

value: human embryonic kidney 293 cells

value: WT


title: T0_1

value: Eye; Pigmented epithelium; Retina


title: D23-1667_E_rep3

city: Boston

first: Chun-Chin

last: Chen

state: MA

address: 300 Longwood Avenue

institute: BCH

data_processing:
FASTQ files were examined using FASTQC and confirmed high quality per sequence; determined quality trimming not needed.
FASTQ files were mapped to hg19 genome in Rsubread (2.12.0) in R (4.2.2) using align function for local alignment.
Reads are counted in Rsubread using featureCounts default options.
Differential analysis was performed in edgeR (3.40.2) in R (4.2.2). Genes with CPM>0.5 (~10 counts) in more than three samples were selected. Read counts were normalized to library sizes.
Differential comparisons between two genotypes were based on quasi-likelihood F-test.
Assembly: hg19
Supplementary files format and content: Tab delimited text files of raw counts from Rsubread
Supplementary files format and content: Tab delimited text files of normalized CPM values from edgeR

growth_protocol: Hematopoietic differentiation using STEMdiff Hematopoietic Kit (STEMCELL #05310) in human iPSCs following manufacturer’s protocol.

extract_protocol:
RNeasy Micro Kit (Qiagen)
Clontech SMARTseq v2 Low-Input method in a high-throughput system at MIT BioMicro Center

value: iPSC-derived progenitors

value: Euploid


title: D23-1668_T21_rep3

value: Trisomy 21


title: S662D.AL.2

value: hypothalamus


title: D23-1669_T21G1s_rep3

value: Trisomy 21-GATA1s


title: WISC_2611

value: nasopharyngeal epithelial cells and secretions

value: 3:High (10+ illnesses)


title: D23-1670_T21SA2_rep3

value: Trisomy 21-GATA1s-STAG2null


title: ko.Fast.5

value: Male

value: Per2 ko

value: 16 hour Fast


title: T2_4OHT_A

value: Epithelial-like

value: p53-/-, DD-HA-ER-I-PpoI

value: Shield-1 + 4-OHT


title: D23-1665_T21G1s_rep2


title: D23-1666_T21SA2_rep2


title: D23-1664_EG1s_rep2


title: WISC_2601

value: 2 years

value: F

value: 2:Med (6-9 illnesses)


title: D23-1663_T21_rep2

value: iPSC-derived progenitors


title: WISC_2551

value: M


title: T4_CTL_B

value: Eye; Pigmented epithelium; Retina

value: DMSO


title: ko.Fast.3

value: hypothalamus


title: ko.Fast.2


title: WISC_2521

value: nasopharyngeal epithelial cells and secretions

value: 1:Low (0-5 illnesses)


title: D23-1661_T21SA2_rep1

value: Trisomy 21-GATA1s-STAG2null


title: D23-1658_T21_rep1

value: Trisomy 21


title: D23-1660_EG1s_rep1


title: Ctrl.Fast.10

value: Male

value: Control


title: D23-1659_T21G1s_rep1

value: Trisomy 21-GATA1s


title: NC2, HEK293T cells, 72h after RPL24 KD

city: Jerusalem

first: Yonat

last: Tzur

address: Givat Ram Campus

institute: Hebrew University of Jerusalem

data_processing:
Fastq files were generated within BaseSpace using FASTQ Generation
Quality control was performed using FastQC, version 0.11.9. Flexbar (with parameters "-q TAIL -qf Sanger -qw 4 -min-read-length 16") served for adapter trimming and quality based filtering of all raw reads. Small RNA was aligned to the miRBase version 21 using miRExpress 2.1.4 allowing one mismatch but skipping adapter trimming for miR expression, and to the tRNA transcriptome using the MINTmap pipeline with default parameters for tRF expression (using only reads mapping exclusively to the  tRNA space).
Assembly: miRBase 21, MINTmap 1.0
Supplementary files format and content: files include raw counts from miRNAs and tRFs, csv files used as input for DESeq2 analysis

growth_protocol: Cells were grown in a humidified atmosphere at 37oC, 5% CO2 in DMEM. Media was supplemented with 10% FBS, 2mM L-glutamine, 1000 units/ml penicillin, 0.1 mg/ml streptomycin sulfate and 0.25 microgram/ml amphotericin B (Beit-Haemek, Israel).

extract_protocol:
RNA was extracted using the miRNeasy kit (Qiagen) following manufacturer's instructions
Libraries were constructed from 800 ng of RNA (NEBNext, Multiplex Small RNA library prep kit for Illumina, New England Bioloabs, Ipswich MA, USA)

treatment_protocol: HEK293T cells were seeded in 24 well plates and transfected the next day with 50nM of siPOOLs targeting RPL24 or control non-targeting siPOOLs (ON-TARGETplus siRNA, Horizon, United Kingdom). 48 hours post siPOOL transfection; cells were transfected with miR-608 plasmids, to test RPL24 depletion on miR-608 levels. 24 hours post plasmid transfection (and 72h post siPOOL transfection) the cells were harvested and RNA was extracted using the miRNeasy kit (Qiagen).

value: non-targeting siPOOLs

value: day 72


title: NC3, HEK293T cells, 72h after RPL24 KD


title: WISC_2511

value: 2 years


title: D23-1657_E_rep1

value: Euploid


title: ko.Fast.1

value: Per2 ko

value: 16 hour Fast


title: Ctrl.Fast.9


title: NC1, HEK293T cells, 72h after RPL24 KD


title: WISC_2471

value: F

value: 2:Med (6-9 illnesses)


title: ko.Fast.4


title: WISC_2461

value: M

value: 3:High (10+ illnesses)


title: WISC_2441

value: nasopharyngeal epithelial cells and secretions


title: KD2, HEK293T cells, 72h after RPL24 KD

value: RPL24 KD, siPOOLs


title: KD3, HEK293T cells, 72h after RPL24 KD


title: Ctrl.Fast.7

value: hypothalamus


title: WISC_2491

value: 1:Low (0-5 illnesses)


title: D23-1662_E_rep2

value: iPSC-derived progenitors


title: Ctrl.Fast.8

value: Male

value: Control


title: KD1, HEK293T cells, 72h after RPL24 KD


title: ATAC-seq_Time_0h_CHD4_shRNA_rep2

city: Grand Forks

first: Motoki

last: Takaku

state: ND

address: W221 Biomedical Sciences 1301 N. Columbia Road

institute: University of North Dakota

description: ATAC_Time_0h_CHD4_shRNA.merged_reps.9ntFootPrint.normDepth.bigWig

data_processing:
Reads were filtered based on a mean base quality score >20.
Adapter sequences were removed with the TrimGalore! function.
Reads were mapped to the hg19 genome using Bowtie 0.12.8 with parameters '-I 0 -X 2000 -m 1'.
The offset parameters suggested by Buenrostro et al (Nat. Methods, 2013) were applied to each mapped read.
Alignments to chrM were filtered out with samtools.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Signal tracks were generated from either the full ATAC-seq fragment or only the 9bp footprint at 5' ends of reads, via conversion to bedGraph via Bedtools v2.17.0 genomeCoverageBed followed by conversion to bigWig format by UCSC utility bedGraphToBigWig.
Peak calls were made by PeaKDEck with parameters '-sig 0.0001 -bin 300 -back 3000 -npBack 2500000'.
Assembly: hg19
Supplementary files format and content: coverage tracks in bigWig format
Supplementary files format and content: peak calls in BED format

growth_protocol: DMEM High glucose + 10% FBS

extract_protocol:
MinElute (before PCR, Qiagen) and AMPure XP (after PCR, Beckman Coulter) were used for DNA purification.
Cells were lysed with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100). Nuclei were treated with Tn5 Transposase (Illumina). The total of 8 PCR cycles were performed to recover and amplify the DNA fragments at open chromatin.

treatment_protocol: For transient GATA3 expression, DOX (1 µg/ml at final) was added to medium. For CHD4 knockdown, MDA-MB-231 cells were infected with lentiviruses encoding CHD4 shRNA. After overnight incubation, the meidum was replaced with fresh medium and the cells were further incubated for 2 days until DOX induction.

tag: passages

tag: time point


title: ATAC-seq_Time_0h_CHD4_shRNA_rep1


title: WISC_2351


title: Ctrl.Fast.6


title: ATAC-seq_Time_0h_control_shRNA_rep1

description: ATAC_Time_0h_control_shRNA.merged_reps.9ntFootPrint.normDepth.bigWig


title: Ctrl.Fast.5


title: ATAC-seq_Time_0h_control_shRNA_rep2


title: Ctrl.Fast.4


title: WISC_2291


title: ATAC-seq_Time_12h_control_shRNA_rep2

description: ATAC_Time_12h_control_shRNA.merged_reps.9ntFootPrint.normDepth.bigWig


title: WISC_2251


title: Ctrl.Fast.3


title: ATAC-seq_Time_12h_CHD4_shRNA_rep1

description: ATAC_Time_12h_CHD4_shRNA.merged_reps.9ntFootPrint.normDepth.bigWig


title: ATAC-seq_Time_12h_control_shRNA_rep1


title: ATAC-seq_Time_48h


title: ATAC-seq_Time_12h


title: Ctrl.Fast.1


title: ATAC-seq_Time_6h


title: Ctrl.AL.10

value: Ad Libitum Fed


title: ATAC-seq_Time_3h


title: ATAC-seq_Time_0h


title: WISC_2221


title: WISC_2191


title: WISC_2201


title: HEK293T,RESTART v3-TGA-tRNA,rep 2

city: Beijing

first: Wenqing

last: Liu

institute: Peking University

description: detect tRNA expression level in wildtype HEK293T cells with RESTART v3-TGA treatment

data_processing:
Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.6) for quality control and adapter trimming. The key parameters were: --illumina --length 60 -e 0.3. The first 10-nucleotide random barcode at the 5’ end was removed by umi_tools (version 1.0.0).
Cleaned reads were mapped to the tRNA reference (hg38, NCBI Refseq) using bwa mem(0.7.17-r1188) with default parameters. A maximum of 3 mismatches were allowed for the mapped reads.
The tRNA counts were quantified by HTSeq(version 1.14), and tRNAs with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The tRNA expression level was quantified by FPKM.
Assembly: GRCh38
Supplementary files format and content: Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.6) for quality control and adapter trimming. The key parameters were: --illumina --length 60 -e 0.3. The first 10-nucleotide random barcode at the 5’ end was removed by umi_tools (version 1.0.0). Cleaned reads were mapped to the tRNA reference (hg38, NCBI Refseq) using bwa mem(0.7.17-r1188) with default parameters. A maximum of 3 mismatches were allowed for the mapped reads. The tRNA counts were quantified by HTSeq(version 1.14), and tRNAs with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The tRNA expression level was quantified by FPKM.

extract_protocol:
total RNA was extracted from cells using TRIzol reagent (Life Technologies)
RNA libraries were prepared using modified eCLIP library construction, NEBNext Small RNA library kits (NEB) and SMARTer Stranded Total RNA-Seq kits (v3) - Pico Input mammalian (Takara) Library Prep Kit following manufacturer's protocols.

value: Epithelial

value: human embryonic kidney 293 cells

value: WT


title: ATAC-seq_Time_24h


title: Ctrl.AL.9


title: WISC_2181

value: 2 years


title: CHD4_ChIP-seq_GATA3plus-MDA-MB-231_rep1

data_processing:
Reads were filtered based on a mean base quality score >20.
Reads were mapped to hg19 genome using Bowtie 0.12.8 with parameters '-I 0 -X 2000 -m 1'.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
Coverage tracks generated with Bedtools v2.17.0 genomeCoverageBed after converting paired-end reads to a single fragment, then format conversion via UCSC utility bedGraphToBigWig.
Peak calling was performed with HOMER v4.1 at default parameters.
Assembly: hg19
Supplementary files format and content: coverage tracks in bigWig format
Supplementary files format and content: peak calls in BED format

extract_protocol:
For ChIP, AMPure XP (Beckman Coulter) was used to purify DNAs.
ChIP-seq libraries were prepared by NEXTFLEX Rapid DNA-Seq kit (PerkinElmer).

tag: chip antibody

value: CHD4 Abcam (Abcam, ab70469)


title: ATAC-seq_Time_12h_CHD4_shRNA_rep2


title: Ctrl.AL.8


title: CHD4_ChIP-seq_GATA3minus-MDA-MB-231_rep2


title: WISC_2231

value: F


title: WISC_2171


title: CHD4_ChIP-seq_GATA3minus-MDA-MB-231_rep1


title: Ctrl.AL.7


title: CHD4_ChIP-seq_T47D_rep2

value: CHD4 Abcam (Abcam, ab72418)


title: Ctrl.Fast.2

value: 16 hour Fast


title: Ctrl.AL.6


title: CHD4_ChIP-seq_T47D_rep1


title: CHD4_ChIP-seq_CR3_rep1

value: CR3 (T47D GATA3 WT/R330fs)


title: WISC_2081

value: nasopharyngeal epithelial cells and secretions

value: 2:Med (6-9 illnesses)


title: WISC_2151

value: 3:High (10+ illnesses)


title: Ctrl.AL.5

value: hypothalamus


title: Ctrl.AL.4


title: GATA3_ChIP-seq_Time_24h

value: GATA3 serum (home made)


title: GATA3_ChIP-seq_Time_12h


title: GATA3_ChIP-seq_Time_6h


title: CHD4_ChIP-seq_GATA3plus-MDA-MB-231_rep2


title: WISC_2031

value: 1:Low (0-5 illnesses)


title: WISC_2061


title: GATA3_ChIP-seq_Time_3h


title: WISC_2021


title: CHD4_ChIP-seq_CR3_rep2


title: GATA3_ChIP-seq_Time_0h


title: Ctrl.AL.2

value: Male

value: Control


title: Ctrl.AL.3

value: Ad Libitum Fed


title: WISC_1991

value: M


title: Ctrl.AL.1


title: VIC-CD151 low CMs 3

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.18) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
HTSeq (v0.11.2) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.6.1) and its package DESeq2 (v1.26.0) were performed.
Genome_build: GRCh38

source_name: VIC-CD151 low CMs

growth_protocol: For hiPSCs, AK02N (Ajinomoto) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol:
RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
TruSeq Standed Total RNA (Illumina)

treatment_protocol: For atrial cardiomyocytes, StemPro-34 supplemented with 2 mM L-glutamine, 4x10-4 M monothioglycerol (MTG), 50 μg/ml ascorbic acid (AA), 150 μg/ml transferrin, bFGF (5 ng/ml), activin A (4 ng/ml),  BMP4 (3 ng/ml), VEGF (10 ng/mL), IWP-3 (1 μM), SB431542 (5.4 μM) and 1 μM RA. For ventricular cardiomyocytes, StemPro-34 supplemented with 2 mM L-glutamine, 4x10-4 M monothioglycerol (MTG), 50 μg/ml ascorbic acid (AA), 150 μg/ml transferrin, bFGF (5 ng/ml), activin A (6 ng/ml),  BMP4 (10 ng/ml), VEGF (10 ng/mL), IWP-3 (1 μM), SB431542 (5.4 μM) and Dorsomorphin (0.6 μM).

value: hiPSC-cardiomyocytes

tag: differentiation condition

value: VCM inducing condition

tag: sort condition

value: CD151 low


title: WISC_1981

value: 2 years

value: F


title: GATA3_ChIP-seq_Time_48h

tag: cell line


title: VIC-CD151 low CMs 1

tag: cell type


title: VIC-CD151 high CMs 1

source_name: VIC-CD151 high CMs

value: CD151 high


title: VIC-CD151 low CMs 2


title: VIC-CD151 high CMs 2


title: WISC_1931


title: WISC_1941


title: AIC-CD151 low CMs 1

source_name: AIC-CD151 low CMs

value: ACM inducing condition


title: AIC-CD151 high CMs 3

source_name: AIC-CD151 high CMs


title: WISC_1921

value: nasopharyngeal epithelial cells and secretions


title: colonic epithelium, Smad4 knockout, DSS treated, replicate 1

city: Hoboken

first: Thompson

last: Hui

state: New Jersey

address: McLean 327

department: Chemistry and Chemical Biology

institute: Stevens Institute of Technology

data_processing:
Raw sequencing reads were cleaned by Novogene using in-house Perl scripts
Clean reads were aligned to the mm9 reference genome using Hisat2
Aligned reads were quantified by featureCounts
The aligned reads were quantified for gene expression levels using featureCounts
Assembly: mm9
Supplementary files format and content: tab-delimited text file including raw counts for each file

source_name: colonic epithelium

growth_protocol: The mice were maintained on standared chow diet, temperature, and humidity controlled animal facility with 12 hour light/dark cycle

extract_protocol:
Epithelium was isolated from the whole colon using 5mM EDTA/PBS buffer and rocked for ~ one hour to seperate the epithelium from the mesenchyme. The isolated crypt epithelium was washed thrice with PBS, pelleted and solubilized in Trizol for RNA extraction. All the aforementioned processes were carried at 4 degrees Celsius. The quality for the RNA was confirmed by Novogene prior to sequencing.
The PolyA enrichment procedure was used for library preparation

treatment_protocol: Adult wild type and Smad4 knockout mice were admimistered 2.5% Dextran Sulphate Sodium ad libitum in drinking water for three days.

value: colonic epithelium

value: colonic epithelial cells

tag: genotype

value: Smad4 knockout

tag: treatment

value: DSS treated


title: AIC-CD151 high CMs 2


title: colonic epithelium, Smad4 knockout, DSS treated, replicate 2

tag: tissue


title: AIC-CD151 high CMs 1


title: WISC_1911

tag: Sex

value: 1:Low (0-5 illnesses)


title: AIC-CD151 low CMs 2


title: 4175 Fus4

city: Miami

first: Ankita

middle: Padma

last: Sankar

state: Florida

address: 1580 NW 10th Ave, Batchelor Children's Research Institute

institute: University of Miami

data_processing:
Gene mapping was conducted by The Weizmann Institute of Science INCPM Bioinformatics core
Cutadapt was used to trim poly A/T stretches and Illumina adapter sequences
Reads below 30 base pairs were discared
Trimmed reads were mapped to the Homo sapiens reference genome (GRCh38/hg38) using STAR alignment and Ensembl gene annotations (EndtoEnd and outFilterMismatchNoverLmax: 0.04)
Htseq-count was used to identify gene expression levels and differentially expressed genes were identified with DESeq2 (betaPrior, cooksCutoff and independent filtering: false)
Assembly: hg38
Supplementary files format and content: Excel file includes raw counts, normalized counts, and relative comparisons for each sample and group

growth_protocol: MDA-MB-231-4175 TNBC cells were maintained in RPMI supplemented with 10% FBS and antibiotics and cultured in incubator at 37C

extract_protocol:
RNA was extraction by using a combination of TRIzol and Qiagen RNAeasy Mini Kit
RNA libraries for RNA-seq were constructed using NEBNext Ultra II RNA kit

treatment_protocol: Vasculogenic mimicry (VM) tube formation was induced upon the addition of MDA-MB-231-4175 TNBC cells to a 6-well cell culture plate coated with matrigel basement membrane. The formation of VM was inhibited upon the addition of our novel anti-EGFR-E-P125A antibody-drug conjugate to cells plated on matrigel basement membrane.

value: breast adenocarcinoma

value: VM inhibited


title: 4175 Fus5


title: colonic epithelium, wildtype, DSS treated, replicate 2

value: Wildtype


title: colonic epithelium, wildtype, DSS treated, replicate 3


title: VIC-CD151 high CMs 3


title: 4175 Fus3


title: AIC-CD151 low CMs 3


title: WISC_1901

tag: farm status

value: 2:Med (6-9 illnesses)


title: colonic epithelium, wildtype, DSS treated, replicate 1


title: 4175 Fus2


title: WISC_1882

tag: num respiratory_illnesses_by_2yrs

value: 3:High (10+ illnesses)


title: 4175 3D5

value: VM induced


title: colonic epithelium, Smad4 knockout, untreated, replicate 3

value: untreated


title: 4175 3D4


title: 4175 3D2


title: WISC_1861

value: 2 years

value: M

tag: collected 2018


title: 4175 3D3


title: WISC_1801

tag: age


title: colonic epithelium, Smad4 knockout, untreated, replicate 1


title: 4175 2D4

value: no VM induced


title: WISC_1771

value: F


title: 4175 2D3


title: 4175 2D2


title: mixed samples (H_98_48h; H_97_pre; H_97_48h; L_38)

city: Hannover

first: Reinhold

last: Förster

address: Carl-Neuberg-Str. 1

department: Institute of Immunology

institute: Hannover Medical School

description: H_98_48h: A0254 anti-human Hashtag 4 (Biolegend 394607; AGTAAGTTCAGCGTA); H_97_pre: A0255 anti-human Hashtag 5 (Biolegend 394609; AAGTATCGTTTCGCA); H_97_48h: A0252 anti-human Hashtag 2 (Biolegend 394603; TGATGGCCTATTGGG); L_38: A0251 anti-human Hashtag 1 (Biolegend 394601; GTCAACTCTTTAGCG)

data_processing:
Demultiplexing, barcode processing, gene counting and aggregation were performed with Cell Ranger v.4.0.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Tab separated values files and matrix files

source_name: PBMC

extract_protocol:
Thawed PBMC were rested for 1hour in RPMI 1640 supplemented medium.
Single-cell transcriptome sequencing were performed on FACS sorted PBMCs isolatingsinglet liveCD3-CD19- cells and later utilizingthe Chromium Single-Cell 5′ Library Gel Bead and Construction Kit according to the user guidelines.

value: PBMC

tag: participant id

value: 48h; pre; 48h; pre

tag: response group

value: HR; HR; HR; LR


title: colonic epithelium, wildtype, untreated, replicate 4

value: colonic epithelium

value: colonic epithelial cells


title: mixed samples (L-39; L_39_24h; H_99_pre; H_99_24h)

description: L-39: A0254 anti-human Hashtag 4 (Biolegend 394607; AGTAAGTTCAGCGTA); L_39_24h: A0255 anti-human Hashtag 5 (Biolegend 394609; AAGTATCGTTTCGCA); H_99_pre:  A0256 anti-human Hashtag 6 (Biolegend 394611; GGTTGCCAGATGTCA); H_99_24h: A0251 anti-human Hashtag 1 (Biolegend 394601; GTCAACTCTTTAGCG)

value: L-39:SNX; H_99:QHMH

value: pre; 24h; pre; 24h

value: LR; LR; HR; HR


title: colonic epithelium, Smad4 knockout, untreated, replicate 4

value: Smad4 knockout


title: colonic epithelium, wildtype, untreated, replicate 3

value: Wildtype


title: mixed samples (L_37_24h; L_37_48h; H_18_24h; H_18_48)

description: L_37_24h: A0254 anti-human Hashtag 4 (Biolegend 394607; AGTAAGTTCAGCGTA) ; L_37_48h: A0252 anti-human Hashtag 2 (Biolegend 394603; TGATGGCCTATTGGG); H_18_24h: A0253 anti-human Hashtag 3 (Biolegend 394605;  TTCCGCCTCTCTTTG ) ; H_18_48: A0257 anti-human Hashtag 7 (Biolegend 394613; TGTCTTTCCTGCCAG)

value: L_37:RQSI; H_18:RRRS


title: WISC_1741

value: nasopharyngeal epithelial cells and secretions

value: 1:Low (0-5 illnesses)


title: WISC_1761

value: 2 years

value: 3:High (10+ illnesses)


title: OP_37

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101)
TPM values calculated using kallisto v0.44.0
Assembly: GRCh38.p13 primary genome assembly
Supplementary files format and content: tab-delimited text files: Read_counts.txt — uniquely aligned read counts for genes

source_name: musculus vastus lateralis

extract_protocol:
A frozen muscle sample (~10-15 mg) was lysed by the RLT buffer (Qiagen, Germany) using a drill homogenizer and total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration and integrity were evaluated by a fluorimetric assay (Qubit 4, ThermoScientific, USA) and capillary electrophoresis (TapeStation, Agilent, Germany), respectively.
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)

value: musculus vastus lateralis

value: female

tag: healthy/patient

value: patient


title: 4175 2D5

value: breast adenocarcinoma

value: no VM induced


title: OP_36


title: WISC_1641

value: F

value: 2:Med (6-9 illnesses)


title: colonic epithelium, wildtype, untreated, replicate 2

value: colonic epithelium

value: colonic epithelial cells

value: untreated


title: OP_35


title: mixed samples (H-29; H_99_48h; H_98_pre; H_98_24h)

description: H-29: A0251 anti-human Hashtag 1 (Biolegend 394601; GTCAACTCTTTAGCG); H_99_48h: A0255 anti-human Hashtag 5 (Biolegend 394609; AAGTATCGTTTCGCA); H_98_pre: A0256 anti-human Hashtag 6 (Biolegend 394611; GGTTGCCAGATGTCA); H_98_24h: A0258 anti-human Hashtag 8 (Biolegend 394615; CTCCTCTGCAATTAC)

value: PBMC

tag: time point

value: pre; 48h; pre; 24h

value: HR; HR; HR; HR


title: colonic epithelium, wildtype, untreated, replicate 1

value: Wildtype


title: colonic epithelium, Smad4 knockout, untreated, replicate 2

value: Smad4 knockout


title: WISC_1841

value: nasopharyngeal epithelial cells and secretions

value: 2 years

value: 1:Low (0-5 illnesses)


title: WISC_1561

value: M


title: OP_32

value: musculus vastus lateralis

value: female

value: patient


title: OP_33


title: OP_34


title: mixed samples (L-37; H-18, H-14-48; L_39_48)

description: L-37:  A0251 anti-human Hashtag 1 (Biolegend 394601; GTCAACTCTTTAGCG); H-18: A0255 anti-human Hashtag 5 (Biolegend 394609; AAGTATCGTTTCGCA), H-14-48: A0256 anti-human Hashtag 6 (Biolegend 394611; GGTTGCCAGATGTCA); L_39_48: A0257 anti-human Hashtag 7 (Biolegend 394613; TGTCTTTCCTGCCAG)

value: pre; pre; 48h; 48h

value: LR; HR; HR; LR


title: WISC_1511


title: mixed samples (L-40; L_40_24h; L40_48h; H_14; H_14_24h)

description: L-40: A0254 anti-human Hashtag 4 (Biolegend 394607; AGTAAGTTCAGCGTA); L40-24h: A0252 anti-human Hashtag 2 (Biolegend 394603; TGATGGCCTATTGGG); L_40_48h:  A0253 anti-human Hashtag 3 (Biolegend 394605;  TTCCGCCTCTCTTTG ); H-14:  A0257 anti-human Hashtag 7 (Biolegend 394613; TGTCTTTCCTGCCAG); H_14_24h: A0258 anti-human Hashtag 8 (Biolegend 394615; CTCCTCTGCAATTAC)

value: LR; LR; LR; HR; HR


title: SclCre;V617F;IL-1R1-/-GFP-6

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Read quality was assessed with the FastQC tool (version 0.11.5)
Reads were mapped to the mouse genome mm10 with STAR (version 2.7.10a) with default parameters, except filtering out multimapping reads with more than 10 alignment locations (outFilterMultimapNmax=10) and filtering reads without evidence in the spliced junction table (outFilterType=“BySJout”). The mm10 genome reference was supplemented with CreERT2, induceable Homo_sapiens_JAK2_V617F construct and pEGFP sequences.
All subsequent analyses were performed using the R software (version 4.2.2) and Bioconductor 3.16 packages. The featureCounts function from the Bioconductor Rsubread package (version 2.0.1) was used to count the number of reads (5' ends) overlapping with the exons of each gene (Ensembl release 102) assuming an exon union model
Assembly: mm10
Supplementary files format and content: gene_counts.tsv.gz: gzipped text file with tab-separated RNA-seq read counts for each gene; each row contains the annotation and raw counts per gene; columns correspond to: 1. Ensembl ID, 2.-26. read counts per gene and sample. Counts on the CreERT2, pEGFP and Homo_sapiens_JAK2_V617F construct (exons 3 to 12 and exons 13 to 25 separately) are listed at the end of the file

source_name: Bone marrow

growth_protocol: Bone marrow cells were harvested from sacrificed mice and FACS stained and sorted directly in RNA extraction buffer (PicoPure)

extract_protocol:
Bone-marrow long-term hematopoietic stem cells (HSC; Lin−Sca1+cKit+CD48−CD150+) were FACS sorted directly into PicoPure extraction buffer and frozen at -80°C after a lysis step. Overall the samples were processed in 2 batches, 2 weeks apart (resp. 2 and 4 weeks after tamoxifen induction)
RNA from all 25 c\frozen samples was extracted using the Picopure RNA isolation kit (Applied Biosystems). The quality and concentration of total RNA was determined on Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico Assay.
Unstranded RNA-seq libraries were prepared using the SMART-Seq v4 kit (Takara).

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)

tag: time

value: 4 weeks after tamoxifen induction


title: WISC_1701

value: F


title: WISC_1431


title: SclCre;V617F;IL-1R1-/-GFP-4

value: 2 weeks after tamoxifen induction


title: OP_28

value: male


title: OP_29


title: SclCre;V617F;IL-1R1-/-GFP-7


title: OP_30


title: WISC_1411

value: 3:High (10+ illnesses)


title: OP_26


title: OP_25


title: SclCre;V617F;IL-1R1-/-GFP-3


title: WISC_1401

value: nasopharyngeal epithelial cells and secretions


title: OP_24


title: SclCre;V617F;IL-1R1-/-GFP-2


title: OP_23


title: OP_22


title: OP_21


title: SclCre;V617F;IL-1R1-/-GFP-5


title: SclCre;V617F;IL-1R1-/-GFP-1


title: SclCre;V617F;IL-1b-/-GFP-6


title: MG1655 invitro N-lim S phase RNA_biol rep 2

city: STILLWATER

first: Tyrrell

last: Conway

state: OKLAHOMA

address: 307 Life sciences east, OKLAHOMA STATE UNIVERSITY

department: Microbiology and Molecular Genetics

institute: Oklahoma state university

description: RNA-Seq of stationary phase Escherichia coli MG1655 wild type grown in vitro in MOPS minimal media containing low nitrogen

data_processing:
Sequencing reads were mapped to the reference genome (accession number:U00096.3) using bowtie2
SAM files were converted to BAM format and sorted and indexed them using SAMtools
The BAM files were then converted to base count (WIG) files
Using in-house script, normalized WIG files were generated by using a simple global normalization approach in which the count at each base location was multiplied by 1 billion and divided that value by the sum of base counts at all base locations in the file
Assembly: U00096.3
Supplementary files format and content: normWIG

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli grown invitro culture

growth_protocol: Wild type StrR  and ∆glnG StrR CamR cultures were grown on MOPS minimal medium with 0.2% glucose as sole carbon source and high(10 mM NH4Cl) or low nitrogen source( 3 mM NH4Cl) at 37°C  and agitation at 200 rpm. For exponential phase samples, culture samples were harvested during logarithmic phase (OD600=0.4-0.6). For stationary phase samples, culture samples were harvested 30 minutes after the culture entered the stationary phase. 5 ml of cultures were harvested into RNA-protect reagent (Qiagen) at 1:2 dilution and cells were pelleted by centrifugation at 5000rpm for 10 minutes. Cell pellets were stored at -80°C until RNA extraction. To extract RNA from colonized E. coli MG1655∆glnG StrR CamR , the mutant strain was fed to CD-1 male mice and allowed it to stably colonize for 9 days. The mice were then euthanized, cecum was taken out and cecal mucus was extracted and immediately homogenized in 500 µl Hanks salt solution (Thermo scientific), 500 µl PCA and 210 µl 20% SDS . The tubes were kept on ice until further processing for RNA extraction.

extract_protocol:
All in-vitro RNA samples were extracted using the Qiagen RNeasy Mini Kit, following manufacturer’s protocol. For in vivo samples, RNA samples were extracted using phenol chloroform extraction method. DNase treatment was done using DNAse I enzyme (Invitrogen, Cat no. AM2238). The samples were quantified using the Agilent Bioanalyzer (Agilent, Catalog no. G2939BA).
Approximately 100 ng of total RNA from each sample were processed at University of Bern for ribo-depletion with the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, Catalog no. 20037135). RNA libraries were prepared using the TruSeq Stranded Total RNA Library Prep kit. Libraries were sequenced on a NovaSeq™ 6000 system, using 1×100 bp single-end read length.

value: E. coli grown invitro culture

value: WT


title: OP_27


title: OP_20


title: SclCre;V617F;IL-1b-/-GFP-7


title: WISC_1191

data_processing:
Initial processing: Basecalling was performed with CASAVA and samples were demultiplexed with bcl2fastq.
Trimming: We removed Illumina adapter sequences and trimmed read ends to a minimum quality score of 20 using the skewer utility (PMID:24925680).
Expression quantification: Trimmed read pairs were provided to kallisto v0.46.1 (PMID:27043002) to quantify transcript-level expression values using a pre-built index built from Ensembl v96 GRCh38 (https://github.com/pachterlab/kallisto-transcriptome-indices/releases). We summarized the estimated counts values to the gene level using tximport (PMID:26925227).
Exploratory data analysis: Clustering and PCA analysis identified variation associated with whether the sample was collected in 2018. We adjusted for this in downstream analysis.
Assembly: GRCh38 v96
Supplementary files format and content: all_samples_gene_counts.tsv.gz: A compressed, single TSV file that gives the gene-level counts estimated by kallisto and summarized to the gene level using tximport. Column names correspond to sample titles.

extract_protocol:
Coordinators obtained nasal cells and secretions by inserting a swab (#516CS01, Copan Inc., Murrieta, CA) into the nasopharynx, rotating it three times, and then immediately immersing it in a cell lysis buffer (RLT buffer, Qiagen, Ann Arbor MI) to preserved the RNA. The tube containing the swab tip was vortexed, kept at 4C overnight, and cryopreserved at -80C pending RNA extraction (RNeasy Micro Kit, Qiagen).
RNA (1 ng) was fragmented, and cDNA was synthesized using random hexamers (SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian reagents, Takara Inc). Next, we added Illumina-compatible indexed adapters and enzymatically depleted host rRNA. A second round of amplification was used to generate the final sequence library.

value: 2 years

value: 2:Med (6-9 illnesses)


title: WISC_1311


title: WISC_1291

value: 1:Low (0-5 illnesses)


title: WISC_1331


title: MG1655 invitro S phase RNA_biol rep 2

description: RNA-Seq of stationary phase Escherichia coli MG1655 wild type grown in vitro in MOPS minimal media containing high nitrogen


title: MG1655 invitro N-lim S phase RNA_biol rep 1


title: SclCre;V617F;IL-1b-/-GFP-5


title: MG1655 invitro S phase RNA_biol rep 1


title: OP_19

value: musculus vastus lateralis

value: female

value: patient


title: SclCre;V617F;IL-1b-/-GFP-4


title: OP_18


title: WISC_1171


title: WISC_1101


title: SclCre;V617F;IL-1b-/-GFP-3


title: WISC_1081

value: M


title: MG1655 invitro N-lim E phase RNA_biol rep 2

description: RNA-Seq of exponential phase Escherichia coli MG1655 wild type grown in vitro in MOPS minimal media containing low nitrogen


title: OP_17


title: MG1655 glnG N-lim invitro E phase RNA_biol rep 2

description: RNA-Seq of exponential phase Escherichia coli MG1655 ∆glnG grown in vitro in MOPS minimal media containing low nitrogen

value: deltaglnG mutant


title: OP_16


title: MG1655 glnG N-lim invitro E phase RNA_biol rep 1


title: WISC_1001

description: nasopharyngeal swab from two-year-old child


title: SclCre;V617F;IL-1b-/-GFP-1

value: Bone marrow

value: HSCs (Lin-Sca1+cKit+CD48-CD150+)


title: OP_14


title: SclCre;V617F;GFP-7

value: 4 weeks after tamoxifen induction


title: MG1655 glnG mice RNA_biol rep 2

description: RNA-Seq of colonized Escherichia coli MG1655 ∆glnG extracted from mouse cecal mucus

source_name: mouse mucus from the cecum

value: mouse mucus from the cecum


title: SclCre;V617F;GFP-6


title: SclCre;V617F;GFP-5


title: OP_13