title: PRIMAQUINE.PHOSPHATE_3_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: PRIMAQUINE PHOSPHATE


title: Imatinib, Con5, Optimization plate 4, Well M12 [S4881Nr4_M12]

status: Public on Oct 10 2023

type: SRA

city: Göttingen

first: Christopher

last: Bruhn

address: Marie-Curie-Str. 7

country: Germany

institute: Evotec International GmbH

library_source: transcriptomic

data_processing:
Transcriptomic profiling was performed in batches of 382 samples. Each batch contained 22 negative-control (i.e. DMSO-treated) samples, and 15 blocks of compound-treated samples. Every block included 8 compound concentrations, each in triplicate.
Reads were mapped to the human genome (genome-build GRCh38.p13 – accession GCA_000001405.28) using STAR (version 2.7.9a).
Multi-mapped reads, reads with mapping to inter-genic regions (with respect to Ensembl gene annotation information version 104) and reads with ambiguous mapping location (i.e. location associated with more than one gene) were discarded, and UMI-based deduplication was performed.
Sequencing files were demultiplexed and barcodes were stripped.
Assembly: GRCh38.p13 – accession GCA_000001405.28
Supplementary files format and content: processed_data_counts.txt: RNA unique moecular identifier (UMI) counts per gene. The column EnsemblID provides the unique gene identifier. One column is included per sample with column names matching the column "description" in the table "SAMPLES".

molecule: polyA RNA

organism: Homo sapiens

source_name: hiPSC-CM

growth_protocol: human iPSC-derived cardiomyocytes (hiPSC-CMs) were seeded in 384-well plates (Corning® Cat. No.: 3764) pre-coated with a 0.1 µg/mL fibronectin solution (Sigma Cat. No. F1141) in phosphate buffered saline (PBS) containing Mg2+ and Ca2+. Fibronectin pre-coated plates were incubated at 37°C for 3 h (5% CO2, 95% humidity), after which the coating was carefully removed using an automated liquid handling robot (Bravo Agilent). Subsequently, hiPSC-CMs were seeded at 10,000 cells/well and cultured for 10 days in CD-4 media. Media was initially refreshed 24 h post-seeding and then, every 48 h thereafter while the cells were in culture.

extract_protocol:
High-throughput transcriptomics was performed using Evotec’s (semi)-automated ScreenSeqTM platform. Cell lysis was performed in a 384-well plate format followed by well-specific labeling of samples.
Plate RNASeq of polyA RNA (ScreenSeqTM); Purified mRNAs were labeled with a unique molecular identifier (UMI). After pooled cDNA synthesis, adapters containing Illumina’s unique dual indexes were attached for final library preparation and sequenced on a NovaSeq 6000 system.

treatment_protocol: All compounds were dissolved in 100% dimethylsulfoxide (DMSO) (stock solutions). The stock solutions were further diluted in CD-4 media and cells were dosed in triplicate at an eight-point dose response range using a half-log dilution series to achieve a final DMSO concentration of 0.5% (v/v). Vehicle controls were dosed with 0.5% (v/v) DMSO, while positive controls were dosed with sunitinib, a functional and structural cardiotoxicant.

tag: cell line

value: hiPSC-CM

tag: genotype

value: WT

tag: treatment

value: Imatinib, Con5

tag: time


title: Imatinib, Con6, Optimization plate 4, Well O11 [S4881Nr4_O11]

value: Imatinib, Con6


title: AUROTHIOGLUCOSE_5_24.hrs_R1

city: New York City

first: Alessandro

last: Vasciaveo

state: NY

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

country: USA

institute: Columbia University

description:
PLATE-Seq
first-experiment-counts.csv

data_processing:
Reads were mapped against the human reference genome version Grch38 using the STAR aligner.
Assembly: human genome version Grch38
Supplementary files format and content: CSV tables with raw counts. Sample names on the columns and human gene symbols on the rows.

growth_protocol: SK-N-Be2 cells were seeded in a 96 w plate at a density of 10 000 cells/well and incubated overnight.

extract_protocol:
Following treatment, wells were rinsed twice with cold PBS, and 40 µL of Buffer TCL was added to the each well and frozen at -20°C.
Library prep and sequencing were performed at Columbia’s high-throughput screening core and the JP Sulzberger Genome center, following published protocols (Bush, et al. Nat Commun 2017)
PLATESeq for the first three experiments (see Bush, et al., Nat. Commun. 2017)
RNASeq for the last (TruSeq experiment)

treatment_protocol: The following day, compounds were sequentially diluted from DMSO stock solutions to create desired concentrations, with DMSO at 0.1%. Duplicate plates were created by randomizing 90 lethal molecules across the plate, with the inclusion of six DMSO-only control wells. Following the addition of compounds, the plates were incubated for 24 h.

tag: disease

value: neuroblastoma

tag: cell type

value: neuroblast

value: MYCNA

value: AUROTHIOGLUCOSE

tag: replicate

value: 24 hrs

tag: concentration


title: Imatinib, Con6, Optimization plate 4, Well M11 [S4881Nr4_M11]


title: PROSCILLARDIN_A_0.15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv


title: CYCLOSPORINE_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: CYCLOSPORINE


title: NSC69187_3_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv


title: BUTOCONAZOLE_10_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: BUTOCONAZOLE


title: Imatinib, Con7, Optimization plate 4, Well M10 [S4881Nr4_M10]

value: Imatinib, Con7


title: Imatinib, Con7, Optimization plate 4, Well N10 [S4881Nr4_N10]


title: QUINACRINE.HYDROCHLORIDE_10_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: QUINACRINE HYDROCHLORIDE


title: CLOXACILLIN.SODIUM_1_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: CLOXACILLIN SODIUM


title: Control..DMSO...R3_NA_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: Control- DMSO - R3


title: Imatinib, Con8, Optimization plate 4, Well O9 [S4881Nr4_O9]

value: Imatinib, Con8


title: NSC255109_7.5_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv


title: Imatinib, Con8, Optimization plate 4, Well M9 [S4881Nr4_M9]


title: DMSO, Con0, Optimization plate 4, Well O8 [S4881Nr4_O8]

value: DMSO, Con0


title: NCC46386954_3_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv


title: Azauridine_10_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: Azauridine


title: Control..DMSO...R2_NA_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: Control- DMSO - R2


title: DMSO, Con0, Optimization plate 4, Well N8 [S4881Nr4_N8]

value: hiPSC-CM

value: WT


title: DMSO, Con0, Optimization plate 4, Well O7 [S4881Nr4_O7]


title: Imatinib, Con6, Optimization plate 4, Well N11 [S4881Nr4_N11]

value: Imatinib, Con6


title: DMSO, Con0, Optimization plate 4, Well N7 [S4881Nr4_N7]


title: DMSO, Con0, Optimization plate 4, Well M7 [S4881Nr4_M7]


title: ARTESUNATE_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblastoma

value: neuroblast

value: ARTESUNATE


title: DMSO, Con0, Optimization plate 4, Well M8 [S4881Nr4_M8]


title: TENIPOSIDE_3_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: MYCNA

value: TENIPOSIDE

value: 24 hrs


title: Imatinib, Con7, Optimization plate 4, Well O10 [S4881Nr4_O10]

value: Imatinib, Con7


title: FpWT_2

city: Tulln

first: Harald

last: Berger

state: NOE

address: Konrad-Lorenzstraße 43

department: DAGZ

country: Austria

institute: Universität f. Bodenkultur Wien

data_processing:
Obtained sequences were de-multiplexed, quality controlled, filtered using trimmomatic 0.36
Mapping was performed using BWA  and reverse transcripts were counted using python script HTSeq .
Normalization and statistics were done using R/Bioconductor and the limma and edgeR packages, using mean-variance weighting (voom) and TMM normalisation .
Assembly: SUB13518710, "Re-sequencing of Fusarium proliferatum NRRL62905", accession number CP128300-CP128312
Supplementary files format and content: tab deliminated text file containing raw counts, log2 RPKM values, log2 differential transcription and p-values of diff. Transcription.

organism: Fusarium proliferatum

growth_protocol: For fungal liquid cultivations, mycelia were pre-cultured in 100 mL Darken medium   in a 300 mL Erlenmeyer flask for 3 days in the dark (30°C, 180 rpm). Then, 0.5 mL of the pre-culture was transferred to ICI media supplemented  with either 6 mM  glutamine  sole nitrogen source .  Fungal cultures were incubated on an orbital shaker at 180 rpm, 30°C for 3 dpi .

extract_protocol:
Total RNA for subsequent sequencing was extracted using TRIzol Reagent as described above, and sent to the Vienna BioCenter (Vienna, Austria) for quality control, library preparation and sequencing.
Vienna BioCenter (Vienna, Austria) performed quality control, library preparation and sequencing for poly A enriched RNA.  Library prep and sequencing was performed using poly-A enrichment kit (NEB) and Nextera Library prep kit.

tag: strain

value: biol rep 2


title: DMSO, Con0, Optimization plate 4, Well M6 [S4881Nr4_M6]


title: DMSO, Con0, Optimization plate 4, Well N6 [S4881Nr4_N6]


title: Imatinib, Con8, Optimization plate 4, Well N9 [S4881Nr4_N9]


title: DIGITOXIN_0.15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: DIGITOXIN


title: NSC80997_10_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv


title: DMSO, Con0, Optimization plate 4, Well O5 [S4881Nr4_O5]


title: DMSO, Con0, Optimization plate 4, Well M5 [S4881Nr4_M5]


title: GRAMICIDIN_3_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: GRAMICIDIN


title: DMSO, Con0, Optimization plate 4, Well O4 [S4881Nr4_O4]


title: Thiothixene_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: Thiothixene


title: Fpkmt6_T1_2


title: DMSO, Con0, Optimization plate 4, Well O6 [S4881Nr4_O6]

value: DMSO, Con0


title: PRAZOSIN.HYDROCHLORIDE_10_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: PRAZOSIN HYDROCHLORIDE


title: DMSO, Con0, Optimization plate 4, Well M4 [S4881Nr4_M4]


title: DMSO, Con0, Optimization plate 4, Well N4 [S4881Nr4_N4]


title: Fpkmt6_T1_1

value: biol rep 1


title: DMSO, Con0, Optimization plate 4, Well O2 [S4881Nr4_O2]

value: hiPSC-CM


title: Root midsection, P limiting, rep 4 [PLM4]

city: Davis

first: Siobhan

last: Brady

state: California

address: One Shields

department: Plant Biology and Genome Center

institute: UC Davis

data_processing:
A custom perl script partitioned the reads into individual libraries based on the barcode and trimmed reads. FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to check the quality of each sequenced library.
Five of the 32 libraries were excluded from analysis due to poor sequence quality.
Reads were aligned to the S. lycopersicum reference transcriptome ITAG 3.1) (Fernandez-Pozo et al. 2014) with bowtie 1.2.2 (Langmead, 2010) (http://bowtie-bio.sourceforge.net/index.shtml).
Reads were aggregated in count tables using a custom script . Differential gene analysis was performed on normalized read counts using the method of trimmed mean of M-values (TMM) with the calcNormFactors function in edgeR (Robinson et al., 2010) and the limma (Ritchie et al., 2015) Bioconductor packages in R.
A linear model was used to determine the effects of developmental stage and phosphate by developmental state on differential gene expression. S. lycopersicum and S. pennellii were analyzed separately but used the same pipelines and thresholds for analysis. Multiple testing correction was performed using the ashR package in R. P-values are set below 0.05.
Assembly: ITAG 3.1

molecule: total RNA

organism: Solanum pennellii

source_name: 35S:TRAP construct-containing tomato seedlings

growth_protocol: Plants were grown for 8 to 10 days after germination in a growth chamber at 25C in 12H light and 12H night on plant growth media similar to MS without the addition of phosphate or with phosphate

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit (ZYMO).
RNA libraries were prepared using Breath Adapter Directional sequencing (BrAD-seq) a strand-specific 3-prime RNA-seq library prep protocol
Libraries were pooled, barcoded, and submitted to the UC Davis DNA Technologies Core and were sequenced on Illumina HiSeq2000 SR50

tag: cultivar

value: cv LA0716

tag: age

value: 8 to 10 days-after germination

tag: tissue

value: approximately 2 cm of tissue halfway between the root-shoot junction and the root tip

value: Limiting phosphate


title: Root midsection, P limiting, rep 3 [PLM3]


title: DMSO, Con0, Optimization plate 4, Well M3 [S4881Nr4_M3]

value: WT


title: DMSO, Con0, Optimization plate 4, Well N3 [S4881Nr4_N3]


title: OXYQUINOLINE.HEMISULFATE_3_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblastoma

value: neuroblast

value: MYCNA

value: OXYQUINOLINE HEMISULFATE


title: DMSO, Con0, Optimization plate 4, Well N2 [S4881Nr4_N2]


title: DMSO, Con0, Optimization plate 4, Well M2 [S4881Nr4_M2]


title: BROXALDINE_5_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: BROXALDINE

value: 24 hrs


title: Control..no.DMSO...R1_NA_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: Control- no DMSO - R1


title: DMSO, Con0, Optimization plate 4, Well O1 [S4881Nr4_O1]


title: DMSO, Con0, Optimization plate 4, Well N5 [S4881Nr4_N5]


title: DMSO, Con0, Optimization plate 4, Well O3 [S4881Nr4_O3]


title: Root midsection, P limiting, rep 2 [PLM2]


title: Root midsection, P limiting, rep 1 [PLM1]


title: DMSO, Con0, Optimization plate 4, Well M1 [S4881Nr4_M1]


title: DMSO, Con0, Optimization plate 4, Well N1 [S4881Nr4_N1]


title: Root midsection, P sufficient, rep 4 [PSM4]

value: Sufficient phosphate


title: Imatinib, Con1, Optimization plate 4, Well L24 [S4881Nr4_L24]

value: Imatinib, Con1


title: Podofilox_2_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: Podofilox


title: Imatinib, Con1, Optimization plate 4, Well K24 [S4881Nr4_K24]


title: Imatinib, Con1, Optimization plate 4, Well J24 [S4881Nr4_J24]


title: Root midsection, P sufficient, rep 2 [PSM2]


title: Root midsection, P sufficient, rep 3 [PSM3]


title: BENZOXIQUINE_7.5_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: BENZOXIQUINE


title: Imatinib, Con2, Optimization plate 4, Well L23 [S4881Nr4_L23]

value: hiPSC-CM

value: Imatinib, Con2


title: IVERMECTIN_10_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: IVERMECTIN


title: Imatinib, Con2, Optimization plate 4, Well K23 [S4881Nr4_K23]


title: Root midsection, P sufficient, rep 1 [PSM1]

value: cv LA0716

value: 8 to 10 days-after germination

value: approximately 2 cm of tissue halfway between the root-shoot junction and the root tip


title: DACTINOMYCIN_0.25_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblastoma

value: DACTINOMYCIN


title: FLUPHENAZINE.HYDROCHLORIDE_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblast

value: MYCNA

value: FLUPHENAZINE HYDROCHLORIDE


title: Root tips, P limiting, rep 4 [PLT4]

value: 1 cm segment from the root tip

value: Limiting phosphate


title: Imatinib, Con3, Optimization plate 4, Well L22 [S4881Nr4_L22]

value: WT

value: Imatinib, Con3


title: Imatinib, Con3, Optimization plate 4, Well K22 [S4881Nr4_K22]


title: NSC13151_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: 24 hrs


title: Root tips, P limiting, rep 3 [PLT3]


title: Imatinib, Con4, Optimization plate 4, Well K21 [S4881Nr4_K21]

value: Imatinib, Con4


title: Imatinib, Con2, Optimization plate 4, Well J23 [S4881Nr4_J23]

value: hiPSC-CM


title: Imatinib, Con4, Optimization plate 4, Well J21 [S4881Nr4_J21]


title: Imatinib, Con3, Optimization plate 4, Well J22 [S4881Nr4_J22]


title: Imatinib, Con4, Optimization plate 4, Well L21 [S4881Nr4_L21]


title: TIOGUANINE_1_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: TIOGUANINE


title: Imatinib, Con5, Optimization plate 4, Well L20 [S4881Nr4_L20]

value: Imatinib, Con5


title: Imatinib, Con5, Optimization plate 4, Well K20 [S4881Nr4_K20]


title: Imatinib, Con6, Optimization plate 4, Well L19 [S4881Nr4_L19]

value: Imatinib, Con6


title: Root tips, P limiting, rep 1 [PLT1]

value: cv LA0716

value: 8 to 10 days-after germination


title: Imatinib, Con6, Optimization plate 4, Well K19 [S4881Nr4_K19]


title: Root tips, P limiting, rep 2 [PLT2]


title: ARTENIMOL_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblastoma

value: ARTENIMOL


title: Imatinib, Con7, Optimization plate 4, Well L18 [S4881Nr4_L18]

value: Imatinib, Con7


title: CYPROHEPTADINE_HCL_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblast

value: MYCNA


title: Root tips, P sufficient, rep 2 [PST2]

value: 1 cm segment from the root tip

value: Sufficient phosphate


title: SULOCTIDIL_10_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: SULOCTIDIL


title: Root tips, P sufficient, rep 4 [PST4]


title: 11518X19

city: Salt Lake City

first: Gennie

last: Parkman

state: UT

address: 2000 Circle of Hope, Rm 5263

department: Oncological Sciences

institute: University of Utah

data_processing:
Purified libraries were qualified on an Agilent Technologies 2200 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583)
The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824)
Individual libraries were normalized to 10 nM and equal volumes were pooled in preparation for Illumina sequence analysis
DNA sequences were determined using the HiSeq 50 Cycle Single-Read Sequencing version 4
Sequencing libraries (25 pM) were chemically denatured and applied to an Illumina HiSeq v4 single read flow cell using an Illumina cBot
Hybridized molecules were clonally amplified and annealed to sequencing primers with reagents from an Illumina HiSeq SR Cluster Kit v4-cBot (GD-401-4001)
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCSv2.2.38 and RTA v1.18.61), a 50 cycle single-read sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4002)
Generated reads mapped to reference genome
Differential expression analysis performed using DESeq2 variance stabilizing transformation
Assembly: hg19
Supplementary files format and content: Table containing counts for each sample counted using featureCounts against the NCBI hg19 release 75 gene annotation file
Supplementary files format and content: Filtered variant calls on RNAseq file using GATK

source_name: melanoma

extract_protocol:
Frozen primary tumor samples embedded in OCT were macrodissected. For RNA extraction and DNase treatment, the Roche High Pure miRNA Isolation Kit was used in accordance with the manufacturer's protocol (5080576001).
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold. Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples. Stranded RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold per the manufacturer’s instructions (RS-122-2301 and RS-122-2302).

value: melanoma


title: Imatinib, Con8, Optimization plate 4, Well K17 [S4881Nr4_K17]

value: WT

value: Imatinib, Con8


title: Root tips, P sufficient, rep 1 [PST1]


title: OXETHAZINE_5_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: OXETHAZINE

value: 24 hrs


title: Root tissue - MH-seq_rep2

city: East Lansing

first: Jiming

last: Jiang

state: MICHIGAN

address: 612 WILSON ROAD

department: Department of Plant Biology

institute: Michigan State University

library_source: genomic

data_processing:
Adapters were removed with trimmomatic v0.36 using the parameters “ILLUMINACLIP:/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30”.
The MH-seq reads were mapped to soybean Williams 82 reference genome (http://www.phytozome.net/soybean) using BWA (0.7.15-r1140) with default parameters.
F-seq was used to identify MHSs with a 200-bp bandwidth.
Genome_build: Gmax_275_v2.0
Supplementary_files_format_and_content: bed files were generated using F-seq; peak files.
Supplementary_files_format_and_content: wig files were generated using F-seq.

molecule: genomic DNA

organism: Glycine max

source_name: Root

growth_protocol: The trifoliate leaves and roots were collected from seedlings at stage V2. The seeds were collected from plants at stage R1. The soybean plants were grown in green house with 12 h (28 °C) light and 12 h dark (25 °C). The flower tissues were collected from the R1 stage plants grown in the experimental field.

extract_protocol:
The collected material was ground into fine powder in liquid nitrogen. Then the powder (0.5g for leaf and 1 g for flower, seed and root) was fixed with 1% of final concentration of formaldehyde for 10 min and followed by neutralization with 0.125 M glycine for 5 min. Next, the nuclei were prepared following previous protocols. The purified nuclei were suspended in 0.8 ml MNase digestion buffer (MNB, 10% sucrose, 50 mM Tris-HCl, pH 7.5, 4 mM MgCl2, and 1 mM CaCl2) and divided into 4 of 1.5 ml eppendorf tubes. The aliquoted nuclei were cleaved at 37°C for 10 mins by using a series of MNase (N3755-50UN, Sigma) in 0, 0.01, 0.03 and 0.1 unit, respectively. After terminating digestion with 10 mM EDTA, the cleaved nuclei with 200 mM NaCl were incubated at 65 °C for 4h in order to reverse cross-linking. The DNA was extracted by adding 400 ul CTAB and incubated at 65°C for 15 min. The subsequent step was performed by following CTAB method.
The extracted DNA was separated by running 2% of agarose gel in 1x TAE buffer. We recovered the DNA fragment with size less than 100 bp to prepare MH-seq library. Illumina library following standard Illumina library preparation procedures.

value: Williams 82

value: Root

value: Stage V2


title: Root tips, P sufficient, rep 3 [PST3]

value: cv LA0716

value: 8 to 10 days-after germination


title: Imatinib, Con6, Optimization plate 4, Well J19 [S4881Nr4_J19]

value: hiPSC-CM

value: Imatinib, Con6


title: Root tissue - MH-seq_rep1


title: Imatinib, Con8, Optimization plate 4, Well L17 [S4881Nr4_L17]


title: Imatinib, Con7, Optimization plate 4, Well J18 [S4881Nr4_J18]

value: Imatinib, Con7


title: Imatinib, Con7, Optimization plate 4, Well K18 [S4881Nr4_K18]


title: Imatinib, Con5, Optimization plate 4, Well J20 [S4881Nr4_J20]

value: Imatinib, Con5


title: Sunitinib, Con2, Optimization plate 4, Well K15 [S4881Nr4_K15]

value: Sunitinib, Con2


title: Imatinib, Con8, Optimization plate 4, Well J17 [S4881Nr4_J17]


title: Sunitinib, Con2, Optimization plate 4, Well L15 [S4881Nr4_L15]


title: 11518X18


title: Sunitinib, Con1, Optimization plate 4, Well K16 [S4881Nr4_K16]

value: Sunitinib, Con1


title: Sunitinib, Con1, Optimization plate 4, Well L16 [S4881Nr4_L16]


title: 11518X15


title: 11518X17


title: Sunitinib, Con2, Optimization plate 4, Well J15 [S4881Nr4_J15]


title: 11518X16


title: Seed tissue - MH-seq_rep2

source_name: Seed

growth_protocol: The trifoliate leaves and roots were collected from seedlings at stage V2. The seeds were collected from plants at stage R4. The soybean plants were grown in green house with 12 h (28 °C) light and 12 h dark (25 °C). The flower tissues were collected from the R1 stage plants grown in the experimental field.

value: Seed

value: Stage R4


title: Sunitinib, Con3, Optimization plate 4, Well J14 [S4881Nr4_J14]

value: WT

value: Sunitinib, Con3


title: Sunitinib, Con3, Optimization plate 4, Well L14 [S4881Nr4_L14]


title: Flower tissue - MH-seq_rep2

source_name: Flower

value: Flower

value: Stage R1


title: Sunitinib, Con3, Optimization plate 4, Well K14 [S4881Nr4_K14]


title: Sunitinib, Con4, Optimization plate 4, Well K13 [S4881Nr4_K13]

value: Sunitinib, Con4


title: Sunitinib, Con1, Optimization plate 4, Well J16 [S4881Nr4_J16]


title: Seed tissue - MH-seq_rep1

value: Williams 82


title: Leaf tissue - MH-seq_rep2

source_name: Leaf

value: Leaf

value: Stage V2


title: Sunitinib, Con5, Optimization plate 4, Well L12 [S4881Nr4_L12]

value: Sunitinib, Con5


title: 11518X12

value: melanoma


title: 11518X11


title: 11518X14


title: Sunitinib, Con5, Optimization plate 4, Well K12 [S4881Nr4_K12]

value: hiPSC-CM


title: 11518X13


title: Sunitinib, Con5, Optimization plate 4, Well J12 [S4881Nr4_J12]


title: 11518X10


title: Leaf tissue - MH-seq_rep1


title: Sunitinib, Con6, Optimization plate 4, Well J11 [S4881Nr4_J11]

value: Sunitinib, Con6


title: 11518X9


title: Sunitinib, Con4, Optimization plate 4, Well L13 [S4881Nr4_L13]


title: Sunitinib, Con6, Optimization plate 4, Well L11 [S4881Nr4_L11]


title: Sunitinib, Con6, Optimization plate 4, Well K11 [S4881Nr4_K11]


title: Flower tissue - MH-seq_rep1


title: 11518X8


title: Sunitinib, Con7, Optimization plate 4, Well L10 [S4881Nr4_L10]

value: Sunitinib, Con7


title: Sunitinib, Con4, Optimization plate 4, Well J13 [S4881Nr4_J13]


title: Gingiva_metformin

city: London

first: Vitor

last: Neves

state: London

address: Great Maze Pond, Floor 17, Guy's Hospital

department: Centre for Host-Microbiome Interactions

country: United Kingdom

institute: King's College London

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The data was demultiplexed using bcl2fastq software from Illumina.
Cellranger 7.0.1 was used to analyse the raw data for barcode processing, generating the counts and clusters.
Loupe browser version 6 was used for further downstream analysis.
Assembly: mm10
Supplementary files format and content: tab separated values & matrix file from cellranger output.

organism: Mus musculus

source_name: gingiva

extract_protocol:
Using scalpel and tweezers, the maxillary gingival neck was carefully excised. Following dissection, the mouse gingivae were cut in small pieces and transferred to a 15ml falcon tube with PBS + 2% FBS with 2 mg/ml of Collagenase Type II and 1 mg/ml of DNAse Type I (Merck), and incubated for 20–30 min at 37 °C shaking (120 rpm) with homogenization of the suspension every 3-4 minutes. After incubation, the cell suspensions were toped up to 12ml using using PBS + 2% FBS and filtered in using a 40µm cell strainer.
Library was performed according to the manufacturer instructions (10x Genomics)

value: gingiva

tag: condition

value: Metformin treatment


title: Gingiva_control

description: 10X Genomics

value: Healthy Sample


title: Disease_gingiva_metformin

description: 10X Genomics

value: Disease sample treated with Metformin


title: 11518X7


title: Sunitinib, Con7, Optimization plate 4, Well J10 [S4881Nr4_J10]

value: WT


title: Sunitinib, Con7, Optimization plate 4, Well K10 [S4881Nr4_K10]


title: PERHEXILINE_MALEATE_3_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblastoma

value: neuroblast

value: MYCNA

value: 24 hrs


title: Sunitinib, Con8, Optimization plate 4, Well L9 [S4881Nr4_L9]

value: Sunitinib, Con8


title: Sunitinib, Con8, Optimization plate 4, Well J9 [S4881Nr4_J9]


title: Sunitinib, Con8, Optimization plate 4, Well K9 [S4881Nr4_K9]


title: Lidocaine, Con1, Optimization plate 4, Well L8 [S4881Nr4_L8]

value: Lidocaine, Con1


title: Lidocaine, Con1, Optimization plate 4, Well K8 [S4881Nr4_K8]


title: Lidocaine, Con1, Optimization plate 4, Well J8 [S4881Nr4_J8]


title: FpWT_1

value: biol rep 1


title: Disease_gingiva

description: 10X Genomics

value: Disease sample


title: Lidocaine, Con2, Optimization plate 4, Well K7 [S4881Nr4_K7]

value: Lidocaine, Con2


title: CFBEC, treated, rep1

city: Chieti

first: Domenico

last: Mattoscio

address: Via Luigi Polacchi, 11

country: Italy

institute: University of Chieti

data_processing:
snakemake
minimap2
salmon
edgeR
DEXSeq and stageR
Assembly: GRCH38.13
Supplementary files format and content: tsv files containing counts for each sample (indicated with different barcodes as above described)
Supplementary files format and content: tsv files containing counts for each sample (indicated with different barcodes as above described)

source_name: bronchial epithelial cystic fibrosis cells

growth_protocol: Cystic fibrosis bronchial epithelial cells (CFBEC) were isolated from bronchi of patients with the ΔF508/ΔF508 genotype provided Primary Culture Service (Istituto G. Gaslini, Genoa, Italy) as part of the of the Fondazione Ricerca Fibrosi Cistica (Verona, Italy). These cells were cultured on rat tail collagen-coated cell culture Petri dishes in a serum-free medium (LHC9:RPMI 1640, 1:1) with growth factors as described in ref. (21). For further differentiation, CFBEC (2.5 x 106 cells) were grown on Alvetex scaffolds submerged in Ham’s F12, 2 % Ultroser G (Pall Corp., New York) medium for 7-10 days after which they were maintained in air-liquid interface up to 2 weeks.

extract_protocol:
CFBEC cells previously cultured in ALI were collected with 1 mL TRIzol (TRIzol™ Reagent, Sigma) and mixed with chloroform (200 μL/mL of TRIzol). Once the samples have been fixed with chloroform and incubated for 3 minutes at room temperature, the samples were centrifuged (12,000 xg, 15 min ,4 °C). The resulting clear upper aqueous phase (~ 60 % of total volume) was carefully transferred into a clean 1.5 mL tube, mixed with an equal volume of RNAse free 70 % EtOH, and loaded into silica spin columns following the Zymo RNA extraction protocol (Zymo Research).
RNA was quantified using a Nanophotomer (NanoPhotometer® NP80) and then processed according to the Nanopore protocol (Nanopore SQKDCS 109 with EXP-NBD 104 and EXP-NBD 114).

treatment_protocol: Cells were exposed to medium with 3.3 % CF ASN (mix of sputum from 3 different volunteers) in the apical side. RvD1 (10 nM) or ethanol (0.01 %) as a vehicle control was added in the apical and basolateral compartment and CFBEC for 24 h.

value: CFBEC

value: primary

value: deltaF508 mutation in CFTR gene


title: CFBEC, treated, rep3

value: bronchial epithelial cystic fibrosis cells


title: Lidocaine, Con2, Optimization plate 4, Well L7 [S4881Nr4_L7]

value: hiPSC-CM


title: CFBEC, treated, rep2


title: Lidocaine, Con2, Optimization plate 4, Well J7 [S4881Nr4_J7]


title: CFBEC, control, rep3

description: control

value: vehicle


title: Lidocaine, Con3, Optimization plate 4, Well L6 [S4881Nr4_L6]

value: Lidocaine, Con3


title: Lidocaine, Con3, Optimization plate 4, Well K6 [S4881Nr4_K6]

value: WT


title: Lidocaine, Con3, Optimization plate 4, Well J6 [S4881Nr4_J6]


title: NSC319990_15_24.hrs_R1

description:
PLATE-Seq
first-experiment-counts.csv

value: neuroblastoma


title: CFBEC, control, rep2

description: control


title: 11518X2

value: melanoma


title: 11518X1


title: 11518X6


title: Lidocaine, Con4, Optimization plate 4, Well K5 [S4881Nr4_K5]

value: Lidocaine, Con4


title: CFBEC, control, rep1

description: control


title: 11518X5


title: 11518X4


title: PC9 GR cells, Erlotinib +iCCR6 (E+C), Day1 b

city: Seoul

first: Eun-Ji

last: Kwon

address: 1, Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
Read quality was assessed using FastQC (v) and poor-quality bases (Phred score < 20) were eliminated using TrimGalore (v0.6.6)
Trimmed reads were aligned to the human reference genome (GRCh38) using the STAR aligner (v2.7.9a) with default parameters
Gene-level expression values such as transcripts per million (TPM) and read counts were calculated using RSEM (v1.3.3.) with human gene annotation (GRCh38.84)
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: PC9 GR

growth_protocol: PC9 and PC9 GR cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Easy-BLUETM RNA isolation kit (iNtRON Biotechnology) . 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA)
Briefly, the strand-specific protocol included the following steps: (1) strand cDNA synthesis, (2) strand synthesis using dUTPs instead of dTTPs, (3) end repair, A-tailing, and adaptor ligation, and (4) PCR amplification. Each library was then diluted to 8 pM for 76 cycles of paired-read sequencing (2 × 75 bp) on an Illumina NextSeq 500 following the manufacturer’s recommended protocol.

treatment_protocol: PC9 and PC9 GR cells were treated with 2uM Erlotinib and 500nM CCR6 inhibitor

value: PC9 GR

value: non-smallcelllung cancercell

value: Acquired resistance


title: Lidocaine, Con5, Optimization plate 4, Well L4 [S4881Nr4_L4]

value: Lidocaine, Con5


title: Lidocaine, Con4, Optimization plate 4, Well J5 [S4881Nr4_J5]


title: Lidocaine, Con5, Optimization plate 4, Well K4 [S4881Nr4_K4]


title: PC9 GR cells, Erlotinib +iCCR6 (E+C), Day1 a


title: 11518X3


title: Lidocaine, Con5, Optimization plate 4, Well J4 [S4881Nr4_J4]


title: Bir1OEN_3

city: Hanover

first: Elisa

middle: Marie

last: Vesely

state: NH

address: 74 College St

department: Microbiology and Immunology

institute: Dartmouth College

description:
ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX-N 1-446aa (Shlezinger et al 2017)
Sample 12
Bir1Conidia_CPM.csv
Figure1_Bir1OE-N v H2A 2-fold Up_Down SigHitGenes .xlsx

data_processing:
FASTQ Parallel Groomer + Trimmomatic (EupathDB, Galaxy)
HISAT2 + htseq-count (EupathDB, Galaxy)
DESeq2 (EupathDB, Galaxy)
Assembly: Aspergillus fumigatus A1163
Supplementary files format and content: Figure1_Bir1OE-N v H2A 2-fold Up_Down SigHitGenes .xlsx is an excel file that shows the differentially expressed genes in Bir1OE-N cells (Sample 10,Sample 11 , and Sample 12) versus ATCC46645 H2A cells (Sample 4, Sample 5, and Sample 6).
Supplementary files format and content: Bir1Conidia_CPM.csv is a .csv file that is the output of htseq-count for each Sample, organized in column order: gene, sample 1, sample 2, etc.

organism: Aspergillus fumigatus

source_name: Swollen Conidia

growth_protocol: 1x10^7 cells were swollen for 6 hours in 100mL RPMI + 0.5ug/mL voriconazole + 10% FBS  at 37C with 5% CO2, shaking at 50rpm. Cells were centrifuged prior to collection and flash frozen in liquid nitrogen before Trisure RNA extraction.

extract_protocol:
RNA was extracted with Trisure Reagent and Qiagen RNAeasy Kit purification columns. RNA was quantified and checked for quality by Nanodrop and Bioanalyzer prior to library preperation.
RNA was polyA enriched before processing with Illumina NextSeq500 sequencing (High Output 75 cycles, Dartmouth GMBSR Core Facility)

treatment_protocol: Swollen for 6 hours, no chemical treatment prior to collection.

value: Swollen Conidia

value: ATCC46645 +Histone H2A::mRFP fusion + Bir1OX-N 1-446aa


title: Bir1OEN_2

description:
ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX-N 1-446aa (Shlezinger et al 2017)
Sample 11
Bir1Conidia_CPM.csv
Figure1_Bir1OE-N v H2A 2-fold Up_Down SigHitGenes .xlsx


title: Lidocaine, Con6, Optimization plate 4, Well L3 [S4881Nr4_L3]

value: Lidocaine, Con6


title: PC9 GR cells, Erlotinib (E), Day1 b


title: Lidocaine, Con6, Optimization plate 4, Well K3 [S4881Nr4_K3]


title: PC9 GR cells, Erlotinib (E), Day1 a


title: Lidocaine, Con6, Optimization plate 4, Well J3 [S4881Nr4_J3]


title: Lidocaine, Con7, Optimization plate 4, Well L2 [S4881Nr4_L2]

value: Lidocaine, Con7


title: Bir1OE_3

description:
ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX (Shlezinger et al 2017)
Sample 9
Bir1Conidia_CPM.csv

value: ATCC46645 +Histone H2A::mRFP fusion + Bir1OX


title: Lidocaine, Con7, Optimization plate 4, Well K2 [S4881Nr4_K2]


title: PC9 GR cells, Vehicle (DMSO), Day1 b


title: PC9 GR cells, Vehicle (DMSO), Day1 a


title: Lidocaine, Con4, Optimization plate 4, Well L5 [S4881Nr4_L5]


title: Bir1OE_1

description:
ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX (Shlezinger et al 2017)
Sample 7
Bir1Conidia_CPM.csv


title: Lidocaine, Con8, Optimization plate 4, Well K1 [S4881Nr4_K1]

value: Lidocaine, Con8


title: PC9 cells, Erlotinib (E), Day1 b


title: Lidocaine, Con8, Optimization plate 4, Well J1 [S4881Nr4_J1]

value: hiPSC-CM


title: Enalapril, Con1, Optimization plate 4, Well I24 [S4881Nr4_I24]

value: Enalapril, Con1


title: ATCC46645H2AmRFP_3

description:
ATCC46645 +Histone H2A:: mRFP fusion (Shlezinger et al 2017)
Sample 6
Bir1Conidia_CPM.csv
Figure1_Bir1OE-N v H2A 2-fold Up_Down SigHitGenes .xlsx

value: ATCC46645 +Histone H2A::mRFP fusion


title: PC9 cells, Erlotinib (E), Day1 a

value: WT


title: Enalapril, Con1, Optimization plate 4, Well G24 [S4881Nr4_G24]


title: Enalapril, Con1, Optimization plate 4, Well H24 [S4881Nr4_H24]


title: PC9 cells, Vehicle (DMSO), Day1 b


title: ATCC46645H2AmRFP_2

description:
ATCC46645 +Histone H2A:: mRFP fusion (Shlezinger et al 2017)
Sample 5
Bir1Conidia_CPM.csv
Figure1_Bir1OE-N v H2A 2-fold Up_Down SigHitGenes .xlsx


title: Enalapril, Con2, Optimization plate 4, Well H23 [S4881Nr4_H23]

value: Enalapril, Con2


title: ATCC46645H2AmRFP_1

description:
ATCC46645 +Histone H2A:: mRFP fusion (Shlezinger et al 2017)
Sample 4
Bir1Conidia_CPM.csv
Figure1_Bir1OE-N v H2A 2-fold Up_Down SigHitGenes .xlsx


title: Bir1OEN_1

description:
ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX-N 1-446aa (Shlezinger et al 2017)
Sample 10
Bir1Conidia_CPM.csv
Figure1_Bir1OE-N v H2A 2-fold Up_Down SigHitGenes .xlsx


title: Enalapril, Con2, Optimization plate 4, Well I23 [S4881Nr4_I23]


title: Enalapril, Con3, Optimization plate 4, Well I22 [S4881Nr4_I22]

value: Enalapril, Con3


title: ATCC46645_3

description:
A. fumigatus wt strain
Sample 3
Bir1Conidia_CPM.csv

value: A. fumigatus wt strain


title: Bir1OE_2

description:
ATCC46645 +Histone H2A:: mRFP fusion + Bir1OX (Shlezinger et al 2017)
Sample 8
Bir1Conidia_CPM.csv


title: Enalapril, Con2, Optimization plate 4, Well G23 [S4881Nr4_G23]


title: Enalapril, Con3, Optimization plate 4, Well H22 [S4881Nr4_H22]


title: ATCC46645_2

description:
A. fumigatus wt strain
Sample 2
Bir1Conidia_CPM.csv


title: 16-904_3

city: Kensington

first: Sara

last: Ballouz

state: NSW

address: High St

country: Australia

institute: UNSW

description: Nine-banded armadillo

data_processing:
We downloaded the armadillo genome from Ensembl and generated an index file for use within STAR (v2.7).
We mapped reads with STAR (v2.7) and standardized counts to counts per million (CPM) by summing the counts and dividing by 1e6.
We generated personal genomes using g2gtools (v0.2.0). We mapped reads to the personal genomes using STAR. We ran the GATK (v3.6.0) pipeline and IGVtools (v2.3.80) to count reads per SNP.
Genome_build: DasNov3 v95
Supplementary_files_format_and_content: processed_count_data.txt: Count level outputs from STAR per gene.
Supplementary_files_format_and_content: processed_cpm_data.txt: CPMs are converted from the counts.
Supplementary_files_format_and_content: processed_counts_ase_quad_*.txt: ASE level outputs from the GATK pipeline; these counts are per SNP.

organism: Dasypus novemcinctus

source_name: Blood

extract_protocol:
RNA was extracted from the samples with a Maxwell® 16 Total RNA Purification Kit. Library preparation was done with a poly(A) selection kit (KAPA mRNA HyperPrep) to enrich for mRNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Multiplexed paired end sequencing (PE76) was done using an Illumina NextSeq500 on multiple flow cells. We blocked for lane batch effects by splitting the quadruplet samples into pairs and ran two pairs of each set per flow cell.

value: PBMCs

tag: Sex

value: Male

tag: infection status

value: Uninfected

tag: library batch

tag: sequencing flowcell lane

tag: longitudinal sample


title: Lidocaine, Con8, Optimization plate 4, Well L1 [S4881Nr4_L1]

tag: cell line

tag: genotype


title: Enalapril, Con4, Optimization plate 4, Well I21 [S4881Nr4_I21]

tag: treatment

value: Enalapril, Con4

tag: time


title: ATCC46645_1

description:
A. fumigatus wt strain
Sample 1
Bir1Conidia_CPM.csv

tag: cell type

value: Swollen Conidia


title: Lidocaine, Con7, Optimization plate 4, Well J2 [S4881Nr4_J2]


title: Enalapril, Con4, Optimization plate 4, Well H21 [S4881Nr4_H21]


title: 16-903_3

description: Nine-banded armadillo


title: Enalapril, Con4, Optimization plate 4, Well G21 [S4881Nr4_G21]


title: 16-902_3

description: Nine-banded armadillo


title: 16-901_3

description: Nine-banded armadillo


title: Enalapril, Con5, Optimization plate 4, Well H20 [S4881Nr4_H20]

value: Enalapril, Con5


title: PC9 cells, Vehicle (DMSO), Day1 a

value: non-smallcelllung cancercell


title: Enalapril, Con5, Optimization plate 4, Well I20 [S4881Nr4_I20]


title: CD8_Donor2 ([#2]_[#3]_[#4]_[#5]) HTO

city: Seattle

first: Scott

last: Furlan

state: WA

address: 1241 Eastlake Ave E

institute: Fred Hutchinson Cancer Center

description:
([#2] 24h [5/0.2/0.8] activated_[#3] 24h [5/0.2/5] activated_[#4] 24h [5/0/5] activated_[#5] naive)
S2_metadata.txt

library_source: other

data_processing:
BCLs were processed using cellranger arc (multiome library) and BCL2fastq (Totalseq A).  resulting fastq files for ATAC and ATAC were processed using cellranger arc count.  Totalseq A fastq were processed using CITEseq count
Assembly: GRCh38
Supplementary files format and content: csv
Supplementary files format and content: csv
Library strategy: Multiome ATAC+GEX

molecule: protein

source_name: CD8 T cells

growth_protocol: Cryopreserved T cells were defrosted and pre-conditioned for 2h at 37C in RPMI (0.01% BSA). T cells were then activated and cultured for 24h in complete CTL medium in the presence of 50U/mL IL2.

extract_protocol:
nuclei were prepared (CG000365 Rev A) and cells captured (CG000338 Rev B) per manufacterer's specifications with the addition of TotalSeq A hashtag antibodies for sample multiplexing
Library was performed according to the manufacter’s instructions (Single cell Multiome ATAC + Gene Expression Kit, 10x Genomics CG000338 Rev B). TotalSeq A hash library was performed according to the manufacturer's instructions (https://www.biolegend.com/en-us/protocols/totalseq-a-dual-index-protocol).

treatment_protocol: T cell activation was either performed using aCD3/aCD28 dynabeads, or antibody-coated plates using aCD3, aCD28 or CD70DT at indicated doses [aCD3/aCD28/CD70DT; ug/mL]

value: CD8 T cells

tag: hash


title: CD8_Donor2 ([#8]) HTO

description:
([#8] 24h aCD3/aCD28 Bead activated)
S3_metadata.txt


title: 16-304_3

description: Nine-banded armadillo

value: Female


title: Enalapril, Con6, Optimization plate 4, Well I19 [S4881Nr4_I19]

value: Enalapril, Con6


title: CD8_Donor1 ([#1]_[#2]_[#3]) HTO

description:
([#1] naive_ [#2] 24h aCD3/aCD28 Bead activated_[#3] 24h [5/0/5] activated)
S1_metadata.txt


title: Enalapril, Con6, Optimization plate 4, Well G19 [S4881Nr4_G19]

value: hiPSC-CM


title: Enalapril, Con3, Optimization plate 4, Well G22 [S4881Nr4_G22]


title: 16-303_3

description: Nine-banded armadillo


title: Enalapril, Con7, Optimization plate 4, Well I18 [S4881Nr4_I18]

value: Enalapril, Con7


title: CD8_Donor2 ([#8]) ATAC

value: 24h bead activated


title: CD8_Donor2 ([#2]_[#3]_[#4]_[#5]) ATAC

value: 24h activated


title: 16-301_3

description: Nine-banded armadillo


title: Enalapril, Con8, Optimization plate 4, Well I17 [S4881Nr4_I17]

value: WT

value: Enalapril, Con8


title: CD8_Donor1 ([#1]_[#2]_[#3]) ATAC

value: naïve


title: Enalapril, Con8, Optimization plate 4, Well H17 [S4881Nr4_H17]


title: 16-204_3

description: Nine-banded armadillo

value: PBMCs


title: Enalapril, Con7, Optimization plate 4, Well G18 [S4881Nr4_G18]


title: 16-302_3

description: Nine-banded armadillo


title: Enalapril, Con7, Optimization plate 4, Well H18 [S4881Nr4_H18]


title: Enalapril, Con8, Optimization plate 4, Well G17 [S4881Nr4_G17]


title: CD8_Donor2 ([#8]) GEX


title: DMSO, Con0, Optimization plate 4, Well I16 [S4881Nr4_I16]

value: DMSO, Con0


title: 16-203_3

description: Nine-banded armadillo

value: Uninfected


title: CD8_Donor2 ([#2]_[#3]_[#4]_[#5]) GEX


title: Enalapril, Con5, Optimization plate 4, Well G20 [S4881Nr4_G20]


title: DMSO, Con0, Optimization plate 4, Well G16 [S4881Nr4_G16]


title: 16-202_3

description: Nine-banded armadillo


title: CD8_Donor1 ([#1]_[#2]_[#3]) GEX


title: 16-201_3

description: Nine-banded armadillo

value: Mycobacterium leprae


title: DJ,240m, NH4-

city: Madrid

first: Luis

middle: M.

last: Rubio

address: Campus de Montegancedo UPM. Crta. M-40 km 38

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC)

data_processing:
Sample files (FASTQ) were quality-checked with FASTQC.Adapter sequences were removed with trim-galore (2) (--length 75).
Processed reads were aligned against azotobacter genome sequence (GCA_000021045.1_ASM2104v1_genomic.fna) with RNA-STAR
Duplicated alignments (PCR or Optical) were detected and labelled using function MarkDuplicates of picard tools
Alignment files, in SAM format, were compressed, sorted and indexed with the corresponding commands of samtools.
The Azotobacter genes included in annotation file provided (GCA_000021045.1_ASM2104v1_genomic.gtf) were quantified with the function featureCounts (ignoreDup=TRUE, primaryOnly=TRUE, requireBothEndsMapped=TRUE) of Bioconductor package Rsubread.
Assembly: EnsemblBacteria Azotobacter vinelandii DJ (GCA_000021045)
Supplementary files format and content: tab-delimited text file includes RPKM normalized counts for each Sample

organism: Azotobacter vinelandii DJ

source_name: Bacterial cells

extract_protocol:
Total RNA was isolated using a RiboPure-Bacteria kit (Ambion, Life Technologies) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using Illumina protocol

value: Bacterial cells

value: 240m nitrogenase derepression


title: DJ,Control,240m, NH4+

value: 240m MH4+ control


title: DMSO, Con0, Optimization plate 4, Well H16 [S4881Nr4_H16]


title: DMSO, Con0, Optimization plate 4, Well I15 [S4881Nr4_I15]


title: SLK21, Non-ARDS, Time_2

first: Carmen

last: Mikacenic

state: Washington

address: 1201 Ninth Avenue

institute: Benaroyra Research Institute

data_processing:
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination

source_name: BAL

extract_protocol:
BAL taken from patients immediately and 72 hours after intubation on ventilators, whole cells sorted for live CD45+ CD15+ Leukocytes
Cells were loaded onto a 10X Genomics GemCode Single-Cell Instrument per manufacturer instructions for nanodroplet single-cell capture, cell lysis, mRNA rtPCR, and cDNA barcoding within droplets.
NextSeq 10x chemistry

value: BAL

value: Leukocytes


title: SLK21, Non-ARDS, Time_1


title: DMSO, Con0, Optimization plate 4, Well H15 [S4881Nr4_H15]


title: DMSO, Con0, Optimization plate 4, Well G15 [S4881Nr4_G15]


title: DJ,30m, NH4-, plus 15m Ammonium Shock

value: 30m nitrogenase derepression plus 15m ammonium shock


title: DJ,30m, NH4-

value: 30m nitrogenase derepression


title: Enalapril, Con6, Optimization plate 4, Well H19 [S4881Nr4_H19]

value: hiPSC-CM

value: Enalapril, Con6


title: DMSO, Con0, Optimization plate 4, Well I14 [S4881Nr4_I14]


title: DJ,10m, NH4-, plus 15m Ammonium Shock

value: 10m nitrogenase derepression plus 15m ammonium shock


title: SLK23, ARDS, Time_1


title: DMSO, Con0, Optimization plate 4, Well H14 [S4881Nr4_H14]

value: WT


title: DJ,10m, NH4-

value: 10m nitrogenase derepression


title: 15-502_3

description: Nine-banded armadillo

value: Male


title: 15-501_3

description: Nine-banded armadillo

value: PBMCs


title: 15-504_3

description: Nine-banded armadillo


title: SLK12, Non-ARDS, Time_2


title: DMSO, Con0, Optimization plate 4, Well G14 [S4881Nr4_G14]

value: DMSO, Con0


title: 12-104_3

description: Nine-banded armadillo

value: Female


title: SLK12, Non-ARDS, Time_1


title: DMSO, Con0, Optimization plate 4, Well I13 [S4881Nr4_I13]


title: 12-103_3

description: Nine-banded armadillo

value: Mycobacterium leprae


title: SLK7, ARDS, Time_2


title: 15-503_3

description: Nine-banded armadillo


title: 12-102_3

description: Nine-banded armadillo


title: DMSO, Con0, Optimization plate 4, Well H13 [S4881Nr4_H13]


title: SLK23, ARDS, Time_2


title: DMSO, Con0, Optimization plate 4, Well G13 [S4881Nr4_G13]


title: 12-101_3

description: Nine-banded armadillo


title: SLK22, ARDS, Time_1


title: DMSO, Con0, Optimization plate 4, Well I12 [S4881Nr4_I12]


title: 16-904_2

description: Nine-banded armadillo

value: Uninfected


title: SLK8, Non-ARDS, Time_1


title: SLK14, Non-ARDS, Time_1


title: DMSO, Con0, Optimization plate 4, Well H12 [S4881Nr4_H12]


title: 16-903_2

description: Nine-banded armadillo


title: 16-902_2

description: Nine-banded armadillo


title: DMSO, Con0, Optimization plate 4, Well G12 [S4881Nr4_G12]


title: SLK3, ARDS, Time_1


title: DMSO, Con0, Optimization plate 4, Well I11 [S4881Nr4_I11]


title: DMSO, Con0, Optimization plate 4, Well H11 [S4881Nr4_H11]


title: 16-901_2

description: Nine-banded armadillo


title: SLK7, ARDS, Time_1


title: SK-MEL-2_CRISPRi_day7_replicate2

city: Tianjin

first: Mulin

middle: Jun

last: Li

state: Tianjin

address: 22 Qixiangtai Road, Tianjin, Tianjin, China

department: Department of Epidemiology and Biostatistics

country: China

institute: Tianjin Medical University

data_processing:
We first extracted the sgRNA sequence from the 150bp original reads, and the abundance of guides was first determined by the MAGeCK “count” module from the extracted sgRNAs. Second, we removed 1% guides of each sample with lowest count. We used the non-targeting control guides to estimate the size factor for normalization, and estimated significant enrichment according to MAGeCK-RRA algorithm at enhancer level.
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited text files contain sgRNA count
Library strategy: CRISPR interference (CRISPRi) screen

growth_protocol: A375 human melanoma cell line (ATCC, CRL-1619) and A375-KRAB were cultured in Dulbecco's Modified Eagle’s Medium (DMEM; ThermoFisher, 11965092) supplemented with 10% fetal bovine serum (FBS; ThermoFisher, R7007). SK-MEL-2 (ATCC, HTB-68) and SK-MEL-2-KRAB were maintained in Eagle’s Minimum Essential Medium (EMEM; ATCC, 30-2003) supplemented with 10% FBS. All cell lines were cultured at 37°C in a humidified atmosphere containing 5% CO2 and were verified mycoplasma free using the MycoAlert Mycoplasma Detection Kit (Lonza, LT07-218).

extract_protocol:
Genomic DNAs of the two group cells were extracted by FastPure Cell/Tissue DNA Isolation Mini Kit (Vazyme, DC102) for PCR amplification (Vazyme, N616), and the amplified products were subject to library construction using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607) according to the kit’s instructions and then performed the next-generation sequence on a HiSeq X Ten platform. The CRISPRi screen was independently performed for two times.
We first comprehensively curated essential genes associated with melanoma cell growth and drug resistance from published CRISPR/shRNA screening studies. Then, we selected HRR-associated enhancers receiving both H3K27ac and H3K4me1 signals in A375 cells within 1Mb region of each melanoma essential genes. These enhancer regions were further narrowed with chromatin accessibility signal based on ATAC-seq peaks. For the remaining enhancer core regions, we divided each region into several bins consisting of 100bp and scored all eligible sgRNAs in each bin using FlashFry. By selecting the best sgRNA in each bin, the intersected tiling strategy can yield a sgRNA library for all selected enhancers, and a total of 1,000 unmatched sgRNAs were added into the library as negative control. The sgRNA sequences were synthesized by Synbio Technologies and cloned into lentiGuide-Puro vector (Addgene, 52963) in the form of homologous recombination to construct the plasmid library, and then packaged into the lentivirus library using the pMD2.G (Addgene, 12259) and psPAX2 (Addgene, 12260) packaging plasmids for subsequent screening.

treatment_protocol: We generated A375 or SK-MEL-2 cell lines stably expressing Lenti-dCas9-KRAB (Addgene, 89567) transgenes and performed lentiviral transduction of pooled sgRNAs at low multiplicity of infection (MOI) = 0.2. After 24 hours, puromycin was added for selecting the effective infected A375-KRAB or SK-MEL-2 cells. After 7 days, the cells were divided into two groups. One group (day 0) of cells was collected and frozen as a control group, and the other groups (day 7 or 21) of cells were selected at 7 or 21 days.

value: human melanoma cell

tag: time point


title: DMSO, Con0, Optimization plate 4, Well G11 [S4881Nr4_G11]


title: 16-303_2

description: Nine-banded armadillo


title: SK-MEL-2_CRISPRi_day0_replicate2


title: 16-302_2

description: Nine-banded armadillo


title: DMSO, Con0, Optimization plate 4, Well I10 [S4881Nr4_I10]


title: SW480 cells grown as spheroid

type: RNA

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

description: Gene expression data from colorectal cancer cell line

hyb_protocol: Following fragmentation, 5.5 ug of sscDNA were hybridized for 16 hr at 45°C on Clariom_D_Human Arrays. GeneChips were washed and stained in the Affymetrix GeneChipFluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 using default analysis settings and RMA normalization method.

label: biotin

source_name: luciferase transgenic SW480 cells grown as spheroid

label_protocol: Biotinylated sscDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: Red-shifted firefly luciferase transgenic cell lines were cultivated in RPMI1640 medium containing 10 % fetal bovine serum and penicillin/streptomycin at 37°C and 5 % CO2 in a humid atmosphere. In order to generate tumor spheroids, tumor cells resuspended in culture medium were seeded onto 96-well plates, which were coated with 0.7 % agarose, partially supplemented with 10 µg/mL collagen I. Generation of subcutaneous xenograft tumors was performed by inoculation of 5 million tumor cells into the right flank of male athymic nude mice. Tumors were removed from mice when they had reached a volume of approximately one cm3.

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

treatment_protocol: Cell separation from xenografts was performed using a gentleMACS Octo (Miltenyi Biotech, Begisch Gladbach, Germany) by using the Tumor Dissociation Kit, followed by separation using the Mouse Cell Depletion Kit and the Death Cell Removal Kit according to the protocols of the manufacturer.

value: colorectal cancer cell line

value: luciferase transgenic


title: SW48 cells grown as xenograft

source_name: luciferase transgenic SW48 cells grown as xenograft


title: LS1034 cells grown as xenograft

source_name: luciferase transgenic LS1034 cells grown as xenograft


title: SW48 cells grown as spheroid

source_name: Sluciferase transgenic W48 cells grown as spheroid


title: SW480 cells grown as monolayer

source_name: luciferase transgenic SW480 cells grown as monolayer


title: LS1034 cells grown as spheroid

source_name: luciferase transgenic LS1034 cells grown as spheroid


title: DMSO, Con0, Optimization plate 4, Well H10 [S4881Nr4_H10]

source_name: hiPSC-CM


title: A375_CRISPRi_day7_replicate2


title: SK-MEL-2_CRISPRi_day0_replicate1


title: LS1034 cells grown as monolayer

source_name: luciferase transgenic LS1034 cells grown as monolayer


title: 16-304_2

description: Nine-banded armadillo


title: 16-203_2

description: Nine-banded armadillo


title: 16-204_2

description: Nine-banded armadillo


title: DMSO, Con0, Optimization plate 4, Well I9 [S4881Nr4_I9]


title: DMSO, Con0, Optimization plate 4, Well H9 [S4881Nr4_H9]


title: SK-MEL-2_CRISPRi_day7_replicate1


title: A375_CRISPRi_day7_replicate1


title: SW48 cells grown as monolayer

source_name: luciferase transgenic SW48 cells grown as monolayer


title: 16-301_2

description: Nine-banded armadillo


title: DMSO, Con0, Optimization plate 4, Well G10 [S4881Nr4_G10]


title: 16-202_2

description: Nine-banded armadillo


title: DMSO, Con0, Optimization plate 4, Well G9 [S4881Nr4_G9]


title: LS174T cells grown as xenograft

source_name: luciferase transgenic LS174T cells grown as xenograft


title: A375_CRISPRi_day21_replicate2

data_processing:
library strategy: CRISPR interference (CRISPRi) screen
We first extracted the sgRNA sequence from the 150bp original reads, and the abundance of guides was first determined by the MAGeCK “count” module from the extracted sgRNAs. Second, we removed 1% guides of each sample with lowest count. We used the non-targeting control guides to estimate the size factor for normalization, and estimated significant enrichment according to MAGeCK-RRA algorithm at enhancer level.
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain sgRNA count

growth_protocol: A375 human melanoma cell line (ATCC, CRL-1619) were all cultured in Dulbecco's Modified Eagle’s Medium (DMEM; ThermoFisher, 11965092) supplemented with 10% fetal bovine serum (FBS; ThermoFisher, R7007).

extract_protocol:
The sgRNA sequences were synthesized by Synbio Technologies and cloned into lentiGuide-Puro vector (Addgene, 52963) in the form of homologous recombination to construct the plasmid library, and then packaged into the lentivirus library for subsequent screening.
We generated A375 cell lines stably expressing Lenti-dCas9-KRAB (Addgene, 89567) transgenes and performed lentiviral transduction of pooled sgRNAs at low multiplicity of infection (MOI) = 0.2. After 24 hours, puromycin was added for selecting the effective infected A375-KRAB cells. After 7 days, the cells were divided into two groups. One group (day 0) of cells was collected and frozen as a control group, and the other group (day 21) of cells were selected at 21 days.
CRISPR interference (CRISPRi) screen on A375 enhancers

value: human melanoma cell line


title: A375_H3K27ac_HiChIP

data_processing:
library strategy: HiChIP
HiChIP paired-end reads were aligned to the hg19 human genome using the HiC-Pro pipeline with default settings to remove duplicate reads, assign reads to MboI restriction fragments, filter for valid interactions, and generate binned interaction matrices.
Chromatin interactions were filtered from a minimum distance of 20-kb to a maximum of 2-Mb
Assembly: hg19
Supplementary files format and content: bed; HiChIP interactions

extract_protocol:
A375 cells were counted, and ~1.5 × 107 cells were crosslinked with 1% formaldehyde in phosphate-buffered saline (PBS; ThermoFisher, 10010023) at room temperature for 10 min, and then quenched with 0.125 M Glycine (Sigma-Aldrich, 50046) on ice for 5 min. Next, crosslinked cells were lysed in Hi-C lysis buffer (10mM Tris-HCl pH8.0 [ThermoFisher, 15568025], 10mM NaCl [Sigma-Aldrich, S7653], and 0.2% Igepal CA630 [Sigma-Aldrich, I3021]) with 50 μl of protease inhibitors (Sigma, P8340), and nuclei were extracted and digested with MboI restriction enzyme (NEB, R0147) for 2 h. After digestion, nuclei were resuspended in NEB buffer supplemented with DNA polymerase I, Large (Klenow) fragment (NEB, M0210) to fill in the restriction fragment overhangs with Biotin-14-dATP (Life Technologies，19524-016) for 1 h. Proximal ligation was performed with T4 DNA ligase (NEB, M0202M) for 4 h at 16°C and nuclei were harvested. The nuclei were transferred to shear chromatin using a Biorupter system (Diagenode, B01060001). The sheared chromatin was incubated overnight with 8 μl of H3K27ac antibody (Abcam, ab4729), and then Protein A-agarose beads (Millipore, 16-157) were used to capture H3K27Ac-associated chromatin.
The whole H3K27ac-ChIP process was performed with the PierceTM Magnetic ChIP kit (ThermoFisher, 26157), the final DNA was eluted with 15 μl Nuclease-Free Water (ThermoFisher, AM9930). The eluted DNA was sent for DNA biotin pull-down with Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602). Sixty micrograms of DNA were used for PCR amplification, and then AMPure XP beads (Beckman Coulter, A63880) was used to select a size range of 300~600 bp products.

tag: chip antibody

value: H3K27ac (Abcam, #ab4729)


title: A375_CRISPRi_day21_replicate1


title: 16-201_2

description: Nine-banded armadillo


title: Sunitinib, Con1, Optimization plate 4, Well I8 [S4881Nr4_I8]

data_processing:
Transcriptomic profiling was performed in batches of 382 samples. Each batch contained 22 negative-control (i.e. DMSO-treated) samples, and 15 blocks of compound-treated samples. Every block included 8 compound concentrations, each in triplicate.
Reads were mapped to the human genome (genome-build GRCh38.p13 – accession GCA_000001405.28) using STAR (version 2.7.9a).
Multi-mapped reads, reads with mapping to inter-genic regions (with respect to Ensembl gene annotation information version 104) and reads with ambiguous mapping location (i.e. location associated with more than one gene) were discarded, and UMI-based deduplication was performed.
Sequencing files were demultiplexed and barcodes were stripped.
Assembly: GRCh38.p13 – accession GCA_000001405.28
Supplementary files format and content: processed_data_counts.txt: RNA unique moecular identifier (UMI) counts per gene. The column EnsemblID provides the unique gene identifier. One column is included per sample with column names matching the column "description" in the table "SAMPLES".

extract_protocol:
High-throughput transcriptomics was performed using Evotec’s (semi)-automated ScreenSeqTM platform. Cell lysis was performed in a 384-well plate format followed by well-specific labeling of samples.
Plate RNASeq of polyA RNA (ScreenSeqTM); Purified mRNAs were labeled with a unique molecular identifier (UMI). After pooled cDNA synthesis, adapters containing Illumina’s unique dual indexes were attached for final library preparation and sequenced on a NovaSeq 6000 system.

value: Sunitinib, Con1


title: 15-504_2

description: Nine-banded armadillo


title: LS174T cells grown as spheroid

source_name: luciferase transgenic LS174T cells grown as spheroid


title: Lovo cells grown as xenograft

source_name: luciferase transgenic Lovo cells grown as xenograft


title: A375_CRISPRi_day0_replicate2


title: 15-503_2

description: Nine-banded armadillo


title: LS174T cells grown as monolayer

source_name: luciferase transgenic LS174T cells grown as monolayer


title: Sunitinib, Con1, Optimization plate 4, Well H8 [S4881Nr4_H8]

value: hiPSC-CM


title: Lovo cells grown as spheroid

source_name: luciferase transgenic Lovo cells grown as spheroid


title: A375_CRISPRi_day0_replicate1


title: Sunitinib, Con1, Optimization plate 4, Well G8 [S4881Nr4_G8]


title: 15-502_2

description: Nine-banded armadillo

source_name: Blood


title: SW480 cells grown as xenograft

source_name: luciferase transgenic SW480 cells grown as xenograft


title: Sunitinib, Con2, Optimization plate 4, Well I7 [S4881Nr4_I7]

value: Sunitinib, Con2


title: A375_MEF2A_4C

data_processing:
library strategy: 4C-seq
Sequences with adaptor or low quality were abandoned for further analysis. 4C mapping pipeline 4Cseqpipe was used to filter, analysis, and visualize the 4C-seq data
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain near-cis coverage

extract_protocol:
A375 cells were cross-linked by 2% formaldehyde, quenched with 0.125 glycine (Sigma-Aldrich, 50046), lysed with cold lysis buffer (50 mM Tris pH 7.5 (ThermoFisher, 15567027), 0.5% NP-40 (ThermoFisher, FNN0021), 150 mM NaCl (Sigma-Aldrich, S7653), 1% Triton X-100 (ThermoFisher, T8787), 5 mM EDTA (ThermoFisher, 15575020) and 1×protease inhibitors (ThermoFisher, 78425)), digested with NlaIII (NEB, R0125L) or HindIII (NEB, R0104) for 4 h at 37°C while shaking at 800 RPM for more than three times until the digestion efficiency reached over 90%, and then ligated with T4 DNA ligase (NEB, M0202) for overnight in a 7 ml reaction system after enzyme inactivation. The ligation sample was purified using Phenol/Chloroform/Isoamyl Alcohol (25:24:1) (ThermoFisher, 15593-049) before reversing the cross-links by adding Protein K (ThermoFisher, AM2548) for 6 h at 65°C and RNase A (ThermoFisher, 15596-018) for 1 h at 37°C. Next, the DNA samples were digested with DpnII (NEB, R0543L) or NlaIII (NEB, R0125) and ligated with T4 DNA ligase for more than 6 h in a 14 ml reaction system. The ligation product was purified using Phenol/Chloroform/Isoamyl Alcohol (25:24:1) and further purified using the QIAquick PCR Purification Kit (QIAGEN, 28106).
The purified product was amplified by PCR using a high-fidelity DNA polymerase (Vazyme, N616-02) with 8 × 200 ng DNA. 4C-seq library was constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 according to the manufacturer’s description, and sequenced on a HiSeq X Ten Platform.

tag: sample type

value: For MEF2A, the NlaIII-cutting chromosome region harboring MEF2A promoter (GRCh37/hg19 chr15:100,125,127–100,127,180) was designed as the viewpoint (VP), and DpnII was the second enzyme.


title: Sunitinib, Con2, Optimization plate 4, Well H7 [S4881Nr4_H7]

value: WT


title: A375_PTEN_4C

value: For PTEN, the HindIII-cutting chromosome region harboring PTEN promoter (GRCh37/hg19 chr10:89,620,814–89,627,996) was designed as the viewpoint (VP), and NlaIII was the second enzyme.


title: Lovo cells grown as monolayer

source_name: luciferase transgenic Lovo cells grown as monolayer


title: HT29 cells grown as xenograft

source_name: luciferase transgenic HT29 cells grown as xenograft


title: 12-104_2

description: Nine-banded armadillo


title: huam_mouse_mix

city: shanghai

first: Guoqiang

last: Zhou

address: Fudan University, Shanghai, 200438, China

institute: Fudan University School of Life Sciences

library_source: genomic single cell

data_processing:
raw paired-end reads were aligned to the hg38 or hg38_mm10 composite reference genome using Chromap
alignment files were subjected to barcode merging using D2C
MergeBamAlignment was employed to consolidate the data, followed by sorting using the "samtools sort" command.
mtDNA coverage was assessed using "samtools depth."
Peak calling was conducted using the MACK2.
Assembly: hg38 or hg38_mm10
Supplementary files format and content: hg38.bam and depth.txt for diffferent lysis conditions
Supplementary files format and content: 293T_percellaverage_sorted.bam and 3T3_percellaverage_sorted.bam for scATAC-seq data within Hydrogles

organism:
Homo sapiens
Mus musculus

source_name: 293T and 3T3

growth_protocol: Human 293T (ATCC) and Mouse 3T3 cells (ATCC) were maintained in DMEM media supplemented with 10 % fetal bovine serum in humidified at mosphere with 5 % CO2 at 37 ℃. Cells were harvested from a culture dish, underwent a single wash with 1×PBS, and were subsequently quantified using using the Trypan Blue method[37]. Before encapsulation, cells were suspended in a 4.58 % (w/v) dextran solution at a concentration of 1.79 million cells per 200 μL when utilizing a microfluidic device with a 40 μm height. All centrifugation steps were executed at 300 × g for 3 minutes at 4 °C.

extract_protocol:
Lysis Buffer 1 involved immersing 50 µL of the HetHydrogels in 200 µL of TCL lysis buffer (QIAGEN,1031576) supplemented with 1% (v/v) beta-mercaptoethanol (Millipore,444203), followed by a 5-minute room temperature incubation. Lysis Buffer 2 comprised the placement of 50 µL of the HetHydrogels into 200 µL of lysis buffer containing 50 mM Tris-HCl (pH 8.0), 50 mM NaCl, 20 µg/mL Proteinase K (Thermo Scientific, EO0491), and 0.2% SDS, with a subsequent 30-minute incubation at 55°C. Lysis Buffer 3 involved submerging 50 µL of the HetHydrogels in 200 µL of lysis buffer containing 0.1% Triton X-100, 10 mM Tris-HCl (pH 8.0), and 20 µg/mL Proteinase K (Thermo Scientific, EO0491), followed by a 30-minute incubation at 55°C. Lastly, Lysis Buffer 4 consisted of 50 µL of the HetHydrogels in 200 µL of lysis buffer composed of 0.1% Triton X-100, 10 mM Tris-HCl (pH 8.0), and 20 µg/mL Proteinase K (Thermo Scientific, EO0491), with a 30-minute incubation at 55 °C. Additionally, for Lysis Buffer 4, the composition included 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (vol/vol) NP-40, and 1% (vol/vol) BSA, with an incubation step on ice for 3 minutes.
This step is carried out following the standard procedures outlined in the DNBelab C-Series High-Throughput Single-Cell ATAC Library Preparation Kit instruction manual (BGI, 940-000793-00).

treatment_protocol: We dissolved 0.0458 g of Dextran (Yeasen, MW 500K, 61216ES25) and 0.0353 g of PEGDA (Sigma-Aldrich, MW 6K, 701963) in 700 μL of 1 × DPBS. To this solution, we added 100 μL of 4 % (w/v) LAP (Sigma-Aldrich, 900889) and 30 μL of PEGDA (Sigma-Aldrich, MW 575, 437441), finally adjusting the volume to 1 mL with 1 × DPBS. This mixture underwent centrifugation at 16,000g for 30 minutes, inducing liquid-liquid phase separation. Following centrifugation, a clear separation boundary was observed between the upper PEGDA-rich phase and the lower dextran-rich phase. For cell manipulation, we resuspended 1.79 million mammalian cells in 200 μL of the dextran-rich phase using a microfluidic device with a 40 μm height. In our microfluidic system, we used a 3 mL BD syringe for a 2% FS10 (w/w) solution in HFE-7500 (Tunderbio, FSA2). Additionally, two 1 mL BD syringes were allocated for the PEGDA-rich phase and the dextran-rich phase containing cells. These preloaded syringes were securely positioned within the injection pump (Leadfluid, TFD04). Flow rates in the microfluidic system were set as follows: 6.67 μL/min for the oil phase, 1.11 μL/min for the PEGDA-rich phase, and 1.55 μL/min for the Dextran-rich phase. Approximately 200 μL of collected droplets were then subjected to 2 minutes of UV irradiation and subsequently treated with 20%(v/v) PFO in HFE-7500 (Sigma-Aldrich, 370533-25G) to form HetHydrogels.

value: 293T and 3T3

value: human embryonic kidney cell line and mouse embryonic fibroblasts

value: encapsulated in hydrogels


title: HT29 cells grown as monolayer

source_name: luciferase transgenic HT29 cells grown as monolayer


title: 12-103_2

description: Nine-banded armadillo

value: PBMCs

value: Female


title: HCT116 cells grown as xenograft

source_name: luciferase transgenic HCT116 cells grown as xenograft


title: Sunitinib, Con3, Optimization plate 4, Well I6 [S4881Nr4_I6]

first: Christopher

last: Bruhn

address: Marie-Curie-Str. 7

value: Sunitinib, Con3


title: Sunitinib, Con2, Optimization plate 4, Well G7 [S4881Nr4_G7]


title: Sunitinib, Con3, Optimization plate 4, Well H6 [S4881Nr4_H6]


title: 16-904_1

description: Nine-banded armadillo

value: Male

value: Uninfected


title: 16-903_1

description: Nine-banded armadillo


title: 12-102_2

description: Nine-banded armadillo

value: Mycobacterium leprae


title: IRI M tub + EXO rep 2

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

country: Canada

institute: Ottawa Hospital Research Institute

description:
18_tub_IR_EX_M_quant.sf.txt
tub.IR_EX_vs_SHAM_all_ar5.txt
tub.IR_vs_IR_EX_all_ar5.txt
18_tub_IR_EX_M

data_processing:
Reads quantified against transcripts from the GENCODE vM19 assembly using salmon v0.13.1 (flags --gcBias --validateMappings)
Fold change analysis performed using DESeq2
Transcript quantification data read using the tximport library. Count matrix filtered to retain only genes with 5+ reads in at least two samples.
Separate DESeqDataSet objects constructed for endothelial and proximal tubule cells. Technical replicates for sample 9_tub_SHAM_M combined using collapseReplicates(). Calculation of size factors and differential expression using the model '~condition' (SHAM, IRI, IRI+EXO, IRI+MIMIC, IRI+SCB)
Fold changes calculated for tubule and endothelial cells between IRI and SHAM, IR/EXO, IR/MIMIC, IR/SCB; between MIMIC and SHAM; and between EXO and SHAM; using the lfcShrink() function with the 'apeglm' method.
Genome_build: GRCm38
Supplementary_files_format_and_content: Salmon transcript quantification: tab-delimited text
Supplementary_files_format_and_content: DESeq2 differential expression results: tab-delimited text

source_name: Kidney

extract_protocol:
RNA was isolated from PTs or renal endothelial cells from 3 male mice in each experimental group, using the RNeasy Plus Micro Kit (Qiagen Inc., Toronto, Ontario, Canada). RNA quality was assessed using the Fragment Analyzer (Advanced Analytical Technologies, Inc., Ames, LA, USA). Only RNA with RQN scores of >7 was selected for further analysis
Library construction was performed with the NEB Next Ultra II RNA Library Prep Kit for Illumina using the polyA mRNA workflow (New England Biolabs Ltd., Ipswich, MA, USA). For each sample, 20 ng of total RNA was used as input for the library preparation. Following library construction, the samples were pooled to minimize potential sequencing bias and run on NextSeq 500 (Illumina, San Diego, CA, USA). A total of six 75 cycle high output flow cells were run to achieve approximately 40 million reads per sample.

treatment_protocol: Endothelial and proximal tubular cells were isolated from kidneys after enzymatic digestion, CD31+ microbeads were used to obtain endothelial cells and proximal tubular cell were collected by microdissection.

value: Proximal tubular cells

value: Acute Kidney injury treated with exosomes

value: kidney


title: Sunitinib, Con4, Optimization plate 4, Well I5 [S4881Nr4_I5]

city: Göttingen

institute: Evotec International GmbH

value: hiPSC-CM

value: Sunitinib, Con4


title: IRI M tub + mimic rep 1

description:
21_tub_IR_MIMIC_M_quant.sf.txt
tub.IR_vs_IR_MIMIC_all_ar5.txt
tub.IR_MIMIC_vs_SHAM_all_ar5.txt
21_tub_IR_MIMIC_M

value: Acute Kidney injury treated with miR


title: IRI M tub + EXO rep 3

description:
19_tub_IR_EX_M_quant.sf.txt
tub.IR_EX_vs_SHAM_all_ar5.txt
tub.IR_vs_IR_EX_all_ar5.txt
19_tub_IR_EX_M


title: IRI M tub + mimic rep 2

description:
22_tub_IR_MIMIC_M_quant.sf.txt
tub.IR_vs_IR_MIMIC_all_ar5.txt
tub.IR_MIMIC_vs_SHAM_all_ar5.txt
22_tub_IR_MIMIC_M


title: HCT116 cells grown as spheroid

source_name: luciferase transgenic HCT116 cells grown as spheroid

value: colorectal cancer cell line

value: luciferase transgenic


title: HCT116 cells grown as monolayer

source_name: luciferase transgenic HCT116 cells grown as monolayer


title: IRI M tub + EXO rep 1

description:
17_tub_IR_EX_M_quant.sf.txt
tub.IR_EX_vs_SHAM_all_ar5.txt
tub.IR_vs_IR_EX_all_ar5.txt
17_tub_IR_EX_M


title: Sunitinib, Con4, Optimization plate 4, Well H5 [S4881Nr4_H5]

source_name: hiPSC-CM

value: WT


title: 16-902_1

description: Nine-banded armadillo


title: HT29 cells grown as spheroid

source_name: luciferase transgenic HT29 cells grown as spheroid


title: 12-101_2

description: Nine-banded armadillo


title: IRI M tub + SCB rep 3

description:
16_tub_IR_SCB_M_quant.sf.txt
tub.IR_vs_IR_SCB_all_ar5.txt
16_tub_IR_SCB_M

value: Acute Kidney injury treated with scrambled miR


title: Sunitinib, Con4, Optimization plate 4, Well G5 [S4881Nr4_G5]


title: DLD1 cells grown as spheroid

source_name: luciferase transgenic DLD1 cells grown as spheroid


title: 16-901_1

description: Nine-banded armadillo


title: MEL1

type: genomic

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: Genomic DNA extracted from MEL1 hESC cells was genotyped using the Infinium Omni2.5Exome-8 BeadChip array v1.3  (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
Using novoalign v2.07.11 (http://www.novocraft.com/products/novoalign), we mapped the array probe sequences to the GRCh37 (hg19) genome assembly (International Human Genome Sequencing Consortium et al. 2001) and filtered variants with ambiguous probe alignments as previously described in Currin et al. (Currin et al. 2021).
We combined the MEL1 genotypes with 15 samples genotyped on the same chip and 2,504 samples from 1000G project phase 3 release (1000 Genomes Project Consortium et al. 2015). We removed variants not in the 1000G Phase 3 release panel, with missing genotypes in >1 of the 16 genotyped samples, that are likely palindromic variants with MAF>0.4 in the 16 genotyped samples, or with a genotype distribution that deviates from Hardy-Weinberg equilibrium (P-value<1x10−4). After filtering the genotypes, we used the remaining 1,589,371 SNPs for genotype imputation on the Michigan TOPmed Server (Minimac v4; (Das et al. 2016) ). In total, we generated imputed genotypes of all SNPs (r2>0.3)

source_name: MEL1 (INSGFP/W）

label_protocol: standard Illumina protocol

growth_protocol: MEL1 wascultured on Matrigel-coated plates in StemFlex medium (Thermo Fisher Scientific) supplemented with 50 µg/mL Normocin (InvivoGen)

extract_protocol: standard Illumina protocol

tag: gender


title: IRI M tub + SCB rep 2

description:
14_tub_IR_SCB_M_quant.sf.txt
tub.IR_vs_IR_SCB_all_ar5.txt
14_tub_IR_SCB_M

tag: tissue


title: DLD1 cells grown as monolayer

source_name: luciferase transgenic DLD1 cells grown as monolayer


title: Sunitinib, Con5, Optimization plate 4, Well I4 [S4881Nr4_I4]

value: Sunitinib, Con5


title: 16-304_1

description: Nine-banded armadillo

value: PBMCs


title: IRI M tub + SCB rep 1

description:
12_tub_IR_SCB_M_quant.sf.txt
tub.IR_vs_IR_SCB_all_ar5.txt
12_tub_IR_SCB_M


title: Sunitinib, Con5, Optimization plate 4, Well H4 [S4881Nr4_H4]


title: Sunitinib, Con5, Optimization plate 4, Well G4 [S4881Nr4_G4]


title: 16-303_1

description: Nine-banded armadillo

value: Female


title: 16-302_1

description: Nine-banded armadillo


title: DLD1 cells grown as xenograft

source_name: luciferase transgenic DLD1 cells grown as xenograft


title: IRI M PTs rep 3

description:
Re-analysis of GSM4292483
tub.IR_vs_SHAM_all_ar5.txt
tub.IR_vs_IR_MIMIC_all_ar5.txt
tub.IR_vs_IR_EX_all_ar5.txt
tub.IR_vs_IR_SCB_all_ar5.txt
7_tub_IR_M

value: Acute Kidney injury


title: Sunitinib, Con6, Optimization plate 4, Well I3 [S4881Nr4_I3]

value: Sunitinib, Con6


title: 16-301_1

description: Nine-banded armadillo

value: Uninfected


title: Sunitinib, Con6, Optimization plate 4, Well H3 [S4881Nr4_H3]


title: IRI M PTs rep 2

description:
Re-analysis of GSM4292482
tub.IR_vs_SHAM_all_ar5.txt
tub.IR_vs_IR_MIMIC_all_ar5.txt
tub.IR_vs_IR_EX_all_ar5.txt
tub.IR_vs_IR_SCB_all_ar5.txt
4_tub_IR_M

value: Male


title: Sunitinib, Con6, Optimization plate 4, Well G3 [S4881Nr4_G3]


title: 16-203_1

description: Nine-banded armadillo


title: Sham M PTs rep 2

description:
Re-analysis of GSM4292475
tub.IR_vs_SHAM_all_ar5.txt
tub.IR_EX_vs_SHAM_all_ar5.txt
tub.IR_MIMIC_vs_SHAM_all_ar5.txt
6_tub_SHAM_M

value: Proximal tubular cells

value: No injury


title: Sunitinib, Con7, Optimization plate 4, Well I2 [S4881Nr4_I2]

value: Sunitinib, Con7


title: IRI M PTs rep 1

description:
Re-analysis of GSM4292481
tub.IR_vs_SHAM_all_ar5.txt
tub.IR_vs_IR_MIMIC_all_ar5.txt
tub.IR_vs_IR_EX_all_ar5.txt
tub.IR_vs_IR_SCB_all_ar5.txt
3_tub_IR_M

value: kidney


title: Sham M PTs rep 3

description:
Re-analysis of GSM4292476 and GSM4292477
tub.IR_vs_SHAM_all_ar5.txt
tub.IR_EX_vs_SHAM_all_ar5.txt
tub.IR_MIMIC_vs_SHAM_all_ar5.txt
9_tub_SHAM_M


title: 16-202_1

description: Nine-banded armadillo


title: Sham M PTs rep 1

description:
Re-analysis of GSM4292474
tub.IR_vs_SHAM_all_ar5.txt
tub.IR_EX_vs_SHAM_all_ar5.txt
tub.IR_MIMIC_vs_SHAM_all_ar5.txt
5_tub_SHAM_M


title: Colo205 cells grown as spheroid

source_name: luciferase transgenic Colo205 cells grown as spheroid


title: 16-201_1

description: Nine-banded armadillo

source_name: Blood


title: IRI M endo + mimic rep 2

description:
21_endo_IR_MIMIC_M_quant.sf.txt
endo.IR_vs_IR_MIMIC_all_ar5.txt
endo.IR_MIMIC_vs_SHAM_all_ar5.txt
21_endo_IR_MIMIC_M

value: endothelial cells


title: Sunitinib, Con7, Optimization plate 4, Well H2 [S4881Nr4_H2]

value: hiPSC-CM


title: 15-504_1

description: Nine-banded armadillo


title: Sunitinib, Con7, Optimization plate 4, Well G2 [S4881Nr4_G2]


title: Sunitinib, Con8, Optimization plate 4, Well I1 [S4881Nr4_I1]

value: Sunitinib, Con8


title: 15-503_1

description: Nine-banded armadillo


title: IRI M endo + mimic rep 1

description:
20_endo_IR_MIMIC_M_quant.sf.txt
endo.IR_vs_IR_MIMIC_all_ar5.txt
endo.IR_MIMIC_vs_SHAM_all_ar5.txt
20_endo_IR_MIMIC_M

value: Acute Kidney injury treated with miR


title: Sunitinib, Con8, Optimization plate 4, Well H1 [S4881Nr4_H1]

value: WT


title: 16-204_1

description: Nine-banded armadillo


title: IRI M endo + EXO rep 3

description:
19_endo_IR_EX_M_quant.sf.txt
endo.IR_EX_vs_SHAM_all_ar5.txt
endo.IR_vs_IR_EX_all_ar5.txt
19_endo_IR_EX_M

value: Acute Kidney injury treated with exosomes


title: Sunitinib, Con8, Optimization plate 4, Well G1 [S4881Nr4_G1]


title: 15-502_1

description: Nine-banded armadillo


title: IRI M endo + EXO rep 2

description:
18_endo_IR_EX_M_quant.sf.txt
endo.IR_EX_vs_SHAM_all_ar5.txt
endo.IR_vs_IR_EX_all_ar5.txt
18_endo_IR_EX_M


title: Lidocaine, Con1, Optimization plate 4, Well F24 [S4881Nr4_F24]

value: Lidocaine, Con1


title: 15-501_1

description: Nine-banded armadillo

value: PBMCs


title: IRI M endo + EXO rep 1

description:
17_endo_IR_EX_M_quant.sf.txt
endo.IR_EX_vs_SHAM_all_ar5.txt
endo.IR_vs_IR_EX_all_ar5.txt
17_endo_IR_EX_M


title: 12-104_1

description: Nine-banded armadillo

value: Female


title: IRI M endo + SCB rep 3

description:
16_endo_IR_SCB_M_quant.sf.txt
endo.IR_vs_IR_SCB_all_ar5.txt
16_endo_IR_SCB_M

value: Acute Kidney injury treated with scrambled miR


title: 12-103_1

description: Nine-banded armadillo


title: Lidocaine, Con1, Optimization plate 4, Well E24 [S4881Nr4_E24]


title: IRI M endo + SCB rep 2

description:
14_endo_IR_SCB_M_quant.sf.txt
endo.IR_vs_IR_SCB_all_ar5.txt
14_endo_IR_SCB_M


title: Lidocaine, Con1, Optimization plate 4, Well D24 [S4881Nr4_D24]


title: 12-102_1

description: Nine-banded armadillo


title: IRI M endo + SCB rep 1

description:
12_endo_IR_SCB_M_quant.sf.txt
endo.IR_vs_IR_SCB_all_ar5.txt
12_endo_IR_SCB_M


title: Colo205 cells grown as monolayer

description: Gene expression data from colorectal cancer cell line

source_name: luciferase transgenic Colo205 cells grown as monolayer

value: colorectal cancer cell line

value: luciferase transgenic


title: Lidocaine, Con2, Optimization plate 4, Well E23 [S4881Nr4_E23]

value: Lidocaine, Con2


title: 12-101_1

description: Nine-banded armadillo

value: Uninfected


title: Lidocaine, Con2, Optimization plate 4, Well D23 [S4881Nr4_D23]


title: Lidocaine, Con2, Optimization plate 4, Well F23 [S4881Nr4_F23]


title: IRI M endo rep 1

description:
Re-analysis of GSM4292468
endo.IR_vs_SHAM_all_ar5.txt
endo.IR_vs_IR_MIMIC_all_ar5.txt
endo.IR_vs_IR_EX_all_ar5.txt
endo.IR_vs_IR_SCB_all_ar5.txt
3_endo_IR_M

value: Acute Kidney injury

value: Male


title: IRI M endo rep 2

description:
Re-analysis of GSM4292469
endo.IR_vs_SHAM_all_ar5.txt
endo.IR_vs_IR_MIMIC_all_ar5.txt
endo.IR_vs_IR_EX_all_ar5.txt
endo.IR_vs_IR_SCB_all_ar5.txt
4_endo_IR_M

value: kidney


title: CD14, D15, sheep4

first: Isabel

last: García-García

state: Madrid

address: Calle José Antonio Novais, 12

department: Genética, Fisiología y Microbiología

institute: Universidad Complutense de Madrid (UCM)

data_processing:
Quality of raw reads was checked using FastQC v0.11.9
Adapter sequences were trimmed and low-quality reads were removed using fastp v0.20.1, retaining reads with a Phred score higher than 15 and with more than 36 bases
Reads were aligned to the Ovis aries reference genome using subread-align and gene counts were obtained using featureCounts, both included in the Subread v2.0.3 package
Genes with low counts (below 15 reads per group) were removed, counts were normalized and differentially expressed genes (DEGs) were identified using edgeR v3.32.1 . An FDR correction was applied and genes with a q-value<0.05 were considered as DEGs
B cell marker+, CD4+, CD8+ and CD14+ cell samples were individually analyzed, comparing days 3, 7 and 15 post-infection to day 0 (prior to infection).
Relevant DEGs were selected based on the gene ontology (GO) terms associated to each gene. GO terms were obtained using biomaRt v2.46.3
An over-representation analysis (ORA) was performed to identify pathways enriched in DEGs, using clusterProfiler v3.18.1. The Ovis aries specific version of the KEGG (Kyoto Encyclopedia of Genes and Genomes) database was used. An FDR correction was applied and those pathways with a q-value<0.05 were considered significantly enriched in DEGs.
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (Bcells)
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (CD4)
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (CD8)
Supplementary files format and content: tab-delimited text file includes filtered counts for each sample (CD14)

organism: Ovis aries

source_name: blood

extract_protocol:
RNeasy Mini Kit (Qiagen)
SMARTer Ultra Low RNA Kit

value: BTV serotype 8 infection

value: blood

value: Day 15


title: Lidocaine, Con3, Optimization plate 4, Well F22 [S4881Nr4_F22]

value: hiPSC-CM

value: Lidocaine, Con3


title: Lidocaine, Con3, Optimization plate 4, Well E22 [S4881Nr4_E22]

value: WT


title: CD14, D15, sheep1


title: Lidocaine, Con3, Optimization plate 4, Well D22 [S4881Nr4_D22]


title: Sham M endo rep 2

description:
Re-analysis of GSM4292463
endo.IR_vs_SHAM_all_ar5.txt
endo.IR_EX_vs_SHAM_all_ar5.txt
endo.IR_MIMIC_vs_SHAM_all_ar5.txt
6_endo_SHAM_M

value: endothelial cells

value: No injury


title: CD14, D7, sheep4

value: Day 7


title: CD14, D15, sheep3


title: IRI M endo rep 3

description:
Re-analysis of GSM4292470
endo.IR_vs_SHAM_all_ar5.txt
endo.IR_vs_IR_MIMIC_all_ar5.txt
endo.IR_vs_IR_EX_all_ar5.txt
endo.IR_vs_IR_SCB_all_ar5.txt
7_endo_IR_M


title: Lidocaine, Con4, Optimization plate 4, Well F21 [S4881Nr4_F21]

value: Lidocaine, Con4


title: CD14, D7, sheep3


title: CD14, D15, sheep2


title: 293T+LNP23-2

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing: Raw FASTQ sequenced reads where first assessed for quality using FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The reads where then passed through Trimmomatic v0.36 for quality trimming and adapter sequence removal, with the parameters (ILLUMINACLIP: trimmomatic_adapter.fa:2:30:10 TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36) 1. The surviving trimmed read pairs were then processed with Fastp in order to remove poly-G tails and Novaseq/Nextseq specific artefacts 2. Following the quality trimming, the reads were assessed again using FastQC. Post QC and QT, the reads were aligned to the human reference genome GRCh38.81 using HISAT2 3 with the default parameters and additionally by providing the –dta flag. The resulting SAM alignments were then converted to BAM, whilst retaining only the unmapped read pairs using SAMtools 4 v1.9 “samtools view -f 12 -F 256 -b INPUT.sam > OUTPUT.bam”. The resulting unmapped BAM reads were then sorted and converted to fastq reads using samtools sort ”samtools sort -@ 14 -o OUTPUT.sorted.bam INPUT.bam” and samtools fastq “samtools fastq -1 read1.fastq -2 read2.fastq -@ 14 INPUT.sorted.bam”. These unmapped reads where then aligned to the SARS-COV-2 reference genome available through NCBI with the accession NC_045512.2 using HISAT2 with the same parameters that were used in the initial mapping to the human reference. The resulting SAM alignments were then converted to BAM format and coordinate sorted using samtools view and samtools sort respectively. Read groups were then added to the sorted SARS-COV-2 mapped BAM files using Picard AddOrReplaceReadGroups (http://broadinstitute.github.io/picard/). A consensus genome was then generated for each SARS-COV-2 sample using samtools mpileup and ivar 5 version 1.3 with the minimum depth set at 20 “samtools mpileup -A -d 0 -Q 0 INPUT.sorted.bam | ivar consensus -m 20 -p OUTPUT.sars-cov-2-consensus.fasta”. Finally, Qualimap 6 v2.2.2 was used to generate alignment specific QC metrics per sample, both for alignments vs the human reference, as well as the SARS-COV-2 reference. The BAM alignment files were processed using HTseq-count, using the reference annotation file to produce raw counts for each sample.

growth_protocol: The HEK 293T cells were grown in full Dulbecco’s Modified Eagle Medium (DMEM) containing 10% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin (Millipore-Sigma) in the humidified incubator at 37°C with 5% CO2. These cells have been engineered to overexpress the ACE2 receptor for SARS-CoV-2 entry.

extract_protocol:
HEK 293T cells either infected with the SARS-CoV-2 virus or uninfected, treated with LNPs containing mRNA sequences of either the anti-NSP9 nanobody or tdTomato were used for total mRNA isolation by TRI Reagent (Millipore-Sigma) according to the manufacturer’s protocol.
Three biological replicates for each condition were used for transcriptional profiling. The RNA-Seq library was prepared by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with the NextSeq 500/550 sequencing platform (performed at the NYUAD Sequencing Center).

treatment_protocol: Half of the 293T cells was treated with lipid nanoparticles (LNPs) containing mRNA sequence of the Nsp9 nanobody (2NSP23) and the other half treated with tdTomato as a control. Next cells were infected with different variants of SARS-CoV-2 virus. The uninfected samples were also either treated with the nanobody-containing LNPs or tdTomato.


title: Sham M endo rep 1

description:
Re-analysis of GSM4292462
endo.IR_vs_SHAM_all_ar5.txt
endo.IR_EX_vs_SHAM_all_ar5.txt
endo.IR_MIMIC_vs_SHAM_all_ar5.txt
5_endo_SHAM_M


title: CD14, D7, sheep1


title: 293T+LNP23-1


title: CD14, D3, sheep4

value: Day 3


title: Lidocaine, Con5, Optimization plate 4, Well F20 [S4881Nr4_F20]

value: Lidocaine, Con5


title: Sham M endo rep 3

description:
Re-analysis of GSM4292464
endo.IR_vs_SHAM_all_ar5.txt
endo.IR_EX_vs_SHAM_all_ar5.txt
endo.IR_MIMIC_vs_SHAM_all_ar5.txt
9_endo_SHAM_M


title: 293T+LNP45-3


title: Lidocaine, Con5, Optimization plate 4, Well D20 [S4881Nr4_D20]


title: 293T+LNP45-2


title: Lidocaine, Con5, Optimization plate 4, Well E20 [S4881Nr4_E20]


title: CD14, D3, sheep1


title: Lidocaine, Con6, Optimization plate 4, Well F19 [S4881Nr4_F19]

value: Lidocaine, Con6


title: 293T+LNP45-1


title: 293T+UK variant+LNP23-3


title: CD14, D7, sheep2


title: CD14, D0, sheep3

value: Day 0


title: Lidocaine, Con6, Optimization plate 4, Well E19 [S4881Nr4_E19]


title: Lidocaine, Con4, Optimization plate 4, Well E21 [S4881Nr4_E21]


title: 293T+UK variant+LNP23-2


title: Lidocaine, Con6, Optimization plate 4, Well D19 [S4881Nr4_D19]


title: CD14, D0, sheep2


title: Lidocaine, Con4, Optimization plate 4, Well D21 [S4881Nr4_D21]


title: Lidocaine, Con7, Optimization plate 4, Well F18 [S4881Nr4_F18]

value: Lidocaine, Con7


title: CD14, D0, sheep1


title: 293T+UK variant+LNP23-1


title: 293T+UK variant+LNP45-3


title: Lidocaine, Con7, Optimization plate 4, Well E18 [S4881Nr4_E18]


title: CD8, D15, sheep4


title: 293T+UK variant+LNP45-2


title: CD14, D3, sheep3


title: CD8, D15, sheep3


title: Lidocaine, Con7, Optimization plate 4, Well D18 [S4881Nr4_D18]


title: CD14, D0, sheep4


title: Lidocaine, Con8, Optimization plate 4, Well F17 [S4881Nr4_F17]

value: Lidocaine, Con8


title: 293T+UK variant+LNP45-1


title: 15-501_2

description: Nine-banded armadillo

value: PBMCs

value: Male

value: Mycobacterium leprae


title: Lidocaine, Con8, Optimization plate 4, Well E17 [S4881Nr4_E17]


title: CD8, D15, sheep1

value: BTV serotype 8 infection

value: blood

value: Day 15


title: CD8, D15, sheep2


title: 293T+B1.617.X+LNP23-2


title: Lidocaine, Con8, Optimization plate 4, Well D17 [S4881Nr4_D17]

value: hiPSC-CM

value: WT


title: 293T+B1.617.X+LNP23-1


title: CD8, D7, sheep3


title: Enalapril, Con1, Optimization plate 4, Well F16 [S4881Nr4_F16]

value: Enalapril, Con1


title: Enalapril, Con1, Optimization plate 4, Well E16 [S4881Nr4_E16]


title: 293T+B1.617.X+LNP45-3


title: CD8, D7, sheep1

value: Day 7


title: 293T+B1.617.X+LNP45-2


title: CD8, D3, sheep3


title: Enalapril, Con1, Optimization plate 4, Well D16 [S4881Nr4_D16]


title: Enalapril, Con2, Optimization plate 4, Well F15 [S4881Nr4_F15]

value: Enalapril, Con2


title: 293T+B1.617.X+LNP45-1


title: CD8, D0, sheep4


title: Enalapril, Con2, Optimization plate 4, Well E15 [S4881Nr4_E15]


title: CD8, D3, sheep1

value: Day 3


title: 293T+B1.621+LNP23-2


title: 293T+B1.617.X+LNP23-3


title: Enalapril, Con2, Optimization plate 4, Well D15 [S4881Nr4_D15]


title: 293T+B1.621+LNP23-3


title: CD8, D0, sheep3


title: CD8, D0, sheep2


title: CD8, D7, sheep4


title: 293T+B1.621+LNP23-1


title: Sunitinib, Con3, Optimization plate 4, Well G6 [S4881Nr4_G6]

value: Sunitinib, Con3


title: 293T+B1.621+LNP45-3


title: Enalapril, Con3, Optimization plate 4, Well F14 [S4881Nr4_F14]

value: Enalapril, Con3


title: 293T+B1.621+LNP45-2


title: Enalapril, Con3, Optimization plate 4, Well E14 [S4881Nr4_E14]


title: Enalapril, Con3, Optimization plate 4, Well D14 [S4881Nr4_D14]


title: Enalapril, Con4, Optimization plate 4, Well E13 [S4881Nr4_E13]

value: Enalapril, Con4


title: 293T+B1.621+LNP45-1


title: 293T+Omicron+LNP23-3


title: CD4, D15, sheep2


title: Enalapril, Con4, Optimization plate 4, Well D13 [S4881Nr4_D13]


title: CD4, D15, sheep1


title: 293T+Omicron+LNP23-2


title: Enalapril, Con4, Optimization plate 4, Well F13 [S4881Nr4_F13]


title: Enalapril, Con5, Optimization plate 4, Well F12 [S4881Nr4_F12]

value: Enalapril, Con5


title: 293T+Omicron+LNP23-1


title: 293T+Omicron+LNP45-3


title: Enalapril, Con5, Optimization plate 4, Well E12 [S4881Nr4_E12]


title: CD4, D7, sheep3


title: CD8, D0, sheep1

value: Day 0


title: 293T+Omicron+LNP45-2


title: CD4, D15, sheep4


title: 293T+Omicron+LNP45-1


title: Colo205 cells grown as xenograft

source_name: luciferase transgenic Colo205 cells grown as xenograft

value: colorectal cancer cell line

value: luciferase transgenic


title: Enalapril, Con5, Optimization plate 4, Well D12 [S4881Nr4_D12]


title: CD4, D15, sheep3


title: Enalapril, Con6, Optimization plate 4, Well F11 [S4881Nr4_F11]

value: Enalapril, Con6


title: CD4, D7, sheep1

value: BTV serotype 8 infection


title: CD4, D3, sheep4

value: blood


title: Enalapril, Con6, Optimization plate 4, Well E11 [S4881Nr4_E11]


title: Enalapril, Con6, Optimization plate 4, Well D11 [S4881Nr4_D11]


title: Pool_3, PBMC, snATACseq

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

institute: Georgia Institute of Technology

description:
2 male, 1 female
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger software cellranger-arc-2.0.0 for all samples (cellranger-arc-2.0.1 for Sample_0) (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Frozen PBMC
snRNA-seq
snATAC-seq

value: PBMC

tag: number of_donors


title: pTh17

city: TianJin

first: Mengjuan

last: Zhang

state: TianJin

address: No.94 Weijin Road, Nankai District, Tianjin, P. R.China

institute: Nankai University

data_processing:
Clean data with high quality was obtained by filtering Raw data, which removes adapter sequence and reads with low quality.
These clean data were further mapped to pre-defined reference genome generating mapped data.
Assessment on insert size and sequencing randomness were processed on mapped data as library quality control.
Basic analysis on mapped data included gene expression quantification, alternative splicing analysis, novel genes prediction and genes structure optimization.
Assembly: mm10
Supplementary files format and content: Counts for each group
Supplementary files format and content: FPKM values for each group

source_name: spleen

growth_protocol: CD4+ T cells were isolated from spleens and lymph nodes of wild-type mice. 0.5 million CD4+ T cells were cultured in a 24-well plate pre-coated with 10 μg/mL anti-CD3 (BioXCell) and 5 μg/mL anti-CD28 (BioXCell) in PBS. For pTh17 cells differentiation, CD4+ T cells were cultured with the addition of 20 ng/mL IL-6 and 20 ng/mL Activin-A and 10 mg/mL anti-IFNγ and 10 mg/mL anti-IL-4.For npTh17 cell differentiation, CD4+ T cells were cultured with the addition of 2 ng/ mL rhTGFβ1, 20 ng/mL IL-6, 10 mg/mL anti-IFNγ, and 10 mg/mL anti-IL-4.

extract_protocol:
(1) mRNA was isolated by Oligo(dT)-attached magnetic beads.
(2) mRNA was then randomly fragmented in fragmentation buffer.    (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.    (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within size range of 300-400 bp.    (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.

treatment_protocol: After 24h, collect cells and lysis with Trizol

value: spleen

tag: group

value: pathogenic Th17

value: CD4 T