title: eEF2-H699N, MDN1-LS, rep2

value: Cultured cell

value: eEF2-H699N, MDN1-LS

value: No treatment

value: cycloheximide


title: eEF2-H699N, MDN1-LS, rep1

status: Public on Jan 10 2023

type: SRA

city: Bethesda

first: Byung-Sik

last: Shin

state: Maryland

address: 6 Center Dr, BLDG 6, RM 227

country: USA

institute: NIH

library_source: transcriptomic

data_processing:
Library strategy: Ribo-Seq
Sequencing data were provided by NHLBI DNA Sequencing and Genomics Core (NIH)
Linker was removed by cutadapt 2.8 with Python 3.7.5
After sorting the sequences by sample barcodes, PCR duplicates were removed by custom Python script.
rRNAs, tRNAs and other non-coding RNAs were removed by bowtie 1.1.2.
Alignments were done by bowtie 1.1.2 with the option -v 2 -m 1 -a -y --best --strata
Genome_build: Yeast trascriptome of R64-1-1 S288C reference genome assembly (SacCer3) was used. 3' and 5' UTR information was from Pelechano and Steinmetz (Nature 2013) and modified by Ingolia.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Yeast cells were grown to A600 0.6-1.0 in selective media.

extract_protocol:
Yeast cells were lysed by grinding by Freezer Mill. CHO cells were lysed by lysis buffer containing Triton X-100. Ribosomes were collected by sucrose cushion with ultracentrifugation. RNAs were extract by Direct-zol RNA Microprep Kits.
Libraries were prepared according to published protocol by Ingolia (Methods 2017)
Ribosome protected fragments (riboseq)

treatment_protocol: Refer to SAMPLES treatment columns

tag: strain

tag: tissue

tag: genotype

tag: treatment

tag: agent


title: MP-59, condition5-Carbamazepine treated

city: Chicago

first: Minoli

last: Perera

state: Illinois

address: 303 E. Chicago Avenue, Ward 9-188

department: Pharmacology

institute: Northwestern University

data_processing:
RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits and sequenced on an Illumina HiSEQ2500 or 4000 according to Illumina provided protocols.
Post alignment and QC, reads were mapped to genes referenced with comprehensive gene annotation (GENCODE version 25) by HTSeq (version 0.6.1p1) with union mode and minaqual = 20
HTSeq raw counts were supplied for gene expression analysis and were normalized using regularized log transformation and principal component analysis (PCA) using Bioconductor package DESeq2 (version1.20.0)
We calculated TPM (transcript per million) by first normalizing the counts by gene length and then normalizing by read depth (Wagner, Kin, & Lynch, 2012). Gene expression values were filtered based on the expression thresholds > 0.1 TPM in at least 20% of samples and ≥ 6 reads in at least 20% of samples as done in the GTEx consortium (gtexportal.org, Analysis Methods, V7).
We normalized expression values across samples by TMM (trimmed mean of M-values) implemented in edgeR (Robinson & Oshlack, 2010) and then normalized for each gene by inverse normal transformation.
Genome_build: hg37
Assembly: GRCh37.p13
Supplementary files format and content: Sample_MP-XX2count.txt data contain raw count data from Htseq for condition2- Omeprazole drug treatment
Supplementary files format and content: Sample_MP-XX3count.txt data contain raw count data from Htseq for condition3 - Phenobarbital drug treatment
Supplementary files format and content: Sample_MP-XX4count.txt data contain raw count data from Htseq for condition4 - Dexamethasone drug treatment
Supplementary files format and content: Sample_MP-XX5count.txt data contain raw count data from Htseq for condition5 - Carbamazepine drug treatment
Supplementary files format and content: Sample_MP-XX6count.txt data contain raw count data from Htseq for condition6 - Phenytoin drug treatment
Supplementary files format and content: Sample_MP-XX7count.txt data contain raw count data from Htseq for condition7 - Rifampicine  drug treatment
Supplementary files format and content: condition2_Omeprazole_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition2 - Omeprazole drug treatment
Supplementary files format and content: condition3_Phenobarbital_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition3 - Phenobarbital drug treatment
Supplementary files format and content: condition4_Dexamethasone_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition4 - Dexamethasone drug treatment
Supplementary files format and content: condition5_Carbamazepine_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition5 - Carbamazepine drug treatment
Supplementary files format and content: condition6_Phenytoin_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition6 - Phenytoin drug treatment
Supplementary files format and content: condition7_Rifampicine_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition7 - Rifampicine  drug treatment

organism: Homo sapiens

source_name: liver hepatocyte cells

growth_protocol: Cell were plated at a density of 0.6 x 106 cells/well in 500 µL InVitroGro-CP media (BioIVT, Baltimore, MD) in collagen-coated plates with matrigel (Corning, Bedford, MA) overlay and incubated overnight at 37° C. Cultures were maintained in InVitroGro-HI media (BioIVT) supplemented with Torpedo antibiotic mix (BioIVT) per the manufacturer's instructions. The media was replaced every 24 hours for three days.

extract_protocol: RNA was extracted after three days using the RNeasy Plus mini-kit (Qiagen) per manufacturer's instructions. RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits.

treatment_protocol: Hepatocyte suspensions (0.6 x 10^6 cells in 0.5 mL of CP medium) were added to collagen-coated wells of a 24-well plate followed by incubation at 37° C for 4-5 hours to allow cells to adhere. The CP medium was replaced with 0.5 mL of 0.25 mg/mL matrigel solution in HI medium, and plates were incubated overnight at 37° C. The following day, matrigel-medium was replaced with 0.5 mL of induction drug in HI medium with antibiotics and the step was repeated for the next two consecutive days after every 24 hours. We performed the induction experiments using the following six drugs: Omeprazole (50 μM), Phenobarbital sodium (1 mM), Dexamethasone (50 μM), Carbamazepine (50 μM), Phenytoin (75 μM), Rifampicine (25 μM).

tag: gender

value: Male

tag: age

tag: platform

tag: batch

tag: cell type

value: liver hepatocyte cells

value: Carbamazepine drug


title: MP-6, condition5-Carbamazepine treated

description: condition5_Carbamazepine_expression_tmm_normalization_exp.txt

value: Female


title: CHO K1 dph2, rep2

organism: Cricetulus griseus

source_name: CHO K1 cell line

value: Ovary

tag: cell line

value: CHO K1 [ATCC CCL-61]


title: day6_ctrl_011

city: Kyoto city

first: Ryosuke

last: Yamamoto

state: Kyoto pref

address: 54 Kawahara-cho

department: Department of Otolaryngology, Head and Neck Surgery

country: Japan

institute: Kyoto University

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW11

library_source: transcriptomic single cell

data_processing:
Demultiplexing: C1 mRNA Seq HT Demultiplex Script v2.0 (Fluidigm)
Mapping: STAR v2.7.0a
Gene counting: SUBREAD v1.6.3
Normalization: Transcripts per million (TPM), quantile normalization (quminorm v0.1.0), sctransform (sctransform v0.3.3)
Assembly: GRCg6a, GCF_000002315.6
Supplementary files format and content: raw_count_file.txt: Unfiltered, non-normalized count file
Supplementary files format and content: normalized_count_file.txt: Filtered, normalized count file (TPM, quantile normalization)
Supplementary files format and content: normalized_seurat_obj.rds: Filtered, normalized Surat object file  (TPM, quantile normalization, scTransform)

organism: Gallus gallus

source_name: basilar papillae

extract_protocol:
BP specimens were incubated in prewarmed 500 µg/ml thermolysin in medium 199 at 37℃ for 30 min. To stop enzymatic dissociation, specimens were transferred into medium 199 supplemented with 5% FBS. Afterwards, the BP was separated from the surrounding tissues under the stereomicroscope. Then, the samples were transferred into an Eppendorf tube by a pipette. After centrifugation (800g x 5 min) at room temperature, the supernatant was removed. Samples were incubated in an enzyme cocktail containing 50% Accutase and 50% TrypLE Select enzyme for 7 min at 37℃. After gently pipetting 10-20 times, samples were incubated for additional 4 min at 37℃. After inactivation of enzymatic activity with medium 199 supplemented with 5% FBS, further mechanical dissociation by pipetting was performed. Dissociated cells were collected after centrifugation and resuspended in medium 199 supplemented with 5% FBS.
Capture of the single cells and cDNA synthesis were conducted using C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2 (Fluidigm), according to manufacturer’s instruction. Briefly, 12,000 cells of each sample were loaded onto HT IFC, and 400 cells were captured in the IFC. Sequencing libraries were prepared by transposase-assisted tagmentation and enrichment of 3’end of genes using Nextera XT DNA Library Prep Kit (Illumina). The libraries were sequenced on the HiSeq2500 for 25 and 75 cycles paired-end reads.

treatment_protocol: Basilar papillae (BPs) were dissected from the temporal bones (intact) and incubated in the control medium for 24 h (day0_pre). BPs were cultured with 78 microM stereptomycin for 48 h (day2_SM). A part of BPs were maintained additional 96 h in the control medium (day6_SM). Other BPs were cultured in the control medium for 48 h (day2_ctrl) or 144 h (day6_ctrl)

value: basilar papillae

value: 144-h culture


title: day6_ctrl_005

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW05


title: MP-66, condition5-Carbamazepine treated


title: MP-58, condition5-Carbamazepine treated


title: day6_ctrl_007

description:
C1 Single-Cell mRNA seq HT IFC for medium cell size (10-17 µm) and Reagent kit v2
SC457_ROW07


title: CHO K1 dph2, rep1


title: CHO K1 WT, rep2


title: MP-55, condition5-Carbamazepine treated


title: MP-57, condition5-Carbamazepine treated


title: eEF2-WT, MDN1-LS, rep1

value: eEF2-WT, MDN1-LS


title: MP-54, condition5-Carbamazepine treated


title: eEF2-H699N, upf1-del, rep2

value: eEF2-H699N, upf1-del


title: eEF2-H699N, upf1-del, rep1


title: MP-90, condition4-Dexamethasone treated

description: condition4_Dexamethasone_expression_tmm_normalization_exp.txt

value: Dexamethasone drug


title: MP-9, condition4-Dexamethasone treated


title: MP-8, condition4-Dexamethasone treated


title: V3-E13

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw fastq files were processed with Cell Ranger 2.1.1 (10x V2) and 7.0.0 (10x V3) with default mapping arguments.
Reads were mapped to the mouse mm10 genome and counted with GRCm38.89 annotation.
Next, the cellranger aggr command was executed to adjust the sequencing depth of different samples to the same level.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Mus musculus

source_name: mouse placental cells

extract_protocol:
Mouse placental single cells were added to the 10x Chip channels. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs.
RNA libraries were prepared for sequencing using 10x Single Cell 3' Library & Gel Bead Kit v2 and v3  protocol

tag: Stage

value: 13.5 days post coitus

value: placenta


title: MP-78, condition4-Dexamethasone treated


title: V3-E11

value: 11.5 days post coitus


title: MP-77, condition4-Dexamethasone treated


title: eEF2-WT, upf1-del, rep1

value: Cultured cell

value: eEF2-WT, upf1-del


title: V3-E9

value: 9.5 days post coitus


title: MP-76, condition4-Dexamethasone treated

value: Male


title: MP-75, condition4-Dexamethasone treated

value: liver hepatocyte cells


title: eEF2-H699N, UPF1, rep2

value: eEF2-H699N, UPF1

value: No treatment

value: cycloheximide


title: MP-70, condition4-Dexamethasone treated

value: Female


title: eEF2-WT, MDN1-LS, rep2


title: V3-E8

value: 8.5 days post coitus


title: CHO K1 WT, rep1

value: Ovary

value: CHO K1 [ATCC CCL-61]


title: MP-7, condition4-Dexamethasone treated


title: MP-69, condition4-Dexamethasone treated


title: MP-53, condition5-Carbamazepine treated

value: Carbamazepine drug


title: eEF2-WT, UPF1, rep2

value: eEF2-WT, UPF1


title: V3-E7

value: 7.5 days post coitus


title: MP-65, condition4-Dexamethasone treated

value: Dexamethasone drug


title: MP-68, condition4-Dexamethasone treated


title: eEF2-H699N, UPF1, rep1


title: MP-66, condition4-Dexamethasone treated


title: eEF2-WT, upf1-del, rep2


title: eEF2-H699N, KCl, rep2


title: MP-64, condition4-Dexamethasone treated


title: eEF2-WT, UPF1, rep1


title: MP-63, condition4-Dexamethasone treated


title: MP-62, condition4-Dexamethasone treated


title: eEF2-H699N, KCl, rep1


title: MP-61, condition4-Dexamethasone treated


title: mouse placental cells, E12.5

data_processing:
Raw fastq files were processed with Cell Ranger 2.1.1 with default mapping arguments.
Reads were mapped to the mouse mm10 genome and counted with GRCm38.89 annotation.
Next, the cellranger aggr command was executed to adjust the sequencing depth of different samples to the same level.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Mouse placental single cells were added to the 10x Chip channels. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs.
RNA libraries were prepared for sequencing using 10x Single Cell 3' Library & Gel Bead Kit v2  protocol

value: 12.5 days post coitus

value: placenta


title: mouse placental cells, E14.5

value: 14.5 days post coitus


title: eEF2-WT, KCl, rep2

value: Cultured cell


title: mouse placental cells, E09.5

value: 9.5 days post coitus


title: MP-60, condition4-Dexamethasone treated

value: liver hepatocyte cells


title: MP-59, condition4-Dexamethasone treated

value: Male


title: MP-6, condition4-Dexamethasone treated


title: mouse placental cells, E10.5

value: 10.5 days post coitus


title: eEF2-WT, KCl, rep1

value: No treatment

value: cycloheximide


title: MP-67, condition4-Dexamethasone treated


title: MP-58, condition4-Dexamethasone treated


title: mouse placental cells, E08.5

value: 8.5 days post coitus


title: mouse placental cells, E13.5

value: 13.5 days post coitus


title: mouse placental cells, E07.5


title: MP-57, condition4-Dexamethasone treated


title: MP-55, condition4-Dexamethasone treated


title: 7b

city: Corvallis

first: Matthew

middle: M

last: Robinson

state: OR

address: Milam Hall 003

institute: Oregon State University

description: P2 flowcell

data_processing:
Sequencing was performed on an Illumina Nextseq 2000 (San Diego, CA) to produce 100bp Single-End Reads and Illumina CASAVA 1.8 software (San Diego, CA) used for basecalling.
The bioinformatics pipeline included the following steps: Sequence reads assessed for adapters and quality scores using FastQC (Babraham Bioinformatics, Cambridge, Unite Kingdom).
For each sample, sequence reads aligned to the reference genome (Hg38) using salmon v1.4.0.
Sequence reads were quantified for each sample using salmon v1.4.0 (Salmon, Github) and differential expression was assessed using DESeq2 v1.32.0
Assembly: Hg38
Supplementary files format and content: Processed data files are from salmon v1.4.0 in .sf files containing columns for Name, Length, Effective Length, TPM, NumReads

source_name: Human muscle, baseline

extract_protocol:
Total RNA was isolated from ~20 mg of the pre- and post- biopsy samples using Trizol followed by spin-column for cleanup and DNAase treatment (Qiagen, Hilden, Germany). Total RNA was eluted in 50 µl of PCR grade water and concentration was quantified using a spectrophotometer (Nanodrop, Thermo Scientific, Waltham, MA) and integrity via 2100 Bioanalyzer (Agilent, Santa Clara, CA).
Libraries were prepared from total RNA according to Illumina instructions.
Stranded RNA Library Prep was performed on a Wafergen Bio-systems Apollo 324 Robot (Fremont, CA). Libraries were quantified by qPCR.

value: Skeletal Muscle (Quad)

tag: status

value: baseline

value: human skeletal muscle

tag: Sex

value: Female


title: 8b

description: P2 flowcell

source_name: Human muscle, 48hr post exercise

value: 48hr post training

value: 7 sessions of HIIT


title: NEB_Q5_Ultra_II_37C

city: San Francisco

first: Scot

last: Federman

state: CA

address: 499 Illinois St

department: Biochemistry

institute: UCSF

library_source: genomic

data_processing:
Basecalls were performed using bclconvert or bcl2fastq. Count tables were generated using the ScreenProcessing pipeline.
Assembly: NCBI hg19
Supplementary files format and content: Text file with guide and and count
Library strategy: CRISPRi/a library sgRNA counts

molecule: genomic DNA

organism: synthetic construct

source_name: sample was not cloned into a cell

growth_protocol: The K562 cultures were maintained at 500,000 cells / mL density for the duration of 7 days for the essential gene drop-out screens and 9 days for the dasatinib screens.

extract_protocol:
Genomic DNA was extracted using Macherey-Nagel Nucleospin Blood kits following the kit-specific protocols and quantified by Nanodrop.
Detailed protocol is in the supplemental materials. The main highlights are ordering insert oligo pools in both orientations, minimizing over amplification of the insert, and performing gel electrophoresis size selection and extraction at low temperatures.

treatment_protocol: Dasatinib treatment samples (labeled as DASA) had a single dose of 0.75 nM of dasatinib was use as the drug selective pressure. Control samples (labeled as DMSO) were treated with  0.01% DMSO. Treatment was for 72 hours with 6 days of recovery.

value: sample was not cloned into a cell

tag: crispr library

tag: overall design

value: CRISPR guide RNA library cloning optimization


title: MP-54, condition4-Dexamethasone treated

value: Dexamethasone drug


title: Klenow_exo_70C


title: buccal pouch,coated with DMBA (squamous cell carcinoma), rep 3

city: Taiyuan

first: Guohua

last: Song

state: Shanxi

address: Road Xinjian 56, Taiyuan 030001, China

department: Laboratory Animal Center

institute: Shanxi Medical University

data_processing:
After base recognition by CASAVA software, it is converted into original sequencing sequence
After the basic analysis, the qualified sequenceswere mapped onto the reference sequence using the genome alignment analysis softwareBowtie2 (http://computing.bio.cam.ac.uk/local/doc/bowtie2.html)
The mappable sequences were then folded into a secondary structureusing RNAfold software with default parameters. Only the non-coding sequences could form a perfect stem-loopstructure and meet the criteria for miRNAs prediction were then considered to be a novel miRNA candidate.
Quantification of known miRNAs was performed using the present species known miRNA sequences from the mirdeep2 software (v1.1.2) miRBase database (release 22), counting the number of clean reads that match a known miRNA, and normalizing the rpm values
Assembly: hg19

source_name: hamster buccal pouch

extract_protocol:
Gradually extract total RNA from tissues according to the experimental instruction manual in Trizol kit
A total of 18–30 nt RNA fragments were excised, purified from a PAGE gel, and ligated with 5' and 3' adaptors using T4RNA ligase. Reverse transcription followed by PCR was used to create cDNA based on the small RNA ligated with 3' and 5' adapters. Subsequently, the amplified cDNA constructs were purified from agarose gel, in preparationfor sequencing analysis using the Illumina HiSeq 2500 Analyzer (Illumina, CA, USA) according to the manufacturer’sinstructions

value: hamster buccal pouch

value: WT

value: coated with DMBA


title: buccal pouch,coated with DMBA (squamous cell carcinoma), rep 2


title: Klenow_70C


title: 7a

description: P2 flowcell


title: 6b

description: P2 flowcell

value: Male


title: MP-53, condition4-Dexamethasone treated

value: liver hepatocyte cells


title: buccal pouch,coated with DMBA (abnormal hyperplasia), rep 3


title: buccal pouch,coated with DMBA (squamous cell carcinoma), rep 1


title: 4b

description: P2 flowcell


title: MP-8, condition3-Phenobarbital treated

description: condition3_Phenobarbital_expression_tmm_normalization_exp.txt

value: Phenobarbital drug


title: MP-90, condition3-Phenobarbital treated


title: NEB_Q5_Ultra_II_70C


title: 752_element_library_1PCR


title: 752_element_library_15PCR


title: MP-9, condition3-Phenobarbital treated


title: buccal pouch,coated with DMBA (abnormal hyperplasia), rep 2


title: 3a

description: P2 flowcell


title: 6a

description: P2 flowcell


title: Klenow_37C


title: Klenow_exo_37C


title: buccal pouch,coated with DMBA (abnormal hyperplasia), rep 1


title: 3b

description: P2 flowcell


title: MP-78, condition3-Phenobarbital treated


title: buccal pouch,coated with DMBA (simple hyperplasia), rep 3


title: 34b

description: P2 flowcell


title: 34a

description: P2 flowcell


title: buccal pouch,coated with DMBA (simple hyperplasia), rep 2


title: MP-76, condition3-Phenobarbital treated


title: buccal pouch, no treatment (control), rep 3

value: no


title: MP-77, condition3-Phenobarbital treated


title: buccal pouch,coated with DMBA (simple hyperplasia), rep 1


title: 33a

description: P2 flowcell


title: 33b

description: P2 flowcell


title: MP-75, condition3-Phenobarbital treated


title: MP-7, condition3-Phenobarbital treated


title: 32b

description: P2 flowcell


title: buccal pouch, no treatment (control), rep 1


title: buccal pouch, no treatment (control), rep 2


title: MP-68, condition3-Phenobarbital treated


title: WBC_treated_with_cows_milk

type: RNA

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs for each sample was hybridized to The Affymetrix Human Genome ST 2.0 GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 7G

data_processing: Expression values were calculated for each gene using robust multi-array average (RMA) Irizarry et al. (2003), in R 3.4.0  (RMA) Irizarry et al. (2003).

label: biotin

source_name: total peripheral blood WBCs

label_protocol: Samples were prepared according to Affymetrix protocols (Affymetrix, Inc). RNA quality and quantity was tested using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc). Per RNA biotin labeling, 200 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for  GeneChip 2.0 ST chips.

growth_protocol: Total WBCs isolated from 6ml of blood from an FPIES subject were plated into 23 wells of 12-well plates, in RPMI + 10% FBS media.

extract_protocol: RNA from WBCs, after treatment, was isolated using the RNEasy Microkit (Qiagen).

treatment_protocol: Each well containing WBCs isolated from a FPIES subject was treated with individual homogenized foods at 1mg/ml, or with LPS or left untreated.

value: treated ex-vivo with cow milk

value: total peripheral blood WBCs


title: 28b

description: P2 flowcell

value: Skeletal Muscle (Quad)


title: MP-69, condition3-Phenobarbital treated


title: MP-66, condition3-Phenobarbital treated


title: MP-70, condition3-Phenobarbital treated


title: 32a

description: P2 flowcell

value: baseline

value: human skeletal muscle


title: B7E11_p63_sh3_R2

city: Buffalo

first: Satrajit

last: Sinha

state: NY

address: 955 Main Street

institute: University at Buffalo

description:
B7E11_p63_sh3_R2
B7E11_p63KD_counts.txt

data_processing:
RNA-seq - Reads were mapped to the Mus musculus genome (mm10 build) with HISAT2 (v2.1.0), reads aligned to the UCSC mm10 build were quanitifed with featureCounts (v1.5.0), which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location, DESeq1 (v.1.10.1) was used to normalize the read counts and derive TPM values
Assembly: mm10
Supplementary files format and content: featureCounts output containing gene-level read count summaries for each RNA-seq sample

source_name: cell line

extract_protocol:
RNA-seq - RNA was extracted from mouse cancer cell lines (B4B8, B7E3, B7E11) using the Direct-zol Mini-Prep kit
RNA-seq - Illumina TruSeq RNA sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries

value: cell line

value: Mouse Oral Squamous Cell Carcinoma

value: p63 KD


title: B7E11_pGIPZ_R1

description:
B7E11_pGIPZ_R1
B7E11_p63KD_counts.txt


title: 28a

description: P2 flowcell

value: Female


title: B7E11_p63_sh3_R1

description:
B7E11_p63_sh3_R1
B7E11_p63KD_counts.txt


title: B7E11_pGIPZ_R2

description:
B7E11_pGIPZ_R2
B7E11_p63KD_counts.txt


title: WBC_treated_with_lamb

value: treated ex-vivo with lamb


title: WBC_treated_with_beef

value: treated ex-vivo with beef


title: WBC_treated_with_squash

value: treated ex-vivo with squash


title: WBC_treated_with_rice

value: treated ex-vivo with rice


title: WBC_treated_with_chicken

value: treated ex-vivo with chicken


title: 27a

description: P2 flowcell


title: WBC_treated_with_spinach

value: treated ex-vivo with spinach


title: WBC_treated_with_potato

value: treated ex-vivo with potato


title: B7E11_p63_sh2_R2

description:
B7E11_p63_sh2_R2
B7E11_p63KD_counts.txt


title: MP-63, condition3-Phenobarbital treated

value: liver hepatocyte cells

value: Phenobarbital drug


title: MP-65, condition3-Phenobarbital treated

value: Male


title: 1b

description: P2 flowcell

value: Skeletal Muscle (Quad)

value: 48hr post training

value: 7 sessions of HIIT


title: 20a

description: P2 flowcell

value: baseline

value: human skeletal muscle


title: MP-62, condition3-Phenobarbital treated


title: MP-64, condition3-Phenobarbital treated


title: MP-61, condition3-Phenobarbital treated


title: B7E3_PlusDox_p63_R2

description:
B7E3_PlusDox_p63_R2
B7E3_pINDmp63_counts.txt

value: cell line

value: Mouse Oral Squamous Cell Carcinoma

value: B7E3 pIND-Trp63

value: 200ng Dox


title: MP-60, condition3-Phenobarbital treated

value: Female


title: 20b

description: P2 flowcell


title: B7E3_PlusDox_p63_R1

description:
B7E3_PlusDox_p63_R1
B7E3_pINDmp63_counts.txt


title: B7E3_MinusDox_R2

description:
B7E3_MinusDox_R2
B7E3_pINDmp63_counts.txt

value: No Dox


title: 1a

description: P2 flowcell


title: 19b

description: P2 flowcell


title: B7E3_MinusDox_R1

description:
B7E3_MinusDox_R1
B7E3_pINDmp63_counts.txt


title: 19a

description: P2 flowcell


title: 16b

description: P2 flowcell


title: MP-59, condition3-Phenobarbital treated


title: B7E11_p63_sh2_R1

description:
B7E11_p63_sh2_R1
B7E11_p63KD_counts.txt

value: p63 KD


title: WBC_treated_with_wheat_bread

value: treated ex-vivo with wheat bread

value: total peripheral blood WBCs


title: CD45+ IL-22+ cells 12h after intrasplenic cancer cell injection

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
Pair-ended UMI-indexed Illumina reads were demultiplexed with Cellranger (v. 3.0.1) mkfastq followed by CellRanger count to perform alignment to the Mm10 genome, read filtering and UMI counting for each sample.
Assembly: mm10
Supplementary files format and content: Sparse matrix output files from Cellranger

molecule: polyA RNA

source_name: liver

extract_protocol:
After euthanasia of the mice, the liver was removed, cut into small pieces and minced using a scalpel. The tissue was then incubated for 30 min at 37°C on a shaking incubator in HBSS (with Ca2+ and Mg2+) with Collagenase (1 mg/ml) and DNase I (10 U/ml) and supernatant was collected. Leukocytes were further enriched by Percoll gradient centrifugation (GE Healthcare, Chicago, IL). Cells were then FACS sorted to purify CD45+ cells and to obtain IL-22-BFP negative and positive fractions.
Single Cell 3' v2

treatment_protocol: In treated samples, mice were given an intra-splenic injection of 250 μl PBS containing 3x10^5 cancer cells (MC38).

value: liver

value: CD45+ IL-22+ cells


title: WBC_treated_with_green_peas

value: treated ex-vivo with green peas


title: WBC_treated_with_strawberry

value: treated ex-vivo with strawberry


title: MP-58, condition3-Phenobarbital treated

value: Male

value: liver hepatocyte cells

value: Phenobarbital drug


title: WBC_treated_with_pumpkin

value: treated ex-vivo with pumpkin


title: WBC_treated_with_cantaloupe

value: treated ex-vivo with cantaloupe


title: WBC_treated_with_avocavo

value: treated ex-vivo with avocado


title: 16a

description: P2 flowcell

value: Skeletal Muscle (Quad)

value: baseline

value: human skeletal muscle


title: WBC_treated_with_peach

value: treated ex-vivo with peach


title: WBC_treated_with_apple

value: treated ex-vivo with apple


title: MP-57, condition3-Phenobarbital treated


title: CD45+ IL-22- cells 12h after intrasplenic cancer cell injection

value: CD45+ IL-22- cells


title: 14b

description: P2 flowcell

value: 48hr post training

value: Female

value: 7 sessions of HIIT


title: CD45+ IL-22- cells before intrasplenic cancer cell injection

value: liver


title: 14a

description: P2 flowcell


title: MP-54, condition3-Phenobarbital treated


title: MP-53, condition3-Phenobarbital treated


title: Testes, WT

city: Cambridge

first: Amelie

last: Raz

state: Ma

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

description: processed data files include  cell names (barcodes.tsv.gz), gene names (features.tsv.gz), and counts matrix (matrix.mtx.gz). The raw data files includes both paired end reads (R1. fastq and R2.fastq)

data_processing:
Reads were mapped to the DM3 reference genome using the 10X CellRanger pipeline with default parameters. The resulting feature matrix, featuring barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz) is present in the respective processed data files
Assembly: DM3
Supplementary files format and content: barcodes.tsv.gz: list of cell names
Supplementary files format and content: features.tsv.gz: list of gene names
Supplementary files format and content: matrix.mtx.gz: gene expression matrix

organism: Drosophila melanogaster

source_name: testis

extract_protocol:
The testis dissociation protocol was adapted from Witt et al., 2019.  Fresh maceration buffer (10mL Trypsin LE (Gibco) with 20 mg collagenase (Gibco)) was prepared on the day of the dissection. Testes were hand dissected from 1-5 day old male flies in 1x phosphate-buffered saline (PBS), separated from seminal vesicles and transferred immediately into tubes filled with cold PBS, on ice.  Testes were kept in PBS for a maximum of 30 minutes.  Samples were centrifuged at 135 rcf and the PBS removed and replaced with 400 μL marceration buffer.  Testes were incubated in maceration buffer for 30 minutes with gentle vortexing every 10 minutes at room temperature.  Following incubation, samples were pipetted up and down for 15 minutes until all visible chunks were gone and the sample was in approximately a single-cell suspension. Sample was filtered through a 35 μm filter into a polystyrene tube, then transferred into a microcentrifuge tube.  After the sample was centrifuged at 135 rcf for 7 minutes, the supernatant was removed and the pellet resuspended in 1mL calcium- and magnesium-free Hanks’ Balanced Salt Solution (HBSS).  The sample was spun a final time at 137 rcf for 7 minutes.  All but 50 μL of the HBSS supernatant was removed, and the cell pellet was resuspended in the remaining 50 μL.  Cell viability and density was then assayed on a hemocytometer using DIC imaging and Trypan Blue stain.
Cells were processed using the 10x Genomics Chromium Controller and Chromium Single Cell Library and Gel Bead Kit following standard manufacturer’s protocol.  Amplified cDNA libraries were quantified by bioanalyzer and size selected using AMPure beads. Samples were sequenced on a NovaSeq SP.

value: testis

value: germ cells and somatic testis cells

value: OregonR


title: MP-6, condition3-Phenobarbital treated

value: liver hepatocyte cells

value: Phenobarbital drug


title: Lab5rep

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

data_processing:
Rna-seq reads were aligned with STAR-aligner using the genome build Ensembl Bos taurus UMD v3.1
Gene expression values were computed with the function featureCounts from the R package Rsubread.
Assembly: Ensembl Bos taurus UMD v3.1
Supplementary files format and content: tab-delimited .txt files include 2 columns: ensemble feature identifier and raw count number.

organism: Bos taurus

source_name: acetabular labrum

growth_protocol: Each tissue specimen was incubated with growth medium (DMEM/F12 with 1% antibiotics antimycotics and 1% insulin transferrin selenium) in a standard cell culture incubator for 2 days before RNA extraction.

extract_protocol:
Cells were frozen until RNA extraction was performed. RNA was extracted using Trizol reagent (Thermo Fisher) according to the manufacturer’s instructions and purified using the Rneasy Mini Kit (Qiagen) according to manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: acetabular labrum

value: male

tag: disease state

value: healthy (no macroscopic signs of disease)


title: RNA_BM_BRM014

city: Houston

first: H. Courtney

last: Hodges

state: TX

address: 1 Baylor Plaza, BCM 229

department: Department of Molecular & Cellular Biology

institute: Baylor College of Medicine

description: mRNA-seq in bone marrow cells

data_processing:
All reads were processed using the 10x Cell Ranger ARC pipeline v2.0.1.
RNA reads within coding regions as well as DNA accessibility reads were counted and normalized using Cell Ranger ARC v2.0.1
Multiplets were identified using data from both RNA (DoubletFinder v2.0.3) and ATAC (AMULET v1.1) reads, and removed. Singlet barcodes were considered all cells that passed both multiplet detection steps.
Assembly: mm10
Supplementary files format and content: H5 binary files contain both ATAC and RNA matrices of feature read counts for each barcode.

source_name: Bone marrow cells

extract_protocol:
18 hours after the final treatment, bone marrow cells from 3 mice undergoing identical treatments were harvested and pooled. Granulocytes were removed by flow sorting before nuclei permeabilization based on the manufacturer's instructions.
All libraries were barcoded and prepared for sequencing using standard 10x protocols (Multiome ATAC + Gene Expression) and Illumina protocols.

treatment_protocol: BRM014 was suspended in a vehicle of 10% DMSO and 1% methylcellulose, and administered to C57BL/6 mice at a dose of 20 mg/kg via daily oral gavage for 14 days.

value: Bone marrow cells

tag: strain


title: WBC_treated_with_sweet_potato

value: treated ex-vivo with sweet potato

value: total peripheral blood WBCs


title: CD45+ IL-22+ cells before intrasplenic cancer cell injection

tag: tissue

value: CD45+ IL-22+ cells


title: MP-90, condition2-Omeprazole treated

description: condition2_Omeprazole_expression_tmm_normalization_exp.txt

value: Male

value: Omeprazole drug


title: MP-9, condition2-Omeprazole treated

value: Female


title: Lab4rep


title: ATAC_BM_vehicle

description: ATAC-seq in bone marrow cells

library_source: genomic single cell

value: vehicle


title: WBC_treated_with_quinoa

value: treated ex-vivo with quinoa


title: MP-55, condition3-Phenobarbital treated


title: WBC_treated_with_banana

value: treated ex-vivo with banana


title: WBC_treated_with_pear

value: treated ex-vivo with pear


title: WBC_treated_with_breast_milk

value: treated ex-vivo with breast milk


title: ATAC_BM_BRM014

description: ATAC-seq in bone marrow cells


title: Lab2rep


title: Lab1rep


title: MP-78, condition2-Omeprazole treated

value: liver hepatocyte cells


title: WBC_LPS_control

value: treated ex-vivo with LPS (positive control)


title: C57BL/6J_M_Fentanyl_nucleus accumbens_3

city: Charlottesville

first: Charles

middle: R

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

data_processing:
Adaptors from raw sequence files were trimmed using Trimmomatic (https://doi.org/10.1093/bioinformatics/btu170)
HISAT2 was used to align sequence reads to the GRCm38 (mm10) genome reference (https://doi.org/10.1038/nmeth.3317)
StringTie was used for quantification of gene expression
DESeq2 was used to conduct differential gene expression analysis. DESeq2 fits a negative binomial generalized linear model for each gene along with a Wald test for significance testing. A total of three differential analyses were conducted. Significant genes were determined from each analysis using the default Benjamini-Hochberg FDR of <0.05. The three univariate models were fit using strain, sex, and treatment independently (n = 32).
Assembly: mm10
Supplementary files format and content: raw read count matrix where is row is a gene and each column is a sample

source_name: nucleus accumbens

extract_protocol:
Flash frozen tissues were homogenized on ice in RLT buffer (Qiagen) containing 40 mM DTT with a Tissue-Tearor (BiosSpec Products, Inc) at low speed (setting 3) for 10 s. The resulting lysate was extracted with an equal volume of acid-phenol:chloroform (Thermo Fisher, cat# AM9722) and RNA was further purified from the aqueous phase with RNeasy mini kit (Qiagen) following the manufacture's recommendations. Samples were DNased (DNA-free DNA removal kit, Thermo Fisher) and RNA concentrations were determined using a Qubit Fluorimeter (Thermo Fisher). DNA-free total RNA was sent to Psomagen (Rockville, MD) for mRNA-seq. The 32 samples were sequenced to an average read count depth of 14.89 ± 2.9 million.
Libraries were constructed using the Illumina TruSeq Stranded mRNA Library Prep Kit

value: nucleus accumbens

tag: genotype

value: Fentanyl


title: MP-8, condition2-Omeprazole treated

tag: treatment


title: C57BL/6J_M_Fentanyl_nucleus accumbens_4


title: WBC_untreated_control

value: untreated control


title: MP-77, condition2-Omeprazole treated


title: Cart5rep

source_name: articular cartilage

value: articular cartilage

value: male

value: healthy (no macroscopic signs of disease)


title: scRNA_BM_BRM014

description: mRNA in bone marrow cells

data_processing:
All RNA-seq reads were processed using the 10x Cell Ranger pipeline v5.0.1. Fragments were aligned to the mm10 genome assembly using STAR aligner v2.7.2a.
Reads within coding regions were counted and normalized using Cell Ranger v5.0.1
Multiplets were identified using DoubletFinder v2.0.3 and removed.
Assembly: mm10
Supplementary files format and content: TSV and MTX files are tab-delimited text files specifying total numbers of reads overlapping each gene for each unique cell barcode (altogether in MEX format). H5 files are binary files in H5 format containing the matrix of transcript read counts for each barcode.

extract_protocol:
18 hours after the final treatment, bone marrow cells from 3 mice undergoing identical treatments were flushed from femur and tibia bones using PBS supplemented with 3% FBS, and pooled for analysis.
All libraries were barcoded and prepared for sequencing using standard 10x protocols (Single cell 5' RNA-seq) and Illumina protocols.

value: Bone marrow cells


title: scRNA_BM_vehicle

description: mRNA in bone marrow cells


title: RNA_PB_vehicle

description:
mRNA-seq in peripheral blood cells
Multiome_PB_vehicle.h5

source_name: Peripheral blood cells

extract_protocol:
18 hours after the final treatment, peripheral blood cells from 3 mice undergoing identical treatments were obtained and cleared of red blood cells by osmotic shock. Granulocytes were removed by flow sorting before nuclei permeabilization based on the manufacturer's instructions.
All libraries were barcoded and prepared for sequencing using standard 10x protocols (Multiome ATAC + Gene Expression) and Illumina protocols.
Joint ATAC- and RNA-seq

value: Peripheral blood cells


title: C57BL/6J_M_Fentanyl_nucleus accumbens_2


title: C57BL/6J_M_Fentanyl_nucleus accumbens_1


title: RNA_BM_vehicle

description: mRNA-seq in bone marrow cells


title: C57BL/6J_M_Saline_nucleus accumbens_4

value: Saline


title: MP-76, condition2-Omeprazole treated

source_name: liver hepatocyte cells

value: Male

value: Omeprazole drug


title: Cart4rep


title: MP-75, condition2-Omeprazole treated

value: Female


title: Lab3rep

value: acetabular labrum


title: Cart3rep


title: RNA_PB_BRM014

description:
mRNA-seq in peripheral blood cells
Multiome_PB_BRM014.h5


title: ATAC_PB_vehicle

description:
ATAC-seq in peripheral blood cells
Multiome_PB_vehicle.h5

value: vehicle


title: C57BL/6J_M_Saline_nucleus accumbens_3


title: ATAC_PB_BRM014

description:
ATAC-seq in peripheral blood cells
Multiome_PB_BRM014.h5


title: Cart2rep


title: MP-7, condition2-Omeprazole treated


title: C57BL/6J_M_Saline_nucleus accumbens_2


title: Cart1rep


title: MP-69, condition2-Omeprazole treated


title: MP-68, condition2-Omeprazole treated


title: C57BL/6J_M_Saline_nucleus accumbens_1


title: C57BL/6J_F_Fentanyl_nucleus accumbens_4


title: LGR_CRISPRi_V2_Plasmid_HiSeq

value: sample was not cloned into a cell

tag: perturbation type

value: CRISPRa

value: CRISPR guide RNA library cloning optimization


title: LGR_CRISPRa_V2_Plasmid_HiSeq

value: CRISPRi


title: muscle_ct62_young

city: Gainesville

first: Karyn

middle: A

last: Esser

state: Florida

address: 1345 Center Drive

department: PHYSIOLOGY & FUNCTIONAL GENOMICS

institute: University of Florida

data_processing:
Alignment was performed by using HISAT2 software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
The raw count data were normalized to cpm (counts per million reads)
Assembly: GRCm38 (mm10)
Supplementary files format and content: count_216.csv: gene expression count data
Supplementary files format and content: cpm_216.csv: normalized count data (count per million reads)

source_name: muscle

extract_protocol:
Samples were homogenized in Trizol, and RNA extracted accordinng to manufacturer protocol
RNAseq libraries were prepared with Illumina RNA-Seq libraries (Poly A) kit following manufacturer's protocols.

value: muscle

tag: age group

value: young

tag: circadian time


title: A_IHMA_I2

city: Grenoble

first: Manon

last: Janet-Maitre

address: 71 Avenue des Martyrs

country: France

institute: IBS

data_processing:
Library strategy: Tn-seq
Trim sequences
Trimmomatic
Bowtie2
Ht-seq count
DeSeq2

organism: Pseudomonas aeruginosa

source_name: plasma

growth_protocol: Bank growth at 30°C, incubation in plasma/Heat inactivated plasma 3h 37°C on rotating wheel recovering of live bacteria in LB

extract_protocol:
gDNA extraction
Fragmentation, End repair, DA tailing, adaptor ligation, size selection and 2 PCRs

treatment_protocol: Plasma or heat inactivated plasma

value: Heat inactivated plasma (input)


title: muscle_ct62_old

value: old


title: muscle_ct62_aged

value: aged


title: C57BL/6J_F_Fentanyl_nucleus accumbens_3

value: nucleus accumbens

value: Fentanyl


title: MP-67, condition2-Omeprazole treated

data_processing:
RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits and sequenced on an Illumina HiSEQ2500 or 4000 according to Illumina provided protocols.
Post alignment and QC, reads were mapped to genes referenced with comprehensive gene annotation (GENCODE version 25) by HTSeq (version 0.6.1p1) with union mode and minaqual = 20
HTSeq raw counts were supplied for gene expression analysis and were normalized using regularized log transformation and principal component analysis (PCA) using Bioconductor package DESeq2 (version1.20.0)
We calculated TPM (transcript per million) by first normalizing the counts by gene length and then normalizing by read depth (Wagner, Kin, & Lynch, 2012). Gene expression values were filtered based on the expression thresholds > 0.1 TPM in at least 20% of samples and ≥ 6 reads in at least 20% of samples as done in the GTEx consortium (gtexportal.org, Analysis Methods, V7).
We normalized expression values across samples by TMM (trimmed mean of M-values) implemented in edgeR (Robinson & Oshlack, 2010) and then normalized for each gene by inverse normal transformation.
Genome_build: hg37
Assembly: GRCh37.p13
Supplementary files format and content: Sample_MP-XX2count.txt data contain raw count data from Htseq for condition2- Omeprazole drug treatment
Supplementary files format and content: Sample_MP-XX3count.txt data contain raw count data from Htseq for condition3 - Phenobarbital drug treatment
Supplementary files format and content: Sample_MP-XX4count.txt data contain raw count data from Htseq for condition4 - Dexamethasone drug treatment
Supplementary files format and content: Sample_MP-XX5count.txt data contain raw count data from Htseq for condition5 - Carbamazepine drug treatment
Supplementary files format and content: Sample_MP-XX6count.txt data contain raw count data from Htseq for condition6 - Phenytoin drug treatment
Supplementary files format and content: Sample_MP-XX7count.txt data contain raw count data from Htseq for condition7 - Rifampicine  drug treatment
Supplementary files format and content: condition2_Omeprazole_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition2 - Omeprazole drug treatment
Supplementary files format and content: condition3_Phenobarbital_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition3 - Phenobarbital drug treatment
Supplementary files format and content: condition4_Dexamethasone_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition4 - Dexamethasone drug treatment
Supplementary files format and content: condition5_Carbamazepine_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition5 - Carbamazepine drug treatment
Supplementary files format and content: condition6_Phenytoin_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition6 - Phenytoin drug treatment
Supplementary files format and content: condition7_Rifampicine_expression_tmm_normalization_exp.txt contain TMM normalized expression values across samples for condition7 - Rifampicine  drug treatment

extract_protocol: RNA was extracted after three days using the RNeasy Plus mini-kit (Qiagen) per manufacturer's instructions. RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits.

tag: gender

tag: age

tag: platform

value: liver hepatocyte cells


title: muscle_ct58_young

value: Male


title: MP-66, condition2-Omeprazole treated

tag: batch

tag: cell type

value: Omeprazole drug


title: muscle_ct58_old


title: MP-70, condition2-Omeprazole treated

value: Female


title: muscle_ct58_aged


title: A_IHMA_P1

value: Heparinized pooled plasma (output)


title: C57BL/6J_F_Fentanyl_nucleus accumbens_2


title: C57BL/6J_F_Fentanyl_nucleus accumbens_1


title: C57BL/6J_F_Saline_nucleus accumbens_4

value: Saline


title: C57BL/6J_F_Saline_nucleus accumbens_3


title: MP-62, condition2-Omeprazole treated


title: MP-64, condition2-Omeprazole treated


title: A_IHMA_P2


title: IHMA_Tn_Psrg_2

data_processing:
Trim sequences
Trimmomatic
Bowtie2
Ht-seq count
DeSeq2
Supplementary_files_format_and_content: xlsx

source_name: culture

growth_protocol: OD600nm=1 LB 37°C

extract_protocol:
Hot phenol-chloroform RNA extraction and Ribominus
NEBNext Ultra II Directional RNA Library


title: MP-61, condition2-Omeprazole treated


title: IHMA_Tn_Psrg_1


title: C57BL/6J_F_Saline_nucleus accumbens_2


title: muscle_ct54_aged


title: C57BL/6J_F_Saline_nucleus accumbens_1


title: A_IHMA_I1


title: A/J_M_Fentanyl_nucleus accumbens_4

value: A/J


title: muscle_ct50_young


title: muscle_ct50_old


title: MP-60, condition2-Omeprazole treated


title: IHMA_WT_2

value: wild-type


title: IHMA_WT_1


title: Legacy_DASA_2

tag: cell line

value: Addgene #83969

value: 100-fold cell coverage dasatinib screen


title: MP-65, condition2-Omeprazole treated


title: MP-59, condition2-Omeprazole treated


title: muscle_ct50_aged

value: muscle

tag: Sex


title: A/J_M_Fentanyl_nucleus accumbens_2


title: MP-6, condition2-Omeprazole treated


title: MP-58, condition2-Omeprazole treated


title: MP-57, condition2-Omeprazole treated


title: A/J_M_Fentanyl_nucleus accumbens_3


title: muscle_ct46_old


title: muscle_ct54_young

value: young


title: muscle_ct46_young


title: A/J_M_Fentanyl_nucleus accumbens_1


title: MP-55, condition2-Omeprazole treated


title: A/J_M_Saline_nucleus accumbens_4


title: Legacy_DMSO_2

value: CRISPRi

tag: crispr library


title: Legacy_DMSO_1

tag: overall design


title: muscle_ct46_aged


title: A/J_M_Saline_nucleus accumbens_3


title: MP-54, condition2-Omeprazole treated


title: muscle_ct42_young


title: MP-53, condition2-Omeprazole treated


title: A/J_M_Saline_nucleus accumbens_2


title: muscle_ct42_old

value: old


title: A/J_M_Saline_nucleus accumbens_1


title: LGR_DASA_2


title: Legacy_T0_A


title: muscle_ct38_young


title: HH controls_baseline_HC_8060101_SV0

city: Bergen

first: Harleen

last: Grewal

address: The Laboratory Building, 5th floor, 5021

department: Department of Clinical Science

country: Norway

institute: University of Bergen

data_processing:
Demultiplexing using bcl2fastq v2.20.0.422
Alignment of RNAseq fastq files to GRCh38.p10 using hisat2-2.05
Quantification of RNAseq data against genome using featurecount 1.5.2.
Normalization of quantized reads and differential gene expression calculation using DEseq2 1.34.0
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Expression matrix for 144 samples rounded to two digits with group information derived from expression matrix calculated by DEseq2

source_name: Whole blood

extract_protocol:
Peripheral whole blood (approx. 2.5 ml) was drawn into PAXgene blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) and stored at -80°C until RNA extraction (PAXgene Blood RNA kit; PreAnalytiX, Hilden, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Whole Blood

tag: distinct stages of tb

value: HH controls_baseline

tag: age in years

tag: chest x-ray

value: Normal

tag: mtb culture

value: Negative

tag: tst in mm

tag: qft result


title: HH controls_baseline_HC_4710107_SV0

tag: tissue


title: LGR_DMSO_2

tag: perturbation type


title: HH controls_baseline_HC_4020109_SV0

tag: gender

value: Male

value: Abnormal, not TB


title: LGR_DASA_1


title: muscle_ct42_aged

tag: strain

tag: age group

value: aged

tag: circadian time


title: A/J_F_Fentanyl_nucleus accumbens_3

value: nucleus accumbens

tag: genotype

tag: treatment

value: Fentanyl


title: Legacy_DASA_1

tag: cell line


title: HH controls_baseline_HC_7150103_SV0

value: Female


title: A/J_F_Fentanyl_nucleus accumbens_2

value: A/J


title: muscle_ct38_old

tag: Sex


title: A/J_F_Fentanyl_nucleus accumbens_4


title: LGR_DMSO_1

tag: crispr library

tag: overall design


title: muscle_ct38_aged


title: HH controls_baseline_HC_6540103_SV0

tag: distinct stages of tb

tag: age in years


title: A/J_F_Fentanyl_nucleus accumbens_1


title: muscle_ct54_old


title: LGR_T0_B


title: muscle_ct34_young


title: Legacy_T0_B

value: Addgene #83969


title: HH controls_baseline_HC_6540101_SV0

tag: chest x-ray

tag: mtb culture


title: LGR_T0_A

value: 100-fold cell coverage dasatinib screen


title: HH controls_baseline_HC_6010110_SV0

tag: tst in mm

tag: qft result


title: A/J_F_Saline_nucleus accumbens_3

tag: tissue

value: Saline


title: Legacy_200X_2

tag: perturbation type

value: Transduction titration experiments


title: HH controls_baseline_HC_6010102_SV0

tag: gender


title: muscle_ct34_aged

value: muscle

tag: strain

tag: age group


title: A/J_F_Saline_nucleus accumbens_2

tag: genotype


title: muscle_ct30_young

value: young

tag: circadian time


title: A/J_F_Saline_nucleus accumbens_1

tag: treatment


title: muscle_ct30_old

tag: Sex

value: old


title: HH controls_baseline_HC_5290101_SV0

value: Whole Blood

value: HH controls_baseline


title: Legacy_100X_2

tag: cell line

value: CRISPRi

tag: crispr library


title: Legacy_CRISPRa_V2_Plasmid_NextSeq

value: sample was not cloned into a cell

value: CRISPRa

value: Addgene #83978

tag: overall design

value: CRISPR guide RNA library cloning optimization


title: Legacy_100X_1


title: muscle_ct30_aged

value: Male

value: aged


title: Legacy_CRISPRi_V2_Plasmid_NextSeq


title: muscle_ct26_young


title: Legacy_50X_2


title: HH controls_baseline_HC_4440202_SV0

tag: distinct stages of tb

tag: age in years

value: Female

value: Normal

value: Negative


title: HH controls_baseline_HC_3690102_SV0

tag: chest x-ray

tag: mtb culture


title: HH controls_baseline_HC_4440204_SV0

tag: tst in mm

tag: qft result


title: LGR_CRISPRa_V2_Plasmid_NextSeq

tag: perturbation type


title: Legacy_50X_1

value: Addgene #83969


title: LGR_CRISPRi_V2_Plasmid_NextSeq


title: Legacy_10X_2

value: Transduction titration experiments


title: A/J_F_Saline_nucleus accumbens_4

tag: tissue

value: nucleus accumbens

value: A/J

value: Saline


title: muscle_ct34_old

value: muscle

tag: strain

value: old


title: muscle_ct26_aged

tag: age group


title: Legacy_200X_1

value: CRISPRi


title: HH controls_baseline_HC_2360104_SV0

value: Whole Blood

value: HH controls_baseline

tag: gender

value: Abnormal, not TB


title: Legacy_10X_1


title: High yield oil palm leaves SP540

city: Jakarta Timur

first: Ardha

last: Apriyanto

state: DKI Jakarta

address: Puloayang Raya Blok OR I

country: Indonesia

institute: Astra Agro Lestari

data_processing:
Geneious Prime v. 2023
The sequenced reads were trimmed and quality-checked using fastp software
RNA-seq data was quantified using Kallisto software , with default parameters.
The read count data was used for subsequent analysis using DESeq2 packages and NetworkAnalyst 3.0
Assembly: GCF_000442705.1
Supplementary files format and content: tab-delimited text files include gene count values for each sample

organism: Elaeis guineensis

source_name: Leaves

growth_protocol: All individual trees were observed seven years after field planting and four years of consecutive yield recording. The oil palm population were planted in the same field and of the same age at Gunung Sejahtera Ibu Pertiwi Plantation, Kalimantan Tengah, Indonesia.

extract_protocol:
Total RNA was isolated from 500 mg of tissues using the Norgen Total RNA Purification Kit (Norgen Biotek Corp, Canada)  according to the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using TruSeq mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Selected individual trees then categorized as high-, medium-, and low-oil yielding groups from each specific populations.
All the samples were immediately frozen in liquid nitrogen and stored at -80°C until further use.

tag: cultivar

value: Tenera

tag: age

value: 7 years

tag: developmental stage

value: Leaves at frond 17

value: Leaves

tag: population

value: Deli x SP540

value: High yield


title: muscle_ct22_young

tag: Sex

value: Male

value: young

tag: circadian time


title: LGR_200X_2

extract_protocol:
Genomic DNA was extracted using Macherey-Nagel Nucleospin Blood kits following the kit-specific protocols and quantified by Nanodrop.
Detailed protocol is in the supplemental materials. The main highlights are ordering insert oligo pools in both orientations, minimizing over amplification of the insert, and performing gel electrophoresis size selection and extraction at low temperatures.

tag: cell line

tag: crispr library

tag: overall design

value: Transduction titration experiments


title: HH controls_baseline_HC_2040104_SV0

tag: distinct stages of tb

tag: age in years

value: Female

tag: chest x-ray

value: Normal

tag: mtb culture

value: Negative


title: High yield oil palm leaves Yangambi

description: HYYangambi

tag: tissue

value: Deli x Yangambi

tag: treatment


title: High yield oil palm leaves LaMe

description: HYLaMe

value: Deli x LaMe


title: LGR_200X_1

tag: perturbation type

value: CRISPRi


title: HH controls_baseline_HC_20402_SV0

value: Whole Blood

value: HH controls_baseline

tag: gender

tag: tst in mm

tag: qft result


title: HH controls_baseline_HC_1790102_SV0


title: muscle_ct26_old

value: muscle

tag: strain

tag: age group

value: old


title: HH controls_baseline_HC_3510301_SV0


title: HH controls_baseline_HC_5490102_SV0

value: Positive


title: muscle_ct22_old

tag: Sex


title: HH controls_baseline_HC_5480403_SV0


title: Medium yield oil palm leaves LaMe

description: MYLaMe

tag: cultivar

value: Tenera

tag: age

value: 7 years

tag: developmental stage

value: Leaves at frond 17

value: Leaves

tag: population

value: Medium yield


title: LGR_100X_2

tag: cell line

tag: crispr library

tag: overall design

value: Transduction titration experiments


title: Medium yield oil palm leaves Yangambi

description: MYYangambi


title: LGR_50X_2


title: muscle_ct18_old

value: Male

tag: circadian time


title: muscle_ct18_young

tag: tissue

value: young


title: Low yield oil palm leaves SP540

value: Deli x SP540

tag: treatment

value: Low yield


title: LGR_50X_1

tag: perturbation type


title: muscle_ct18_aged

value: aged


title: HH controls_baseline_HC_5480402_SV0

tag: distinct stages of tb

tag: age in years

tag: gender

tag: chest x-ray

value: Normal

tag: mtb culture

value: Negative


title: HH controls_baseline_HC_7600201_SV0

value: Whole Blood

value: HH controls_baseline

value: Female

tag: tst in mm

tag: qft result


title: lung_ct62_young

source_name: lung

value: lung

tag: strain

tag: Sex

tag: age group


title: LGR_10X_2

tag: cell line

value: CRISPRi


title: lung_ct62_old

value: old


title: Medium yield oil palm leaves SP540

tag: cultivar

value: Tenera

tag: age

value: 7 years

tag: developmental stage

value: Leaves at frond 17

tag: population


title: lung_ct62_aged

tag: tissue

tag: circadian time


title: HH controls_baseline_HC_4020108_SV0

tag: distinct stages of tb

value: Positive


title: LGR_10X_1

tag: perturbation type

tag: crispr library

tag: overall design

value: Transduction titration experiments


title: muscle_ct22_aged

value: muscle

value: Male


title: Low yield oil palm leaves LaMe

description: LYLaMe

value: Leaves

value: Deli x LaMe

tag: treatment

value: Low yield


title: LGR_100X_1


title: LGR_100X_Tf_4

value: Genome-wide essential gene drop-out screens


title: HH controls_baseline_HC_3700201_SV0

value: Whole Blood

tag: age in years

tag: gender

tag: chest x-ray

value: Normal

tag: mtb culture

value: Negative

tag: tst in mm


title: LGR_100X_Tf_3

tag: cell line


title: HH controls_baseline_HC_3510202_SV0

value: HH controls_baseline

value: Female

tag: qft result


title: lung_ct58_young

value: lung

tag: strain

tag: Sex

tag: age group

value: young


title: LGR_100X_Tf_2

value: CRISPRi


title: CD3-28, WT, iNeuron

city: Boston

first: Serkan

last: Erdin

state: MA

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
Batch 1B
RNAseq for human SCN2A iNeurons

data_processing:
RNAseq data was processed using a standard workflow, which includes quality assessment of fastq reads using FastQc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Raw sequence reads were trimmed against Illumina adapters using Trimmomatic (v. 0.36) with parameters ILLUMINACLIP:adapter.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:75.
Each bulk RNAseq library of human sample was aligned to human reference genome GRCh37 version 75 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
Differential expression analysis was performed by DESeq2 pipeline.
Quality assessment of alignments were obtained using RNASeQC, RSeQC and SamTools.
Assembly: Human reference genome for bulk RNAseq GRCh37 v75.
Supplementary files format and content: "SCN2A_iNeuron_GRCh37.v75_counts.txt.gz" - gzipped tab delimited text file for raw counts of human cell line bulk RNAseq data
Supplementary files format and content: "SCN2A_iNeuron_RNAseqLibraries_RNASeQC_metrics_experimentalMetaData.txt.gz" gzipped tab delimeted text file for experimental meta data and RNASeQC post alignment QC metrics

growth_protocol: For differentiation of SCN2A  human iPSC models into glutamatergic neurons, Ngn2- neuronal induction was performed as previously described (Ho et al Biomark Insights 2015). Briefly, iPSCs were seeded at a density of 106 cells/mL and transduced with a lentivirus expressing TetO-Ngn2-GFP-Puro or TetO-Ngn2-Puro along with rtTA. Twenty-four hours after transduction, doxycycline was added to initiate Ngn2 expression, and then 24h later the cells were selected with puromycin. Ngn2-glutamatergic iPSC-derived neurons were cultured in neuronal maintenance medium supplemented with BDNF and GDNF growth factors for an additional 22 days. Subsequent experiments were performed with 24 day-old Ngn2-glutamatergic neurons, using 6-34 total replicates per genotype (i.e. WT, heterozygous deletion) per target gene

extract_protocol:
All RNA samples were extracted with Trizol reagent according to the manufacturer’s instruction (Invitrogen).
SCN2A RNAseq libraries were prepared from 200 ng of total RNA using a TruSeq stranded mRNA Sample Prep Kit (Illumina cat# RS-122-2102). Libraries were multiplexed, pooled and sequenced on multiple lanes of the Illumina NovaSeq platform, generating an average of 30.7M paired-end 150 bp-cycle reads for 30 samples (20 SCN2A heterozygous deletion, 10 SCN2A wild-types)

treatment_protocol: We generated SCN2A CRISPR-mediated LoF gene editing models which leveraged a dual-gRNA strategy to promote gene deletions. SCN2A sgRNAs targeted intron 4 and intron 11 (NM_001040142) to generate a 7.5kb partial gene deletion, and the crRNA sequences used were: 5'-tatcgtagggggaccaacc-3' and 5'-gcgtggatctagtgaactt-3'.

tag: cell type

value: induced neuron

tag: genotype

value: SCN2A WT

value: M


title: lung_ct58_aged

tag: tissue

value: aged

tag: circadian time


title: HH controls_baseline_HC_7150102_SV0

tag: distinct stages of tb

value: Positive


title: HH controls_baseline_HC_6770101_SV0


title: CD3-50, Het, iNeuron

description:
Batch 5
RNAseq for human SCN2A iNeurons

value: SCN2A Het


title: LGR_100X_Tf_1

data_processing:
Basecalls were performed using bclconvert or bcl2fastq. Count tables were generated using the ScreenProcessing pipeline.
Assembly: NCBI hg19
Supplementary files format and content: Text file with guide and and count
Library strategy: CRISPRi/a library sgRNA counts

tag: perturbation type

tag: crispr library

tag: overall design


title: lung_ct54_young

value: Male


title: HH controls_baseline_HC_5480201_SV0

tag: age in years

tag: gender


title: Low yield oil palm leaves Yangambi

description: LYYangambi

tag: cultivar

value: Tenera

tag: age

value: 7 years

tag: developmental stage

value: Leaves at frond 17

value: Leaves

tag: population

value: Deli x Yangambi

tag: treatment

value: Low yield


title: CD3-27, WT, iNeuron

tag: cell line

tag: Sex


title: lung_ct54_old

tag: strain

tag: age group

value: old


title: LGR_100X_T0_2

value: Genome-wide essential gene drop-out screens


title: CD3-25, Het, iNeuron

tag: cell type

tag: genotype


title: HH controls_baseline_HC_5290103_SV0

tag: tissue

value: Whole Blood

tag: distinct stages of tb

value: HH controls_baseline

value: Female

tag: chest x-ray

value: Normal

tag: mtb culture

value: Negative

tag: tst in mm

tag: qft result


title: CD3-24, Het, iNeuron

value: induced neuron

value: M


title: CD3-53, Het, iNeuron

description:
Batch 5
RNAseq for human SCN2A iNeurons

value: SCN2A Het


title: LGR_100X_T0_1

tag: perturbation type

value: CRISPRi

tag: crispr library

tag: overall design


title: CD3-16, WT, iNeuron

description:
Batch 1A
RNAseq for human SCN2A iNeurons

value: SCN2A WT


title: lung_ct54_aged

value: lung

value: Male

value: aged

tag: circadian time


title: LGR_1000X_Tf_3


title: HH controls_baseline_HC_4710106_SV0

tag: age in years

tag: gender

value: Positive


title: lung_ct58_old

tag: Sex


title: CD3-15, Het, iNeuron

tag: cell line


title: lung_ct50_young

tag: strain

tag: age group

value: young


title: LGR_1000X_Tf_2


title: lung_ct50_old

value: old


title: HH controls_baseline_HC_4460105_SV0


title: CD2-59, Het, iNeuron

description:
Batch 5
RNAseq for human SCN2A iNeurons

tag: cell type

tag: genotype


title: LGR_1000X_T0

value: Genome-wide essential gene drop-out screens


title: CD2-55, Het, iNeuron

description:
Batch 5
RNAseq for human SCN2A iNeurons


title: HH controls_baseline_HC_4460104_SV0

tag: tissue

value: Whole Blood

tag: distinct stages of tb


title: CD2-52, WT, iNeuron

description:
Batch 5
RNAseq for human SCN2A iNeurons


title: lung_ct50_aged


title: LGR_1000X_Tf_1


title: HH controls_baseline_HC_3550101_SV0

value: HH controls_baseline

tag: chest x-ray

tag: mtb culture


title: CD2-51, WT, iNeuron

description:
Batch 5
RNAseq for human SCN2A iNeurons


title: lung_ct42_young


title: HH controls_baseline_HC_5090201_SV0

tag: tst in mm

tag: qft result


title: HH controls_baseline_HC_2240103_SV0


title: HH controls_baseline_HC_2360102_SV0

value: Female

value: Abnormal, not TB


title: HH controls_baseline_HC_4070102_SV0

value: Normal

value: Negative


title: lung_ct46_aged


title: ChIP_THP1_SMARCA4_DMSO_rep1

description: SMARCA4 ChIP-seq in THP1 cells treated with DMSO

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis.
All bigWig files are unscaled counts and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

growth_protocol: Cells were cultured in 10% FBS RPMI medium using standard approaches.

extract_protocol:
Lysates were obtained from sonicated nuclei crosslinked with either 1% formaldehyde and 2 mM disuccinimidyl glutarate (double cross-linking) for SMARCA4, or 1% formaldehyde alone (single cross-linking) for all other targets. Protein-DNA complexes were isolated by immunoprecipitation.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either 1 uM BRM014, 3 uM DB2313, or an equivalent volume of DMSO for 72 h.

tag: chip antibody

value: Proteintech, 21634-1-AP

tag: treatment

value: DMSO


title: CD2-42, Het, iNeuron

description:
Batch 4
RNAseq for human SCN2A iNeurons

value: induced neuron

value: SCN2A Het

value: M


title: CD2-41, Het, iNeuron

description:
Batch 4
RNAseq for human SCN2A iNeurons


title: lung_ct42_aged

value: lung

value: Male

tag: circadian time


title: lung_ct46_old


title: ATAC_THP1_DB2313_rep2

description: ATAC-seq in THP-1 cells treated with DB2313 for 72 h

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. 200 bp pseudofragments were created at the positions corresponding to the transposition sites, and peak calls were made using MACS 2.1.2 without modeling of fragment size. Reads within peaks were counted using bedtools.
The table of all counts was processed using DESeq2, using default parameters.
Bigwig files were created based on 200 bp pseudofragments, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Assembly: hg38
Supplementary files format and content: Unscaled bigWig files of genome-wide coverage

source_name: THP-1 cells

extract_protocol:
Nuclei were permeabilized and transposed according to the Omni-ATAC protocol.
All libraries were barcoded and prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with either 1 uM BRM014 or an equivalent volume of DMSO for either 24 or 72 h prior to library construction. PMA differentiation of THP-1 cells was performed by addition of 10 nM PMA for 48 h, followed by removal of PMA to allow cells to rest for 24 h. DB2313 treatment was performed by addition of 3 uM DB2313 for 72 h.

value: THP-1 cells


title: ChIP_THP1_SMARCA4_DB2313_rep2

description: SMARCA4 ChIP-seq in THP1 cells treated with DB2313


title: HH controls_baseline_HC_20403_SV0

tag: age in years

value: Positive


title: ChIP_THP1_SMARCA4_DMSO_rep2


title: ATAC_THP1_DB2313_rep1


title: CD2-40, WT, iNeuron

description:
Batch 4
RNAseq for human SCN2A iNeurons

value: SCN2A WT


title: lung_ct42_old

value: old


title: lung_ct46_young

value: young


title: HH controls_baseline_HC_2040106_SV0

value: Whole Blood

value: HH controls_baseline

tag: gender


title: CD2-32, WT, iNeuron

tag: Sex


title: ChIP_THP1_SMARCA4_DB2313_rep1

tag: cell line


title: HH controls_baseline_HC_1380101_SV0

value: Female


title: ChIP_THP1_RUNX1_DMSO_rep2

description: RUNX1 ChIP-seq in THP1 cells treated with DMSO

value: Abcam, ab23980


title: lung_ct38_old

tag: strain


title: CD2-29, Het, iNeuron


title: Incipient TB_followup_NPRIF_5480401_SV12

value: Incipient TB/Non-Progressor_followup

value: Normal

value: Negative


title: Incipient TB_followup_NPRIF_1800203_SV12


title: lung_ct34_young

tag: age group


title: CD2-20, WT, iNeuron

tag: cell type

value: induced neuron


title: CD2-18, Het, iNeuron

tag: genotype

value: SCN2A Het


title: ChIP_THP1_RUNX1_DMSO_rep1

value: DMSO


title: lung_ct38_aged

tag: tissue

value: lung

value: aged


title: Incipient TB_baseline_NPRIB_3700205_SV0

tag: distinct stages of tb

value: Incipient TB/Non-Progressor_baseline

value: Male


title: Incipient TB_baseline_NPRIB_1800203_SV0

tag: chest x-ray

value: Abnormal TB


title: Incipient TB_followup_NPRIF_6690101_SV6

tag: mtb culture


title: CD1-43, Het, iNeuron

description:
Batch 4
RNAseq for human SCN2A iNeurons

value: M


title: CD1-55, Het, iNeuron

description:
Batch 5
RNAseq for human SCN2A iNeurons


title: ChIP_THP1_PU1_DMSO_rep2

description: PU.1 ChIP-seq in THP1 cells treated with DMSO

value: Cell Signaling, 2266s


title: lung_ct34_aged


title: Incipient TB_baseline_NPRIB_6690101_SV0

value: Whole Blood

value: Positive

tag: tst in mm


title: CD1-41, Het, iNeuron

description:
Batch 4
RNAseq for human SCN2A iNeurons


title: ChIP_THP1_PU1_DMSO_rep1


title: lung_ct30_young

value: young


title: lung_ct30_old

value: old


title: lung_ct38_young


title: Incipient TB_followup_NPRIF_6540102_SV12

value: Incipient TB/Non-Progressor_followup

tag: qft result


title: CD1-33, WT, iNeuron

value: SCN2A WT


title: CD2-19, Het, iNeuron


title: ChIP_THP1_RUNX1_BRM014_rep2

description: RUNX1 ChIP-seq in THP1 cells treated with BRM014

tag: chip antibody

value: Abcam, ab23980


title: lung_ct30_aged


title: lung_ct34_old


title: ChIP_THP1_RUNX1_BRM014_rep1

tag: treatment


title: lung_ct26_young

tag: circadian time


title: lung_ct26_old


title: ChIP_THP1_MEIS1_DMSO_rep1

description: MEIS1 ChIP-seq in THP1 cells treated with DMSO

value: Abcam, ab19867


title: lung_ct26_aged


title: lung_ct22_young


title: Incipient TB_followup_NPRIF_5580103_SV12

tag: age in years

value: Normal

value: Negative


title: lung_ct22_old

value: lung


title: CD1-27, Het, iNeuron

value: induced neuron

value: SCN2A Het


title: ChIP_THP1_LMO2_DMSO_rep2

description: LMO2 ChIP-seq in THP1 cells treated with DMSO

value: R&D Systems, AF2726

value: DMSO


title: ChIP_THP1_LMO2_DMSO_rep1


title: lung_ct18_young

value: Male


title: CD1-20, WT, iNeuron

value: M


title: ChIP_THP1_LMO2_BRM014_rep2

description: LMO2 ChIP-seq in THP1 cells treated with BRM014


title: POLE-mutant/TMB-UH_6, CZ2101795S

city: Shanghai

first: Yunjin

last: Wang

state: --- Select a state ---

address: 270 Dongan Road

institute: Fudan University Shanghai Cancer Center

data_processing:
The RNA-seq transcript quantification were then mapped to the human genome hg19 with STAR aligner16.
The corresponding gene expression levels were estimated by RSME.
Assembly: hg19
Supplementary files format and content: count values for each sample

source_name: colorectal cancer

extract_protocol:
TruSeq RNA Exome (Illumina)
For fresh frozen and formalin-fixed, paraffin-embedded (FFPE) tissues, the RNA-seq libraries were constructed using total RNA prepared with TruSeq RNA Exome (Illumina).

value: colorectal cancer

value: POLE-mutant/TMB-UH


title: POLE-mutant/TMB-UH_5, CZ2005188S


title: POLE-mutant/TMB-UH_3, CZ2101265S


title: ChIP_THP1_PU1_BRM014_rep1

description: PU.1 ChIP-seq in THP1 cells treated with BRM014

value: Cell Signaling, 2266s


title: Incipient TB_baseline_NPRIB_6540102_SV0

value: Whole Blood

value: Incipient TB/Non-Progressor_baseline

tag: gender

value: Female

value: Positive


title: kidney_ct62_old

source_name: kidney

value: kidney

tag: Sex

value: old


title: CD1-30, Het, iNeuron

tag: cell line


title: ChIP_THP1_MEIS1_DMSO_rep2

value: Abcam, ab19867


title: Incipient TB_followup_NPRIF_5340201_SV12

value: Incipient TB/Non-Progressor_followup

value: Normal

value: Negative


title: Incipient TB_followup_NPRIF_6010107_SV12


title: ChIP_THP1_PU1_BRM014_rep2


title: Incipient TB_baseline_NPRIB_5340204_SV0


title: CD1-29, Het, iNeuron

value: induced neuron

value: SCN2A Het


title: Incipient TB_baseline_NPRIB_6010107_SV0

value: Male


title: ChIP_THP1_MEIS1_BRM014_rep2

description: MEIS1 ChIP-seq in THP1 cells treated with BRM014


title: Incipient TB_baseline_NPRIB_5580103_SV0

value: Abnormal, not TB


title: ChIP_THP1_MEIS1_BRM014_rep1


title: Incipient TB_followup_NPRIF_5490103_SV12


title: CD1-18, Het, iNeuron

value: M


title: MSI-high/TIB-high_12, CZ2100053F

value: colorectal cancer

value: MSI-high/TIB-high


title: PBMC14_HemaCare-D327210 (10X)

city: La Jolla

first: Paola

last: Benaglio

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: University of California San Diego

data_processing:
Fastq files were processed using the 10x Genomics Cell Ranger ATAC v2.0 pipeline. Reads with MAPQ<30, secondary or unmapped reads, and duplicate reads from the resulting bam files were filtered using samtools.
A sparse m x n matrix containing read counts for m nuclei passing a minimum total read depth threshold of 4000 per nucleus at n  genome 5kb windows was generated.
For clustering scanpy (version 1.5) was used: principal component analysis was performed, and the top 50 principal components were used to calculate the nearest 30 neighbors using the cosine metric. This cosine metric was then used to perform UMAP dimensionality reduction clustering with the parameters ‘min_dist=0.3’, along with further sub-clustering using the Louvain clustering algorithm with the parameters ‘resolution=1.25’.
Clusters and sub-clusters with low read depth, low read count, low fraction of reads in peaks, or being doublets were iteratively removed.
Matrices from different samples were combined and the R package harmony (version 0.1.0) (arguments “theta=c(2,2) and “do_pca=FALSE”) was used to perform batch correction, using sample donor as the covariate. Final clustering was performed on the combined matrix.
Peak calling: reads were shifted by +4 bp (positive strand) and -5 bp (negative strand), extended to 200 bp and centered. Peaks were called with MACS2 from the obtained bed files using the parameters ‘-q 0.05’, ‘-nomodel’, ‘-keep-dup all’, ‘-g hs’, and ‘-B’
Assembly: hg19

source_name: peripheral blood mononuclear cells

growth_protocol: Cryopreserved PBMC samples were thawed, resuspended in 1 mL PBS (with 0.04% FBS) and filtered with 50 μm CellTrics

extract_protocol:
Chromium Next GEM Chip H Single Cell Kit
Cells were centrifuged and permeabilized with 100 μl of chilled lysis buffer for 3 min on ice and then washed with 1mL chilled wash buffer. After centrifugation, pellets were resuspended in 100 μL of chilled Nuclei buffer (10x Genomics) in a final concentration of 3,000 to 7,000 of nuclei per μl. 15,300 nuclei (targeting 10,000) were used for each sample.

tag: age

tag: donor id

tag: lot id


title: Incipient TB_baseline_NPRIB_5490103_SV0

value: Whole Blood


title: lung_ct18_old

value: lung

tag: strain

tag: age group


title: lung_ct18_aged

tag: tissue

value: aged


title: CD1-26, Het, iNeuron

tag: cell type

tag: genotype


title: Incipient TB_followup_NPRIF_3690101_SV6

tag: distinct stages of tb

tag: chest x-ray

tag: mtb culture

tag: tst in mm


title: Incipient TB_baseline_NPRIB_5290102_SV0

value: Incipient TB/Non-Progressor_baseline

value: Positive

tag: qft result


title: Incipient TB_followup_NPRIF_5340204_SV12

tag: age in years


title: MSI-high/TIB-high_11, C2000051F


title: POLE-mutant/TMB-UH_4, C2000825S

value: POLE-mutant/TMB-UH


title: kidney_ct62_young

value: kidney

value: young

tag: circadian time


title: MSI-high/TIB-high_10, C2000762S


title: Incipient TB_baseline_NPRIB_5340201_SV0

tag: gender

value: Female

value: Normal


title: Incipient TB_baseline_NPRIB_3690101_SV0

value: Negative


title: ChIP_THP1_input_single_rep1

description: Single cross-link input sample in THP1 cells

tag: cell line

tag: chip antibody

tag: treatment

value: single cross-linking


title: ChIP_THP1_LMO2_BRM014_rep1

value: R&D Systems, AF2726


title: POLE-mutant/TMB-UH_2, CZ2002129S


title: ChIP_THP1_input_single_rep2


title: kidney_ct62_aged

tag: Sex

value: Male


title: PBMC13_HemaCare-D166991 (10X)

tag: age

tag: donor id

tag: lot id


title: Incipient TB_followup_NPRIF_5290102_SV12

tag: tissue

value: Incipient TB/Non-Progressor_followup


title: ChIP_THP1_input_double_rep1

description: Double cross-link input sample in THP1 cells

value: double cross-linking


title: ChIP_THP1_input_double_rep2


title: POLE-mutant/TMB-UH_1, CZ2002267S

value: colorectal cancer

tag: genotype


title: kidney_ct58_young

tag: strain

tag: age group


title: MSI-high/TIB-high_9, CZ2004113S

value: MSI-high/TIB-high


title: PBMC15_HemaCare-D328704 (10X)


title: kidney_ct54_young


title: MSI-high/TIB-high_8, C2000907S


title: kidney_ct58_aged


title: PBMC12_HemaCare-D328701 (10X)


title: PBMC10_HemaCare-D179395 (10X)


title: MSI-high/TIB-high_7, CZ2004238S


title: kidney_ct54_old

value: old


title: Incipient TB_followup_NPRIF_2360105_SV12

value: Whole Blood

tag: distinct stages of tb

tag: chest x-ray

tag: mtb culture


title: Incipient TB_followup_NPRIF_2040105_S12

tag: age in years

tag: tst in mm

tag: qft result


title: kidney_ct50_young

tag: circadian time


title: PBMC8_HemaCare-D327201 (10X)


title: Incipient TB_baseline_NPRIB_2740105_SV0

value: Incipient TB/Non-Progressor_baseline

tag: gender

value: Abnormal, not TB


title: kidney_ct54_aged

value: aged


title: Incipient TB_baseline_NPRIB_2360105_SV0

value: Positive


title: PBMC9_HemaCare-D316208 (10X)


title: MSI-high/TIB-high_6, CZ2100897S


title: Incipient TB_followup_NPRIF_2740105_SV12


title: Incipient TB_baseline_NPRIB_2040105_SV0


title: MSI-high/TIB-high_4, CZ2100117S


title: kidney_ct50_old

value: kidney


title: ATAC_THP1_PMA_rep2

description: ATAC-seq in THP-1 cells treated with PMA

data_processing:
ATAC-seq reads were aligned to the hg38 genome assembly using Bowtie v2.4.1.
Fragments with read qualities greater than 10 were considered for further analysis. 200 bp pseudofragments were created at the positions corresponding to the transposition sites, and peak calls were made using MACS 2.1.2 without modeling of fragment size. Reads within peaks were counted using bedtools.
The table of all counts was processed using DESeq2, using default parameters.
Bigwig files were created based on 200 bp pseudofragments, with intermediate files created using bedtools 2.28.0. All bigWig files are unscaled and require scaling before comparison across samples.
Genome_build: hg38
Supplementary_files_format_and_content: Unscaled bigWig files of genome-wide coverage

treatment_protocol: Cells were treated with either 1 uM BRM014 or an equivalent volume of DMSO for either 24 or 72 h prior to library construction. PMA differentiation of THP-1 cells was performed by addition of 10 nM PMA for 48 h, followed by removal of PMA to allow cells to rest for 24 h.

tag: cell line

value: THP-1 cells

tag: marker

value: WT

tag: treatment

value: PMA


title: Incipient TB_followup_NPRIF_1380102_SV12

value: Normal

value: Negative


title: MSI-high/TIB-high_5, CZ2100171F


title: kidney_ct58_old

tag: Sex

value: Male


title: MSI-high/TIB-high_3, C2000969S


title: ATAC_THP1_DMSO_rep2

description: ATAC-seq in THP-1 cells treated with DMSO

value: DMSO


title: MSI-high/TIB-high_2, C2000166S


title: ATAC_THP1_DMSO_rep1


title: ATAC_THP1_BRM014-72h_rep2

description: ATAC-seq in THP-1 cells treated with BRM014 for 72 h

value: BRM014 for 72 h


title: kidney_ct46_old


title: MSI-high/TIB-high_1, C2000862S

value: colorectal cancer


title: Incipient TB_followup_NPRIF_5580101_SV12

value: Incipient TB/Non-Progressor_followup


title: ATAC_THP1_PMA_rep1


title: Incipient TB_baseline_NPRIB_1380102_SV0


title: kidney_ct46_aged


title: HEKa + Activated [HEKTNFIL173_1]

city: Monroe

first: Jean Christopher

last: Chamcheu

state: Louisiana

address: 1800 Bienville drive

department: Basic Pharmaceutical and Toxicological Sciences

institute: University of Louisiana Monroe

data_processing:
Raw data quality control
Illumina NovaSeq 6000
fastq trimming
Reads mapping to the reference genome
Assembly:  Homo Sapiens  (GRCh38/hg38)
Supplementary files format and content: gene_count.xls

source_name: Human Epidermal Keratinocyte cell line (HEKa)

growth_protocol: Activated with 10ng/mL TNFα+ 20ng/mL IL17A for 24h

extract_protocol:
All groups were harvested in trizol and immidiately transferred to -80℃ fridge.
A magnetic bead system was used to separate messenger RNA from total RNA.  Second strand cDNA was synthesized using either dUTP (for directional library) or dTTP (for non-directional library) after fragmentation. This library was ready for amplification and purification following end repair and A-tailing. We had the directional library ready for amplification and purification after end repair and A-tailing. The library was quantified using Qubit, and the size distribution was detected with a bioanalyzer. Amount of data and effective library concentration will be pooled and sequenced on Illumina platforms.  The index-coded samples were clustered as directed by the manufacturer. These were then sequenced on an Illumina platform to obtain paired-end reads.

treatment_protocol: 3h of pretreatment with fisetin alone or in combination with rapamycin and then activate with 10 ng/mL TNFα+ 20ng/mL IL17A for 24h

tag: cell type

value: Skin cells

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A

value: 10 ng/mL TNFα+ 20ng/mL IL17A


title: Incipient TB_baseline_NPRIB_5580101_SV0

tag: tissue

value: Whole Blood

value: Incipient TB/Non-Progressor_baseline

value: Female

value: Abnormal TB


title: Incipient TB_baseline_NPRIB_4020104_SV0

value: Positive


title: kidney_ct46_young

value: kidney

value: young


title: ATAC_THP1_BRM014-72h_rep1

value: THP-1 cells

value: WT


title: Incipient TB_followup_NPRIF_4020104_SV12

value: Normal

value: Negative


title: kidney_ct42_old

value: Male

value: old


title: kidney_ct42_young


title: ATAC_THP1_BRM014-24h_rep2

description: ATAC-seq in THP-1 cells treated with BRM014 for 24 h

value: BRM014 for 24 h


title: HEKa + Activated + Treatment with Rapamycin 3 [HEKT17_RAP3_1]

value: Skin cells

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A + 100nM Rapamycin

value: 10 ng/mL TNFα+ 20ng/mL IL17A + 100nM Rapamycin


title: HEKa + Activated [HEKTNFIL171_1]

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A

value: 10 ng/mL TNFα+ 20ng/mL IL17A


title: kidney_ct42_aged

value: aged


title: Incipient TB_followup_NPRIF_3550106_SV12

value: Whole Blood

value: Incipient TB/Non-Progressor_followup


title: kidney_ct38_young

value: kidney


title: Incipient TB_baseline_NPRIB_3550106_SV0

value: Incipient TB/Non-Progressor_baseline

value: Abnormal TB

value: Positive


title: ATAC_MV411_DMSO_rep2

description: ATAC-seq in MV-4-11 cells treated with DMSO

source_name: MV-4-11- cells

value: MV-4-11- cells

value: WT

value: DMSO


title: HEKa + Activated + Treatment with Rapamycin 2 [HEKT17_RAP2_1]


title: ATAC_MV411_DMSO_rep1


title: kidney_ct38_old

value: Male

value: old


title: HEKa + Activated + Treatment with Rapamycin 1 [HEKT17_RAP1_1]

value: Skin cells


title: Incipient TB_followup_NPRIF_3310101_SV12

value: Normal

value: Negative


title: kidney_ct38_aged


title: Incipient TB_baseline_NPRIB_3310101_SV0

value: Female


title: ATAC_MV411_BRM014-72h_rep2

description: ATAC-seq in MV-4-11 cells treated with BRM014 for 72 h

value: BRM014 for 72 h


title: HEKa + Activated [HEKTNFIL172_1]

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A

value: 10 ng/mL TNFα+ 20ng/mL IL17A


title: HEKa + Activated + Treatment with Methotrexate 3 [HEKT17_MET3_1]

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A + 1μM Methotrexate

value: 10 ng/mL TNFα+ 20ng/mL IL17A + 1μM Methotrexate


title: ATAC_MV411_BRM014-72h_rep1


title: kidney_ct34_young

value: kidney

value: young


title: ATAC_THP1_BRM014-24h_rep1

value: THP-1 cells

value: BRM014 for 24 h


title: HEKa + Activated + Treatment with Methotrexate 2 [HEKT17_MET2_1]


title: Incipient TB_followup_NPRIF_2330101_SV12

value: Whole Blood

value: Incipient TB/Non-Progressor_followup

value: Positive


title: ATAC_MV411_BRM014-24h_rep2

description: ATAC-seq in MV-4-11 cells treated with BRM014 for 24 h

value: MV-4-11- cells

value: WT


title: kidney_ct34_old

value: Male

value: old


title: kidney_ct34_aged

value: aged


title: HEKa + Activated + Treatment with Methotrexate 1 [HEKT17_MET1_1]

value: Skin cells


title: ATAC_MV411_BRM014-24h_rep1


title: lung_ct22_aged

value: lung


title: Incipient TB_followup_NPRIF_8060102_SV12

value: Normal

value: Negative


title: Incipient TB_baseline_NPRIB_2330101_SV0

value: Incipient TB/Non-Progressor_baseline

value: Abnormal TB


title: ATAC_MOLM13_DMSO_rep2

description: ATAC-seq in MOLM-13 cells treated with DMSO

source_name: MOLM-13 cells

value: MOLM-13 cells

value: DMSO


title: Incipient TB_baseline_NPRIB_8060102_SV0


title: kidney_ct30_young

value: kidney

value: young


title: HEKa + Activated + Treatment with Fisetin 1 [HEKT17_FIS1_1]

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A + 20μM Fisetin

value: 10 ng/mL TNFα+ 20ng/mL IL17A + 20μM Fisetin


title: HEKa + Activated + Treatment with Fisetin 3 [HEKT17_FIS3_1]


title: ATAC_MOLM13_DMSO_rep1


title: HEKa + Activated + Treatment with Fisetin 2 [HEKT17_FIS2_1]


title: kidney_ct30_old


title: HEKa + Activated + Treatment with Fisetin and Rapamycin 2 [HEKT17_FIRA2_1]

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A + 15μM Fisetin + 100nM Rapamycin

value: 10 ng/mL TNFα+ 20ng/mL IL17A + 15μM Fisetin + 100nM Rapamycin


title: Incipient TB_followup_NPRIF_5490104_SV12

value: Whole Blood

value: Incipient TB/Non-Progressor_followup

value: Positive


title: kidney_ct26_young

value: Male


title: kidney_ct26_old

value: old


title: kidney_ct30_aged

value: aged


title: ATAC_MOLM13_BRM014-72h_rep2

description: ATAC-seq in MOLM-13 cells treated with BRM014 for 72 h

value: WT

value: BRM014 for 72 h


title: Incipient TB_baseline_NPRIB_5490104_SV0

value: Incipient TB/Non-Progressor_baseline

value: Female

value: Normal


title: ATAC_MOLM13_BRM014-72h_rep1

value: MOLM-13 cells


title: Incipient TB_followup_NPRIF_5490101_SV12

value: Negative


title: HEKa + Activated + Treatment with Fisetin and Rapamycin 3 [HEKT17_FIRA3_1]

value: Skin cells


title: kidney_ct26_aged

value: kidney


title: ATAC_MOLM13_BRM014-24h_rep2

description: ATAC-seq in MOLM-13 cells treated with BRM014 for 24 h

value: BRM014 for 24 h


title: HEKa + Activated + Treatment with Fisetin and Rapamycin 1 [HEKT17_FIRA1_1]

value: Epilife + 1%HKGS + 1%PEST + TNFα+ IL17A + 15μM Fisetin + 100nM Rapamycin

value: 10 ng/mL TNFα+ 20ng/mL IL17A + 15μM Fisetin + 100nM Rapamycin


title: Incipient TB_baseline_NPRIB_5490101_SV0

value: Whole Blood

value: Abnormal not TB


title: ATAC_MOLM13_BRM014-24h_rep1


title: kidney_ct22_young

value: Male

value: young


title: Incipient TB_followup_NPRIF_4710102_SV12

value: Incipient TB/Non-Progressor_followup

value: Positive


title: HEKa control 3 [HEKCTRL3_1]

value: Epilife + 1%HKGS + 1%PEST


title: HEKa control 2 [HEKCTRL2_1]


title: 3D fibroblasts_3 treated without trehalose

city: Toon

first: Jun

last: Muto

address: Shitsukawa 454

department: Department of Dermatology

institute: Ehime University Graduate School of Medicine

data_processing:
FASTQ files produced by Illimina NEXTSeq were imported to CLC Genomics Workbench software (ver.12.0.3).
Reads with more than 2 ambiguous nucleotides and reads with quality scores less  than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.12.0.3). Long reads with more than 1000 nucleotides and short reads with fewer than 20 nucleotides were also discarded.
The trimmed reads were mapped to the human reference genome GRCh37 release-75 using CLC Genomics Workbench software (ver.12.0.3) with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.12.0.3).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM and TPM values for each sample.

source_name: 3D fibroblasts treated without trehalose

growth_protocol: Normal human epidermal keratinocytes were isolated from normal human skin and cultured under serum-free   conditions, following a previously described method. The cells were used for LSE cultures in their fourth passage. Fibroblasts were isolated from normal human skin and cultured in Dulbecco's modified Eagle medium (DMEM) supplemented with 10% fetal calf serum, and fifth-passage cells were used to construct the LSEs.  (Shirakata Y, Tokumaru S, Yamasaki K, Sayama K, and Hashimoto K. So-called biological dressing effects of cultured epidermal sheets are mediated by the production of EGF family, TGF-beta and VEGF. J Dermatol Sci. 2003;32(3):209-15.)

extract_protocol:
Total RNA was isolated from the fibroblasts or keratinocyte using the RNeasy Mini Kit (Qiagen). Polyadenylated  mRNA was purified with oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs, NEB). Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNextplex Oligos for Illumina.
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences were inserted to cDNA fragments with PCR amplification. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Bioanalyzer. The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina Next-seq DNA sequencer with 75 bp pair-end cycle sequencing kit (Illumina).

treatment_protocol: The method used for LSE preparation was described previously. Briefly, a collagen gel was prepared by mixing six volumes of ice-cold porcine collagen type I solution (Nitta Gelatin) with one volume of 8 × DMEM (Gibco), 10 volumes of 1 × DMEM supplemented with 20% FBS, and one volume of 0.1 N NaOH, of which 1 ml was added to each culture insert (Transwell, Costar) in a six-well culture plate (Costar). Following polymerization of the gel in the inserts at 37°C, two volumes of fibroblast suspension solution 5 × 10e5 cells/ml in 1 × DMEM supplemented with 10% FBS were added to eight volumes of the collagen solution (thus, the final collagen concentration was 0.8 mg/ml). Then, 3.5 ml of the fibroblast-containing collagen solution was applied to each insert. When the fibroblast-containing gel polymerized, DMEM supplemented with 10% FBS and ascorbic acid (final concentration 50 ng/ml) was added with or without trehalose (100 mg/ml). The gel was submerged in culture for 5 days. For 4DF-T1-3 samples, the fibroblasts in the gel with trehalose were harvested after 3 days.  After the fibroblasts contracted the gel, 6 × 10e5 keratinocytes in 60 µl MCDB 153 type II were seeded onto the surface of the contracted gel. The resulting LSE was maintained submerged in culture medium for 2 days. When the keratinocytes reached confluence, the LSE was raised to the air-liquid interface. LSEs were harvested 14 days after airlifting. (Yang L, Shirakata Y, Tamai K, Dai X, Hanakawa Y, Tokumaru S, et al. Microbubble-enhanced ultrasound for gene transfer into living skin equivalents. J Dermatol Sci. 2005;40(2):105-14.)

value: primary fibroblast

value: untreated


title: kidney_ct22_old

value: old


title: kidney_ct50_aged

value: aged


title: 3D fibroblasts_2 treated without trehalose


title: HEKa control 1 [HEKCTRL1_1]


title: 3D fibroblasts_1 treated without trehalose


title: Incipient TB_followup_NPRIF_3720101_SV12

value: Normal


title: Incipient TB_baseline_NPRIB_3720101_SV0

value: Incipient TB/Non-Progressor_baseline

value: Female


title: kidney_ct22_aged

value: kidney


title: Day 30 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 4

city: Melbourne

first: Enzo

last: Porrello

state: Victoria

address: c/o Royal Children’s Hospital

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

description:
mRNA extraction from hPSCCM
mut_d30_rep4

data_processing:
Trimming using the Skewer (version 0.2.2).
Aligned to the human genome (GRCh38.105/hg38) using STAR (version 2.5.3a).
Reads aligning to Ensembl-annotated with a strict mapping quality (Q≥30) were counted with featureCounts (subread 2.0.0).
Genes with > 0.5 counts per million in at least 4 samples were retained for statistical analysis.
Assembly: GRCh38.105/hg38
Supplementary files format and content: Raw counts or filtered counts of sequencing reads.

source_name: stem cell derived cardiomycytes

extract_protocol:
Total RNA was extracted from cells using Trizol reagent and cleaned up with Qiagen RNeasy kit.
Samples were processed at VCGS using Illumina TruSeq stranded mRNA Library Prep kit

value: stem cell derived cardiomycytes

tag: genotype

value: ALPK3 mutant

tag: time point

value: Day 30


title: Day 30 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 3

description:
mRNA extraction from hPSCCM
mut_d30_rep3


title: Incipient TB_followup_NPRIF_3550103_SV12

value: Whole Blood

value: Negative


title: kidney_ct18_old

tag: strain

value: Male

tag: age group


title: kidney_ct18_young

value: young


title: 3D fibroblasts_1 treated with trehalose for 72 hr

source_name: 3D fibroblasts treated with trehalose for 72 hr

value: treated with trehalose for 72 hr


title: Day 30 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 1

description:
mRNA extraction from hPSCCM
mut_d30_rep1


title: Day 30 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 2

description:
mRNA extraction from hPSCCM
mut_d30_rep2


title: Incipient TB_baseline_NPRIB_4710102_SV0

tag: distinct stages of tb

tag: chest x-ray

value: Positive


title: kidney_ct18_aged


title: hypothalamus_ct62_young

source_name: hypothalamus

value: hypothalamus


title: Incipient TB_baseline_NPRIB_3510201_SV0

tag: age in years

value: Abnormal not TB

tag: mtb culture


title: 3D keratinocyte_2 of final LSE without trehalose

source_name: 3D keratinocyte of final LSE without trehalose

value: primary keratinocyte

value: untreated


title: Day 14 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 4

description:
mRNA extraction from hPSCCM
mut_d14_rep4

value: Day 14


title: Incipient TB_followup_NPRIF_3510201_SV12

value: Incipient TB/Non-Progressor_followup

value: Normal

tag: tst in mm

tag: qft result


title: Incipient TB_followup_NPRIF_2990101_SV12


title: hypothalamus_ct62_old

value: old

tag: circadian time


title: Incipient TB_baseline_NPRIB_2990101_SV0

value: Incipient TB/Non-Progressor_baseline

tag: gender


title: hypothalamus_ct62_aged

value: aged


title: 3D keratinocyte_1 of final LSE without trehalose


title: 3D fibroblasts_3 treated with trehalose for 72 hr

value: primary fibroblast


title: Incipient TB_followup_NPRIF_2240101_SV12

value: Whole Blood


title: 3D keratinocyte_3 of final LSE with trehalose

source_name: 3D keratinocyte of final LSE with trehalose

value: treated with trehalose for 14 days


title: 3D keratinocyte_2 of final LSE with trehalose


title: Incipient TB_baseline_NPRIB_3550103_SV0

value: Male


title: 3D fibroblasts_2 treated with trehalose for 72 hr


title: Incipient TB_baseline_NPRIB_2240101_SV0

value: Female


title: 3D keratinocyte_3 of final LSE without trehalose


title: hypothalamus_ct58_old


title: Day 14 ALPK3 mutant hPSC-derived cardiomyocytes - replicate 3

description:
mRNA extraction from hPSCCM
mut_d14_rep3

value: stem cell derived cardiomycytes

value: ALPK3 mutant


title: Day 30 wild-type hPSC-derived cardiomyocytes - replicate 4

description:
mRNA extraction from hPSCCM
wt_d30_rep4

value: wild-type

value: Day 30


title: 3D keratinocyte_1 of final LSE with trehalose


title: hypothalamus_ct58_aged

value: hypothalamus


title: Incipient TB_baseline_NPRIB_1790101_SV0

value: Poistive

value: Positive


title: hypothalamus_ct54_young

value: young