title: Nalm6_WT_Contr_rep2

description:
2379050_Nalm6_WT_baseline_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: WT


title: WholeBlood-MDD-F-503

status: Public on Dec 31 2024

type: SRA

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

library_source: transcriptomic

data_processing:
reads were trimmed using cutadapt v1.18
reads were aligned following the QuickMIRseq pipeline [26] using bowtie v1.2.2 at default parameters
read counts were quantified using HTSeq-count
Assembly: GRCh38.p12
Supplementary files format and content: csv file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

growth_protocol: Not applicable

extract_protocol:
Venous blood passed through LeukoLOCK™ filters (Life Technologies, Ambion), followed by total RNA extraction using ethanol precipitation
MiRNA libraries were prepared using the Bioo Scientific NEXTflex Small RNA-Seq kit v3 (Bioo Scientific), following the manufacturer’s instructions, using 500 ng of total RNA

treatment_protocol: Not applicable

tag: tissue

value: Whole blood

tag: group

value: MDD

tag: Sex

value: Female


title: Bone marrow-derived macrophage-BM_pIL4_K36M3_rep1

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Rd

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Reads were trimmed for quality and adapter sequences using fastp.
Trimmed reads were aligned to the mm10 reference genome using bowtie2.
Aligned reads were deduplicated using Picard.
Peakswere called using MACS2 from the paired endbed file (bedpe) using a false discovery thresh-old of 0.05 (-q 0.05).
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Assembly: mm10
Supplementary files format and content: Normalized bigwig files.

molecule: genomic DNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Wild type, 2-3 months old female C57Bl6 mice were purchased from Jackson laboratories. Mice were sacrificed and bone marrow was isolated form the tibiae and femora of the animals. Red blood cell lysis was carried out and cells were plated in differentiation media containing 10% FBS, Dulbecco’s Modified Eagle’s Medium (DMEM) and 20ng/ml mouse M-CSF (Peprotech). On the third day of differentiation, media was replaced with fresh differentiation media. Cytokine treatments sorting procedures were carried out on the 6th day of differentiation.

extract_protocol:
Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 12 PCR cycles.

treatment_protocol: Macrophages were treated with either IL-4 (20ng/ml) or IFNG (20ng/ml) (Peprotech). For polarization we used 24 hours of IL-4 polarization and 3 hours of IFNG polarization in differentiation media that contained 10% FBS, 1% penicillin/streptomycin and M-CSF (20ng/ml). IL-4 priming was performed as follows: macrophages were polarized with IL-4 (20ng/ml) for 24 hours. Cell were washed three times with serum-free DMEM, then differentiation media was replaced, and cells were rested for an additional 24 hours. Repolarization was performed at this point for 3 hours with IFNG (20ng/ml). Macrophage polarization for cell cycle experiments used 3 hours of polarization with either IL-4 or IFNG (both at a 20ng/ml concentration).

tag: cell type

value: Bone marrow-derived macrophage

tag: strain

value: Bone marrow

tag: genotype

value: wild type

tag: agent

tag: antibody

value: female


title: Bone marrow-derived macrophage-BM_pIL4_K27ac_rep1


title: WholeBlood-MDD-M-513

value: Male


title: WholeBlood-MDD-M-502


title: Bone marrow-derived macrophage-BM_IL4_SMC1A_rep1


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 8

city: Bundoora

first: Christian

last: Aloe

state: VIC

address: Plenty Road

country: Australia

institute: RMIT University

data_processing:
FASTQ files were generated with the Illumina DRAGEN BCL Convert 07.021.609.3.9.3 pipeline
The raw sequencing data was filtered by removing sequencing adapters, and low-quality reads using Trim Galore (v0.6.5)
The cleaned reads were then used in the bioinformatics and statistical analyses.
The cleaned sequence reads were aligned against the Homo sapiens genome (Build version HG38)
The STAR aligner (v2.5.3a) was used to map reads to the genomic sequences
The counts of reads mapping to each known gene were summarised
The transcripts were assembled with the StringTie tool v2.1.4 utilising the reads alignment with hg38 and reference annotation-based assembly option (RABT)
The GENCODE annotation containing both coding and non-coding annotation for human genome version hg38 were used as a guide
Downstream analysis was conducted using RStudio v4.2.2
This was followed by the trimmed mean of M-values (TMM) normalization and differentially expressed genes (DEGs) identification
Assembly: Homo sapiens genome version HG38
Supplementary files format and content: excel of CPM counts
Supplementary files format and content: csv of log normalised counts

source_name: Bronchoalveolar cells

extract_protocol:
RNA was extracted from BALcells using a RNeasy kit (Qiagen, #74106) following the manufacturer’s instructions.
Illumina's TruSeq stranded RNA sample preparation protocol (Illumina, San Diego, California, USA). This protocol includes the following steps: cDNA Synthesis: (Purification of mRNA (via oligo(dT) beads), Fragmentation of mRNA with divalent cations and heat, 1st strand cDNA synthesis (randomly primed), 2nd strand cDNA synthesis; cDNA library preparation: DNA fragment end repair (blunt ending of DNA fragments), 3' Adenylation of DNA fragments, Sequencing adapter ligation (utilizing T-A pairing of adapter and DNA fragments), Amplification of library via PCR

value: Bronchoalveolar cells

value: Complicated Silicosis


title: WholeBlood-MDD-M-509


title: Bone marrow-derived macrophage-BM_pIL4_K27ac_rep2


title: WholeBlood-MDD-F-408


title: Bone marrow-derived macrophage-BM_IL4_NIPBL_rep1

value: NIPBL


title: WholeBlood-MDD-M-504


title: Bone marrow-derived macrophage-BM_IL4_K4M3_rep2


title: miR137OE #6

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

institute: The University of Newcastle

data_processing:
Raw base calls were demultixplexed, subjected to adapter trimming, and converted to fastq format utilising bcl2fastq2 (v.2.20). Lane data for each sample were merged, and per-base sequence quality was assessed via FastQC (v.0.11.8), after which low quality 3´ bases (Phred33 score < 28) and short reads (< 25 nt) were discarded using cutadapt (v.2.10).
Alignment to the reference genome (Rnor_6.0, NCBI) was conducted via HISAT2 (v.2.1.0) and gene-level read counts were obtained using HTSeq (v.0.12.4).
The EdgeR (v.3.36.0) R library was then used to normalise data to library size (counts per million, CPM) and genes with consistently low expression across all libraries were omitted. Samples were then normalised via the trimmed mean of means (TMM) method, dispersion was estimated and variation amongst biological replicates was assessed using multidimensional scaling (MDS) and biological coefficient of variation (BCV) plots.
Assembly: Rnor_6.0, NCBI
Supplementary files format and content: tab-delimited text file containing normalised gene-level read-counts expressed as counts-per-million.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Dorsomedial striatum

growth_protocol: Outbred male Sprague Dawley rats (250–300 g at the time of surgery) were obtained from the Animal Resources Centre (ARC) Western Australia. Rats were housed in pairs on a 12 h light/dark cycle, food, and water ad libitum. All experiments were performed in compliance with Australian Code of Practice for the Care and Use of Animals for Scientific Purposes (University of Newcastle Animal Research Authority 2010-147-420).

extract_protocol:
Animals were deeply anaesthetised and then perfused with ice-cold Diethyl pyrocarbonate (DEPC) treated Phosphate-buffered saline (PBS). Brains were rapidly dissected and flash-frozen using isopentane. RNA was extracted and isolated from tissue samples using TRIzol Reagent as according to manufacturer’s guidelines (Invitrogen, Cat. No. 15596026 and 15596018).
mRNA-Seq was conducted using the Illumina (San Diego, CA, USA) Stranded mRNA Prep, Ligation Kit as per the manufacturer’s instructions. Briefly, 50 ng of total RNA per sample was subjected to poly(A) enrichment via oligo-dT magnetic beads, followed by heat fragmentation and denaturation (94°C, 8 min). Samples were then reverse transcribed, single adenine nucleotides were ligated to cDNA 3´ ends and pre-index anchors were ligated in preparation for dual indexing. cDNA fragments were subsequently amplified via 14 PCR cycles utilising unique dual i7 and i5 indexes (UDP0XXX). The successful production of ~200-600 bp amplicons was validated using an Agilent (Santa Clara, CA, USA) High Sensitivity DNA Kit and Bioanalyzer instrument, after which samples were pooled in equal concentrations and volumes, denatured and diluted. The final pooled library was subjected to 2x151 cycles of paired end sequencing using a NovaSeq6000 instrument and SP v1.5 flow cell.

treatment_protocol: Rats were subjected to bilateral stereotaxic injection of lentivirus pre-miR-137 (HIV-1 derived pMIRNA1/pCDH vector, System Biosciences, 2.97 x 106 Tu/ml) or Control (pCDH empty backbone vector, 7.2 x 106 Tu/ml) into the dorsomedial striatum (AP: -0.3; ML: 2.6; DV: 4.0).

value: Sprague-Dawley rat

value: Dorsomedial striatum

tag: treatment

value: pre-miR-137 lentivirus (dorsomedial striatum)

tag: gender

value: male


title: Bone marrow-derived macrophage-BM_IL4_SMC1A_rep2


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 5


title: miR137OE #4


title: miR137OE #5


title: Nalm6_WT_Contr_rep1

city: Memphis

first: Carolin

last: Escherich

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
2379049_Nalm6_WT_baseline_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

data_processing:
BAM file with duplicate reads marked by GATK, after sequencing reads were mapped to the human genome (GRCh38/hg38) by STAR (version 2.6.0b) and annotation file derived from GENCODE (v31).
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: B-ALL

growth_protocol: RPMI1640 containg 10% FBS

extract_protocol:
total RNA was extracted using Rneasy Mini Kit (Qiagen)
Total RNA library was constructed using an Illumina TrueSeq stranded mRNA library prep kit

treatment_protocol: Inotuzumab Ozogamicin or vehicle control

value: B-ALL

tag: cell line

value: B-lymphoblast

value: control


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 4


title: Bone marrow-derived macrophage-BM_IL4_K4M1_rep2


title: Bone marrow-derived macrophage-BM_pIL4_K4M1_rep1


title: WholeBlood-MDD-M-501

value: Whole blood

value: MDD


title: miR137OE #8


title: Ctrl #4

value: pCDH empty vector lentivirus (dorsomedial striatum)


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 7


title: Ctrl #2


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 6


title: WholeBlood-MDD-F-404

value: Female


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 2


title: Ctrl #1


title: WholeBlood-MDD-M-317


title: WholeBlood-MDD-M-401


title: miR137OE #1


title: WholeBlood-MDD-F-323


title: Bone marrow-derived macrophage-BM_IL4_K4M3_rep1

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type


title: Bone marrow-derived macrophage-BM_IL4_NIPBL_rep2

value: female


title: Ctrl #3


title: Bone marrow-derived macrophage-BM_IL4_K36M3_rep1


title: WholeBlood-MDD-M-322

value: Male


title: miR137OE #3


title: BAL Cells, Silica Exposed, Simple Silicosis, Patient 5

value: Bronchoalveolar cells

value: Simple Silicosis


title: Bone marrow-derived macrophage-BM_IL4_K27ac_rep2


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 1

value: Complicated Silicosis


title: Female SHR EWH5

city: Nanjing

first: Wang

last: Liao

state: Jiangsu

address: No.87 Dingjiaqiao, Hunan Road

country: China

institute: Southeast University

data_processing:
Remove the reads without 3' adapter. Remove the reads without insert fragment. Remove the reads contain too much A/T. Remove the reads which length is out of range. Remove the low-quality reads. Then obtain the clean reads.
The clean reads were mapped to reference genome.
Map reads to mature miRNA and hairping which recorded in miRBase(release 21) to identiy known-miRNA.
DEGseq was used for differential gene expression analysis.
Assembly: rn6
Supplementary files format and content: tpm.txt

source_name: Aorta

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's protocol.
Connecting the 3' adaptor to the total RNA. Connecting the 5' adaptor to the total RNA. RT-PCR. Recycling strips of 138-165bp (15-35nt RNA).

value: Aorta

value: EWH


title: Bone marrow-derived macrophage-BM_IL4_K36M3_rep2


title: WholeBlood-MDD-M-316


title: BAL Cells, Silica Exposed, Simple Silicosis, Patient 6


title: BAL Cells, Silica Exposed, Simple Silicosis, Patient 4


title: WholeBlood-MDD-M-315


title: WholeBlood-MDD-F-314


title: Female SHR EWH3


title: Bone marrow-derived macrophage-BM_CTR_SMC1A_rep1

value: CTR


title: BAL Cells, Silica Exposed, Complicated Silicosis, Patient 3


title: Female SHR EWH6


title: Bone marrow-derived macrophage-BM_CTR_NIPBL_rep2

value: NIPBL


title: BAL Cells, Silica Exposed, Simple Silicosis, Patient 1


title: Female SHR EWH1


title: Bone marrow-derived macrophage-BM_IL4_K4M1_rep1


title: WholeBlood-MDD-M-303


title: Female SHR CNTR6

value: Saline


title: miR137OE #2

value: Sprague-Dawley rat

value: Dorsomedial striatum

value: pre-miR-137 lentivirus (dorsomedial striatum)

value: male


title: Female SHR EWH4


title: BAL Cells, Silica Exposed No Disease, Control Patient 4

value: No Radiological Disease


title: WholeBlood-MDD-F-222

value: Whole blood

value: MDD

value: Female


title: WholeBlood-MDD-M-313

value: Male


title: Bone marrow-derived macrophage-BM_CTR_SMC1A_rep2

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type

value: female


title: BAL Cells, Silica Exposed, Simple Silicosis, Patient 3

value: Bronchoalveolar cells

value: Simple Silicosis


title: BAL Cells, Silica Exposed No Disease, Control Patient 3


title: WholeBlood-MDD-M-311


title: Female SHR CNTR4

value: Aorta


title: BAL Cells, Silica Exposed, Simple Silicosis, Patient 2


title: Female SHR EWH2

value: EWH


title: Bone marrow-derived macrophage-BM_CTR_K4M1_rep2

value: CTR


title: WholeBlood-MDD-M-219


title: Female SHR CNTR2

value: Saline


title: WholeBlood-MDD-F-218


title: WholeBlood-MDD-F-309


title: Bone marrow-derived macrophage-BM_CTR_K4M1_rep1


title: Bone marrow-derived macrophage-BM_CTR_K36M3_rep2


title: Bone marrow-derived macrophage-BM_IL4_K27ac_rep1


title: Bone marrow-derived macrophage-BM_CTR_NIPBL_rep1

value: NIPBL


title: Bone marrow-derived macrophage-BM_CTR_K4M3_rep2


title: BAL Cells, Silica Exposed No Disease, Control Patient 5


title: WholeBlood-MDD-M-302


title: Female SHR CNTR5


title: Human-Patient-Sample 7

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

country: Germany

institute: University Clinics Bonn

data_processing:
Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Assembly: hg38 oder mm10 Ensembl Transcripts release 101
Supplementary files format and content: human_Counts -GSA of gene counts
Supplementary files format and content: human_GSA_results -normalized GSA of transcript counts
Supplementary files format and content: human_Partek_Early_Late_2_Normalization_Normalized_counts -normalized gene counts
Supplementary files format and content: human_Partek_Early_Late_2_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts -gene counts
Supplementary files format and content: Chat-Ribo_ gene counts -GSA of gene counts
Supplementary files format and content: Chat-Ribo_gsa_result -normalized GSA of transcript counts
Supplementary files format and content: Partek_Chat-Ribo-IM3h_Normalization_Normalized_counts -normalized gene counts
Supplementary files format and content: Partek_Chat-Ribo-IM3h_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts -gene counts
Supplementary files format and content: Partek_Chat-Ribo-IM24h_Normalization_Normalized_counts -normalized gene counts
Supplementary files format and content: Partek_Chat-Ribo-IM24h_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts -gene counts

source_name: Small bowel muscularis externa

extract_protocol:
Muscularis externa was prepared from small bowel and subjected to an immunoprecipitation protocol for RiboTag (Leven et al 2021, Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells,  https://doi.org/10.1111/nmo.14309). Input samples were generated from total lysate while IP samples underwent the entire precipitation process and were purified afterwards.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Patient samples were collected during surgeryin ice cold krebs-buffer and processed directly after collection. Muscularis externa was prepared from small bowel and subjected to an immunoprecipitation protocol for RiboTag (Leven et al 2021, Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells,  https://doi.org/10.1111/nmo.14309).

value: Small bowel muscularis externa

value: early


title: ST-12-072_LU_S1

city: Morgantown

first: Pius

last: Joseph

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division/Toxicology and Molecular Biology Branch

institute: National Institute for Occupational Safety and Health (NIOSh)

data_processing:
Reads were quasi-mapped using Salmon v1.1
Each library was run on two different lanes. Each run was quantified separately, resulting in two salmon output archives per sample.
Genome_build: Rnor6
Supplementary_files_format_and_content: Salmon count file
Supplementary_files_format_and_content: samples.txt: text file containing experimental setup

source_name: lung tissue

growth_protocol: The rats were housed in groups of 3 rats/cage and maintained on a 12-hour light-dark cycle in a temperature (68-72oF) and humidity (30-70%) controlled room with free access to filtered tap water and Teklad rodent diet (Envigo, Indianapolis, IN).

extract_protocol:
Total RNA was isolated using the miRNeasy Kit (Qiagen, Inc, Valencia, CA)
Next generation sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc, San Diego, CA)

treatment_protocol: The rats were housed in groups of 3 rats/cage and divided into 4 groups (n=6) and exposed to air (control) tobacco smoke (80 mg/m3, twice weekly, 6 months), crystalline silica (15 mg/m3, 6 hours/day, 5 days) or crystalline silica (15 mg/m3, 6 hours/day, 5 days) followed by tobacco smoke (80 mg/m3, twice weekly, 6 months) by whole-body inhalation (exposure period). Following the 6 months exposure period, all four groups of rats were maintained approximately for an additional 6 months without any further exposure (recovery period).

value: Fischer

value: lung

value: Crystalline Silica + tobacco smoke

value: male


title: Human-Patient-Sample 6

value: late


title: WholeBlood-MDD-F-210

value: Whole blood

value: MDD

value: Female


title: BAL Cells, Chronic Cough, Control Patient 1

value: Bronchoalveolar cells

value: No Radiological Disease

value: Male


title: ST-12-071_LU_S4


title: Bone marrow-derived macrophage-BM_CTR_K27ac_rep1

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type

value: female


title: ST-12-070_LU_S7


title: BAL Cells, Chronic Cough, Control Patient 2


title: Female SHR CNTR3

value: Aorta

value: Saline


title: Human-Patient-Sample 5

value: Small bowel muscularis externa

value: early


title: WholeBlood-MDD-M-215


title: WholeBlood-MDD-F-216


title: Human-Patient-Sample 8


title: Bone marrow-derived macrophage-BM_CTR_K36M3_rep1

value: CTR


title: retina-RKO-ffc-08

city: 广州

first: haoyu

last: zuo

address: 天河区金穗路7号

institute: 中山眼科中心

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Reference genome and gene model annotation files were downloaded from genome website directly.
Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed. Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the GOseq R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used KOBAS software to test the statistical enrichment of differential expression genes in KEGG pathways.
Assembly: Genome_build: mm9
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: retina

extract_protocol:
Total RNA was extracted from retinas using the TRIzol reagent according to the manufacturer’s instruction.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: retina

value: Phb2 flox/flox, RHO-cre


title: Bone marrow-derived macrophage-BM_CTR_K4M3_rep1


title: WholeBlood-MDD-M-207

value: Whole blood


title: ST-12-069_LU_S10

value: Fischer

value: lung

value: Crystalline Silica + tobacco smoke

value: male


title: Human-Patient-Sample 4

value: late


title: retina-RKO-ffc-06


title: WholeBlood-MDD-F-211

value: MDD

value: Female


title: Bone marrow-derived macrophage-BM_CTR_K27ac_rep2

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type


title: Female SHR CNTR1

value: Aorta

value: Saline

value: female


title: retina-RKO-ffc-07


title: ST-12-068_LU_S13


title: Human-Patient-Sample 3

value: Small bowel muscularis externa

value: early


title: WholeBlood-MDD-F-205


title: WholeBlood-MDD-M-202

value: Male


title: Human-Patient-Sample 2


title: Human-Patient-Sample 1


title: WholeBlood-MDD-M-208

value: Whole blood


title: ST-12-66_LU_S19

value: Fischer

value: tobacco smoke


title: ST-12-067_LU_S16

value: lung

value: Crystalline Silica + tobacco smoke


title: ST-12-065_LU_S22

value: male


title: retina-Ctrl-ff-03

value: retina

value: Phb2 flox/flox


title: WholeBlood-Control-F-198

value: Control

value: Female


title: retina-Ctrl-ff-04


title: WholeBlood-Control-M-197


title: retina-Ctrl-ff-02


title: R_D09_T12_CAR

city: Basel

first: Rocio

last: Castellanos Rueda

state: --None--

address: Mattenstrasse 26

department: D-BSSE

country: Switzerland

institute: ETH

data_processing:
Identification of CAR-BC  and 10X barcode using Biostrings R package
Assembly: CAR_barcode_identity.csv
Supplementary files format and content: .csv file containing CAR library identity
Supplementary files format and content: .rds file with preprocessed data of all the samples combined

source_name: T cells

growth_protocol: Primary human T cells derived from healthy donors were activated with CD3/CD28 Dynabeads at 1:1 ratio in T cell growth medium (X-VIVO 15 medium, 5% FBS, 50 μM β-mercaptoethanol,100 U/mL IL2). After 2 days, cells were engineered to integrate a pooled CAR signaling library into the TRAC locus using CRISPR-Cas9 genome editing and cultured in T cell growth medium. TCR-/CAR+ cells were FACS-sorted 6 days later and rested for 6 additional days.

extract_protocol:
Single cell V(D)J enriched library preparation was done following the the Chromium Single Cell V(D)J Reagent Kits User Guide (CG000086 Rev M; 10x Genomics) and sequenced on the Illumina NovaSeq platform.
At days 0, 6 and 12 of the RAS assay, CAR library T cells were co-cultured with SKBR3-GFP cells for 6h in 30 IU/mL of IL-2. Following this time, the co-cultures were stained using DRAQ7, and the live GFP- negative population was sorted using a FACS
In SAMPLE description
scRNA-seq + scCITEseq + scCARseq

treatment_protocol: Repeated antigen stimulation assay: co-culture of library T cells at 1:1 E:T ratio with SKBR3-GFP cells in T cell growth media with 30 U/mL IL2. Every 3 days the co-culture was reset.

tag: sort

value: Live/GFP-

value: T cells

tag: individual

value: Donor 9

tag: time

value: RAS T12

tag: library type

value: scCARseq


title: ST-12-063_LU_S5


title: retina-RKO-ffc-05

value: Phb2 flox/flox, RHO-cre


title: S_D09_T12_CAR


title: ST-12-064_LU_S2


title: T_D09_T12_CAR


title: WholeBlood-Control-F-199


title: WholeBlood-Control-F-196


title: retina-Ctrl-ff-01


title: Q_D09_T0_CAR

value: RAS T0


title: WholeBlood-Control-M-195

value: Whole blood

value: Male


title: Bone marrow-derived macrophage-BMDMCTR_Rep1

data_processing:
Reads were trimmed for quality and adapter sequences using fastQC.
Trimmed reads were aligned to the mm10 reference genome using bowtie2.
Aligned reads were processed with HiC-Pro pipeline
Contact matrices were created with Juicer
Loop calling was performed with Homer
Assembly: mm10
Supplementary files format and content: Normalized contact matrices and chromatin interaction loops

extract_protocol: Hi-C was performed by following the reported HiChIP protocol and omitting the protein immunoprecipitation step42. Briefly, 106 bone marrow-derived macrophages were crosslinked with 1% formaldehyde for 10-minutes. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated in lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0) by rotating the cells for 1-hour at 4C. Nuclear pellet was resuspended in 0.5% SDS solution and incubated at 62C for 10 minutes. SDS was quenched by the addition of 10% Triton-X. Chromatin was digested with 8U of MboI enzyme overnight at 37C. Biotin fill-in was performed for 1-hour at 37C, followed by proximity ligation for 6-hours at room temperature. After proximity ligation, nuclei were subjected to Proteinase K digestion and decrosslinking overnight at 68C. DNA was column purified (Minelute, Qiagen), and sonicated to a size distribution of 200-500bp. DNA was subjected to streptavidin bead binding to pull-down biotinylated DNA that represents ligation junctions. Tn5 was used to create libraries by on bead tagmentation with sequencing adapters, followed by PCR. Libraries were quantified by Qubit and size distribution was assessed with Bioanalyzer.

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type

value: female

value: CTR


title: ST-12-062_LU_S8

value: Fischer

value: lung

value: tobacco smoke

value: male


title: Substantia nigra, SIRT3-overexpressed, rep5

city: Daegu

first: Jun-Yeong

last: Lee

address: Daehak-ro 80, Buk-gu

department: School of Life Sciences

country: South Korea

institute: Kyungpook National University

data_processing:
Alignment, HISAT2 v2.1.0, default options
Read count calculation, HTSeq2 v0.12.4, default options
Normalization and DEG determination, DESeq2 v1.34.0, default options
Assembly: mm10
Supplementary files format and content: txt, normalized read count table

source_name: Substantia nigra

extract_protocol:
Total RNA was isolated from the SN of 3-month-old mice, indicating a month after AAV administration, using TRIzol reagent (Life Technologies, #15596026). The isolated RNA was further purified using the miRNeasy Mini kit (217004, Qiagen Hilden, Germany) following the manufacturer's instructions. The concentration of total RNA was determined using the Quant-IT RiboGreen assay (Invitrogen, #R11490). To evaluate the integrity of the RNA samples, an analysis was performed using the TapeStation RNA screentape (Agilent, #5067-5576). Only high-quality RNA samples with an RNA integrity number (RIN) greater than 7.0 were selected for subsequent RNA library construction.
A library was prepared independently using 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, #RS-122-2101). Briefly, mRNA containing poly‐A tails was purified and collected molecules using poly‐T‐attached magnetic beads. The mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The resulting fragmented RNA was reverse transcribed into first-strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. Subsequently, second-strand cDNA synthesis was performed using DNA Polymerase I, RNase H, and dUTP. These cDNA fragments underwent end repair, followed by the addition of a single 'A' base and ligation of adapters. The products are then purified and enriched with PCR to create the final cDNA library.
The libraries were quantified using KAPA Library Quantification kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, # 5067-5582). The indexed libraries were then submitted for paired-end (2x100 bp) sequencing on an Illumina NovaSeq platform (Illumina, Inc., San Diego, CA) at Macrogen Incorporated (Seoul, Korea).

value: Substantia nigra


title: WholeBlood-Control-F-193

value: Control

value: Female


title: Substantia nigra, SIRT3-overexpressed, rep6


title: Substantia nigra, SIRT3-overexpressed, rep4


title: N_D17_T6_CAR

value: Live/GFP-

value: T cells

value: Donor 17

value: RAS T6

value: scCARseq


title: WholeBlood-Control-F-194

value: Whole blood


title: ST-12-060_LU_S14

value: Crystalline Silica


title: ST-12-059_LU_S17


title: ST-12-058_LU_S20


title: Substantia nigra, SIRT3-overexpressed, rep3


title: O_D09_T0_CAR

value: Donor 9

value: RAS T0


title: WholeBlood-Control-F-192


title: ST-12-057_LU_S23


title: M_D17_T6_CAR


title: WholeBlood-Control-F-191


title: L_D17_T6_CAR

extract_protocol:
Single cell gene expression library preparation was done following the the Chromium Single Cell V(D)J Reagent Kits User Guide (CG000086 Rev M; 10x Genomics) and sequenced on the Illumina NovaSeq platform.
At days 0, 6 and 12 of the RAS assay, CAR library T cells were co-cultured with SKBR3-GFP cells for 6h in 30 IU/mL of IL-2. Following this time, the co-cultures were stained using DRAQ7, and the live GFP- negative population was sorted using a FACS
In SAMPLE description
scRNA-seq + scCITEseq + scCARseq


title: Substantia nigra, SIRT3-overexpressed, rep1


title: Substantia nigra, GFP-overexpressed, rep6

value: AAV-GFP


title: Substantia nigra, SIRT3-overexpressed, rep2


title: ST-12-055_LU_S6

value: Fischer


title: ST-12-056_LU_S3

value: lung


title: P_D09_T0_CAR


title: ST-12-054_LU_S9

value: Air


title: J_D09_T6_CAR


title: WholeBlood-Control-M-190

value: Male


title: WholeBlood-Control-M-189


title: WholeBlood-Control-M-188


title: ST-12-061_LU_S11

value: tobacco smoke

value: male


title: I_D09_T6_CAR


title: Substantia nigra, GFP-overexpressed, rep4

value: Substantia nigra


title: Substantia nigra, GFP-overexpressed, rep5


title: Substantia nigra, GFP-overexpressed, rep3


title: H_D17_T12_CAR

value: Live/GFP-

value: RAS T12


title: WholeBlood-Control-F-187

value: Control

value: Female


title: ST-12-053_LU_S12


title: ST-12-052_LU_S15


title: ST-12-051_LU_S18


title: B_D17_T0_CAR

value: T cells

value: Donor 17

value: scCARseq


title: G_D17_T0_CAR


title: WholeBlood-Control-M-186

value: Whole blood


title: WholeBlood-Control-F-185


title: E_D17_T12_CAR


title: WholeBlood-Control-M-183


title: Substantia nigra, intact, rep6

value: WT


title: A_D17_T0_CAR

value: RAS T0


title: ST-12-050_LU_S21

value: Fischer


title: WholeBlood-Control-F-182


title: Substantia nigra, intact, rep5


title: S_D09_T12_CITE_ADT

description:
S_D09_T12_barcodes.tsv.gz
S_D09_T12_features.tsv.gz
S_D09_T12_matrix.mtx.gz

library_source: other

data_processing:
Allignment and transcript counting: cellranger v6.0.0
Assembly: Feature_reference.csv
Supplementary files format and content: 10x format single cell surface protein expression matrices
Supplementary files format and content: .rds file with preprocessed data of all the samples combined

molecule: protein

extract_protocol:
Single cell surface protein library preparation was done following the the Chromium Single Cell Cell 3’ Reagent Kits v3.1 with Feature Barcode technology for Cell Surface Protein (Dual Index; User guide CG000317 Rev D; 10x Genomics) and sequenced on the Illumina NovaSeq platform.
At days 0, 6 and 12 of the RAS assay, CAR library T cells were co-cultured with SKBR3-GFP cells for 6h in 30 IU/mL of IL-2. Following this time, the co-cultures were stained using DRAQ7, and the live GFP- negative population was sorted using a FACS
In SAMPLE description
scRNA-seq + scCITEseq + scCARseq

value: Donor 9

value: ADT


title: ST_12_48_S47_L001

data_processing:
Reads were quasi-mapped using Salmon v1.1
Genome_build: Rnor6 (transcriptome)
Supplementary_files_format_and_content: Salmon count file (.sf) and metadata

extract_protocol:
Total RNA was isolated using the miRNeasy Kit (Qiagen, Inc, Valencia, CA)
next generation sequencing libraries prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc, San Diego, CA)

treatment_protocol: The rats were divided into 4 groups (n=6) and exposed to air (control) tobacco smoke (80 mg/m3, twice weekly, 12 months), crystalline silica (15 mg/m3, 6 hours/day, 5 days) or crystalline silica (15 mg/m3, 6 hours/day, 5 days) followed by tobacco smoke (80 mg/m3, twice weekly, 12 months) by whole-body inhalation.

value: lung

value: crystalline silica + tobacco smoke


title: WholeBlood-Control-M-181

value: Male


title: Substantia nigra, intact, rep4

value: Substantia nigra


title: Substantia nigra, GFP-overexpressed, rep2

value: AAV-GFP


title: ST_12_47_S41_L001


title: ST-12-049_LU_S24

value: Air

value: male


title: Q_D09_T0_CITE_ADT

description:
Q_D09_T0_barcodes.tsv.gz
Q_D09_T0_features.tsv.gz
Q_D09_T0_matrix.mtx.gz

value: Live/GFP-


title: Substantia nigra, intact, rep2


title: T_D09_T12_CITE_ADT

description:
T_D09_T12_barcodes.tsv.gz
T_D09_T12_features.tsv.gz
T_D09_T12_matrix.mtx.gz

value: T cells

value: RAS T12


title: Substantia nigra, GFP-overexpressed, rep1


title: WholeBlood-Control-M-179

value: Control


title: WholeBlood-Control-F-180

value: Whole blood

value: Female


title: WholeBlood-Control-F-184


title: ST_12_45_S29_L001


title: P_D09_T0_CITE_ADT

description:
P_D09_T0_barcodes.tsv.gz
P_D09_T0_features.tsv.gz
P_D09_T0_matrix.mtx.gz

value: RAS T0


title: WholeBlood-Control-F-178


title: R_D09_T12_CITE_ADT

description:
R_D09_T12_barcodes.tsv.gz
R_D09_T12_features.tsv.gz
R_D09_T12_matrix.mtx.gz


title: O_D09_T0_CITE_ADT

description:
O_D09_T0_barcodes.tsv.gz
O_D09_T0_features.tsv.gz
O_D09_T0_matrix.mtx.gz


title: WholeBlood-Control-M-177


title: ST_12_43_S17_L001


title: P21_LIN28A.positive_cKO 2.1

city: Pullman

first: Nathan

middle: C

last: Law

state: WA

address: 100 Dairy Road

department: School of Molecular Biology

institute: Washington State University

description: NanoString WTA generated from mouse testis cross-section

data_processing:
Raw sequencing reads were demultiplexed and probe counts corresponding to each gene were quantified using the NanoString GeoMX NGS Pipeline (v. 2.3.3.10).
Count matrices were then analyzed in R software (v. 4.3.0) using the GeomxTools package (v. 3.4.0).
Low-quality libraries were omitted from downstream analysis by selecting libraires with a Gene Detection Rate >= 1-5%.
Assembly: NanoString Mouse NGS Whole Transcriptome Atlas RNA (v1.0)
Supplementary files format and content: .dcc files contain probe counts
Supplementary files format and content: Annotation files (xlsx) contain genotype, ROI, segment, and QC information corresponding to each library.
Supplementary files format and content: .ini index files for each developmental age (P6 and P21)
Supplementary files format and content: .stats files contain segment QC statistics
Library strategy: GeoMx

source_name: testis

extract_protocol:
Sections from each tissue were generated at 5 μm thickness and prepared according to NanoString GeoMx NGS FFPE protocol with minor modifications. Briefly, slides were incubated at 60°C for 30-60 minutes. Then, slides were sequentially incubated for 5 mins in xylene three times, 100% EtOH two times, 95% EtOH one time, and 1X PBS one time. To retrieve the target antigen, hydrated slides were first placed in 95°C DEPC H2O for 10 seconds, followed by 99-100°C 1X Tris-EDTA (pH 9.0) for 20 mins. Slides then washed in 1X PBS for 5 mins and incubated in 0.1ug/mL proteinase K for 15 mins at 37°C. Slides were then washed for 5 mins in 1X PBS one time, 10% neutral buffered formalin (NBF) one time, NBF stop buffer (0.1M Tris EDTA, 0.01M Glycine) two times, and another 1X PBS once. For in situ hybridization, 200μL of Buffer R, 25μL of WTA probe mix, and 25μL of DEPC H2O were added per slide. The slides were covered with a glass coverslip and incubated overnight in a humidity chamber at 37°C. The next day, slides were briefly submerged in 2X saline-sodium citrate buffer (SSCB). Then, off-target probes were removed using stringent wash solution (equal part formamide and 4X SSCB) twice at 37°C for 25 mins each, followed by 2X SSCB two times for 2 mins each. Blocking was done by adding 200uL of Buffer W per slide and incibated inside a humidity chamber for 30 mins. Buffer W was then removed from the slide and replaced with unconjugated primary antibodies and SYTO13 mixture that was diluted to the appropriate concentration using Buffer W and incubated in a humidity chamber for 1 hr at RT. Slides were then quickly washed with 2x SSCB twice, followed by 3 mins 2x SSCB washes three times. Slides were then incubated with secondary antibodies diluted in Buffer W for 30 min at RT in a humidified chamber. Slides were then washed 2x in SSCB buffer and directly imaged for RNA collection using a NanoString GeoMx Digital Spatial Profiler (DSP) and GeoMx DSP Control center software (v. 3.0.0.109). For overall gene expression signatures between control and cKO, three circular regions of interest (ROIs) of approximately 600-650 mm in diameter were randomly placed over three different cross-sections of each animal for technical replication. For phenotype-specific regions, tubules were grouped based on containing only a single layer of spermatogonia or containing an incomplete compliment of spermatocytes within the tubule cross-sections. ROIs were then segmented to capture undifferentiated spermatogonia or advanced germ cells separately by thresholding fluorescent signal corresponding to SYTO13+LIN28A+DDX4+ and SYTO13+LIN28A-DDX4+ within each ROI. A minimum of 50 nuclei were captured within each segmented population.
cDNA libraries were generated according to the manufacturers protocol.
NanoString WTA

value: testis

tag: lin28a status

value: cKO

tag: age


title: N_D17_T6_CITE_ADT

description:
N_D17_T6_barcodes.tsv.gz
N_D17_T6_features.tsv.gz
N_D17_T6_matrix.mtx.gz

value: Donor 17

value: RAS T6

value: ADT


title: WholeBlood-Control-M-175

tag: tissue

value: Male


title: P21_LIN28A.positive_Control 1.1


title: WholeBlood-Control-F-174

tag: group


title: Substantia nigra, intact, rep3

value: Substantia nigra

value: WT


title: ST_12_46_S35_L001

value: lung

value: crystalline silica + tobacco smoke


title: M_D17_T6_CITE_ADT

description:
M_D17_T6_barcodes.tsv.gz
M_D17_T6_features.tsv.gz
M_D17_T6_matrix.mtx.gz

value: Live/GFP-


title: P21_LIN28A.positive_Control 1.2


title: ST_12_35_S5_L001

value: tobacco smoke


title: L_D17_T6_CITE_ADT

description:
L_D17_T6_barcodes.tsv.gz
L_D17_T6_features.tsv.gz
L_D17_T6_matrix.mtx.gz

value: T cells


title: ST_12_34_S45_L001


title: J_D09_T6_CITE_ADT

description:
J_D09_T6_barcodes.tsv.gz
J_D09_T6_features.tsv.gz
J_D09_T6_matrix.mtx.gz

value: Donor 9


title: WholeBlood-Control-F-173

value: Whole blood

value: Control

tag: Sex


title: WholeBlood-Control-M-171


title: Substantia nigra, intact, rep1


title: P21_LIN28A.positive_Control 2.1


title: ST_12_33_S39_L001


title: P21_LIN28A.positive_cKO 2.3


title: I_D09_T6_CITE_ADT

description:
I_D09_T6_barcodes.tsv.gz
I_D09_T6_features.tsv.gz
I_D09_T6_matrix.mtx.gz

tag: cell type


title: ST_12_44_S23_L001


title: ST_12_32_S33_L001


title: WholeBlood-Control-M-170


title: H_D17_T12_CITE_ADT

description:
H_D17_T12_barcodes.tsv.gz
H_D17_T12_features.tsv.gz
H_D17_T12_matrix.mtx.gz

value: RAS T12


title: P21_LIN28A.positive_cKO 2.2

value: testis


title: WholeBlood-Control-F-169

value: Female


title: ST_12_31_S27_L001


title: P21_LIN28A.positive_cKO 1.3

value: cKO


title: ST_12_36_S11_L001


title: P21_LIN28A.positive_Control 2.3


title: WholeBlood-Control-F-168


title: E_D17_T12_CITE_ADT

description:
E_D17_T12_barcodes.tsv.gz
E_D17_T12_features.tsv.gz
E_D17_T12_matrix.mtx.gz

value: Donor 17


title: ST_12_24_S21_L001

value: crystalline silica


title: G_D17_T0_CITE_ADT

description:
G_D17_T0_barcodes.tsv.gz
G_D17_T0_features.tsv.gz
G_D17_T0_matrix.mtx.gz

value: RAS T0

value: ADT


title: WholeBlood-Control-F-167


title: B_D17_T0_CITE_ADT

description:
B_D17_T0_barcodes.tsv.gz
B_D17_T0_features.tsv.gz
B_D17_T0_matrix.mtx.gz


title: ST_12_23_S15_L001


title: WholeBlood-Control-M-166

value: Male


title: P21_LIN28A.positive_Control 2.2


title: P21_LIN28A.positive_Control 1.3


title: A_D17_T0_CITE_ADT

description:
A_D17_T0_barcodes.tsv.gz
A_D17_T0_features.tsv.gz
A_D17_T0_matrix.mtx.gz


title: ST_12_22_S9_L001

value: lung


title: WholeBlood-Control-F-165


title: ST_12_21_S3_L001


title: P21_LIN28A.positive_Diff Pheno 3


title: T_D09_T12_GEX

library_source: transcriptomic single cell

data_processing:
Allignment and transcript counting: cellranger v6.0.0
Assembly: GRCh38
Supplementary files format and content: 10x format single cell gene expression matrices
Supplementary files format and content: .rds file with preprocessed data of all the samples combined

extract_protocol:
Single cell gene expression library preparation was done following the the Chromium Single Cell Cell 3’ Reagent Kits v3.1 with Feature Barcode technology for Cell Surface Protein (Dual Index; User guide CG000317 Rev D; 10x Genomics) and sequenced on the Illumina NovaSeq platform.
At days 0, 6 and 12 of the RAS assay, CAR library T cells were co-cultured with SKBR3-GFP cells for 6h in 30 IU/mL of IL-2. Following this time, the co-cultures were stained using DRAQ7, and the live GFP- negative population was sorted using a FACS
In SAMPLE description
scRNA-seq + scCITEseq + scCARseq

value: GEX


title: WholeBlood-Control-M-162

extract_protocol:
Venous blood passed through LeukoLOCK™ filters (Life Technologies, Ambion), followed by total RNA extraction using ethanol precipitation
MiRNA libraries were prepared using the Bioo Scientific NEXTflex Small RNA-Seq kit v3 (Bioo Scientific), following the manufacturer’s instructions, using 500 ng of total RNA


title: WholeBlood-Control-F-161


title: R_D09_T12_GEX

value: Live/GFP-


title: S_D09_T12_GEX

description:
S_D09_T12_barcodes.tsv.gz
S_D09_T12_features.tsv.gz
S_D09_T12_matrix.mtx.gz


title: ST_12_19_S37_L001

value: Crystalline Silica


title: WholeBlood-Control-F-160


title: ST_12_20_S43_L001


title: P21_LIN28A.positive_Diff Pheno 2


title: ST_12_12_S31_L001

value: Air


title: P21_LIN28A.positive_cKO 1.2


title: WholeBlood-Control-F-158


title: P21_LIN28A.positive_cKO 1.1


title: WholeBlood-Control-F-159


title: WholeBlood-Control-F-157


title: P21_LIN28A.positive_Spg Pheno 3


title: P21_LIN28A.positive_Spg Pheno 1


title: P_D09_T0_GEX

value: T cells

value: Donor 9


title: ST_12_10_S19_L001


title: O_D09_T0_GEX


title: N_D17_T6_GEX

value: RAS T6


title: ST_12_09_S13_L001


title: WholeBlood-Control-F-155

value: Whole blood

value: Control


title: P21_LIN28A.positive_Diff Pheno 1

value: testis


title: P21_LIN28A.positive_Spg Pheno 2

value: cKO


title: ST_12_08_S7_L001


title: L_D17_T6_GEX

value: Donor 17


title: M_D17_T6_GEX


title: Q_D09_T0_GEX

description:
Q_D09_T0_barcodes.tsv.gz
Q_D09_T0_features.tsv.gz
Q_D09_T0_matrix.mtx.gz


title: P21_LIN28A.positive_Diff Pheno 4


title: WholeBlood-Control-M-152


title: ST_12_07_S1_L001


title: J_D09_T6_GEX


title: P21_LIN28A.negative_Control 2.1


title: set-9(red8);set-26 (tm3526), rep2, small RNA-seq

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
RPKM values were calculated for all protein coding genes.
bigwig files were calculated using the "bamCoverage" tool with "--binSize 10 --normalizeUsing RPKM --filterRNAstrand forward (or reverse)" parameters
Assembly: WS190(ce6)
Supplementary files format and content: bigwig files
Supplementary files format and content: set9set26_RNA_sRNA_bayseq.xlsx (see SuperSeries)

organism: Caenorhabditis elegans

source_name: dissected gonads

growth_protocol: C. elegans were cultured on NGM plates with OP50 at 20ºC.

extract_protocol:
RNA was extracted by using TRIZOL, phenol, and chloroform. DNase I was used to remove DNA.
Ligation-based sRNA-seq, 5’-linker ligation is independent of the 5’-mono phosphate of the small RNAs, 5' barcodes: mixture of AGCG, CGTC, GTTA, TATG
small RNA-seq

value: dissected gonads


title: WholeBlood-Control-F-151

data_processing:
reads were trimmed using cutadapt v1.18
reads were aligned following the QuickMIRseq pipeline [26] using bowtie v1.2.2 at default parameters
read counts were quantified using HTSeq-count
Assembly: GRCh38.p12
Supplementary files format and content: csv file includes raw counts for each sample

value: Female


title: WholeBlood-Control-M-154


title: P21_LIN28A.negative_Control 2.2


title: set-9(red8);set-26 (tm3526), rep1, small RNA-seq


title: WholeBlood-Control-F-150


title: P21_LIN28A.negative_cKO 1.1


title: set-26 (tm3526), rep2, small RNA-seq


title: H_D17_T12_GEX

value: RAS T12


title: WholeBlood-Control-M-149

value: Male


title: ST_12_11_S25_L001

value: lung


title: set-26 (tm3526), rep1, small RNA-seq


title: G_D17_T0_GEX

value: RAS T0

value: GEX


title: P21_LIN28A.negative_cKO 2.3


title: set-9 (red8), rep2, small RNA-seq

value: set-9 (red8)


title: B_D17_T0_GEX

value: Live/GFP-


title: WholeBlood-Control-F-145


title: A_D17_T0_GEX

value: T cells


title: P21_LIN28A.negative_Control 1.1


title: P21_LIN28A.negative_Control 1.3


title: set-9 (red8), rep1, small RNA-seq


title: RMK0138C_CFC2_line, day 31 diff, rep6 [2023A427]

city: Marseille

first: Heather

last: Etchevers

address: 27 boulevard Jean Moulin

department: INSERM U1251

institute: INSERM/Aix-Marseille Univ

data_processing:
The quality of sequencing reads was assessed using fastQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw sequencing reads were aligned on the human reference genome GRCh38 using STAR (v2.7.2b). Bam files were indexed and sorted using Samtools (v1.7). After mapping, the number of reads per feature ( GENCODE v34 annotations) was determined using StringTie v2.1.6.
Genes differentially expressed between conditions were identified using a Wald test in the DESeq2 package (v1.34.0). Transcripts with an adjusted P-value for FDR (False Discovery Rate) below 0.05 were assigned as significantly differentially expressed.
Assembly: GRCh38
Supplementary files format and content: Tab-separated text, gene count matrix

extract_protocol:
For pellets of wild-type (WT) or BRAF Q257R/+ human induced pluripotent stem cell (hiPSC)-derived uncommitted Schwann cell precursors (SCP, at P18) or engaged SCP (at P31), total RNA was extracted using the NucleoSpin RNA Plus S kit (#740984; Macherey-Nagel). RNA concentrations were measured using a NanoDrop TM 1000 Spectrophotometer (Thermo Fisher Scientific).
Librairies were constructed following the instructions of the KAPA mRNA HyperPrep kit (Roche, #KR1352-v7.21) using 1 μg total RNA. After conversion to cDNA, librairies were multiplexed after ligation of a 6 basepair index and PCR amplification. Quality and quantity of librairies were assessed individually before multiplexing using a Bioanalyzer High Sensitivity DNA microfluidics chip (Agilent Technologies) and quantified spectrophotometrically on a Qubit™ using the dsDNA High Sensitivity Kit (Thermofisher). Normalized equimolar quantities of cDNA librairies were loaded using a total of 400 pM on an Illumina NovaSeq 6000 using a SP flowcell.
RNA-seq for Differential Gene Expression, 25 M paired-end sequences, 2*101 basepair reads per sample

treatment_protocol: All cell lines underwent the same differentiation protocol. Most cells were differentiated along the same 90-day protocol ("diff1") in independent wells, with lysis of one triplicate on d18 and another from the same plate on d31.  The RMK0138C line was re-differentiated a second time from frozen hiPSC in parallel with a third control cell line, not sampled for RNA-sequencing ("diff2").

value: immature Schwann-like

value: BRAF Q257R


title: WholeBlood-Control-M-143

value: Whole blood


title: WholeBlood-Control-M-146

value: Control


title: I_D09_T6_GEX

value: Donor 9

value: RAS T6


title: P21_LIN28A.negative_Control 1.2

value: testis


title: WholeBlood-Control-M-144


title: WT, rep 2, small RNA-seq

value: dissected gonads

value: WT


title: WT,  rep 1, small RNA-seq


title: set-9(red8);set-26 (tm3526), rep2, RNA-Seq

extract_protocol:
RNA was extracted by using TRIZOL, phenol, and chloroform. DNase I was used to remove DNA. rRNA was depleted using anti-rRNA DNA oligoes and RNase H.
RNA libraries were made by using SMARTer Stranded Total RNA-Seq Kit (Takara).
SMARTer Stranded Total RNA-Seq


title: P21_LIN28A.negative_cKO 2.2

value: cKO


title: RMK0138C_CFC2_line, day 31 diff, rep5 [2023A426]


title: WholeBlood-Control-M-142

value: Male


title: P21_LIN28A.negative_cKO 1.3


title: P21_LIN28A.negative_Control 2.3


title: set-9(red8);set-26 (tm3526), rep1, RNA-Seq


title: RMK0138C_CFC2_line, day 31 diff, rep4 [2023A425]


title: WholeBlood-Control-F-141

value: Female


title: E_D17_T12_GEX

value: Donor 17

value: RAS T12


title: WholeBlood-Control-M-147


title: set-26 (tm3526), rep2, RNA-Seq


title: P21_LIN28A.negative_cKO 1.2


title: RMK0138C_CFC2_line, day 31 diff, rep3 [2023A424]


title: WholeBlood-Control-M-140


title: WholeBlood-Control-F-139


title: P21_LIN28A.negative_Diff Pheno 1


title: set-9 (red8), rep2, RNA-Seq

value: set-9 (red8)


title: RMK0138C_CFC2_line, day 31 diff, rep1 [2023A422]


title: RMK0056C_CFC1_line, day 31 diff, rep3 [2023A421]


title: P21_LIN28A.negative_Diff Pheno 3


title: set-9 (red8), rep1, RNA-Seq


title: P21_LIN28A.negative_cKO 2.1


title: WholeBlood-Control-M-138


title: WholeBlood-Control-F-137


title: P21_LIN28A.negative_Diff Pheno 4


title: RMK0056C_CFC1_line, day 31 diff, rep2 [2023A420]


title: set-26 (tm3526), rep1, RNA-Seq


title: WT, rep 2, RNA-Seq


title: P21_LIN28A.negative_Diff Pheno 2


title: RMK0056C_CFC1_line, day 31 diff, rep1 [2023A419]


title: AG08H control clone, day 31 diff, rep3 [2023A418]

value: BRAF WT


title: P6_LIN28A.positive_Neg

value: Background


title: P6_LIN28A.positive_cko2.3


title: AG08H control clone, day 31 diff, rep2 [2023A417]

value: immature Schwann-like


title: WholeBlood-Control-M-133


title: RMK0138C_CFC2_line, day 31 diff, rep2 [2023A423]

value: BRAF Q257R


title: P6_LIN28A.positive_cko3.1


title: WholeBlood-Control-F-136

value: Whole blood


title: hFF15 control clone, day 31 diff, rep2 [2023A415]


title: P6_LIN28A.positive_Het1.1

value: Control


title: Library_6_rep_2

city: Albuquerque

first: Christos

last: Argyropoulos

state: New Mexico

address: 1 University of New Mexico MSC 04-2785

department: Internal Medicine

institute: University of New Mexico

description:
ERCC (10.4 fmoles)
PAP
Flow Cell Used: FLO-FLG001  There are two processed files  in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. A 2nd ERCC source was used for these experiments (stored at -20oC)

data_processing:
Custom bioinformatics workflow in python to identify the adaptors and classify reads as well formed (adapters present at both 5' and 3' end), naked (no adapters could be identified) , fusion (multiple adapters that did not conform to a well formed read) and partial (only one adapter either a 5' or 3' could be identified in the data)
Adapters were identified by blastn searches, and an adapter was considered to be present if at least 80% of its sequence was present in the read at an epsilon value of 0.001 or less. After mapping, adapters were trimmed from within python
Reorientation of the reads to identify those sequenced from the 3'->5' direction took place using the adapter orientation
PolyA trimming took place by custom regular expression matches using python's regex module
Inserts (defined as the part of the read surviving the trimming of adapters and polyA tails were mapped to the reference database using blastn. Identification required an e-value of 0.001 or less, and the top scoring alignment (smallest e-value) was assigned to each read
Assembly: a) Mmusculus.39.cDNAncRNA that included  all non-coding RNAs and cDNAs from the Genome Reference Consortium Mouse Build 39  b) Mmusculus.39.cDNAncRNA_spike that enhanced the mouse database with the sequences of the ERCC spike-in mix c) ERCC+10 microRNAs and d) ERCC + entire miRbase
Supplementary files format and content: Tab separated file which contains the counts for each RNA species identified, the type of RNA insert and the quality of the run
Supplementary files format and content: Each library was mapped to multiple databases to explore the false positives and negatives by each technique

organism: synthetic construct

source_name: synthethic sample

growth_protocol: Mice were housed in humidity-, temperature-, and light/dark-controlled rooms and cared for by trained individuals according to the Institutional Animal Care and Use Committees (IACUC) approved-protocols at the University of Cincinnati and the University of New Mexico.

extract_protocol:
Synthetic RNA in water for the synthetic libraries.  Jejunal RNA was extracted using the TRI Reagent method (Molecular Research Center; Cincinnati, OH). RNA samples were stored at -80o C until needed for Illumina sequencing.
Library construction followed Nanopore's instruction for the SQKPCS109  kit, except for samples that included a poly-adenylation step. Those samples were subjected to a 15 PAP reaction, followed by cold inactivation of the PAP enzyme. Then the entire product was used as input to the SQKPCS109  protocol without an intermediate cleanup. Biological samples were subjected to a PAP step, except for those designated as "R10" : they were processed with the unmodified Nanopore protocol. Number of PCR cycles: biological samples subjected to the unmodified Nanopore protocol :10, Biological samples subjected to PALS-NS : 18, , Libraries 1-4 & Libraries 1-5 (up to 10 fold dilution) : 15, Library 5 100fold diluted 19, Library 5 1000 fold diluted 22
RNAseq with or without an optional polyadenylation step. Synthetic libraries were made under conditions of sham polyadenylation, in which all the re-agents for the reaction except the PAP enzyme were included in the mix. These sham polyadenylated samples were subjected to the same conditions (incubation and cold treatment) as their PAP counterparts.

treatment_protocol: Mice were fed either a carbohydrate control or 60% fructose diet (Envigo, Indianapolis, IN) for 5 weeks.  Mice were euthanized with an overdose of pentobarbital sodium and jejunum were harvested, cleaned of dietary material, snap frozen and stored at -80o C.

value: synthethic sample


title: P6_LIN28A.positive_Het1.3


title: WholeBlood-Control-F-132


title: WholeBlood-Control-F-131


title: RMK0138C_CFC2_line, day 18 diff, rep6 [2023A413]

value: Schwann cell precursor-like


title: Library_6_rep_1


title: hFF15 control clone, day 31 diff, rep1 [2023A414]


title: WholeBlood-Control-F-130


title: C666-1 MCL-1 cell line, Guide2, slide1

type: RNA

city: Gelugor

first: Nethia

last: Mohana Kumaran

state: Penang

address: Persiaran Sains

department: School of Biological Sciences

country: Malaysia

institute: Universiti Sains Malaysia

description: Gene expression

hyb_protocol: 0.825μg of Cy3-labeled cRNA with specific activity =/>6 pmol Cy3/ug cRNA was fragmented at 60 °C for 30 min in a reaction volume of 25 μL containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent following the manufacturers’ instructions. After fragmentation step, 25μl of the mixture were then combined with 25ul of 2× Hi-RPM Hybridization Buffer and immediately hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K (Design ID: 072363) for 17 hours at 65 °C in a rotating Agilent microarray hybridization oven. After hybridization, microarrays were washed for 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 min with 37 °C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were immediately scanned using Agilent SureScan Microarray Scanner (G4900DA) with 3 μm resolution at wavelengths of 532 nm (Cy3) using the extended dynamic range (10–100 %) setting.

data_processing: Normalized intensities were extracted using the Agilent Feature Extraction 11.5.1.1 Software with protocol GE1_1200_Jun14.

source_name: C666-1 MCL-1 cell line, Guide2

label_protocol: The concentration of all RNA samples were normalized to 50ng before the preparation of Cyanine-3 (Cy3) labeled cRNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent, Valencia, Ca) according to manufacturer’s instructions. Cy3 labeled cRNA was then purified by RNeasy Mini Kit (Qiagen, Valencia, CA) to purify the amplified cRNA samples. Dye incorporation and cRNA yield were checked with the NanoVue™ Plus Spectrophotometer (GE Healthcare, UK).

growth_protocol: The cells were cultured in RPMI-complete media and incubated in a humidified incubator at 37°C with 5% carbon dioxide.

extract_protocol: Cells were trypsinized and centrifuged at 500 g (Sigma 3-16PK, rotor number:12171) for 5 minutes. The cell pellet was washed with 1X PBS and re-centrifuged at the same speed for another 5 minutes. The PBS (supernatant) was removed and 1 ml of TRIzol was added to the cell pellet and re-suspended several times for the cells to undergo complete lysis. The mixture was incubated at room temperature for 5 minutes. Next, 0.2 ml of chloroform was added to the mixture and the tubes were inverted vigorously for about 15 seconds. The tubes were then incubated at room temperature for 5 minutes. After 5 minutes, the samples were centrifuged at 12000 g (Sigma 3-16PK, rotor number:12171) for 15 minutes at 4 °C. Phase separation was observed. Approximately, 0.45 ml of the uppermost layer (RNA) was transferred into a new 1.5 ml tube. Equal volume of isopropanol was added to each tube and mixed well. The mixture was then incubated at room temperature for 5 minutes prior to centrifugation at 12000 g (Sigma 3-16PK, rotor number:12171) for 5 minutes. The supernatant was removed and the pellet was re-suspended in 1 ml of ice cold 75% (v/v) ethanol and re-pelleted at 7500 g (Sigma 3-16PK, rotor number:12171) for 5 minutes at 4 °C. Next, the RNA pellet was air dried at room temperature for 3-5 minutes and dissolved in 30 μl nuclease free water. The RNA yield and purity of the total extracted RNA, were assessed using the Nanodrop 1000TM. Absorbance of the sample was measured at 260 nm and 280 nm wavelengths and the 260/280 ratio was used to assess RNA purity. The RNA samples were considered pure when the 260/280 ratio fall between 1.8-2.0.

value: MCL-1 knockout


title: C666-1 wildtype cell line, slide1

description: Gene expression

source_name: C666-1 cell line

value: Wildtype


title: WholeBlood-Control-M-135


title: WT,  rep 1, RNA-Seq

value: dissected gonads

value: WT


title: Library_5_dilut1000_rep_2

description:
LiM+HiM+ERCC , mix of 0.047 fmole microRNA (in high and low concentrations differing by two fold) and 0.01 fmole ERCC
PAP
Flow Cell Used: FLO-FLG001 .  There are two processed files  in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. Batch of ERCC stored at -20oC


title: WholeBlood-Control-F-129


title: WholeBlood-Control-F-134


title: RMK0138C_CFC2_line, day 18 diff, rep5 [2023A412]


title: WholeBlood-Control-F-127


title: Library_5_dilut1000_rep_1


title: RMK0138C_CFC2_line, day 18 diff, rep4 [2023A411]


title: P6_LIN28A.positive_Het3.2

value: testis


title: AG08H control clone, day 31 diff, rep1 [2023A416]


title: WholeBlood-Control-F-126

value: Female


title: HK-1 MCL-1 knockout cell line, Guide2, slide1

description: Gene expression

source_name: HK-1 MCL-1 knockout cell line, Guide2


title: P6_LIN28A.positive_Het2.1


title: Library_5_dilut100_rep_2

description:
LiM+HiM+ERCC , mix of 0.47 fmole microRNA (in high and low concentrations differing by two fold) and 0.1 fmole ERCC
PAP
Flow Cell Used: FLO-FLG001 .  There are two processed files  in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. Batch of ERCC stored at -20oC


title: RMK0138C_CFC2_line, day 18 diff, rep3 [2023A410]


title: P6_LIN28A.positive_cko3.2

value: cKO


title: Library_5_dilut100_rep_1


title: P6_LIN28A.positive_Het3.1


title: RMK0138C_CFC2_line, day 18 diff, rep2 [2023A409]


title: WholeBlood-Control-F-124

source_name: Whole blood


title: HK-1 wildtype cell line, slide1

description: Gene expression

source_name: HK-1 cell line


title: P6_LIN28A.positive_cko2.1


title: RMK0138C_CFC2_line, day 18 diff, rep1 [2023A408]


title: Library_5_dilut10_rep_2

description:
LiM+HiM+ERCC , mix of 4.72 fmole microRNA (in high and low concentrations differing by two fold) and 1.04 fmole ERCC
PAP
Flow Cell Used: FLO-FLG001 .  There are two processed files  in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. Batch of ERCC stored at -20oC


title: P6_LIN28A.positive_cko3.3

description: NanoString WTA generated from mouse testis cross-section


title: RMK0056C_CFC1_line, day 18 diff, rep3 [2023A407]


title: WholeBlood-Control-M-122

value: Male


title: Library_5_dilut10_rep_1


title: RMK0056C_CFC1_line, day 18 diff, rep2 [2023A406]


title: WholeBlood-Control-F-123


title: WholeBlood-Control-F-121


title: P6_LIN28A.positive_Het2.2


title: Library_4_rep_2

description:
ERCC (10.4 fmoles)
Sham PAP
Flow Cell Used: FLO-MIN106 and FLO-FLG001 (for the replicate). There are two processed files for each sequencing replicate in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. ERCC stored at -80oC to simulate effects of long term storage


title: WholeBlood-Control-F-118


title: P6_LIN28A.positive_Het1.2


title: Library_5_dilut01

description:
LiM+HiM+ERCC , mix of 47.2 fmole microRNA (in high and low concentrations differing by two fold) and 10.4 fmole ERCC
PAP
Flow Cell Used: FLO-FLG001 for both replicates.  There are two processed files for each sequencing replicate in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. Batch of ERCC stored at -20oC


title: RMK0056C_CFC1_line, day 18 diff, rep1 [2023A405]


title: Library_3_rep_2

description:
ERCC (10.4 fmoles)
PAP
Flow Cell Used: FLO-FLG001 for both replicates.  There are two processed files for each sequencing replicate in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. ERCC stored at -80oC to simulate effects of long term storage


title: P6_LIN28A.positive_cko1.2


title: AG08H control clone, day 18 diff, rep3 [2023A404]


title: WholeBlood-Control-M-116


title: WholeBlood-Control-F-125


title: Library_2_rep_2

description:
LiM+HiM+ERCC , mix of 1270 fmole microRNA (in high and low concentrations differing by two fold) and 10.4 fmole ERCC
Sham PAP
Flow Cell Used: FLO-MIN106 and FLO-FLG001 (for the replicate). There are two processed files for each sequencing replicate in this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. ERCC stored at -80oC to simulate effects of long term storage


title: P6_LIN28A.positive_cko2.2


title: AG08H control clone, day 18 diff, rep2 [2023A403]


title: WholeBlood-Control-F-113


title: AG08H control clone, day 18 diff, rep1 [2023A402]


title: Library_1_rep_2

description:
LiM+HiM+ERCC , mix of 1270 fmole microRNA (in high and low concentrations differing by two fold) and 10.4 fmole ERCC
PAP
Flow Cell Used: FLO-MIN106 . There are two processed files for this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. ERCC stored at -80oC to simulate effects of long term storage


title: P6_LIN28A.positive_Het3.3


title: WholeBlood-Control-F-111


title: P6_LIN28A.positive_Het2.3


title: Library_4_rep_1

description:
ERCC (10.4 fmoles)
Sham PAP
Flow Cell Used: FLO-MIN106 . There are two processed files for this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. ERCC stored at -80oC to simulate effects of long term storage


title: Library_3_rep_1

description:
ERCC (10.4 fmoles)
PAP
Flow Cell Used: FLO-MIN106 . There are two processed files for this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. ERCC stored at -80oC to simulate effects of long term storage


title: WholeBlood-Control-F-109


title: hFF15 control clone, day 18 diff, rep2 [2023A400]


title: P6_LIN28A.positive_cko1.1


title: P6_LIN28A.positive_cko1.3


title: Library_2_rep_1

description:
LiM+HiM+ERCC , mix of 1270 fmole microRNA (in high and low concentrations differing by two fold) and 10.4 fmole ERCC
Sham PAP
Flow Cell Used: FLO-MIN106 . There are two processed files for this run, one mapped against ERCC and the 10 microRNAs used in the experiment, and the other mapped against the entire miRbase and the ERCC mix. ERCC stored at -80oC to simulate effects of long term storage


title: hFF15 control clone, day 18 diff, rep1 [2023A399]


title: WholeBlood-Control-F-107


title: type IIb myofibers, trained_2

city: Beijing

first: Minghong

last: Leng

address: No.38, Xueyuan Road, Beijing, China

institute: Health Science Center

description:
EE_2
readcount.txt
fpkm_genename.txt

data_processing:
The adaptor sequences and low-quality sequence reads were removed from the data sets. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome.
Sequenced reads were mapped to mouse mm10 genome assembly using Tophat2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file of raw count for all samples
Supplementary files format and content: tab-delimited text file of FPKM value for all samples
Supplementary files format and content: tab-delimited text files of FPKM value for each sample

source_name: type IIb myofibers isolated from extensor digitorum longus

growth_protocol: Male C57BL/6J mice were housed in the controlled facilities with 12h light/ 12h dark cycle at 23±3℃ provided with ad libitum food and water.

extract_protocol:
RNA was extracted with lysis buffer prepared according to the manufacturer’s instructions (SMART-Seq HT kit, Takara).
cDNA was synthesis and amplified using SMART-Seq HT kit according to the manufacturer’s instructions. Then the cDNA was purified with AMPure XP system (Beckman Coulter, A63880) and quantified by QuantiFluor dsDNA System (Promega, E2670). Sequencing libraries were created with the Nextera XT kit (Illumina, FC-131-1024) using 1 ng cDNA according to the manufacturer’s instructions.

treatment_protocol: Mice were trained on the treadmill for 6 weeks (12-16 m/min for 60 min, 5 d/week) and  euthanized three days after the last treadmill running. Extensor digitorum longus and soleus muscles were dissected immediately and digested with 2 mg/ml collagenase in DMEM at 37 ℃ for 60 min (for extensor digitorum longus) and 90 min (for soleus). Then, the fibers were disassociated by gently pipetting the muscles up and down in DMEM. Each myofiber was cut into two parts under stereo microscope. One part of myofiber was solubilized in 1× protein loading buffer for 10 min at 100 ℃ for MHC isoform identification and the rest part was immediately lysed in 1× lysis buffer for sequencing.

tag: strain

value: 8 weeks

value: male

value: endurance trained


title: Cut_and_Run_MCF7_H_IgG

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

data_processing:
library strategy: Cut&Run
Quality control of raw ChIP-seq, CUT&RUN and 4C-seq reads was performed using Fastqc.
CTCF-ChIP-seq paired-end sequencing fastq files were mapped to human hg38 genome using Bowtie2 (Langmead and Salzberg, 2012). Sam files were converted into bam files and sorted by Samtools (Li et al., 2009). Peaks were called using MACS v2.1.2. Each bam file was converted into bigwig files using DeepTools bamCoverage (Ramirez et al., 2014).
The CUT&RUN reads were mapped to the human genome hg38 utilizing Bowtie2. To call peaks, we used MACS2 using an IgG bam file as a control. Each bam file was converted into bigwig files using DeepTools bamCoverage (Ramirez et al., 2014).
4C-seq reads were processed using pipe4C (Krijger P.H.L. et al., 2020) using default parameters in the configuration file.
Assembly: GRCh38
Supplementary files format and content: bigWig

growth_protocol: MCF7 cells were cultured in media recommended by American Type Cell Culture in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol:
MCF7 breast cancer cell line was kept in duplicate under Normoxia (21% oxygen) or Hypoxia (1% oxygen) for 24 hours before performing CTCF-ChIP-seq (Shukla et al., 2011; Khoury et al., 2020) and CTCF-CUT&RUN assay (Skene et al., 2018; Sharma et al, 2023). For 4C-seq, MCF7 cells  transduced with lentivirus expressing either shRNA control (shControl) or shRNA specific for CTCF (shCTCF) were kept in Normoxia or Hypoxia and the 4C-seq experiment was performed based on (Splinter et al., 2012; Krijger et al., 2020)  using NlaIII and DpnII as restriction enzymes.
All the DNA libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.
150 bp paired-end ChIP-seq using Illumina NovaSeq X Plus, 50 bp paired-end CUT&RUN using Illumina NovaSeq 6000, 100 bp paired-end 4C-seq using Illumina NovaSeq 6000

treatment_protocol: MCF7 breast cancer cell line was kept under Normoxia (21% oxygen) or Hypoxia (1% oxygen) for 24 hours before performing CTCF-ChIP-seq or CTCF-CUT&RUN or 4C-seq

value: Breast cancer cell line (luminal)

tag: chip antibody

value: Normal Rabbit IgG (CST, #2729S)


title: WholeBlood-Control-M-106

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

value: Whole blood


title: type IIb myofibers, trained_3

description:
EE_3
readcount.txt
fpkm_genename.txt

value: type IIb myofibers isolated from extensor digitorum longus


title: WholeBlood-Control-F-110

value: Control


title: 127_WT_DMSO

city: Praha 6

first: Karel

last: Muller

address: Rozvojová 263

department: Lab. of hormonal regulations in plants

country: Czech Republic

institute: Institute of Experimenal Botany of the Czech Academy of Sciences

data_processing:
reads were quality filterred by rcorrector and Trimmomatic
transcript quantification and normalization done by Salmon v1.3.0 with parameters--seqBias, --gcBias, --PosBias, --numBootstraps 30
Assembly: Arabidopsis thaliana, TAIR10 cds library, version 20101214
Supplementary files format and content: sf files generated by Salmon software, include TPM values

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis thaliana plants were cultivated at 22°C, 10h/14h light cycle until four-weeks old

extract_protocol:
RNeasy Mini Kit (Qiagen).
NEBNext Ultra II Directional RNA Library prep kit

treatment_protocol: Fully expanded mature rosette leaves (three  per plant) of Col-0 or sid2, were treated by infiltration of 1 µM of latrunculin B or 0.01% DMSO by needleless syringe. After 24h, leaves were detached, samples were fixed in liquid nitrogen and total RNA was extracted using RNAeasy Mini kit (Qiagen).

value: leaf

tag: genotype

value: WT Col-0

value: DMSO


title: Library_1_rep_1

value: synthethic sample


title: WholeBlood-Control-F-105


title: type IIb myofibers, untrained_3

description:
CE_3
readcount.txt
fpkm_genename.txt

value: untrained


title: type IIb myofibers, trained_1

description:
EE_1
readcount.txt
fpkm_genename.txt


title: hFF15 control clone, day 18 diff, rep3 [2023A401]

value: Schwann cell precursor-like

value: BRAF WT


title: Cut_and_Run_MCF7_H_CTCF_2

value: CTCF (CST, #3418S)


title: type IIb myofibers, untrained_2

description:
CE_2
readcount.txt
fpkm_genename.txt


title: WholeBlood-Control-M-104

value: Male


title: 125_WT_DMSO


title: WholeBlood-Control-M-103


title: 126_WT_DMSO


title: 124_WT_latB

value: latB


title: Cut_and_Run_MCF7_N_CTCF_2


title: Cut_and_Run_MCF7_H_CTCF_1


title: type IIb myofibers, untrained_1

description:
CE_1
readcount.txt
fpkm_genename.txt

value: 8 weeks

value: male


title: WholeBlood-Control-M-102


title: 123_WT_latB


title: WholeBlood-Control-M-101


title: Cut_and_Run_MCF7_N_CTCF_1

value: Breast cancer cell line (luminal)


title: type I myofibers, trained_3

description:
ES_3
readcount.txt
fpkm_genename.txt

source_name: type I myofibers isolated from soleus

value: type I myofibers isolated from soleus

value: endurance trained


title: type I myofibers, trained_2

description:
ES_2
readcount.txt
fpkm_genename.txt


title: 122_WT_latB


title: type I myofibers, trained_1

description:
ES_1
readcount.txt
fpkm_genename.txt


title: PMA-stimulated THP1 cells, 6h, 100 nM AM580 and 100 nM Calcitriol, replicate 3

city: DEBRECEN

first: LAJOS

last: SZELES

address: NAGYERDEI KRT 98

country: Hungary

institute: UNIVERSITY OF DEBRECEN

description: hs_THP1_6h_AM580+Caclcitriol_rep3(normalized)

data_processing:
Sequence reads were aligned to the hg38 genome assembly using HISAT2
BAM files were imported to the StrandNGS program (Strand Life Sciences Pvt., Bangalore, India)
lowly expressed in all 4 conditions were excluded
differentially expressed genes were determined by ANOVA with Benjamini-Hochberg procedure (adjustedp-value < 0.05), Tukey post-hoc tests (p-value < 0.05) and filtering on fold change
Assembly: hg38
Supplementary files format and content: table containing log2 transformed normalized expression values, as determined by DESeq in StrandNGS

source_name: THP-1 human leukemia monocytic cell line

extract_protocol:
RNA was isolated using Quick-RNA Miniprep Kit (ZYMO research).
RNA-seq libraries were prepared from total RNA using an Ultra II RNA Sample Prep kit (New England BioLabs)

tag: stimulation

value: phorbol-12-myristate-13-acetate (PMA) for 16h

value: 100 nM AM580 and 100 nM Calcitriol

value: wt


title: Cut_and_Run_MCF7_N_IgG

value: Normal Rabbit IgG (CST, #2729S)


title: 121_sid2_DMSO

value: leaf

tag: treatment

value: DMSO


title: MCF7_shCTCF_H_COL5A1_promoter_4C_1

data_processing:
library strategy: 4C-seq
Quality control of raw ChIP-seq, CUT&RUN and 4C-seq reads was performed using Fastqc.
CTCF-ChIP-seq paired-end sequencing fastq files were mapped to human hg38 genome using Bowtie2 (Langmead and Salzberg, 2012). Sam files were converted into bam files and sorted by Samtools (Li et al., 2009). Peaks were called using MACS v2.1.2. Each bam file was converted into bigwig files using DeepTools bamCoverage (Ramirez et al., 2014).
The CUT&RUN reads were mapped to the human genome hg38 utilizing Bowtie2. To call peaks, we used MACS2 using an IgG bam file as a control. Each bam file was converted into bigwig files using DeepTools bamCoverage (Ramirez et al., 2014).
4C-seq reads were processed using pipe4C (Krijger P.H.L. et al., 2020) using default parameters in the configuration file.
Assembly: GRCh38
Supplementary files format and content: bigWig


title: PMA-stimulated THP1 cells, 6h, 100 nM AM580 and 100 nM Calcitriol, replicate 2

description: hs_THP1_6h_AM580+Caclcitriolrep2(normalized)

value: THP-1 human leukemia monocytic cell line


title: 120_sid2_DMSO


title: type I myofibers, untrained_3

description:
CS_3
readcount.txt
fpkm_genename.txt

value: untrained


title: MCF7_shControl_H_COL5A1_promoter_4C_2


title: 119_sid2_DMSO


title: PMA-stimulated THP1 cells, 6h, 100 nM Calcitriol, replicate 2

value: 100 nM Calcitriol


title: PMA-stimulated THP1 cells, 6h, 100 nM AM580 and 100 nM Calcitriol, replicate 1

description: hs_THP1_6h_AM580+Caclcitriol_rep1(normalized)


title: MCF7_shControl_H_COL5A1_promoter_4C_1


title: PMA-stimulated THP1 cells, 6h, 100 nM Calcitriol, replicate 3


title: type I myofibers, untrained_1

description:
CS_1
readcount.txt
fpkm_genename.txt


title: PMA-stimulated THP1 cells, 6h, 100 nM Calcitriol, replicate 1


title: type I myofibers, untrained_2

description:
CS_2
readcount.txt
fpkm_genename.txt


title: MCF7_shControl_N_COL5A1_promoter_4C_2


title: T-ALL28 [CITE-Seq]

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Raw FASTQ sequencing data was processed for downstream analysis using CellRanger version 6.0.0 (10X Genomics).
ADT and RNA counts were generated from raw sequencing data using the SC5P-R2 mode for 5 prime paired end read analysis and expected cells were estimated at 26000.
The single-cell analyses were carried out using the Seurat v4.3.022 in R. CellRanger h5 files were imported directly into Seurat.
Antibody derived tags (ADTs) were normalized to spike-in murine IgG.
Cells with less than 200 genes and more than 20% mitochondrial gene counts were removed
Hashtag oligos (HTOs) were demultiplexed using the HTODemux function at 0.99 percentile.
TCR clonotypes were reviewed manually to assign sample-specific clonotypes
Cells of samples expressing clonotypes from other samples were marked as doublets
Cells that were negative by HTO-based assignment or marked as doublet by HTO or clonotypes were filtered out.
Assembly: GENCODE human reference genome v38
Supplementary files format and content: Gene expression – Raw counts
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Bone Marrow

extract_protocol:
Cells aliquoted for CITE-Seq were washed 3X with CITE-Seq staining buffer (CSM; 2% BSA, 0.01% Tween in PBS) in conical bottom polypropylene FACS tubes. After washing, cells were resuspended in 50μl of CITE-Seq antibody mix containing 0.1μg CITE-Seq antibody (BioLegend, see Table X) per sample. Next, 0.1μg Hashtag oligos (HTO, Biolegend, table X) were added to each sample individually, and samples were incubated for 30 minutes in the dark at RT. Each library was made up of 4 hashed samples, including 3 malignant and 1 healthy bone marrow specimen. After staining, cells were washed 3X with CSM, counted, pooled evenly and delivered to the Princess Margaret Genomics Center (PMGC) for single cell sequencing preparation using the 10X platform.
Library construction was carried out with the Chromium Next GEM Single Cell 5ʹ Kit v2 (cat#1000263) for Whole transcriptome gene expression library, the 5' Feature barcoding kit (cat#1000541) for Antibody Derived Tag library and the Chromium Single Cell Human TCR Amplification Kit (cat#1000252) for the VDJ library all following manufacturor's recommendations

value: Bone Marrow

tag: disease

value: primary TALL

value: primary human BM mononuclear cells

value: WT


title: 116_sid2_latB

value: latB


title: 441376

city: Beerse

first: Nádia

last: Conceição-Neto

address: Turnhoutseweg 30

country: Belgium

institute: Janssen R&D

data_processing:
Read alignment: Cell Ranger pipeline (version 7). Filtering: Cells with less than 1,000 Unique Molecular Identifiers (UMIs) or less than 200 genes or more than 25% mitochondrial counts were removed.
Assembly: mm10
Supplementary files format and content: rds
Supplementary files format and content: R object

source_name: liver

extract_protocol:
Male C57BL/6 mice (4–5-week-old, Wuxi Apptec, Shanghai, China) were either transduced via the tail vein with 1x1011 viral genome equivalents (vge) per mouse of rAAV-HBV1.3 (n=5)  (FivePlus Molecular Medicine Institute, Beijing, China) or rAAV vector control (n=5), which contained an empty rAAV capsid and rAAV containing a short sequence of the CMV promoter and BGH poly A tail flanked with inverted AAV-ITR or kept naïve (n=5). IHICs isolated via mechanical digestion of the liver were processed according to the 10x Chromium Single-cell V(D)J Reagent Kits User Guide and loaded on to the Chromium 10x platform using the 5’ v1.1 chemistry (10x Genomics). Libraries were sequenced on a NovaSeq 6000 platform (PE150) (Illumina) to an average ~50,000 reads per cell.
10x 5'

value: liver

value: IHIC

value: Male

value: naïve


title: MCF7_shControl_N_COL5A1_promoter_4C_1

tag: cell line

value: Breast cancer cell line (luminal)


title: 441383


title: 118_sid2_latB


title: 441378


title: 117_sid2_latB


title: PMA-stimulated THP1 cells, 6h, 100 nM AM580, replicate 3

value: phorbol-12-myristate-13-acetate (PMA) for 16h

value: wt


title: MCF7_shCTCF_H_COL5A1_promoter_4C_2


title: T-ALL27 [CITE-Seq]


title: wrky48_HS-3

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Assembly: TAIR 10
Supplementary files format and content: tab-deliminated files included mean normalized counts for each sample

growth_protocol: Arabidopsis thaliana wild-type Col-0 (var Columbia-0) and homozygous knockout mutants (Col-0 background) wrky48-1 (Salk_066438C) were grown in peat pellets (Jiffy-7; http://www.jiffygroup.com/) at 23°C under long-day growth conditions (12-h light from 7 AM to 7 PM; 50 μmol m−2 s−1/12-h dark from 7 PM to 7 AM).

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Individual high light stress (HL) and heat stress (HS), and combined HL and HS (HL+HS) were applied in parallel using 30-day-old Arabidopsis plants (wild-type Col-0 and wrky48-1). HL was applied by exposing plants to 900 µmol m−2 s−1 at 23 °C for 8 h. HS was applied by subjecting plants to 40 °C, 50 µmol m−2 s−1, for 8 h. HL+HS was performed by simultaneously subjecting plants to 900 µmol m−2 s−1 of light stress and 40°C for 8 h. Control (CT) plants were maintained at 50 µmol m−2 s−1 and 23°C throughout the entire experiment.

value: leaf


title: PMA-stimulated THP1 cells, 6h, 100 nM AM580, replicate 2


title: T-ALL26 [CITE-Seq]


title: wrky48_HS-2


title: 441372


title: PMA-stimulated THP1 cells, 6h, 100 nM AM580, replicate 1


title: 441374


title: T-ALL25 [CITE-Seq]


title: wrky48_HS-1


title: PMA-stimulated THP1 cells, 6h, vehicle (DMSO:EtOH), replicate 3

value: vehicle (DMSO:EtOH)


title: 441348

value: AAV-control


title: wrky48_HL-HS-3


title: T-ALL24 [CITE-Seq]


title: T-ALL23 [CITE-Seq]


title: PMA-stimulated THP1 cells, 6h, vehicle (DMSO:EtOH), replicate 2

value: THP-1 human leukemia monocytic cell line


title: T-ALL22 [CITE-Seq]


title: wrky48_HL-HS-1


title: wrky48_HL-HS-2


title: PMA-stimulated THP1 cells, 6h, vehicle (DMSO:EtOH), replicate 1


title: 441324


title: 441323


title: wrky48_HL-2

source_name: highlight

value: highlight


title: PMA-stimulated THP1 cells, 1h, 100 nM Calcitriol, VDR ChIP-seq, replicate 2

data_processing:
alignment with bwa using default parameters
bam generation with Picard tools using SortSam, AddOrreplaceReadGroups, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, MarkDuplicates with default parameters
tag directory generation with HOMER makeTagDirectory
Model-based analysis of ChIP-seq version 2 (MACS2) was used for predicting summits of the peaks using q value cutoff (q) = 0.001.
Assembly: hg38
Supplementary files format and content: bedgraph

extract_protocol:
The cells were cross-linked with 2 mM disuccinimidyl glutarate for 40 minutes and 1% methanol-free formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sheared using a Diagenode Bioruptor sonicator. Precipitated and washed samples were purified using NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel).
Indexed libraries were prepared from ChIP-DNA using a TruSeq ChIP Sample Preparation Kit (Illumina).

value: 100 nM Calcitriol

tag: antibody


title: wrky48_HL-3


title: PMA-stimulated THP1 cells, 1h, vehicle (DMSO:EtOH), VDR ChIP-seq, replicate 2


title: T-ALL20 [CITE-Seq]

value: Bone Marrow

value: primary TALL


title: wrky48_HL-1


title: PMA-stimulated THP1 cells, 1h, 100 nM Calcitriol, VDR ChIP-seq, replicate 1


title: T-ALL19 [CITE-Seq]

value: primary human BM mononuclear cells

value: WT


title: MPAL4 [CITE-Seq]


title: 441269

value: liver

value: AAV-HBV


title: PMA-stimulated THP1 cells, 1h, vehicle (DMSO:EtOH), VDR ChIP-seq, replicate 1


title: PMA-stimulated THP1 cells, 1h, 100 nM AM580, RAR ChIP-seq, replicate 2


title: 441147

value: IHIC

value: Male


title: wrky48_CT-3

source_name: Control

value: No treatment


title: wrky48_CT-2


title: ETP-ALL8 [CITE-Seq]


title: 441326


title: T-ALL21 [CITE-Seq]


title: PMA-stimulated THP1 cells, 1h, 100 nM AM580, RAR ChIP-seq, replicate 1

value: phorbol-12-myristate-13-acetate (PMA) for 16h


title: 441087


title: 441322


title: ETP-ALL7 [CITE-Seq]


title: wrky48_CT-1


title: ETP-ALL6 [CITE-Seq]


title: PMA-stimulated THP1 cells, 1h, vehicle (DMSO:EtOH), RAR ChIP-seq, replicate 2

value: wt


title: PMA-stimulated THP1 cells, 1h, vehicle (DMSO:EtOH), RAR ChIP-seq, replicate 1


title: 441287


title: col_HS-3

value: leaf

value: wild type Col-0


title: immune cells, EL4 subcutaneous tumour, psgl1 ko, rep6

city: guangzhou

first: wang

middle: l

last: x

state: guangdong

address: zhongshan

department: immunity

institute: sysu

data_processing:
Sequence reads were trimmed for adaptor sequence sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to mm10 using hisat2 package
Read count extraction, ordering and quantification were performed using samtools and htseq package
Assembly: mm10
Supplementary files format and content: tab-delimited text files include COUNT values for each Sample

source_name: CD45 positive cells

growth_protocol: vector or PSGL1 KO EL4 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C, and then 500000 EL4 cells/mouse were injected subcutaneously into the right flank of 6- to 8-week-old mice

extract_protocol:
almost 20 days after inoculation, graft EL4 tumour tissues were resected and digested into single cell suspension. After that, CD45 positive immune cells were sorted for RNA-seq with flow cytometry. Total RNA was extracted from sorted immune cells with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions, and >1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: CD45 positive cells

value: immune cell

value: CD45 positive cells were sorted from psgl1 ko el9 tumour tissue


title: col_HS-2


title: T-ALL18 [CITE-Seq]


title: col_HS-1


title: ETP-ALL5 [CITE-Seq]


title: immune cells, EL4 subcutaneous tumour, psgl1 ko, rep5

value: CD45 positive cells were sorted from psgl1 ko el8 tumour tissue


title: T-ALL17 [CITE-Seq]

value: Bone Marrow


title: col_HL-HS-3


title: immune cells, EL4 subcutaneous tumour, psgl1 ko, rep4

value: CD45 positive cells were sorted from psgl1 ko el7 tumour tissue


title: Uninfected with K67 Nrf2 Inhibitor addition Rep2 [UIK-2]

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

institute: University of Arkansas for Medical Sciences

data_processing:
RNA reads were assessed for quality of sequencing using FastQC.  Adaptors and low-quality bases (%Q30 < 20) were trimmed to a minimum of 36 base pairs using Trimmomatic [50].
Reads that passed quality control were aligned to the reference genomes GRCh38 Ensemble release 99
Differential expression and linear modeling was performed using Limma voom with quality weights [52-54].  Briefly, raw counts were obtained from bam files using Subread’s featuresCount function and transformed to log2 counts per million (CPM) [55].  Low expressed genes were filtered out and libraries normalized by trimmed mean of M-values [56].  Linear modeling and differential expression were performed and sorted by log fold change.  Genes with an FDR p-value < 0.05 and FC > 2 were considered significant.
Assembly: GRCh38 Ensemble release 99
Supplementary files format and content: Raw counts in csv file

source_name: THP-1 human monocytes (TIB-202)

growth_protocol: THP-1 human monocytes (TIB-202) were obtained from the American Type Culture Collection (ATCC) and cultured in RPMI1640 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.  THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA; 200 nM) overnight to differentiate monocytes into adherent macrophage-like cells.

extract_protocol:
Cells were cultured in T-25 culture flasks, treated with inhibitors, infected with WT or icmD::Tn C. burnetii, and harvested in TRIzol (Thermofisher).
Illumina Truseq

treatment_protocol: C. burnetii cultivation.  Wild type (Nine Mile II; clone 4; RSA439), icmD::Tn, and mCherry-expressing C. burnetii were cultured for 7 days at 37°C with 5% CO2 and 2.5% O2 in acidified citrate cysteine medium (ACCM).  icmD::Tn mutant cultures contained kanamycin (350 g/mL) and mCherry-expressing bacterial cultures contained chloramphenicol (3 g/mL) for selection.  Cultures were pelleted via centrifugation, washed three times with sucrose phosphate (SP) buffer, and stored in SP buffer at -80°C prior to use.  All infections were performed for 48 h using a multiplicity of infection = 10-25.  Cells were cultured in T-25 culture flasks, treated with inhibitors, infected with WT or icmD::Tn C. burnetii, and harvested in TRIzol (Thermofisher).

value: THP-1 human monocytes (TIB-202)

value: Macrophage


title: Uninfected with K67 Nrf2 Inhibitor addition Rep1 [UIK-1]


title: immune cells, EL4 subcutaneous tumour, psgl1 ko, rep3

value: CD45 positive cells were sorted from psgl1 ko el6 tumour tissue


title: col_HL-HS-2


title: Uninfected Rep3 [UI-3]

value: Uninfected


title: immune cells, EL4 subcutaneous tumour, psgl1 ko, rep2

value: CD45 positive cells were sorted from psgl1 ko el5 tumour tissue


title: T-ALL15 [CITE-Seq]

value: primary TALL

value: primary human BM mononuclear cells

value: WT


title: Uninfected Rep2 [UI-2]


title: immune cells, EL4 subcutaneous tumour, psgl1 ko, rep1

value: CD45 positive cells were sorted from psgl1 ko el4 tumour tissue


title: col_HL-HS-1

value: leaf


title: col_HL-3

value: wild type Col-0

value: highlight


title: Lip_LNAME_rep3

city: Charlottesville

first: Brant

middle: E

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia

data_processing:
The paired-end reads were mapped to the hg38 reference genome using STAR (v 2.7.9a). Gene counts were generated with FeatureCounts in the Rsubread (v. 2.8.8) package. DESeq2 (v. 1.34.0) was used to calculate log fold change and adjusted p-values. The adjusted p-values were then adjusted for multiple comparisons between groups by the Benjamini-Hochberg procedure using p.adjust().
Assembly: hg38
Supplementary files format and content: csv file of  raw counts
Supplementary files format and content: csv file of counts normalized with DESeq2
Supplementary files format and content: csv file of differential expression results compared to control group
Supplementary files format and content: csv file of differential expression results compared to lipid treated group

source_name: Human Adipose Microvascular Endothelial Cells

extract_protocol:
RNA was isolated using Quick-RNA MiniPrep Kit (Genesee Scientific: 11-328). When necessary, samples were further concentrated and purified with the RNeasy MinElute Cleanup Kit (Qiagen: 74804).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.


title: Uninfected Rep1 [UI-1]


title: 441031

value: liver

value: IHIC

value: Male

value: AAV-HBV


title: Lip_LNAME_rep2

value: Human Adipose Microvascular Endothelial Cells


title: immune cells, EL4 subcutaneous tumour, Control, rep6

value: CD45 positive cells

value: immune cell

value: CD45 positive cells were sorted from vec-EL8 tumour tissue


title: col_HL-1


title: Uninfected with K67 Nrf2 Inhibitor addition Rep3 [UIK-3]

value: THP-1 human monocytes (TIB-202)

value: Macrophage


title: Lip_LNAME_rep1


title: immune cells, EL4 subcutaneous tumour, Control, rep7

value: CD45 positive cells were sorted from vec-EL9 tumour tissue


title: Ionomycin Oxidative Stress positive control Rep 3 [ion-3]


title: T-ALL16 [CITE-Seq]

value: Bone Marrow

value: primary TALL

value: primary human BM mononuclear cells


title: Ionomycin Oxidative Stress positive control Rep 1 [ion-1]


title: col_CT-3

value: leaf

value: No treatment


title: Ionomycin Oxidative Stress positive control Rep 2 [ion-2]


title: Lip_DETA_rep3


title: Lip_DETA_rep2


title: immune cells, EL4 subcutaneous tumour, Control, rep5

value: CD45 positive cells were sorted from vec-EL7 tumour tissue


title: col_CT-2

value: wild type Col-0


title: Infected with WT + K67 (Nrf2 Inhibitor) Rep1 [IK-3]

value: Infected with WT + K67 (Nrf2 Inhibitor)


title: col_CT-1


title: Lip_DETA_rep1


title: immune cells, EL4 subcutaneous tumour, Control, rep3

value: CD45 positive cells were sorted from vec-EL5 tumour tissue


title: Infected with WT + K67 (Nrf2 Inhibitor) Rep2 [IK-2]


title: immune cells, EL4 subcutaneous tumour, Control, rep4

value: CD45 positive cells were sorted from vec-EL6 tumour tissue


title: immune cells, EL4 subcutaneous tumour, Control, rep2

value: CD45 positive cells were sorted from vec-EL4 tumour tissue


title: Lip_rep3

value: Human Adipose Microvascular Endothelial Cells

value: Lip


title: Infected with WT + K67 (Nrf2 Inhibitor) Rep1 [IK-1]


title: col_HL-2

value: highlight


title: Col-0_t30h_rep2

city: Rostock

first: Andreas

middle: Sven

last: Richter

address: Albert-Einstein-Strasse 3

department: Institute for Biosciences

institute: University of Rostock

description:
WT_30_2
Col0_24hHL+6hNL_fpkm.csv

data_processing:
removing reads containing adapter, reads containing ploy-N and low quality reads
mapping: Hisat2 v2.0.5
calculation of FPKM: featureCounts v1.5.0-p3
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: csv / FPKM

source_name: total leaf

growth_protocol: 4-week old Arabidopsis plants grown in short-day condition (10h light/14h dark) subjected to high light 2h after the onset of light.

extract_protocol:
Citric acid (Oñate-Sánchez and Vicente-Carbajosa, 2008)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library followed by  end repair, A-tailing, adapter ligation, size selection, enzyme digestion, amplification, and purification

treatment_protocol: 2h normal light (100µmol photons m-2 s-1 ) > 24 h continous high light (500µmol photons m-2 s-1) > 6h normal light

value: total leaf

value: Col-0 (WT)

value: 24h high light + 6 h normal light