title: sham operation group-3

first: Sen-Lin

last: Hou

address: West China Hospital, Sichuan University, 37 Guoxue Alley, Chengdu

department: Institute of Thoracic Oncology

institute: West China Hospital

description:
Library name: Sham3
10x Genomics

data_processing:
Raw sequencing reads were processed with the DNBc4tools pipeline (v2.1.2) using default and recommended settings. FASTQ files generated from the DNBSEQ-T7 sequencing system were aligned to the GRCh38 reference genome using the STAR algorithm. Unique Molecular Identifiers (UMIs) were counted, and non-cell-associated barcodes were removed to create individual Gene-Barcode matrices for each sample. Finally, a comprehensive gene-barcode matrix containing barcoded cells and their corresponding gene expression data was generated.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Left lung after transplantation

extract_protocol:
Lung tissues were transported on ice in a sterile culture dish containing 10 mL of 1× Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. No. 14190144) to remove any residual storage solution. Lung tissues were minced into small pieces on ice and digested using an enzymatic solution composed of 0.25% Trypsin (Thermo Fisher, Cat. No. 25200-072) and 10 µg/mL DNase I (Sigma, Cat. No. 11284932001) dissolved in PBS supplemented with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. No. SV30087.02). The digestion was performed at 37°C with gentle shaking at 50 r.p.m. for approximately 40 minutes. Dissociated cells were harvested every 20 minutes to maximize cell yield and viability. Cell suspensions were filtered through a 40-μm nylon cell strainer, and any remaining red blood cells were lysed using 1× Red Blood Cell Lysis Solution (Thermo Fisher, Cat. No. 00-4333-57). Afterward, the cells were washed with 1× DPBS containing 0.4% FBS. Cell viability was assessed using a 0.4% acridine orange/propidium iodide (AO/PI) stain with the Countstar Rigel S2 (Countstar, Shanghai). The processed samples were subsequently sent to Majorbio Biopharm Technology Co., Ltd. (Shanghai, China) for further analysis.
Single-cell libraries were prepared following the protocol provided by the DNBelab C4 Single-Cell RNA Preparation Kit. Briefly, cells were diluted to a final concentration of 1,000 cells/mL and loaded into the microfluidic chip's cell reservoir. Barcoded beads and droplet generation oil were sequentially introduced into the respective reservoirs. Droplets were generated and collected via the DNBelab C4 system, with mRNA captured by barcoded beads for reverse transcription. The resultant complementary DNA (cDNA) was amplified using polymerase chain reaction (PCR), purified, and quantified with the Qubit dsDNA Assay Kit (Invitrogen, Cat. No. Q32854). For library preparation, 3′-end transcripts underwent cDNA fragmentation, size selection, end repair, A-tailing, adapter ligation, PCR-based indexing, and library cyclization. These steps followed the manufacturer's guidelines, with purification and quantification carried out using the Qubit ssDNA Assay Kit (Thermo Fisher Scientific, Cat. No. Q10212). Sequencing was performed on the DNBSEQ-T7 platform (PE150) using the DNBSEQ-T7RS Reagent Kit (FCL PE150, version 3.0). Majorbio Biopharm Technology Co., Ltd. (Shanghai, China) conducted the sequencing and bioinformatic analyses.

value: Left lung after transplantation

value: pneumonocyte

value: sham operation


title: HSW-15-3_2

status: Public on Mar 25 2025

type: SRA

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

country: Canada

institute: Agriculture and AgriFood Canada

description: Library name: MBFgIsolatesRNA-05

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling
reads trimmed using trimmomatic v0.36 for adapter sequences and low-quality reads
trimmed reads mapped to F. graminearum using hisat2
count data generated using featureCounts
Differential expression analysis performed using DESeq2
Assembly: F. graminearum PH-1 (ASM24013v3)
Supplementary files format and content: tab delimited count data sheets

molecule: polyA RNA

organism: Fusarium graminearum

source_name: Mycelia

growth_protocol: Isolates were cultured in 60mm petri plates (Catalog No:  FB0875713A, Fisherbrand)in Potato Dextrose Agar (PDA - Catalog No:  0013-17-6, Difco) with Streptomycin sulfate (Catalog No: S6501-010, SIGMA-Aldrich). Plates were incubated at 20C for 7days

extract_protocol:
Mycelia was ground and RNA extraction was performed using the Trizol Reagent (Ambion), according to the manufacturer’s instructions. RNA was quantified using Agilent 2100 Bioanalyzer with the Agilent RNA 6000 Nano Kit
RNA libraries were prepared for sequencing using standard illumina protocols

tag: tissue

value: Mycelia

tag: genotype

tag: treatment

value: PDA + Streptomycin sulfate


title: Bd3-1,control,rep23

city: Cambridge

first: Jie

last: Yun

state: MA

address: 77 MASS

department: CEE

country: USA

institute: MIT

data_processing:
Raw sequence reads were trimmed by Trimmomatic (trimmomatic-0.39) with 2:30:10:1:true and Cutadapt (v2.10)to remove adapters and poly(A) tails with -a A{20} and -m 25
Reads were aligned to reference transcriptome using Bowtie2 (v2.4.0) with seedlength -L 25 and mismatch allowance -n 2 and other default parameters suggested by next step RSEM
Reads with the same unique molecular identifier (UMI) and aligned to the same genes were removed to eliminate PCR bias during library generation using a custom script
RNA-Seq by Expectation-Maximization (RSEM, 1.3.3) was used to estimate counts to account for non-specifically aligned reads with --estimate-rspd
Assembly: Bdistachyon_556_v3.2.transcript_primaryTranscriptOnly and LT558597 Bd21 plastome
Supplementary files format and content: csv file includes raw counts for each samples

molecule: total RNA

organism: Brachypodium distachyon

source_name: leaf

growth_protocol: Plants were grown in growth chambers with 50% humidity, 500 mmol photons m-2 s-1 light intensity and a controlled temperature of 25oC day/20oC night (12h/12h). Plants were bottom watered with tap water (pH=5-6) every other day throughout the experiment, supplemented with DYNA-GRO GROW Liquid Plant Food 7-9-5 (Dyna-Gro, Richmond, CA, USA) over the first 32 days.

extract_protocol:
Approximately 100mg of tissue was used for RNA extraction using Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer instructions, followed by DNase treatment (On-Column DNase I Digestion Set, Sigma-Aldrich, USA). 25ng of RNA for 214 samples were aliquoted at a normalized concentration of 5 ng/μL for sequencing
MIT BioMicro Center performed RNA-seq library construction and sequencing following the approach of High-Throughput 3' Digital Gene Expression with 26 + 80 bases pair-end run with 6 nucleotide index

treatment_protocol: Starting the 33rd day after sowing, control plants were watered to 85% FC every night while dry-down plants were allowed to decrease their soil water content to 55% FC over 6 days (5% decrease each day) by daily bringing soil water content to the specified water contents.

value: leaf

tag: cell type

value: bulk

value: control


title: HCC78 dCas9-KRAB-MeCP2 sgNT RNA-seq Rep2

city: Boston

first: Matthew

last: Meyerson

address: 44 Binney St

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
NKX2-1_RNAseq_TPM.csv
JLP-R090

data_processing:
Paired-end RNA-seq reads were trimmed using Trimmomatic (v. 0.36) for properly paired reads and to remove any TruSeq adapter sequences. RNA-seq reads were mapped to the human reference genome (hg38) using STAR (Dobin et al., 2013) version 2.3.1 with default parameters.
Raw read counts were generated with Rsubread featureCounts against the hg38 refFlat annotation from UCSC—reads were allowed to map to multiple annotations (allowMultiOverlap=T) but we only counted the primary alignment of each read (primaryOnly=T). Significance was assessed using the R package DESeq2. Significantly changing genes were assessed with a Bonferri-corrected p value≤1e-3 and a fold change≥1.5 to determine set of significantly changing genes. Transcripts per million (TPM) were determined from featureCounts raw counts normalized per million total reads.
Assembly: GRCh38
Supplementary files format and content: Transcripts per million normalized reads for the hg38 refFlat annotation.

organism: Homo sapiens

growth_protocol: Cell lines were cultured in RPMI + 10% Fetal Bovine Serum + 1X PenStrep

extract_protocol:
RNA was extracted from cell pellets stored at -80°C using an RNeasy Mini Kit (Qiagen) with on-column DNase digestion using RNase-Free DNase Set (Qiagen). RNA was eluted in RNase-free ddH2O, and quantified by nanodrop. RNA integrity was determined using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Electrophoresis Bioanalyzer, all RNA samples used for RNA-seq had a RNA integrity number (RIN) > 9.0.
1000-2000µg of RNA was polyA-selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB). Final libraries were quantified using Qubit, pooled, and sequenced by Broad Walk-Up Sequencing on a Nextseq 500 using 2x40bp sequencing.

treatment_protocol: Cells were spinfected with knockdown constructs at day 0, changed over to hard selection (1µg/mL puromycin) on day 1, then reduced to low selection (0.5µg/mL puromycin) on day 4. On day 7 post-infection, cells were harvested for RNA extraction.

tag: cell line

value: lung adenocarcinoma

value: dCas9-KRAB-MeCP2 sgNT


title: Bd21,control,rep24


title: sham operation group-1

city: Chengdu

country: China

description:
Library name: Sham1
10x Genomics

library_source: transcriptomic single cell

organism: Mus musculus


title: HSW-15-3_1

description: Library name: MBFgIsolatesRNA-04


title: sham operation group-2

description:
Library name: Sham2
10x Genomics


title: HCC78 dCas9-KRAB-MeCP2 sgE764 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R091

value: dCas9-KRAB-MeCP2 sgE764


title: Bd3-1,drought,rep24

value: drought


title: untreated IRI_transplanted left lung-3

description:
Library name: IR3
10x Genomics

value: untreated IRI


title: HCC78 dCas9-KRAB-MeCP2 sgNT RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R089


title: Bd21,control,rep23


title: untreated IRI_transplanted left lung-2

description:
Library name: IR2
10x Genomics


title: HSW-15-1_3

description: Library name: MBFgIsolatesRNA-03


title: HSW-15-27 _1

description: Library name: MBFgIsolatesRNA-07


title: HSW-15-1_2

description: Library name: MBFgIsolatesRNA-02


title: NCI-H358 dCas9-KRAB-MeCP2 sgE764 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R088


title: Bd21,drought,rep22


title: Bd21,drought,rep21


title: HSW-15-1_1

description: Library name: MBFgIsolatesRNA-01


title: untreated IRI_transplanted left lung-1

description:
Library name: IR1
10x Genomics


title: NCI-H358 dCas9-KRAB-MeCP2 sgE764 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R087


title: baicalein-treated_transplanted left lung-3

description:
Library name: BI3
10x Genomics

value: baicalein-treated


title: Muscle_Control5_rep2(RNA-seq)

city: Beijing

first: Wei

last: Tao

address: No.5 Yiheyuan Road

department: School of Life Sciences

institute: Peking University

description: Library name: Sample4

data_processing:
The raw sequencing data were processed using trim_galore (version  0.6.10) to remove adapters and low-quality reads
The trimmed reads were then mapped to the hg38 or mm10 reference genome using hisat2 (version 2.2.1), and the SAM files were converted to sorted BAM files using samtools (version 1.7)
The gene expression count matrix was obtained using featureCounts (version 2.0.6) and normalized with DESeq2 (version 1.34.0)
Assembly: hg38, mm10
Supplementary files format and content: Tab-delimited text files include normalized values for each sample

source_name: muscle

extract_protocol:
Total RNA was extracted from cells for the construction of sequencing libraries using TRIzol® (Invitrogen, 15596018)
RNA libraries were prepared for sequencing using Illumina protocols

value: muscle

value: WT


title: Bd3-1,drought,rep23


title: NCI-H358 dCas9-KRAB-MeCP2 sgNT RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R086


title: baicalein-treated_transplanted left lung-2

description:
Library name: BI2
10x Genomics


title: NCI-H358 dCas9-KRAB-MeCP2 sgNT RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R085


title: Bd21,control,rep22


title: Muscle_NALA_rep2(RNA-seq)

description: Library name: Sample2

value: NALA


title: baicalein-treated_transplanted left lung-1

description:
Library name: BI1
10x Genomics

value: Left lung after transplantation


title: Bd3-1,control,rep22


title: NCI-H2087 dCas9-KRAB-MeCP2 sgE764 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R083


title: Muscle_NALA_rep1(RNA-seq)

description: Library name: Sample1


title: NCI-H2087 dCas9-KRAB-MeCP2 sgE764 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R084


title: Muscle_Sedentary_rep2(CUT&Tag)

description: Library name: Sample28

data_processing:
Clean data were mapped to the hg38 or mm10 reference genome using bowtie2 (version 2.2.5).The sorted bam files were converted to bigwig format using bamCoverage (version 3.5.1)
The normalized signal was visualized in Integrative Genomics Viewer (IGV, version 2.11.3). deepTools (version 3.5.1) was used to calculate signal scores between ±3 kb from the transcriptional start site and create profiles
Peak calling was performed using MACS2 (version 2.2.7.1). DESeq2 (version 1.34.0) and MACS2 (version 2.2.7.1) were used to identify altered peaks
Peaks distribution and annotation were analyzed using ChIPseeker (version 1.30.3)
Assembly: hg38, mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag experiments were performed according to the CUT&Tag Assay Kit manual (Vazyme, TD903). Briefly, cell pellets were collected at 600 × g for 5 min, washed with wash buffer, and incubated with ConA beads for 10 min at room temperature in 8-strip tubes. Subsequently, the cell–ConA bead complexes were incubated with anti-H3K9la (PTM BIOLABS, PTM1419RM) at 4℃ overnight and a secondary antibody for 1 h at room temperature. The pA/G-Tnp transposon mediated the transposition reaction, and TTBL mediated DNA fragmentation. DNA extraction beads were used to extract CUT&Tag-enriched DNA
CUT&Tag libraries were prepared for sequencing using established protocols


title: NCI-H2087 dCas9-KRAB-MeCP2 sgNT RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R082


title: PC9 EF1a-NKX2-1 Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R064


title: Bd21,control,rep21


title: Muscle_Sedentary_rep1(CUT&Tag)

description: Library name: Sample27


title: Bd21,drought,rep20


title: MRC5_static_9

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

country: Spain

institute: Instituto de Investigación Sanitaria del Principado de Asturias

description: MRC5 were preconditioned by supernatants from non-stretched A549 during 24 hours

data_processing:
Basecalling was performed using the default Ion Torrent software
trimming was performed using the fastp software v0.20.1
Counts were calculated using the pseudoalignment tool salmon v1.9 with the default parameters for mapping-based quantification and the hg38 salmon partial index
Transcript counts were imported into R using the packages Annotationhub and tximport to obtain gene counts
Assembly: GRCh38
Supplementary files format and content: transcript counts

extract_protocol:
MRC5 samples were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries were prepared using the Ion Ampliseq Trascriptome Human Gene Expression Kit (Ion Torrent)

value: lung fibroblast

tag: preconditioning

value: Static

value: supernatants from non-stretched A549


title: Bd3-1,control,rep21


title: Bd3-1,drought,rep22


title: Muscle_Running_rep2(CUT&Tag)

description: Library name: Sample26


title: MRC5_stretch_10

description: MRC5 were preconditioned by supernatants from stretched A549 during 24 hours

value: Stretch

value: supernatants from stretched A549


title: Bd3-1,drought,rep21

value: leaf

value: bulk


title: Muscle_Running_rep1(CUT&Tag)

description: Library name: Sample25


title: NCI-H2087 dCas9-KRAB-MeCP2 sgNT RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R081

value: lung adenocarcinoma


title: Muscle_Control5_rep1(RNA-seq)

description: Library name: Sample3


title: MRC5_stretch_8


title: CRL1506

type: RNA

city: San Miguel de Tucuman

first: Leonardo

last: Albarracin

address: Chacabuco 145

country: Argentina

institute: CERELA

description: Gene expression after 3 hours after the stimulation with the TLR4 agonist.

hyb_protocol: cRNA was synthesized.

scan_protocol: After scanning the slides using an Agilent microarray scanner, Dedicated software was used to quantify the fluorescent signal at each spot.

data_processing: Raw intensity data from Agilent-065570 Mus musculus 8x60K Gene Expression arrays were processed using the limma package in R. Background correction was performed using the normexp method with an offset of 50. Between-array normalization was conducted using the quantile normalization method. Probe summarization and log2 transformation were applied before statistical analysis.

source_name: Raw 264.7 mouse macrophage cells

label_protocol: Label total RNA using Low Input Quick Amp Labeling Kit (Agilent) cRNA was synthesized.

extract_protocol: Total RNA was isolated from Lactobacilli-treated and control macrophages using RNeasy Mini Kit (Qiagen, Tokyo, Japan) and treated with DNase.

value: RAW macrophages


title: Muscle_Young_rep2(CUT&Tag)

description: Library name: Sample24


title: PC9 SFFV-NKX2-1 Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R068


title: LPS


title: CRL1505


title: MRC5_static_7


title: Muscle_Young_rep1(CUT&Tag)

description: Library name: Sample23


title: PC9 SFFV-NKX2-1 Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R067


title: Bd21,drought,rep19


title: MRC5_stretch_6


title: Bd21,control,rep20

value: control


title: Muscle_Aging_rep2(CUT&Tag)

description: Library name: Sample22


title: MRC5_static_5


title: Bd21,drought,rep18

value: drought


title: Muscle_Aging_rep1(CUT&Tag)

description: Library name: Sample21


title: PC9 EF1a-NKX2-1 Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R063


title: Bd3-1,control,rep20


title: PC9 hPGK-NKX2-1 Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R061


title: PC9 hPGK-NKX2-1 Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R062


title: MRC5_stretch_4


title: PC9 UBC-NKX2-1 Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R066


title: MRC5_static_3


title: Bd3-1,drought,rep20


title: Muscle_Control4_rep2(CUT&Tag)

description: Library name: Sample20


title: Muscle_Control4_rep1(CUT&Tag)

description: Library name: Sample19


title: MRC5_stretch_2


title: PC9 UBC-NKX2-1 Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R065


title: PC9 EF1a-GFP Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R060


title: Muscle_MS-275_rep2(CUT&Tag)

description: Library name: Sample18


title: Bd21,control,rep19


title: Bd3-1,control,rep19


title: MRC5_static_1


title: PC9 EF1a-GFP Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R059


title: Muscle_MS-275_rep1(CUT&Tag)

description: Library name: Sample17


title: Bd21,control,rep18


title: NCI-H441 shNKX2-1(8) Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R106


title: Bd3-1,control,rep18


title: A549_stretch_senescent_6

extract_protocol:
A549 samples were homogeneized in Trizol and total RNA was extracted by isopropanol precipitation.
Libraries were prepared using the Ion Ampliseq Trascriptome Human Gene Expression Kit (Ion Torrent)

value: lung adenocarcinoma epithelial cell

value: cyclic stretch


title: Bd3-1,drought,rep19


title: NCI-H441 shNKX2-1(7) Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R104


title: Sample 9 Mouse Liver, Cold Exposure TFEB ChIP-Seq

city: Madison

first: Thomas

last: Kizzar

state: Wisconsin

address: 711 S Dickinson St Apt 2

department: Biochemistry

institute: University of Wisconsin-Madison

description: Library name: Sample 9 Cold

library_source: genomic

data_processing:
Sequenced reads were checked for: sequencing quality, insert length, read concordance, duplications, and adapters via FastP and then aligned to the mouse genome (UCSC build mm10) via bowtie2 v2.2.5 using the sensitive end-to-end read alignment mode. Aligned reads are sorted and indexed with SAMtools 1.9 and peaks are called at p<0.05 and q<0.05 (separately) using the input/IgG as the background control with the MACS2.  Primary and differential peaks were annotated for their positioning relative to genomic elements with Homer v4.11. De novo and known motif analysis were carried out with Homer. Pathway ontology information was generated by inputting genes differentially bound in cold or RT into geneontology.org for ‘Reactome’ pathway results
Assembly: mm10
Supplementary files format and content: .bdg file format. Aligned with bowtie2 v2.2.5; sorted and indexed with SAMtools 1.9; peak calling using MACS2; annotation with Homer v4.11.

molecule: genomic DNA

source_name: Liver

growth_protocol: Chromatin immunoprecipitation was performed on livers from individually housed male C57BL/6J mice (11 weeks old) that were placed at 4°C without food for 6 hours or kept at RT with ad libitum access to food (n=2 per group). All mice had ad libitum access to water.

extract_protocol:
1. Weigh 100 mg of frozen tissue (25 mg/IP) on dry ice from each sample, place each sample into one well of a 6 well tissue culture dish on wet ice with 1 mL cold PBS + PIC (5 uL PIC (200x)/1mL PBS). Chop liver into small pieces. Transfer chopped liver (with 1mL pipette tip with tip cut off) and PBS to Eppendorf tubes.  2. Add 93.7 uL of 16% EM grade formaldehyde to make a final concentration of 1.5% and incubate at room temp for 10 minutes rotating.  3. Add 110 uL of 10 x glycine per 1mL of PBS + PIC and incubate at room temp for 5 minutes rotating.  4. Centrifuge at 500 g for 5 minutes at 4°C. Remove supernatant, resuspend in 1 mL cold PBS + PIC and spin down again at 500 g for 5 minutes at 4°C. Remove supernatant and resuspend in 1mL cold PBS + PIC  5. Transfer to the 2mL Dounce on ICE and Dounce with pestle A for 10 strokes, followed by pestle B for 20 strokes. Transfer samples back to Eppendorf tubes.  6. Spin samples at 2000g for 5 minutes at 4°C.
SimpleChIP Plus Enzymatic Chromatin IP Kit was used according to manufacturer’s instructions. Briefly, 100mg of tissue was used per mouse and two immunoprecipitations were performed with rabbit anti-TFEB antibody, and two immunoprecipitations were performed with normal rabbit IgG control. ChIP DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit. Purified immunoprecipitated and input DNA was quantified and assessed for sheering using the Qubit dsDNA HS Assay Kit and Agilent DNA HS chip, respectively. Samples were prepared according the TruSeq ChIP Sample Preparation kit. Libraries were size selected for an average insert size of 350 bp using SPRI-based bead selection. Quality and quantity of the finished libraries were assessed using an Agilent Tapestation and Qubit dsDNA HS Assay Kit, respectively. Paired end 150bp sequencing was performed on the NovaSeq 6000 by the UW-Madison Biotechnology Center.

treatment_protocol: Liver samples were flash frozen and stored at -80 degrees Celcius after harvest and then dry weighed at ~100 mg tissue per sample for extraction.

value: Liver

value: 6 Hours, Cold Exposure


title: Sample 10 Mouse Liver, Cold Exposure TFEB ChIP-Seq

description: Library name: Sample 10 Cold


title: Sample 4 Mouse Liver, Room Temperature TFEB ChIP-Seq

description: Library name: Sample 4 RT

value: Room Temperature


title: NCI-H441 shNKX2-1(8) Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R105


title: A549_stretch_senescent_5


title: Bd21,drought,rep17


title: A549_stretch_senescent_4


title: NCI-H441 shNKX2-1(7) Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R103


title: Sample 2 Mouse Liver, Room Temperature TFEB ChIP-Seq

description: Library name: Sample 2 RT


title: A549_doxo_2

value: Doxorubicin


title: Bd21,control,rep17


title: NCI-H441 shNKX2-1(6) Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R102


title: A549_doxo_3


title: Bd21,control,rep27


title: NCI-H441 shNKX2-1(6) Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R101


title: Bd3-1,control,rep17


title: Bd3-1,drought,rep18


title: NCI-H441 shNKX2-1(5) Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R100


title: A549_stretch_senescent_7


title: LLC cell line, serum-starved, 24h, rep4

city: Wuhan

first: Xinghui

last: Cao

address: Hangkong Road 13, Wuhan, China

institute: Huazhong University of Science and Technology

description: Library name: Star-4

data_processing:
After the integrity of RNA was further verified by 1.0% agarose gel electrophoresis, paired-end sequencing was performed on the Illumina Novaseq 6000 sequencing platform to obtain high-quality transcriptome outcomes. Total RNA was subjected to data processing and quality control, including obtaining the high-quality clean reads, detecting the stability of AT and CG and analyzing redundancy of reads.
Assembly: mm10
Supplementary files format and content: tab-delinited text file includeds raw counts for each Sample
Supplementary files format and content: txt file include FPKM for each Sample

source_name: LLC cell line

growth_protocol: LLC cell lines were cultured in DMEM (Gibco) supplemented with 10% FBS (Newzerum) at 37 °C in 5% CO2-95% air.

extract_protocol:
Two phenol-chloroform methods were used to purify RNA.
First, isolate the total RNA from the specimens by employing suitable methodologies, such as the phenol-chloroform extraction technique, which exploits the differential solubility of RNA in organic solvents, or column-based purification systems that rely on the specific binding properties of RNA to stationary phases. Subsequently, conduct a rigorous quality control assessment on the RNA samples to guarantee their structural integrity and high purity. This can be accomplished by visualizing the 28S and 18S ribosomal RNA (rRNA) bands on an electropherogram or agarose gel, where the intensity and distinctness of these bands serve as indicators of RNA integrity. Additionally, measure the RNA Integrity Number (RIN) using a bioanalyzer, which provides a quantitative evaluation of RNA quality based on its fragmentation pattern. In the case of whole-transcriptome sequencing, it is imperative to deplete ribosomal RNA (rRNA) to selectively enrich the transcripts of biological interest. For messenger RNA sequencing (mRNA-seq), specifically target and enrich polyadenylated (poly-A) transcripts, which are characteristic of mature mRNAs. Following these enrichment steps, convert the RNA into complementary DNA (cDNA) through the process of reverse transcription, utilizing reverse transcriptase enzymes that catalyze the synthesis of DNA from an RNA template. Subsequently, ligate adapters to the cDNA fragments. These adapters play a crucial role in the subsequent sequencing process, providing essential binding sites for the sequencing platform and enabling the proper orientation and attachment of the cDNA molecules. Finally, carry out polymerase chain reaction (PCR) amplification to exponentially increase the quantity of DNA, thereby constructing the cDNA library. Once the library is successfully constructed, it is primed and ready for sequencing on the appropriate next-generation sequencing platform, which will generate the necessary data for downstream transcriptomic analysis.

treatment_protocol: LLC cells stimulated with UV or MW for 24 hours were collected.

value: LLC cell line

value: lung cancer cells

tag: time


title: LLC cell line, serum-starved, 24h, rep2

description: Library name: Star-2


title: LLC cell line, serum-starved, 24h, rep3

description: Library name: Star-3


title: A549_stretch_Non_senescent_8

description: A549 were exposed to cyclic stretch for 24 hours and after 6 days in culture those negative for Bgal were sorted

tag: senescent

value: No


title: LLC cell line, serum-starved, 24h, rep1

description: Library name: Star-1


title: Bd21,control,rep16


title: NCI-H441 shNKX2-1(2) Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R097


title: LLC cell line, ultraviolet irradiation, 24h, rep4

description: Library name: UV-4


title: Bd21,drought,rep15


title: NCI-H441 shNKX2-1(2) Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R098


title: A549_stretch_Non_senescent_6


title: Bd21,drought,rep16


title: A549_stretch_Non_senescent_7


title: A549_stretch_Senescent_5

description: A549 were exposed to cyclic stretch for 24 hours and after 6 days in culture those positive for Bgal were sorted

value: Yes


title: A549_doxo_1


title: NCI-H441 shNKX2-1(1) Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R095


title: NCI-H441 shNKX2-1(1) Set2 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R096


title: Bd3-1,drought,rep17


title: Bd3-1,control,rep15


title: A549_stretch_Senescent_4


title: LLC cell line, microwave, 24h, rep4

description: Library name: MW-4


title: LLC cell line, ultraviolet irradiation, 24h, rep2

description: Library name: UV-2


title: Bd3-1,control,rep16


title: A549_stretch_Non_senescent_2


title: Bd3-1,drought,rep16


title: NCI-H441 shLuc RNA-seq Rep2 Set2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R094

value: shLuc


title: LLC cell line, microwave, 24h, rep3

description: Library name: MW-3


title: Bd21,control,rep15

value: leaf


title: NCI-H441 shLuc RNA-seq Rep1 Set2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R093


title: A549_stretch_Senescent_1


title: NCI-H1975 hPGK-NKX2-1 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R058


title: LLC cell line, ultraviolet irradiation, 24h, rep3

description: Library name: UV-3


title: Bd21,drought,rep14

value: bulk


title: NCI-H441 shNKX2-1(5) Set2 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R099

value: lung adenocarcinoma


title: LLC cell line, microwave, 24h, rep1

description: Library name: MW-1


title: CN 30478 [S001C27]

city: Saskatoon

first: Isobel

last: Parkin

address: 107 Science Pl

institute: Agriculture and Agri-Food Canada

data_processing:
Raw RNA-seq data were filtered using Trimmomatic (version 0.32) with the following settings (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10; SLIDINGWINDOW:4:15; LEADING:15; TRAILING:15; MINLEN:55) to remove adapter and low-quality sequences. For expression profiling, clean reads were aligned to the C .sativa reference genome using STAR (version 2.7.10a) and gene expression levels were summarized by featureCounts (version 2.0.1).
Assembly: Camelina sative; GCF_000633955.1
Supplementary files format and content: raw_counts.txt, which contains the raw count number summarized by featureCounts

organism: Camelina sativa

source_name: Leaves

extract_protocol:
We collected the fully expanded true leaves from the young seedlings of C .sativa to extract their total RNA using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
The concentration and integrity of total RNA were examined by BioAnalyzer with RNA 6000 Nano Kit (Agilent). cDNA sequencing libraries were constructed according to the standard TruSeq RNA library preparation guide

value: Leaves

value: plant cell

tag: flower time_(days_to_50_%_flowering)


title: Bd21,control,rep14

value: control


title: LLC cell line, ultraviolet irradiation, 24h, rep1

description: Library name: UV-1


title: Licalla [S001C39]

value: Licalla


title: LLC cell line, control, 24h, rep4

description: Library name: Control-4


title: NCI-H1975 hPGK-NKX2-1 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R057


title: A549_stretch_Senescent_3

value: lung adenocarcinoma epithelial cell

value: cyclic stretch


title: NCI-H1975 EF1a-NKX2-1 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R056


title: Bd21,drought,rep13

value: drought


title: LLC cell line, control, 24h, rep3

description: Library name: Control-3


title: CN 30478 [S001C1F]


title: NCI-H1975 EF1a-NKX2-1 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R055


title: Bd3-1,drought,rep15


title: CN 30478 [S001C1D]


title: Bd3-1,control,rep14


title: LLC cell line, control, 24h, rep2

description: Library name: Control-2


title: LLC cell line, microwave, 24h, rep2

description: Library name: MW-2


title: Bd3-1,drought,rep14


title: CN 30475 [S001C1E]


title: CN 30475 [S001C28]


title: LLC cell line, control, 24h, rep1

description: Library name: Control-1


title: Bd3-1,control,rep13


title: CN 30475 [Cs146]


title: Bd21,control,rep13


title: PC9 EF1a-NKX2-1 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R048


title: CN 114270 [Cs137]


title: Bd21,drought,rep12


title: CN 114270 [S001C3F]


title: NCI-H1975 EF1a-GFP RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R054


title: PC9 EF1a-GFP RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R045


title: CN 114270 [Cs121]


title: Bd21,drought,rep11


title: Bd3-1,control,rep12


title: CN 114262 [S001C48]


title: CN 114262 [Cs130]


title: Bd21,control,rep12


title: C57BL/6J, Vehicle 3

city: gwangju

first: Darren

middle: Reece

last: Williams

address: school of life science, 123, Cheomdangwagi-ro, Buk-gu, Gwangju, Republic of Korea

country: South Korea

institute: Gwangju Institute of Science and Technology

description: Library name: Sample 3

data_processing:
Trimmomatic 0.38,HISAT2 version 2.1.0, Bowtie2 2.3.4.1,StringTie version 2.1.3b
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each sample
Supplementary files format and content: csv files incllude TPM values for each sample

source_name: Tibialis anterior muscle

extract_protocol:
RNA was harvested using TRIzol™ Reagent(Invitrogen). Total RNA was used for construction of sequencing libraries
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit following manufacturer's protocols

value: Tibialis anterior muscle

tag: Sex

value: Male

tag: age

value: 24 months

value: Vehicle


title: C57BL/6J, BML-260 3

description: Library name: Sample 6


title: C57BL/6J, BML-260 1

description: Library name: Sample 4


title: Lung memory B cells on day 77 (biol rep 2)

city: Maywood

first: Yee Ling

last: Wu

state: Illinois

address: 2160 S. First Ave

department: Microbiology and Immunology

institute: Loyola University Chicago

description:
Library name: AN-76B
10X Genomics

data_processing:
Barcode processing and gene counting wer performed using Cell Ranger (v8) to generate processed data files for each library.
Assembly: GRCm38 - mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: Lung

extract_protocol:
Mice were injected with fluorophore-conjugated anti-CD45 3 minutes before sacrifice to label circulating cells. Cells were isolated from the lungs by mincing tissue and digesting in 2 mL solution of 750 U/mL collagenase I and 200 U/mL DNase I in RPMI for 45 minutes at 37 C. Digested lungs were passed through 70 micron cell strainers, diluted with 10 mL of 30% Percoll in RPMI and centrifuged for 930 g for 10 minutes with no brake. Red blood cells were lysed for 5 mins at RT in ACK lysis buffer and cells were washed and resuspended in PBS + 2% FBS. Cells were isolated from mediastinal lymph nodes by mushing through 70 micron cell strainers followed by washing and resuspending in PBS + 2% PBS. Isolated cells were stained with anti-CD19, anti-CD38, anti-GL7, and anti-IgD antibodies and resuspended in PBS + 2% FBS + DAPI (1:2000).Cells were sorted as live (DAPI negative), non-circulating (i.v. anti-CD45 negative), B220+ CD38+ GL7- IgD-. Sorted cells were washed and resuspended in PBS without calcium or magnesium + 0.05% BSA.
Libraries were prepared using 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3 (Dual Index). 2 biological replicates per time point (day 21 and day 77) were included and 2,500 cells per sample were loaded into individual wells of Chromium Next GEM Chip G and partitioned into Gel Bead-In Emulsions (GEM) and barcoding by 10X Genomics Chromium Controller. Reverse transcription, cDNA amplification, and library construction were performed according to manufacturer's instructions including addition of Illumina i5 and i7 index sequences.

treatment_protocol: Ragweed pollen and ovalbumin (OVA) were administered to mice intranasally for 5 days under isofluorane anesthesia in week 1 and 5 days of OVA alone in weeks 2 and 3.

value: Lung

value: Memory B cells

value: BALB/cJ

value: 16-17 weeks


title: PC9 EF1a-NKX2-1-dTag 2hr-dTagV-1 Rep2

description:
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1_Rep2
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A086

data_processing:
We analyzed our ATAC-seq data using a pipeline modeled off PEPATAC (Smith et al., 2021). We used skewer (v. 0.2.2) to pair reads and remove any Nextera adapters from fastq files. We performed two rounds of read removal, mapping paired-end reads to the rCRSd (mtDNA) and human_rDNA reference genomes from refgenie (http://refgenomes.databio.org/index), using bowtie2 (v. 2.2.9) and mapping parameters (-k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --un-conc $dir), and retaining unmapped reads to either genome. We then mapped reads to the hg38 (GRCh38_noalt_as) bowtie2 reference genome using parameters (--very-sensitive -X 2000).
We filtered reads using samtools view (-f 2 -q 10 -@ 8 -b) for quality and then using picard (v. 2.27.4) (MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true). We also quantified insert metrics using picard (CollectInsertSizeMetrics, M=0.5).
We converted each ATAC-seq BAM file to a bed file using bedtools bamtobed. For each read, we corrected the Tn5 insertion bias for (-4/+5 for –/+ strand) in the bed tile using awk (awk 'BEGIN {OFS="\t"} {if ($6 =="+") print $1,$2-4,$2-4; else print $1,$3+5,$3+5 }'). We then sorted these Tn5 sites, and removed any sites that corrected to outside the hg38 reference genome.
We used bedtools makewindows (-w 100) (v. 2.26.0) to make 100bp windows of the chr1-22,X,Y for hg38. We used bedtools map (-c 2 -o count) to map the individual Tn5 cut sites to the 100bp genome-wide windows. We normalized this bedgraph file such that each 100bp window is the number of Tn5 cut sites per 10M Tn5 cut sites mapped to hg38. We converted this to a bigwig for visualization using bedGraphToBigWig.
For ATAC-seq differential analyses, we merged all ATAC-seq BAM files for a cell line assayed (NCI-H2087, NCI-H441, NCI-H1975, PC9), and called peaks on this merged BAM file using macs2 (v. 2.1.1) with parameters (-q 1e-3 -f BAMPE --nomodel). We used the summits generated by this peak calling, extended by 200bp on each side to generate 400bp windows, and filtered for peaks outside hg38. We mapped Tn5 corrected cut sites to these windows using bedtools map. These counts were used for DESeq2 differential analysis—differential peaks were called based on a Bonferroni-corrected p-value ≤ 1e-2 and a fold-change ≥ 1.5.
Assembly: GRCh38
Supplementary files format and content: bw - bigwig of Tn5 cut sites in 100bp windows genome-wide normalized per 10M insertions in called peaks by cell line
Supplementary files format and content: csv - raw counts mapped to each ATAC-seq peak called by cell line.

extract_protocol:
ATAC-seq samples were prepared according to the Omni-ATAC protocol (Corces et al., 2017). Cells were tagmented using Illumina Tn5 enzyme, purified using a Zymo DNA Clean and Concentrator-5 Kit.
ATAC-seq gDNA samples were PCR amplified for 5 cycles using NEBNext Ultra II Master Mix. Additional amplification was determined using qPCR on a QStudio 6 FLX real-Time PCR System, with the only modification being inclusion of ROX passive dye for qPCR. Samples were amplified for 2-3 additional cycles, column purified again using a post-ATAC-seq Zymo DNA Clean and Concentrator-5 Kit. Libraries were quantified by qPCR or Qubit and pooled. ATAC-seq libraries were sequenced by Broad Walk-Up Sequencing on a Nextseq 500 using 2x40bp sequencing.

treatment_protocol: Cells were spinfected with constructs at day 0, changed over to hard selection (1µg/mL puromycin) on day 1, then reduced to low selection (0.5µg/mL puromycin) on day 4. On day 7 or day 10 post-infection, cells were counted using a ViCell XR, and 50K fresh cells were harvested for ATAC-seq.


title: Lung memory B cells on day 77 (biol rep 1)

description:
Library name: AN-76A
10X Genomics


title: C57BL/6J, BML-260 2

description: Library name: Sample 5


title: Bd21,drought,rep10

value: leaf

value: bulk


title: PC9 EF1a-NKX2-1-dTag 2hr-dTagV-1 Rep1

description:
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1_Rep1
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A085

value: lung adenocarcinoma


title: CN 113760 [S001C52]

value: Leaves

value: plant cell


title: CN 113760 [S001C3D]


title: Bd21,control,rep11

value: control


title: PC9 EF1a-NKX2-1-dTag 2hr-dTagV-1NEG Rep2

description:
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_Rep2
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A084


title: Lung memory B cells on day 21 (biol rep 1)

description:
Library name: AN-21A
10X Genomics

value: 8-9 weeks


title: PC9 EF1a-NKX2-1 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R047


title: PC9 EF1a-NKX2-1-dTag 2hr-dTagV-1NEG Rep1

description:
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_Rep1
PC9_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A083


title: Bd3-1,drought,rep12


title: CN 113760 [Cs085]


title: PC9 EF1a-GFP-dTag 2hr-dTagV-1 Rep1

description:
PC9_EF1a-GFP-dTag_2hr-dTagV-1_Rep1
PC9_EF1a-GFP-dTag_2hr-dTagV-1_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A081


title: Bd3-1,control,rep11


title: PC9 EF1a-GFP-dTag 2hr-dTagV-1 Rep2

description:
PC9_EF1a-GFP-dTag_2hr-dTagV-1_Rep2
PC9_EF1a-GFP-dTag_2hr-dTagV-1_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A082


title: WT scRNAseq

city: Palo Alto

first: Alex

last: Dalal

state: California

address: CT Surgery, 870 Quarry Rd Ext

department: Cardiothoracic Surgery

institute: Stanford University

description:
Library name: WT_8wk
10x Genomics

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from NovaSeq 6000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) genome, cell barcodes and unique molecular identifiers were filtered and corrected using the cellranger count pipeline (cellranger-6.1.2)
The final output filtered expression matrices were imported into the Seurat package in R and built into Seurat objects using the CreateSeuratObject function.
Standard quality control measures were then taken to exclude outliers representing doublets/clumps and free RNA. Cells with greater than 5% mitochondrial gene content were excluded Data normalization, scaling and regression by mitochondrial content were then performed using the SCTransform command in Seurat.
Assembly: mm10
Supplementary files format and content: Processed data files(.csv format) are exported expression matrices from the SCT assay within the Seurat package in R. Columns represent individual cell barcodes, rows represent features (genes) and numerical values represent the normalized expression data.

source_name: Thoracic aorta

extract_protocol:
The aortic root was dissected completely and divided below the aortic valve. The ascending aorta was divided at the takeoff of the brachiocephalic artery. Aortas were transferred to a separate dish and rinsed in HBSS. Specimens were combined into groups with age, genotype, and sex-matched animals as biologic diversity. The aortas were then digested in enzymatic solution containing 2U/mL Liberase TM (Roche #05401127001) and 2U/mL elastase (Worthington #LS002279) in Hanks buffered saline solution (HBSS) for one hour. The cell suspension was filtered through a 70uM strainer, centrifuged and resuspended in cold HBSS. Suspensions were processed with FACS to exclude debris. Samples were then processed using a 10x Genomics microfluidics chip to generate barcoded Gel Bead-In Emulsions (GEMs) according to manufacturer protocols.
Individual sample libraries were generated from single cell GEM captures using the Chromium 3' version 3 library prep protocol (10X Genomics). QC was performed following cDNA generation and final library construction.

value: Thoracic aorta

value: 8 weeks

value: WT


title: Bd21,drought,rep9

value: drought


title: LDS scRNAseq

description:
Library name: LDS_8wk
10x Genomics

value: pooled male and female


title: CN 113757 [S001C40 ]


title: CN 113757 [Cs086]


title: NCI-H1975 EF1a-GFP RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R053


title: C57BL/6J, Vehicle 2

description: Library name: Sample 2

value: Tibialis anterior muscle

value: Male

value: 24 months

value: Vehicle


title: PC9 EF1a-GFP RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R046


title: cardiac tissues from mice in SD model group with oxygen treatment,rep2

city: Shanghai

first: Yunkai

last: Zhang

address: 800 Xiangyin Road

institute: Naval Medical University

description:
Library name: Oxygen2
Oxygen2

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads for each sample were generated. Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs).
Assembly: GRCm39
Supplementary files format and content: xls

source_name: cardiac tissues

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: cardiac tissues

tag: strain

value: SD Model with oxygen treatment

tag: batch


title: CN 114262 [S001C54]


title: C57BL/6J, Vehicle 1

description: Library name: Sample 1


title: Bd3-1,drought,rep13

value: leaf

value: bulk


title: Lung memory B cells on day 21 (biol rep 2)

description:
Library name: AN-21B
10X Genomics

value: Lung

value: Memory B cells

value: BALB/cJ


title: CN 113757 [Cs083]

value: Leaves

value: plant cell


title: cardiac tissues from mice in SD model group with oxygen treatment,rep1

description:
Library name: Oxygen1
Oxygen1


title: PC9 EF1a-GFP-dTag 2hr-dTagV-1NEG Rep2

description:
PC9_EF1a-GFP-dTag_2hr-dTagV-1NEG_Rep2
PC9_EF1a-GFP-dTag_2hr-dTagV-1NEG_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A080

value: lung adenocarcinoma


title: Bd3-1,drought,rep11


title: CN 113757 [Cs065]


title: PC9 EF1a-GFP-dTag 2hr-dTagV-1NEG Rep1

description:
PC9_EF1a-GFP-dTag_2hr-dTagV-1NEG_Rep1
PC9_EF1a-GFP-dTag_2hr-dTagV-1NEG_merge.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A079


title: cardiac tissues from mice in SD model group,rep2

description:
Library name: Model2
Model2

value: WT

value: SD Model


title: CN 113754 [S001C4A]


title: cardiac tissues from mice in SD model group,rep1

description:
Library name: Model1
Model1


title: PC9 hPGK-NKX2-1 RNA-seq Rep1

description:
NKX2-1_RNAseq_TPM.csv
JLP-R049


title: cardiac tissues from mice in Blank group,rep2

description:
Library name: Blank2
Blank2


title: Bd3-1,drought,rep10

value: drought


title: NCI-H1975 EF1a-NKX2-1-dTag 2hr-dTagV-1 Rep1

description:
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1_Rep1
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A093


title: NCI-H1975 EF1a-NKX2-1-dTag 2hr-dTagV-1NEG Rep2

description:
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_Rep2
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A092


title: CN 113754 [S001C32 ]


title: Bd3-1,control,rep9

value: control


title: CN 113754 [S001C29 ]


title: cardiac tissues from mice in Blank group,rep1

description:
Library name: Blank1
Blank1


title: NCI-H1975 EF1a-NKX2-1-dTag 2hr-dTagV-1NEG Rep1

description:
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_Rep1
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1NEG_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A091


title: Bd3-1,control,rep10


title: Bd21,control,rep9


title: CN 113754 [Cs068]


title: NCI-H1975 EF1a-GFP-dTag 2hr-dTagV-1 Rep2

description:
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1_Rep2
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A090


title: WT_1

middle: V.

last: Riella

address: 149 13th Street

department: Medicine

institute: Massachusetts General Hospital

data_processing:
Trimm adaptor with FASTP 0.23.4
Abudance estimation with Salmon 1.10.1 with GRCm39 transcriptome reference
Differential expression analysis and normalization with DESeq2 3.19
Assembly: GRCm39
Supplementary files format and content: CSV is a normalized counts from DESeq2 R package

source_name: Tissue

extract_protocol:
Total RNA was isolated from flow-sorted splenic DCs using RNAeasy Plus (Qiagen).
Dual-indexed libraries were generated using Takara/Clontech Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian reagents (Takara)

value: Tissue


title: CN 113754 [Cs088]


title: Bd21,drought,rep8


title: NCI-H1975 EF1a-GFP-dTag 2hr-dTagV-1 Rep1

description:
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1_Rep1
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A089


title: EKO_2

value: KO


title: NCI-H1975 EF1a-GFP-dTag 2hr-dTagV-1NEG Rep1

description:
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1NEG_Rep1
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1NEG_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A087


title: Bd21,drought,rep7


title: EKO_1


title: CN 113750 [S001C55]


title: CN 113750 [Cs101]


title: Bd21,control,rep8


title: CN 113750 [S001C4B]


title: CN 113746 [S001C4F]


title: PC9 EF1a-NKX2-1 Rep1 Set2

description:
PC9_EF1a-NKX2-1_Rep1_Set2
PC9_EF1a-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A057


title: sgASH1L_3

city: Houston

first: Chenling

last: Meng

state: TX

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

description: 10X Genomics

data_processing:
The raw data of scRNA-seq was processed by CellRanger 6.1.2 (10X Genomics) and then analyzed using Bioturing (https://academic.bioturing.com/login)
Assembly: mm10
Supplementary files format and content: Tap seperated value files and matrix files

source_name: Metastatic bone tumors

extract_protocol:
Control and ASH1L-knockout metastatic bone tumors were dissected, minced, and digested into single-cell suspension using Collagenase A (Sigma, 11088793001) at 37°C for 45min with continuously gentle shaking. The dissociated tissues were centrifuged at 500xg for 5 min, followed by further digestion with 0.25% Trypsin (Corning, 25053CI) at 37°C for 5 min. The samples were filtered using a 70uM strainer (Falcon, 352350) and centrifuged at 500xg at 4°C for 5 min, followed by incubation in 1x RBC lysis buffer (Biolegend, 420302) at RT for 5 min. After washing with cold DMEM, the cells were collected and resuspended in cold PBS containing 0.04% BSA (Ambion, AM2616), followed by measurement of cell number and viability.
The scRNA-seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 30 V3 Reagent Kits (10X Genomics) according to the manufacturer’s recommendations. Libraries were subsequently sequenced on NovaSeq 6000 (Illumina) with a paired-end 50-base pair (50PE) reading strategy.

value: Metastatic bone tumors

value: Murine prostate cancer cellls

value: Male, 6 weeks of age

value: ASH1L Knockout


title: CN 113746 [S001C47]


title: WT_2


title: Bd3-1,drought,rep9

extract_protocol:
Approximately 100mg of tissue was used for RNA extraction using Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer instructions, followed by DNase treatment (On-Column DNase I Digestion Set, Sigma-Aldrich, USA). 25ng of RNA for 214 samples were aliquoted at a normalized concentration of 5 ng/μL for sequencing
MIT BioMicro Center performed RNA-seq library construction and sequencing following the approach of High-Throughput 3' Digital Gene Expression with 26 + 80 bases pair-end run with 6 nucleotide index

value: leaf

value: bulk


title: sgASH1L_2

description: 10X Genomics


title: Bd21,control,rep10


title: Bd3-1,control,rep8


title: Bd21,control,rep7


title: CN 113746 [Cs098]


title: PC9 SFFV-NKX2-1 Rep2 Set2

description:
PC9_SFFV-NKX2-1_Rep2_Set2
PC9_SFFV-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A062


title: NCI-H1975 EF1a-GFP-dTag 2hr-dTagV-1NEG Rep2

description:
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1NEG_Rep2
NCI-H1975_EF1a-GFP-dTag_2hr-dTagV-1NEG_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A088


title: PC9 SFFV-NKX2-1 Rep1 Set2

description:
PC9_SFFV-NKX2-1_Rep1_Set2
PC9_SFFV-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A061


title: sgASH1L_1

description: 10X Genomics


title: Bd21,drought,rep6


title: CN 113742 [S001C60]


title: PC9 hPGK-NKX2-1 Rep2 Set2

description:
PC9_hPGK-NKX2-1_Rep2_Set2
PC9_hPGK-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A056


title: sgASH1L_4

description: 10X Genomics


title: Bd3-1,control,rep7


title: CN 113742 [S001C3C]


title: sgCtrl_3

description: 10X Genomics

value: contorl


title: PC9 hPGK-NKX2-1 Rep1 Set2

description:
PC9_hPGK-NKX2-1_Rep1_Set2
PC9_hPGK-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A055


title: Bd3-1,drought,rep7


title: CN 113742 [Cs095]


title: sgCtrl_2

description: 10X Genomics


title: Bd21,drought,rep5


title: CN 113736 [S001C57]


title: Bd3-1,control,rep6


title: CN 113736 [S001C4C]


title: 24W_scATACseq

city: Ikoma

first: Taito

last: Matsuda

country: Japan

institute: Nara Institute of Science and Technology

description: 10X Genomics

library_source: genomic single cell

data_processing:
Fastq files from sequencing were demultiplexed and then used as input for Cell Ranger (v2.2.0), and aligned to the mm10 reference genome for assignment of reads to single cells. To detect age-related gene expression changes, we conducted an integrated analysis using the IntegrateData function of the Seurat package (v4.1.0). Two datasets were confirmed as anchors using the FindIntegrationAnchors function, after which the anchors were used to integrate the three datasets using the IntegrateData function. We then performed a PCA analysis on the integrated dataset36. Using Seurat’s non-linear dimensional reduction algorithm RunUMAP, we clustered cells using variable genes. Differential gene expression analysis was performed using the FindAllMarkers function in Seurat.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matirix files

source_name: Hippocampus

extract_protocol:
P5, 12w, and 24w Nestin-EGFP mice were euthanized, and each brain was promptly harvested. The DG was quickly microdissected under a dissection scope and minced with a scalpel. The dissociated DG was transferred into prewarmed papain (25 U/mL) solution and incubated at 33 ℃ for 45 min. The suspension was then washed with 2 mL Minimum Essential Medium α (Gibco) containing 5% BSA to stop enzyme activity, mechanically dissociated by gentle pipetting with a fire-polished Pasteur pipette, and centrifuged at 130 × g for 5 min. The cell pellet was then resuspended in 2 mL of Hanks’ balanced salt solution (HBSS) containing 250 U/mL DNase and centrifuged at 130 × g for 5 min, after which the cells were suspended in HBSS. The cells were sorted on a FACS Aria II (BD Biosciences), with 7-AAD (559925, BD Pharmingen) added to exclude nonviable cells from the analysis. Cells dissociated from the DG of WT mice were used to draw gates for EGFP+ and EGFP− cell populations. The EGFP+ cells were sorted into N2 medium and centrifuged at 200 × g at 4 ℃ for 10 min. The supernatant was carefully removed, leaving 30 µL to resuspend the cell pellet. One microliter of cells was mixed with 10 µL Trypan Blue to determine cell viability. For scRNA-seq and scATAC-seq analyses, 700–1200 cells/µL were used.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics).

value: Hippocampus

value: EGFP-positive cells


title: PC9 UBC-NKX2-1 Rep1 Set2

description:
PC9_UBC-NKX2-1_Rep1_Set2
PC9_UBC-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A059


title: 12W_scATACseq

description: 10X Genomics


title: NCI-H1975 EF1a-NKX2-1-dTag 2hr-dTagV-1 Rep2

description:
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1_Rep2
NCI-H1975_EF1a-NKX2-1-dTag_2hr-dTagV-1_merge.bw
NCI-H1975_NKX2-1_ATAC_RawCts.csv
JLP-A094


title: Bd21,control,rep6

data_processing:
Raw sequence reads were trimmed by Trimmomatic (trimmomatic-0.39) with 2:30:10:1:true and Cutadapt (v2.10)to remove adapters and poly(A) tails with -a A{20} and -m 25
Reads were aligned to reference transcriptome using Bowtie2 (v2.4.0) with seedlength -L 25 and mismatch allowance -n 2 and other default parameters suggested by next step RSEM
Reads with the same unique molecular identifier (UMI) and aligned to the same genes were removed to eliminate PCR bias during library generation using a custom script
RNA-Seq by Expectation-Maximization (RSEM, 1.3.3) was used to estimate counts to account for non-specifically aligned reads with --estimate-rspd
Assembly: Bdistachyon_556_v3.2.transcript_primaryTranscriptOnly and LT558597 Bd21 plastome
Supplementary files format and content: csv file includes raw counts for each samples


title: PC9 EF1a-GFP Rep2 Set2

description:
PC9_EF1a-GFP_Rep2_Set2
PC9_EF1a-GFP_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A054


title: P5_scATACseq

description: 10X Genomics


title: PC9 EF1a-GFP Rep1 Set2

description:
PC9_EF1a-GFP_Rep1_Set2
PC9_EF1a-GFP_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A053


title: Bd3-1,drought,rep6


title: CN 113736 [Cs063]

value: Leaves

value: plant cell


title: NCI-H441 shNKX2-1(8) Rep2 Set2

description:
NCI-H441_shNKX2-1_8_Rep2_Set2
NCI-H441_shNKX2-1_8_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A052

value: lung adenocarcinoma


title: Bd21,drought,rep4


title: CN 113731 [S001C34]


title: sgCtrl_1

description: 10X Genomics


title: PC9 UBC-NKX2-1 Rep2 Set2

description:
PC9_UBC-NKX2-1_Rep2_Set2
PC9_UBC-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A060


title: CByB6F1 normal + BMF pool 1

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

data_processing:
The raw data was processed through the perl scripts developed by parse Biosciences (https://www.parsebiosciences.com/technology/data-analysis/)
Paired-end reads were mapped to the mm10 genome with Hisat2 v2.0.5
Assembly: mm10

source_name: Mouse Bone Marrow

extract_protocol: Libraries were generted using the cell fixation and single-cell whole-transcriptome kits from Parse Biosciences (Seattle, WA).

treatment_protocol: To enrich for megakaryocytes, BM Cells were flushed from sterna and tibias, and filtered through 100 um mesh, subsequently passed through a 10 µm pluriStrainer™. Small cells passed through the strainer, while large cells were retained above the strainer. Large cells were then eluted from the top of the pluriStrainer™. BM cells enriched with MKs were processed using the cell fixation and single-cell whole-transcriptome kits from Parse Biosciences (Seattle, WA) according to the manufacturer’s instructions. Cells from 20 BMF mice at day 14 and from 10 normal CByB6F1 mice were pooled as BMF and control groups respectively.

value: male

value: 2-5 months

tag: subject

value: pool 1


title: CByB6F1 normal + BMF pool 2

value: pool 2


title: NCI-H441 shNKX2-1(8) Rep1 Set2

description:
NCI-H441_shNKX2-1_8_Rep1_Set2
NCI-H441_shNKX2-1_8_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A051


title: CN 113731 [S001C21 ]


title: Bd21,drought,rep3

value: drought


title: Bd3-1,control,rep5

value: control


title: CN 113731 [Cs087]


title: NCI-H441 shNKX2-1(7) Rep1 Set2

description:
NCI-H441_shNKX2-1_7_Rep1_Set2
NCI-H441_shNKX2-1_7_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A049


title: CN 113736 [S001C3E ]


title: Bd3-1,drought,rep8


title: CN 113731 [Cs056]


title: Bd3-1,drought,rep5


title: SMARTA, rLCMV, ctrl

city: Milano

first: Chiara

last: Laura

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

data_processing:
Raw sequencing data were demultiplexed with the mkfastq application (Cell Ranger v.6.0.2). UMI-Tools (v.1.0.0) whitelist and extract commands were used to identify and select the number of cell barcodes to use in downstream analysis. Reads were mapped to the reference genome using STAR v.2.5.3a and assigned to genes with featureCounts v.1.6.4. GRCm38 was used as the reference genome. Bam files were sorted with samtools (v1.9). Finally, Umi-Tools count was used to processing the UMIs aligned to each gene in each cell to find the number of distinct, error-corrected UMIs mapping to each gene. The UMI count tables of each cellular barcode were used for further analysis.
Single cell data analysis was performed using Seurat (v4.0.2) (Stuart et al., 2019).
High quality cells were obtained after applying a filter of at least 200 genes expressed per cell and only genes expressed in at least 5 cells were retained. Moreover, cells with more than 10% of reads mapped to mitochondrial genes were also excluded from the analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata with unique cell name, UMAP coordinates, condition and cluster

source_name: popliteal LNs

extract_protocol: Single cells were processed on the Chromium platform (10x) using the Chromium Next GEM Single Cell 3’ v3.1 (Dual Index). After quality controls and quantification on TapeStation instrument (Agilent), libraries were sequenced on NovaSeq 6000 platform (Illumina) generating around 18,000 reads/cell

value: popliteal LNs

value: CD4 T cells

tag: infection

value: rLCMV


title: SMARTA, Naive


title: Bd21,control,rep5

city: Cambridge

last: Yun

institute: MIT

value: leaf


title: CN 113726 [S001C43 ]


title: Bd3-1,drought,rep4

value: bulk


title: NCI-H441 shNKX2-1(7) Rep2 Set2

city: Boston

last: Meyerson

institute: Dana-Farber Cancer Institute

description:
NCI-H441_shNKX2-1_7_Rep2_Set2
NCI-H441_shNKX2-1_7_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A050


title: NCI-H441 shNKX2-1(6) Rep2 Set2

description:
NCI-H441_shNKX2-1_6_Rep2_Set2
NCI-H441_shNKX2-1_6_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A048


title: CN 113726 [S001C35]


title: NCI-H441 shNKX2-1(5) Rep1 Set2

description:
NCI-H441_shNKX2-1_5_Rep1_Set2
NCI-H441_shNKX2-1_5_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A045


title: SMARTA, rLCMV, rep2

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata with unique cell name, plate barcode, cell barcode and cell type

extract_protocol: Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. Briefly, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}


title: SMARTA, rLCMV, aIFNg


title: SMARTA, rLCMV, rep4


title: SMARTA, rLCMV, rep3


title: Bd21,drought,rep2

first: Jie

address: 77 MASS


title: NCI-H441 shNKX2-1(5) Rep2 Set2

first: Matthew

address: 44 Binney St

description:
NCI-H441_shNKX2-1_5_Rep2_Set2
NCI-H441_shNKX2-1_5_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A046


title: SMARTA, rLCMV, rep1


title: Bd21,control,rep4


title: CN 113726 [Cs064]


title: NCI-H441 shNKX2-1(2) Rep2 Set2

description:
NCI-H441_shNKX2-1_2_Rep2_Set2
NCI-H441_shNKX2-1_2_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A042


title: Bd3-1,control,rep4


title: PC9 hPGK-NKX2-1 RNA-seq Rep2

description:
NKX2-1_RNAseq_TPM.csv
JLP-R050

data_processing:
Paired-end RNA-seq reads were trimmed using Trimmomatic (v. 0.36) for properly paired reads and to remove any TruSeq adapter sequences. RNA-seq reads were mapped to the human reference genome (hg38) using STAR (Dobin et al., 2013) version 2.3.1 with default parameters.
Raw read counts were generated with Rsubread featureCounts against the hg38 refFlat annotation from UCSC—reads were allowed to map to multiple annotations (allowMultiOverlap=T) but we only counted the primary alignment of each read (primaryOnly=T). Significance was assessed using the R package DESeq2. Significantly changing genes were assessed with a Bonferri-corrected p value≤1e-3 and a fold change≥1.5 to determine set of significantly changing genes. Transcripts per million (TPM) were determined from featureCounts raw counts normalized per million total reads.
Assembly: GRCh38
Supplementary files format and content: Transcripts per million normalized reads for the hg38 refFlat annotation.

extract_protocol:
RNA was extracted from cell pellets stored at -80°C using an RNeasy Mini Kit (Qiagen) with on-column DNase digestion using RNase-Free DNase Set (Qiagen). RNA was eluted in RNase-free ddH2O, and quantified by nanodrop. RNA integrity was determined using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Electrophoresis Bioanalyzer, all RNA samples used for RNA-seq had a RNA integrity number (RIN) > 9.0.
1000-2000µg of RNA was polyA-selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB). Final libraries were quantified using Qubit, pooled, and sequenced by Broad Walk-Up Sequencing on a Nextseq 500 using 2x40bp sequencing.


title: CN 113724 [S001C5B]


title: CN 113726 [S001C5E]


title: SMARTA, rVSV, rep6

value: rVSV


title: Bd3-1,control,rep3


title: SMARTA, rVSV, rep5


title: NCI-H441 shNKX2-1(6) Rep1 Set2

description:
NCI-H441_shNKX2-1_6_Rep1_Set2
NCI-H441_shNKX2-1_6_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A047


title: CN 113724 [S001C44]


title: NCI-H441 shNKX2-1(2) Rep1 Set2

description:
NCI-H441_shNKX2-1_2_Rep1_Set2
NCI-H441_shNKX2-1_2_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A041


title: Bd21,control,rep3


title: NCI-H441 shNKX2-1(1) Rep2 Set2

description:
NCI-H441_shNKX2-1_1_Rep2_Set2
NCI-H441_shNKX2-1_1_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A040


title: SMARTA, rVSV, rep4


title: CN 113724 [Cs089]


title: NCI-H441 shNKX2-1(1) Rep1 Set2

description:
NCI-H441_shNKX2-1_1_Rep1_Set2
NCI-H441_shNKX2-1_1_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A039


title: NCI-H441 shLuc Rep2 Set2

description:
NCI-H441_shLuc_Rep2_Set2
NCI-H441_shLuc_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A038

value: shLuc


title: CN 113723 [S001C2F ]


title: Bd3-1,drought,rep3


title: SMARTA, rVSV, rep3


title: SMARTA, rVSV, rep2


title: CN 113723 [S001C3B]


title: Bd21,control,rep2


title: Bd3-1,control,rep2


title: CN 113723 [Cs081]


title: NCI-H2087 shNKX2-1(8) RNA-seq Rep2

description:
JLP-R038
NKX2-1_RNAseq_TPM.csv


title: Bd3-1,drought,rep2


title: NCI-H441 shLuc Rep1 Set2

description:
NCI-H441_shLuc_Rep1_Set2
NCI-H441_shLuc_merge_Set2.bw
NCI-H441_shNKX2-1_ATAC_RawCts.csv
JLP-A037


title: SMARTA, rVSV, rep1


title: CN 113723 [Cs060]


title: SMARTA, Naive, rep4


title: Bd21,drought,rep1


title: CN 113721 [S001C41]


title: NCI-H2087 shNKX2-1(8) RNA-seq Rep1

description:
JLP-R037
NKX2-1_RNAseq_TPM.csv


title: NCI-H2087 shNKX2-1(1) RNA-seq Rep2

description:
JLP-R036
NKX2-1_RNAseq_TPM.csv


title: CN 113721 [S001C37]


title: SMARTA, Naive, rep3


title: Bd3-1,drought,rep1


title: Bd21,control,rep1


title: NCI-H2087 shNKX2-1(1) RNA-seq Rep1

description:
JLP-R035
NKX2-1_RNAseq_TPM.csv


title: CN 113721 [Cs090]


title: SMARTA, Naive, rep2


title: Bd3-1,control,rep1


title: NCI-H2087 shLuc RNA-seq Rep2

description:
JLP-R034
NKX2-1_RNAseq_TPM.csv


title: WT female scRNAseq

description:
10x Genomics
processed_data_mouse.csv

data_processing:
The sequenced data were processed into expression matrices with the ‘Cell Ranger Single cell software suite 3.1.0’. Raw base-call files from NovaSeq 6000 sequencer were demultiplexed to first generate FASTQ files using the cellranger mkfastq pipeline.
Reads were aligned to the mouse (mm10-3.0.0) genome, cell barcodes and unique molecular identifiers were filtered and corrected using thecellranger countpipeline (cellranger-6.1.2)
The final output filtered expression matrices were imported into the Seurat package in R and built into Seurat objects using the CreateSeuratObject function.
Standard quality control measures were then taken to exclude outliers representing doublets/clumps and free RNA. Cells with greater than 5% mitochondrial gene content were excluded Data normalization, scaling and regression by mitochondrial content were then performed using the SCTransform command in Seurat.
Assembly: mm10
Supplementary files format and content: Processed data files(.csv format) are exported expression matrices from the SCT assay within the Seurat package in R. Columns represent individual cell barcodes, rows represent features (genes) and numerical values represent the normalized expression data.

value: Thoracic aorta

value: Female

value: 24 weeks

value: WT


title: NCI-H2087 shLuc RNA-seq Rep1

description:
JLP-R033
NKX2-1_RNAseq_TPM.csv

value: lung adenocarcinoma


title: WT male scRNAseq

description:
10x Genomics
processed_data_mouse.csv

value: Male


title: CN 113717 [S001C5D ]

value: Leaves

value: plant cell


title: Hybrid,drought,rep5

data_processing:
Raw sequence reads were trimmed by Trimmomatic (trimmomatic-0.38) with 2:30:10:1:true and Cutadapt (v 3.7) to remove adapters and poly(A) tails, and filter for >75nt reads with -a A{20} -m 75
Reads were aligned to diploid genome using Bowtie (v1.2.2) -q -a --best --strata --sam -v 3 -m 100
Raw counts were estimated using emase from alntools (v0.1.1) -m 4 to account for non-specifically aligned reads
Assembly: Reads were aligned to Bdistachyon_556_v3.0.fa using STAR (v2.6.1b) with --alignSJoverhangMin 30 --alignSJDBoverhangMin 10 with two passes
Assembly: Variants calling was done with gatk (v4.2.5.0) with --dont-use-soft-clipped-bases, and variants are filtered by QD < 2.0, QUAL < 30.0, SOR > 3.0, FS > 60.0, MQ < 20.0, MQRankSum < -12.5, ReadPosRankSum < -8.0, then filtered with vcffilter (v1.0.2) -f "FILTER = PASS"|vcffilter -g "GT = 1/1" | vcffixup - | vcffilter -f "AC > 0" and only variants found in more than 50% of the samples are included with e.g., bcftools (v1.8) isec -n +3
Assembly: Deploid genome (Bd21 and Bd3-1) and gtf is generated with variants called after filteration, using g2gtools (v0.2.7) from the genome Bdistachyon_556_v3.0.fa and Bdistachyon_556_v3.2.gene_complete.gtf
Supplementary files format and content: csv file includes raw counts for each samples

extract_protocol:
Approximately 100mg of tissue was used for RNA extraction using Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA) according to the manufacturer instructions, followed by DNase treatment (On-Column DNase I Digestion Set, Sigma-Aldrich, USA). 100ng of RNA for samples were aliquoted for sequencing
MIT BioMicro Center performed RNA-seq library construction and sequencing following NEB Ultra II Directional RNA with Poly(A) Selection (New England Biolabs, Ipswich, MA) 150 + 150 bases pair-end run with 8 + 8 nucleotide indexes

value: Hybrid

value: drought


title: CN 113717 [S001C5A ]


title: NCI-H441 shNKX2-1(8) RNA-seq Rep2

description:
JLP-R026
NKX2-1_RNAseq_TPM.csv


title: Hybrid,control,rep5

value: control


title: Bd3-1,drought,rep3


title: LDS female scRNAseq

description:
10x Genomics
processed_data_mouse.csv


title: NCI-H441 shNKX2-1(8) RNA-seq Rep1

description:
JLP-R025
NKX2-1_RNAseq_TPM.csv


title: LDS male scRNAseq

description:
10x Genomics
processed_data_mouse.csv


title: Hybrid,control,rep4


title: CN 113717 [Cs070]


title: NCI-H441 shNKX2-1(1) RNA-seq Rep2

description:
JLP-R024
NKX2-1_RNAseq_TPM.csv


title: CN 113717 [Cs067]


title: Bd3-1,control,rep5


title: CD8-WT1(WT1)

city: Beijing

first: Yujia

last: Wang

state: Beijing

address: 38 Xueyuan Road, Haidian District

department: Department of Immunology

institute: Peking university school of basic medical sciences

data_processing:
Quality control of Raw data: raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts.
Paired-end clean reads were aligned to the reference genome using Hisat2. Featurecount was used to count the reads numbers mapped to each gene.
EdgeR was used for differential expression analysis. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
GO and KEGG enrichment analysis of differentially expressed gene sets were implemented by the topG （http://www.bioconductor.org/packages/release/bioc/html/topGO.html） and KOBAS package, respectively.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CD8+ T cells

extract_protocol:
On the day10 of LCMV Cl13 infection, 2×106 CD8+ T cells were sorted by flow cytometry and collected. RNA was purified and concentration were then examined using NanoDrop 2000, RNA integrity and quantity were measured using the Agilent 2100/4200 system.
The library was constructed using standard Illumina library construction process. After library construction, the concentration of library was measured by the Qubit fluorometer. The accurate concentration of cDNA library was again examined using qPCR. The size distribution of library was detected by agarose gel electrophoresis. After library preparation and pooling of different samples, the samples were subjected for Illumina sequencing.

value: CD8+ T cells


title: SMARTA, Naive, rep1

value: popliteal LNs

value: CD4 T cells


title: CD8-WT2(WT2)


title: CN 113717 [Cs066]

data_processing:
Raw RNA-seq data were filtered using Trimmomatic (version 0.32) with the following settings (ILLUMINACLIP:TruSeq3-PE.fa:2:30:10; SLIDINGWINDOW:4:15; LEADING:15; TRAILING:15; MINLEN:55) to remove adapter and low-quality sequences. For expression profiling, clean reads were aligned to the C .sativa reference genome using STAR (version 2.7.10a) and gene expression levels were summarized by featureCounts (version 2.0.1).
Assembly: Camelina sative; GCF_000633955.1
Supplementary files format and content: raw_counts.txt, which contains the raw count number summarized by featureCounts


title: NCI-H441 shLuc RNA-seq Rep2

description:
JLP-R022
NKX2-1_RNAseq_TPM.csv


title: NCI-H441 shNKX2-1(1) RNA-seq Rep1

description:
JLP-R023
NKX2-1_RNAseq_TPM.csv


title: Hybrid,control,rep3

value: leaf

value: bulk


title: CN 113716 [S001C3A ]


title: CN 113717 [S001C62 ]


title: Bd21,drought,rep3


title: NCI-H441 shLuc RNA-seq Rep1

description:
JLP-R021
NKX2-1_RNAseq_TPM.csv

value: shLuc


title: Hybrid,drought,rep4


title: CN 113716 [Cs078]


title: CD8-KO1(cKO1)


title: CN 113716 [S001C36]


title: NCI-H441 sgNKX2-1 RNA-seq Rep3

description:
JLP-R020
NKX2-1_RNAseq_TPM.csv


title: Bd21,control,rep3


title: Plasmodium falciparum treated with 5mM GlcN (repeat 1)

city: Shenyang

first: Yiwei

address: 120 Dongling Road

institute: Shenyang Agricultural University

description: Library name: B10jia

data_processing:
scRNA-seq filtering and analysis Use Seurat v.2.2 for downstream analysis. Genes expressed in fewer than two cells were filtered out. Cells with more than 200 genes and less than 10% mitochondrial genes were further processed.The variation coefficient of genes was calculated with Seurat. A k-nearest neighbor graph was constructed from Euclidean distances in the space of the first 10 significant principal components. Louvain Modularity optimization algorithm was utilized to cluster the cells in the graph and clustering results were visualized by using t-distributed Stochastic Neighbor Embedding (tSNE) project. The Cells expressing high levels of genes encoding hemoglobin were discarded.
Assembly: PlasmoDB-66_Pfalciparum3D7
Supplementary files format and content: matrix files

organism: Plasmodium falciparum 3D7

source_name: parasite

extract_protocol:
PfAP2-V parasites in the ring, trophozoite, and schizont stages were treated for one cycle in 5 mM GlcN . Parasite survival was monitored using Hoechst 33342 (Beyotime, #C1027, China) according to the manufacturer's instructions, and all pure iRBCs were obtained by sorting using an Aria III flow cytometer (BD Biosciences, USA).
Two single-cell libraries were obtained using the protocol provided with the Chromium™ Single Cell 3 Reagent Kit (V3 Chemistry). The final library pool was sequenced on an Illumina NovaSeq 6000 instrument using 150-base-pair paired-end reads.

value: parasite


title: NCI-H441 sgNKX2-1 RNA-seq Rep2

description:
JLP-R019
NKX2-1_RNAseq_TPM.csv


title: Plasmodium falciparum treated with 0mM GlcN (repeat 1)

description: Library name: B9_


title: CN 113716 [Cs062]

extract_protocol:
We collected the fully expanded true leaves from the young seedlings of C .sativa to extract their total RNA using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s protocol.
The concentration and integrity of total RNA were examined by BioAnalyzer with RNA 6000 Nano Kit (Agilent). cDNA sequencing libraries were constructed according to the standard TruSeq RNA library preparation guide


title: Bd21,drought,rep2

source_name: leaf


title: CN 113706 [S001C46]


title: NCI-H441 sgNT RNA-seq Rep3

description:
JLP-R017
NKX2-1_RNAseq_TPM.csv

value: sgNT


title: Hybrid,control,rep2


title: Plasmodium falciparum treated with βOHB (repeat 3)

data_processing:
scRNA-seq filtering and analysis Downstream analysis was performed with Seurat v.2.2. Data were filtered to remove cells with high mitochondrial reads (>10%), low-quality gene detection (<200 or >10000) and high red blood cell marker gene reads (>10%). Furthermore, Scrublet was used to remove cells that may have been double-celled. Dimensionality reduction of the data was performed by using principal component analysis (PCA) on the basis of the first 2000 highest variable genes. A k-nearest neighbor graph was constructed from Euclidean distances in the space of the first 10 significant principal components. The Louvain modularity optimization algorithm was utilized to cluster the cells in the graph, and the clustering results were visualized using uniform manifold approximation and projection (UMAP).
Assembly: PlasmoDB-66_Pfalciparum3D7
Supplementary files format and content: matrix files

extract_protocol:
P. falciparum 3D7 parasites at the ring, trophozoite, and schizont stages were exposed to IC50 concentrations (7.3 mM) of βOHB for 96 hours (two growth cycles). MitoTracker Green (Invitrogen, #M-7512, USA) was used according to the manufacturer’s instructions to monitor the viability of parasites, and all pure iRBCs were obtained by sorting with an Aria III flow cytometer (BD Biosciences, USA).
The protocol provided in the Chromium™ Single Cell 3 Reagent Kit (V3 Chemistry) was used to obtain six single-cell libraries. The final library pool was sequenced on an Illumina NovaSeq 6000 instrument using 150-base-pair paired-end reads.

value: βOHB


title: Plasmodium falciparum treated with βOHB (repeat 2)


title: Hybrid,drought,rep3


title: PC9 EF1a-NKX2-1 Rep2 Set2

description:
PC9_EF1a-NKX2-1_Rep2_Set2
PC9_EF1a-NKX2-1_merge_Set2.bw
PC9_NKX2-1_ATAC_RawCts.csv
JLP-A058

data_processing:
We analyzed our ATAC-seq data using a pipeline modeled off PEPATAC (Smith et al., 2021). We used skewer (v. 0.2.2) to pair reads and remove any Nextera adapters from fastq files. We performed two rounds of read removal, mapping paired-end reads to the rCRSd (mtDNA) and human_rDNA reference genomes from refgenie (http://refgenomes.databio.org/index), using bowtie2 (v. 2.2.9) and mapping parameters (-k 1 -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --un-conc $dir), and retaining unmapped reads to either genome. We then mapped reads to the hg38 (GRCh38_noalt_as) bowtie2 reference genome using parameters (--very-sensitive -X 2000).
We filtered reads using samtools view (-f 2 -q 10 -@ 8 -b) for quality and then using picard (v. 2.27.4) (MarkDuplicates VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true). We also quantified insert metrics using picard (CollectInsertSizeMetrics, M=0.5).
We converted each ATAC-seq BAM file to a bed file using bedtools bamtobed. For each read, we corrected the Tn5 insertion bias for (-4/+5 for –/+ strand) in the bed tile using awk (awk 'BEGIN {OFS="\t"} {if ($6 =="+") print $1,$2-4,$2-4; else print $1,$3+5,$3+5 }'). We then sorted these Tn5 sites, and removed any sites that corrected to outside the hg38 reference genome.
We used bedtools makewindows (-w 100) (v. 2.26.0) to make 100bp windows of the chr1-22,X,Y for hg38. We used bedtools map (-c 2 -o count) to map the individual Tn5 cut sites to the 100bp genome-wide windows. We normalized this bedgraph file such that each 100bp window is the number of Tn5 cut sites per 10M Tn5 cut sites mapped to hg38. We converted this to a bigwig for visualization using bedGraphToBigWig.
For ATAC-seq differential analyses, we merged all ATAC-seq BAM files for a cell line assayed (NCI-H2087, NCI-H441, NCI-H1975, PC9), and called peaks on this merged BAM file using macs2 (v. 2.1.1) with parameters (-q 1e-3 -f BAMPE --nomodel). We used the summits generated by this peak calling, extended by 200bp on each side to generate 400bp windows, and filtered for peaks outside hg38. We mapped Tn5 corrected cut sites to these windows using bedtools map. These counts were used for DESeq2 differential analysis—differential peaks were called based on a Bonferroni-corrected p-value ≤ 1e-2 and a fold-change ≥ 1.5.
Assembly: GRCh38
Supplementary files format and content: bw - bigwig of Tn5 cut sites in 100bp windows genome-wide normalized per 10M insertions in called peaks by cell line
Supplementary files format and content: csv - raw counts mapped to each ATAC-seq peak called by cell line.


title: NCI-H441 sgNT RNA-seq Rep2

description:
JLP-R016
NKX2-1_RNAseq_TPM.csv


title: CN 113706 [S001C42]


title: Bd3-1,drought,rep2


title: NCI-H441 sgNT RNA-seq Rep1

description:
JLP-R015
NKX2-1_RNAseq_TPM.csv


title: CN 113706 [S001C38]


title: Plasmodium falciparum treated with βOHB (repeat 1)


title: CN 113704 [S001C61]


title: Plasmodium falciparum treated with PBS (repeat 3)

value: PBS


title: NCI-H2087 sgNKX2-1 RNA-seq Rep3

description:
JLP-R014
NKX2-1_RNAseq_TPM.csv

value: lung adenocarcinoma


title: Bd3-1,drought,rep1


title: Bd3-1,control,rep4


title: Plasmodium falciparum treated with PBS (repeat 2)


title: NCI-H2087 sgNKX2-1 RNA-seq Rep2

description:
JLP-R013
NKX2-1_RNAseq_TPM.csv


title: CN 113704 [Cs141]


title: CN 113704 [Cs107]


title: NCI-H441 sgNKX2-1 RNA-seq Rep1

description:
JLP-R018
NKX2-1_RNAseq_TPM.csv


title: Plasmodium falciparum treated with PBS (repeat 1)


title: NCI-H2087 sgNKX2-1 RNA-seq Rep1

description:
JLP-R012
NKX2-1_RNAseq_TPM.csv


title: Bd3-1,control,rep3


title: HEK_tRNAseqKO2_S12_R1_001

city: Frederick

first: Colin

department: RNA Biology Laboratory

institute: NCI

description:
HEK_tRNAseqKO2
HEK293_ThumpKOvsWT_diffexpr-results.csv

data_processing:
*library strategy: tRNAseq
Reads  were processed using the minm-tRNAseq pipeline.
Assembly: hg38
Supplementary files format and content: Differential expression of tRNA isodecoders

extract_protocol:
total RNA were extracted and subjected to small RNA enrichment.
tNRAs were size-selected through electrophoresis, ligated to a 3'adpater, reverse transcribed. cDNA was circularized. Libraries were then prepared by PCR amplification.

value: kidney embryonic

value: KO


title: CN 113702 [S001373]

value: Leaves

value: plant cell


title: Bd21,control,rep2


title: HEK_tRNAseqKO1_S11_R1_001

description:
HEK_tRNAseqKO1
HEK293_ThumpKOvsWT_diffexpr-results.csv


title: HEK_tRNAseqWT2_S10_R1_001

description:
HEK_tRNAseqWT2
HEK293_ThumpKOvsWT_diffexpr-results.csv

value: WT


title: NCI-H2087 sgNT RNA-seq Rep1

description:
JLP-R009
NKX2-1_RNAseq_TPM.csv


title: CN 113702 [S00135D]


title: Bd21,control,rep1

value: control


title: HEK_tRNAseqWT1_S9_R1_001

description:
HEK_tRNAseqWT1
HEK293_ThumpKOvsWT_diffexpr-results.csv


title: NCI-H2087 sgNT RNA-seq Rep2

description:
JLP-R010
NKX2-1_RNAseq_TPM.csv


title: Bd3-1,control,rep2


title: NCI-H358 sgNKX2-1 RNA-seq Rep3

description:
JLP-R008
NKX2-1_RNAseq_TPM.csv


title: Hybrid,drought,rep2

value: Hybrid

value: drought


title: ThumpKO2disome

description:
Disome footprints
Disome_5occupancy15.csv

data_processing:
*library strategy: Disome-seq
3’ adapter (NNNNNNCACTCGGGCACCAAGGA) was trimmed off using skewer, and 4 random nucleotides included in the RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed. Trimmed reads were aligned to human ribosomal and non-coding RNA sequences using STAR10. Unmapped reads were then mapped to an hg19 transcriptome file.
Assembly: hg19
Supplementary files format and content: Metagene analysis at translation start sites from all the datasets.

growth_protocol: Cells were grown in Dulbecco’s modified medium (DMEM) supplemented with 10% fetal bovine serum, 2 mM L-glutamin e and maintained in a 5% CO2 humidified incubator .

extract_protocol:
Cells were harvested in lysis buffer (20 mM Tris-Cl [pH 8], 150 mM KCl, 15 mM MgCl2, 1% Triton X100, 1 mM DTT, 0.1 mg/mL cycloheximide, supplemented with 1X cOmplete™ Mini Protease Inhibitor Cocktail).
Footprints were size-selected through electrophoresis, ligated to a 3'adpater, reverse transcribed. cDNA was circularized. Libraries were then prepared by PCR amplification.


title: CN 113699 [S001366]


title: Bd3-1,control,rep1


title: ThumpKO1disome


title: CN 113702 [S001C2B]


title: CN 113699 [S00135E]


title: Hybrid,control,rep1


title: NCI-H358 sgNT RNA-seq Rep3

description:
JLP-R005
NKX2-1_RNAseq_TPM.csv


title: NCI-H358 sgNKX2-1 RNA-seq Rep1

description:
JLP-R006
NKX2-1_RNAseq_TPM.csv


title: CN 113698 [S001C2E]


title: CN 113698 [S00136C]


title: NCI-H2087 sgNT RNA-seq Rep3

description:
JLP-R011
NKX2-1_RNAseq_TPM.csv


title: Bd21,drought,rep1


title: CN 113698 [S001363]


title: Hybrid,drought,rep1


title: RiboSeq_ThumpKO4

description:
Monosome footprints
RiboSeq_5occupancy15..csv

data_processing:
*library strategy: Ribo-seq
3’ adapter (NNNNNNCACTCGGGCACCAAGGA) was trimmed off using skewer, and 4 random nucleotides included in the RT primer (RNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC/iSP18/TTCAGACGTGTGCTCTTCCGATCTGTCCTTGGTGCCCGAGTG) were removed. Trimmed reads were aligned to human ribosomal and non-coding RNA sequences using STAR10. Unmapped reads were then mapped to an hg19 transcriptome file.
Assembly: hg19
Supplementary files format and content: Metagene analysis at translation start sites from all the datasets.


title: CN 113695 [S001368]


title: Nephrectomy 1-4

city: Ediburgh

first: Maximilian

last: Reck

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: The 980-plex ISH probe panel previously described was prepared by denaturing at 95°C for 2min and placing on ice. The ISH probe mix was prepared using 1nM ISH probes in 1X Buffer R and 0.1U/μL SUPERaseIn RNase Inhibitor (Thermo Fisher, AM2696). Samples were then incubated with the probe mix at 37°C overnight. On the next day slides were washed with 50% formamide (VWR) in 2X SSC at 37°C for 25 min, rinsed twice with 2X SSC for 2 min at room temperature. Before antibody incubation slides were treated with blocking buffer with DAPI nuclear stain for 15min. For visualization of cell morphology antibodies against PanCK, CD45 and CD3 from the CosMx Segmentation and Supplemental Markers Kit were chosen and incubated at room temperature for 1 hours. Finally, after washing with 2X SSC for 2 min at room temperature a custom-made slide covers were attached to the sample slide to form a flow cell.

scan_protocol: RNA readouts were acquired used previously described by manufacturer protocols. Briefly, the assembled flow cells were loaded onto the SMI instrument and washed with reporter was buffer. Initially the flow cell was washed and a median of 12 and total of 141 field of views (FOVs) were defined inside which RNA was detected. The imaging procedure was repeated in 16 reporter pools, with each imaging repeated 8 times to increase RNA detection sensitivity. Each cycle was initiated with flowing 100µL of the Reporter Pool into the flow cell and incubating for 15min followed by flushing with 1ml of Reporter Wash Buffer. The wash buffer was replaced with imaging buffer and nine Z-stack images (0.8 um step size) of each FOV were acquired. Each cycle was completed with UV cleavage of fluorophores on the reporter probes and washing using Strip Wash buffer. Following RNA readouts DAPI and the 3 membrane antibodies were acquired by capturing nine Z-stack images after washing with Reporter Washing Buffer.

data_processing: Image processing and feature extraction followed the Nanostring pipeline which first extracts XYZ locations of individual transcripts. After image registration, feature detection and localisation the Z-stack images of nuclear and cell membrane markers were used define cell boundaries using a machine learning algorithm. Cell segmentation boundaries were used to assign transcripts to cells and subcellular compartments from which a count matrix was generated. Pipeline outputs included a cell by gene matrix, cell segmentation polygons, and cell meta data.

label: SMI imaging barcodes

source_name: Biopsy tissue

label_protocol: After rinsing with nuclease free water and incubated with 1:1000 diluted fiducials (Bangs Laboratory) in 2X SSCT (2X saline sodium citrate, 0.001% Tween 20) for 5min at room temperature. After PBS washes were fixed with 10% neutral buffered formalin for 5min at room temperature. After rinsing with Tris-glycine buffer (0.1M glycine, 0.1M Tris-base) and a 5min wash with PBS samples were blocked using 100 mM N-succinimidyl acetate (Thermo Fisher, 464750250) in NHS-acetate buffer (0.1M NaP, 0.1% Tween pH 8) for 15 min at room temperature. Samples were rinsed with 2X saline sodium citrate (SSC) for 5 min and samples were covered with an Adhesive SecureSeal Hybridization Chamber (Grace Bio-Labs).

extract_protocol: 5mm sections were cut from FFPE embedded tissue blocks and adhered to Superfrost Plus slides (VWR, 631-0108). Slides were deparaffinized with two 5min Xylene washed and two 2min 100% ethanol washes followed by proteinase K (3μg/ml; Thermo Fisher, AM2546) digestion (40°C for 30 min) and heat induced epitope retrieval at 100°C for 15 min in buffer ER1 (Leica, AR9961).

treatment_protocol: Nephrectomy and biopsy tissue was fixed with in neutral buffered formalin and embedded in paraffin. 5µm sections  were cut.

value: Four nephrectomy samples  with advanced pyelonephritis


title: NCI-H358 sgNKX2-1 RNA-seq Rep2

description:
JLP-R007
NKX2-1_RNAseq_TPM.csv


title: RiboSeq_ThumpKO3


title: CN 113695 [S001367]

institute: Agriculture and Agri-Food Canada


title: HCC364 H3K4me1

data_processing:
We trimmed paired end ChIP-seq reads using Trimmomatic (v. 0.36) for properly paired reads and to remove any TruSeq adapter sequences. We aligned to the hg38 reference genome (GRCh38_noalt_as) using bowtie2 (v. 2.2.9) with parameters “-k 1” and converted to a final BAM file with samtools (v. 1.9).
To generate genome-wide occupancy tracks, we used macs2 (v. 2.1.1) with parameters “-g hs -f BAM --nomodel -B --SPMR” to generate a per million normalized genome-wide track, and then converted to a bigwig file using bedGraphToBigWig.
Narrow ChIP-seq peaks were called using macs2 (v. 2.2.7.1) with parameters “g hs -q qe-3 -f BAMPE --nomodel” against an input control generated from sample cells. Peak calls were filtered against ENCODE hg38 blacklist regions using bedtools subtract with parameter “-A” to remove peaks with any overlap.
Assembly: GRCh38
Supplementary files format and content: bw - SPMR ChIP-seq occupancy tracks generated by MACS2
Supplementary files format and content: narrowPeak - Peak calls by MACS2 for ChIP-seq against input control.

extract_protocol:
Cells were prepared according to standard ChIP-seq protocols, see paper for full protocol. Briefly, thawed cells were rinsed twice, resuspended in Covaris Shearing Buffer, aliquoted to an 8 tube microTUBE strip (Covaris) at 5M cells (130µL) per tube, and sonicated on a Covaris LE220 at PIP 300/DF 15/CBP 200 for 20min total at 2min intervals. Sheared chromatin was incubated with ChIP antibody in ChIP buffer rotating overnight at 4°C. The next day, ChIP lysates were rotated with 30µL dynabeads for 2hr at 4°C, 12 total washed, 3 each of Wash Buffer 1, Wash Buffer 2, Wash Buffer 3, and Wash Buffer 4. Bead pellet was resuspended in elution buffer, and heated at 65°C for 1hr at 1000rpm, to eluted supernatnet added 1µL RNase (Roche) and incubated at 37°C for 30min at 1000rpm, then added 3µL of Proteinase K (Lifetech) and incubated at 65°C for 3hr at 1000rpm. ChIP DNA was purified using SPRISelect beads, eluted in 20µL of 10mM Tris-HCl pH 8. DNA concentration was quantified using Quant-IT dsDNA HS assay.
Libraries were prepared with eluted ChIP DNA using the NEBNext Ultra II DNA Library Prep Kit. Final libraries were quantified using Qubit, pooled, and sequenced by Broad Walk-Up Sequencing on a Nextseq 500 using 2x40bp sequencing.

treatment_protocol: Cells were trypsinized, counted, and fixed in culture media at 1% formaldehyde at 37°C for 10min, quenched in 0.125M glycine for 5min at 37°C, PBS washed, pelleted, stored at -80°C.

tag: chip antibody


title: Biopsy 4-6

value: Three biopsies with  IgA nephropathy


title: CN 113699 [S00136F]


title: RiboSeq_ThumpKO1


title: NCI-H358 sgNT RNA-seq Rep1

description:
JLP-R003
NKX2-1_RNAseq_TPM.csv


title: CN 113694 [S001372]


title: WT1disome


title: RiboSeq_WT4


title: Biopsy 7-9


title: Biopsy 1-3

value: Three biopsies with minimal change disease


title: HCC364 NKX2-1

value: NKX2-1 (Abcam Cat#ab137061 Lot#YJ050719CS)


title: CN 113694 [S001371]


title: CN 113694 [S001361]


title: HCC364 H3K27ac


title: NCI-H358 sgNT RNA-seq Rep2

description:
JLP-R004
NKX2-1_RNAseq_TPM.csv


title: RiboSeq_WT3


title: NCI-H441 Input

value: No antibody


title: RiboSeq_WT2


title: CN 113692 [Cs008]


title: HCC364 Input


title: RiboSeq_ThumpKO2


title: RiboSeq_WT1


title: NCI-H441 H3K27ac


title: CN 113692 [Cs007]