title: ATF4_input_rep2

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

data_processing:
The fastq.gz files of sequence tag returned by the Illumina Pipeline was trimmed by Trim Galore and aligned to the mm10 assembly by Bowtie2. Peaks are called by MACS2 in a pooling mode with default parameters; briefly, the two independent ATF4 ChIP-seq are calculated against their two input samples. For subsequent visualization of ChIP-Seq results, bigwig files were generated using the DeepTools “bamCoverage” script integrated in Galaxy server using “Normalized to reads per kilobase per million(RPKM)”. DeepTools “computeMatrix” and “plotHeatmap” functions were used to generate heatmaps.
Assembly: mm10
Supplementary files format and content: bigwig flle of bamcoverage for each sample.
Supplementary files format and content: Excel file including ATF4 ChIP-seq binding peaks.

source_name: spleen

extract_protocol:
Treg cells (enriched CD4+CD25+ cells, 24 million per replicate) were cross-linked with 1% formaldehyde in PBS for 10 min at room temperature and the reaction was quenched by 0.125 M glycine. Cells were washed with ice-cold PBS, pelleted, snap-frozen in liquid nitrogen, and stored at −80 °C. On the day of ChIP, cells were thawed on ice and incubated in cell lysis buffer (10 mM HEPES-KOH pH 7.9, 1 mM EDTA, 85 mM KCl, 1% NP-40, 0.5 mM sodium butyrate, 1 mM PMSF, and 1x protease inhibitor cocktail) for 10 min. Nuclear pellets were resuspended in shearing buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.5 mM EGTA, 1 mM EDTA, 0.1% SDS, 1%NP-40, 0.5 mM DTT, 0.4% sodium deoxycholate, 0.5 mM sodium butyrate, 1 mM PMSF, and 1x protease inhibitor cocktail) and sheared in a Covaris E220 sonicator. After centrifugation, the supernatant was diluted 1.1-fold with 10% Triton X-100 and 1% of the supernatant was kept as ChIP input. For immunoprecipitation, the supernatant was incubated with ATF4 antibody pre-bound to 20 ul of Protein A+G Dynabeads overnight at 4 °C. On the next day, the beads were collected and washed three times with WB I (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 0.5mM sodium butyrate, 1 mM PMSF, and 1x protease inhibitor cocktail), three times with WB III (10 mM Tris-HCl pH 7.5, 250 mM LiCl, 1 mM EDTA, 1%Triton X-100, 0.7% sodium deoxycholate, 0.5 mM sodium butyrate, 1 mM PMSF, and 1x protease inhibitor cocktail), and twice with TET (10 mM Tris-HCl pH 7.5, 0.2% Tween-20, 1 mM EDTA, 0.5 mM sodium butyrate, 1 mM PMSF, and 1x protease inhibitor cocktail). The beads were resuspended in 25 ul of TT (10mM Tris-HCl pH 7.5, 0.05% Tween-20) for on-bead library preparation by using NEBNext Ultra II DNA library prep kit (NEB) according to the manufacturer’s protocol. DNA was eluted, crosslinks reversed by adding 4.5 ul of 5 M NaCl, 4 ul of 10% SDS, 3 ul of 0.5 M EDTA, 1 ul of 20 mg/ml proteinase K, and 20 ul of water, incubated at 55 °C for 1 h, and then incubated at 65 °C for 30 min. DNA was purified with 2 ul of SpeedBeads in 20% PEG 8000/1.5 M NaCl and eluted with 25 ul of TT. The eluted DNA was amplified and purified with 2 ul of SpeedBeads in 20% PEG 8000/2.5 M NaCl. The library was size selected using PAGE/TBE gel and sequenced on NovaSeq 6000.
Libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB) according to the manufacturer’s protocol.

value: spleen

value: CD4+CD25+ Treg cells


title: WT-5-2

status: Public on Mar 31 2025

type: SRA

city: Hong Kong

first: Xin

last: DENG

address: 1/F, Block 1, To Yuen Building, City University of Hong Kong, 31 To Yuen Street, Kowloon Tong

department: Department of Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

library_source: genomic

data_processing:
Raw reads were trimmed by Trim Galore with default parameters.
ChIP-seq reads were mapped to the P. aeruginosa genomes (NC_002516) using Bowtie2 (Version 2.3.4.1). Only the uniquely mapped reads were kept for the subsequent analyses.
Binding peaks (q < 0.05) were identified using MACS2 software (version 2.1.1.20160309).
Assembly: P. aeruginosa genomes (NC_002516)
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial cell

extract_protocol:
P. aeruginosa  was cultured in LB medium until mid-log phase (OD600 = 0.6), then treated with 1% formaldehyde for 10 min at 37℃. After quenching and lysis, cells were subjected to sonication to produce 100–300 bp DNA fragments.
ChIP-seq libraries were constructed using NEXTflex ChIP-Seq kit (Bio Scientific), and agarose gel was used to cut DNA fragments between 150 and 250 bp.

tag: strain

tag: cell type

value: bacterial cell

tag: chip antibody

value: Anti-vsv

tag: genotype

value: WT


title: TNFdARE mouse 4

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

country: USA

institute: Bioinformatic Solutions LLC

description: Library name: dARE 94VR

library_source: transcriptomic

data_processing:
Reads generated were mapped to the mouse genome (mm10) by gSNAP, expression (FPKM) derived by Cufflinks and differential expression analyzed with ANOVA in R. Genes significant at a p < 0.05 were submitted to pathway analysis using R, and genes significant p < 0.05 were submitted to KEGG pathway analysis using Enrichr.
Assembly: MM10
Supplementary files format and content: Microsoft Excel format

molecule: total RNA

organism: Mus musculus

source_name: Platelet

growth_protocol: Whole blood was drawn from three TNFdARE mice and three  littermates of 8-12 weeks.

extract_protocol:
RNA was extracted from isolated washed platelets of mice (healthy littermattes and the TNFdARE, n4 each). The extraction was performed with the TRIzol reagent (Invitrogen). Then, RNA was treated with DNase (Qiagen), and purified with columns (Qiagen).
Libraries from extracted RNA were then sequenced as dual pass 150 bp reads on the Illumina NovaSeq 6000 sequencer by the University of Colorado Medical Campus Cancer Center Genomics Shared Resource Core Facility (RRID:SCR_021984).

treatment_protocol: 5.2 month old male mice were euthanized, humeri was extracted.

tag: tissue

value: Platelet

tag: cell line

value: Female

value: Hematopoietic cell

value: TNFdAre +

tag: treatment

value: Baseline

tag: batch


title: WT-5-1


title: TNFdARE mouse 3

description: Library name: dARE 18M

value: Male


title: ChIP-Seq_Rpb3_Salivary_glands_NHS_rep1

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq, FAIRE-Seq and RNA-Seq reads were aligned to the dm6 genome by HISAT2 (using UseGalaxy.eu online tools)
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: Aligned reads were sorted to have MAPQ>5. BigWig files were generated using  bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library. Final BigWIgs were generated The final bigwig files (representing the protein binding profiles) were obtained using bigwigcompare tool by computing a ratio between the ChIP signal and the Input (all Inputs were preliminary smoothed over a 1 kb window). For the H3K27Ac ChIP-Seqs the Input was substracted from the signal. FAIRE-Seq data were not normalized by Input and presented as a number of reads. The final bigwig files (representing the protein binding profiles) were obtained using bigwigcompare tool by computing a ratio between the ChIP signal and the Input (all Inputs were preliminary smoothed over a 1 kb window). For the H3K27Ac ChIP-Seqs the Input was substracted from the signal. FAIRE-Seq data were not normalized by Input and presented as a number of reads.

organism: Drosophila melanogaster

source_name: Salivary glands were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

growth_protocol: The Drosophila melanogaster of hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (=hsp-e23; capable of expressing E23 after treatment with the heat shock) and Oregon-R-modENCODE (corresponds to Bloomington stock 25211) stock were used. All flies were raised at 25°C on standard agar medium.

extract_protocol:
ChIP protocol: crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated with the NEBNext UltraTM II Directional RNA Library Prep Kit. FAIRE-Seq protocol was perfomed exactly as previously described in Simon et al (2012) Nat protocols, 7:256-267.
DNA and RNA-Seq libraries were prepared for sequencing using standard Illumina NEBNext protocols

treatment_protocol:
no treatment
For the RNA-Seq and ChIP-Seq experiments, hsp-e23 larvae (or Oregon-R larvae) of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation. Dissections were performed manually in PBS/0.1% NP-40. Tissues targeted for RNA-Seqs were collected directly into TRI-reagent. Dissected salivary glands and brains (brains were taken with eye/antennal discs) aimed for ChIP-Seqs and FAIRE-Seqs were accumulated in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice not more than 1 hour. After the dissection, tissues were warmed to room temperature and fixated by addition of FA up to 1% for 10 min. The fixation was stopped by addition of 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

tag: sample id

value: hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (described in a current study)

tag: chip antibodies

value: anti-Rpb3 (1–275 aa) antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )

value: no treatment


title: WT-7-1


title: ATF4_input_rep1


title: WT-4-2


title: FAIRE-Seq_Salivary_glands_HS_rep1

source_name: Salivary glands dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

extract_protocol:
ChIP protocol: crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation. Total RNA was extracted with the TRI reagent (Ambion). PolyA comprising RNA fraction was isolated with the NEBNext UltraTM II Directional RNA Library Prep Kit. FAIRE-Seq protocol was perfomed exactly as previously described in Simon et al (2012) Nat protocols, 7:256-267.
DNA and RNA-Seq libraries were prepared for sequencing using standard Illumina NEBNext protocols
ChIP-Seq, RNA-Seq, FAIRE-Seq and total DNA sequencing

treatment_protocol:
hsp-e23 larvae of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation.
For the RNA-Seq and ChIP-Seq experiments, hsp-e23 larvae (or Oregon-R larvae) of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation. Dissections were performed manually in PBS/0.1% NP-40. Tissues targeted for RNA-Seqs were collected directly into TRI-reagent. Dissected salivary glands and brains (brains were taken with eye/antennal discs) aimed for ChIP-Seqs and FAIRE-Seqs were accumulated in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice not more than 1 hour. After the dissection, tissues were warmed to room temperature and fixated by addition of FA up to 1% for 10 min. The fixation was stopped by addition of 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

tag: developmental stage

value: heat shock


title: ChIP-Seq_Rpb3_Brains_NHS_rep1

source_name: Brains/eye-antennal discs were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation


title: FAIRE-Seq_Salivary_glands_NHS_rep2

value: wandering larvae 4-6 hours before puparium formation


title: WT-4-1


title: ChIP-Seq_EcR-full_Brains_NHS_rep1

value: Brains/eye-antennal discs were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

value: EcR-full antibodies against full-length EcR-A isoform NM_165461 were obtained in our lab and described in this manuscript for the first time.


title: FAIRE-Seq_Salivary_glands_NHS_rep1


title: WT-3-2


title: Input_Brains_NHS_rep1

source_name: Brains/eye-antennal discs dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation

value: Brains


title: CRE18-4

city: Saint-Hyacinthe

first: Michael

last: Bérubé

state: QC

address: 3200, Sicotte street

country: Canada

institute: University of Montreal

description: Mutant 4

data_processing:
Fastq data was processed using the GenPipes v.3.1.2 pipeline.
Briefly, raw reads were quality and adaptor trimmed using Trimmomatic, then aligned to the mm10 (mouse) reference genome using the STAR aligner.
Library technical quality was assessed using Picard-tools (http://broadinstitute.github.io/picard) v.1.92 and Samtools (http://www.htslib.org/) v.1.1.
PCR duplicates and fragments with poor mapping quality (q < 255) were filtered out.
Gene transcription levels was quantitated over annotated Ensembl genes, and differential gene expression was measured between Ad-eGFP and Ad-Cre condition using DESeq2 (corrected p-value < 0.05, LOG2 fold-change > 1.5)
Assembly: mm10 (mouse) reference genome
Supplementary files format and content: FPKM

source_name: Primary culture

growth_protocol: Granulosa cells were cultured in MEM containing 1% fetal bovine serum, 0.25 nM sodium pyruvate, and 3 mM L-glutamate. GCs were seeded in 96-well culture plates (each well receiving the granulosa cells isolated from 0.5 ovary) and incubated for 3h at 37ºC in 5% CO2/95% air. Culture medium was then replaced with serum-free medium for 2h before the treatments

extract_protocol:
RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol
250 ng RNA was used for ribosomal RNA depletion using the NEBNext rRNA Depletion Kit (Cat# E6310X) according to the manufacturer’s instructions.
Double-stranded cDNA was then synthesized using the NEBNext Ultra II RNA First Strand Synthesis (Cat# E7771) and the NEBNext Ultra II Directional RNA Second Strand Synthesis (Cat# E7550L) modules.
Libraries were constructed using NEBNext Ultra II End Repair/dA-Tailing (Cat# E7546L) and NEBNext Ultra II Ligation (Cat# E7595L) modules.
Each library was amplified for 9 PCR cycles using NEBNext High-Fidelity 2X PCR Master Mix (Cat# M0541L) and NEBNext Multiplex Oligos for Illumina (UDI) (Cat# E6440S)

treatment_protocol: Primary culture of mouse preovulatory granulosa cells infected with Adenovirus-Cre (or  Adenovirus-eGFP as control) during 18h.

value: Ovary

value: Granulosa cells

value: Ad-Cre

tag: time


title: ChIP-Seq_Rpb3_Salivary_glands_NHS_rep2

value: Salivary glands were dissected from hsp-e23 wandering larvae 4-6 hours before puparium formation


title: Input_Salivary_glands_HS_rep1


title: WT-3-1

value: bacterial cell

value: Anti-vsv

value: WT


title: Input_Salivary_glands_NHS_rep1


title: ChIP-Seq_Crol_Brains_NHS_Oregon_rep1

source_name: Salivary glands dissected from Oregon-R wandering larvae 4-6 hours before puparium formation

value: Oregon-R-modENCODE (Bloomington stock 25211)

value: Antibodies against Crol (a.a. 1–188, isoform PA) were generated and described previously (Erokhin et al. 2023).


title: ChIP-Seq_EcR-C-end_Salivary glands_NHS_rep1

value: hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (described in a current study)

value: EcR-C end antibodies against an antigen corresponding to amino acids Ile-691 to Ala-878 of the EcR-B isoform (NM 165465) were described and characterized previously (Kovalenko et al. 2019).


title: ChIP-Seq_Crol_Salivary_glands_Oregon_NHS_rep1

value: no treatment


title: CRE18-2

description: Mutant 2


title: WT-2-2


title: FAIRE-Seq_Brains_NHS_rep1


title: WT-2-1


title: ChIP-Seq_H3K27Ac_Brains_NHS_rep1

value: Active motif antibodies against Histone H3K27Ac (39133)


title: CRE18-1

description: Mutant 1


title: WT-1-2


title: ChIP-Seq_PolII_Ser2P_Brains_NHS_rep1

value: wandering larvae 4-6 hours before puparium formation

value: Antibodies against RNA polymerase II CTD repeat (phospho S2) (Ab5095) were purchased from Abcam


title: ATF4_ChIP-seq_rep2

value: spleen

value: CD4+CD25+ Treg cells


title: FAIRE-Seq_Salivary_glands_HS_rep2

value: heat shock


title: GFP18-4

description: Control 4

value: Ovary

value: Granulosa cells

value: Ad-eGFP


title: ATF4_ChIP-seq_rep1


title: ChIP-Seq_H3K27Ac_Salivary_glands_HS_rep1


title: ChIP-Seq_H3K27Ac_Salivary_glands_NHS_rep2


title: ChIP-Seq_H3K27Ac_Salivary_glands_HS_rep2


title: WT-1-1

value: bacterial cell


title: GFP18-3

description: Control 3


title: ChIP-Seq_H3K27Ac_Salivary_glands_NHS_rep1


title: CRE18-3

description: Mutant 3

value: Ad-Cre


title: GFP18-2

description: Control 2


title: GFP18-1

description: Control 1


title: ChIP-Seq_CBP_Nejire_Salivary_glands_HS_rep1

value: anti-CBP/p300/Neijre  (125–310 aa) antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: RPE, Sync (M), CUT&Tag, rep4

city: Hefei

first: Yan

last: Yang

state: Anhui

address: No.373 Huangshan Road

country: China

institute: University of Science and Technology of China

description: Library name: CUT_Tag_M4

data_processing:
Raw sequencing reads were trimmed for adapters using fastp, and mapped to the human genome (hs1) using Bowtie2. Alignments were converted to bigWig file for visualization using bedtools. Peaks were called from alignments using MACS2.
Assembly: hs1
Supplementary files format and content: bigWig files including SAF-A CUT&Tag read density normalized with spiked-in E. coli DNA
Supplementary files format and content: narrowPeak including the genomic localization of SAF-A CUT&Tag peaks
Library strategy: CUT&Tag

organism: Homo sapiens

extract_protocol:
CUT&Tag was performed according to a commercially available kit (Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro, Vazyme, TD904). Briefly, 100,000 cells were immobilized on ConA magnetic beads and permeablized. 1 pg E. coli DNA was added for spike-in calibration. Primary antibodies used are anti-SAFA (Abcam, ab180952).
Sequencing of the library was conducted on Illumina Novaseq (PE150) platform (Novogene).

value: WT


title: RPE, Sync (M), CUT&Tag, rep3

description: Library name: CUT_Tag_M3


title: ChIP-Seq_PAF1_Brains_NHS_rep1

value: Brains

value: anti-PAF1 (1–234 aa) antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: ChIP-Seq_CBP_Nejire_Salivary_glands_NHS_rep2

value: hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (described in a current study)


title: RPE, Async, CUT&Tag, rep4

description: Library name: CUT_Tag_A4


title: Multiplex

city: Buffalo

first: Santosh

last: Patnaik

state: NY

address: Elm and Carlton

institute: Roswell Park Cancer Center

library_source: transcriptomic single cell

data_processing:
Paired-end fastq data generated by the sequencer instrument were processed through on-cloud Parse Biosciences Trailmaker pipeline with split-pipe v1.2.1, GRCm39 mouse reference, and default parameters. All fastq data files were co-processed to generate per-cell per-gene count matrix, cell metadata (sample origin, gene count, etc.), and list of all detected genes.
Assembly: GRCm39-1-1-3c in the Parse Biosciences Trailmaker cloud platform
Supplementary files format and content: Compressed unfiltered (raw) count matrix (per cell, per gene), cell metadata (including sample origin), and gene list files for all samples as a whole as generated by on-cloud Parse Biosciences Trailmaker pipeline with split-pipe v1.2.1. Refer to sample.tsv for sample metadata.

source_name: Multiple mouse lung carcinoma

extract_protocol:
Dissected tumors were dissociated in GentleMACS device with Miltneyi Biotec Mouse Tumor Dissociation Kit (product 130-096-730). All tumors of a given experiment were processed together. The cell suspensions were then enriched for live cells with Miltenyi Biotec Dead Cell Removal Kit (130-090-101). Cells were then fixed with Parse Biosciences Cell Fixation Kit v2 and stored at -80 ºC for 2-6 months depending on the cell-line. Thawed cells were counted with propidium iodide staining on a Nexcelom cell counter.
Instructions and reagents for the Parse Biosciences Evercode Whole Transcriptome v3 for 100k Cells were used. Two wells with a total of 5k cells were used per sample. Three rounds of combinatorial barcoding were performed. Overall, the use of the platform results in sequencing data files (fastq) containing reads from single cells from all samples.

value: Subcutaneous tumor

value: Mouse lung carcinoma

value: Wild-type C57BL/6

value: Diet


title: ChIP-Seq_CBP_Nejire_Salivary_glands_NHS_rep1

value: wandering larvae 4-6 hours before puparium formation

value: no treatment


title: ChIP-Seq_PAF1_Salivary_glands_HS_rep1

value: heat shock


title: Non-MPR-3

city: Tianjin

first: Lili

state: Tianjin

address: Huanhuxi Road, Tiyuanbei, Hexi District

institute: Tianjin Medical University Cancer Institute and Hospital

description: Library name: Sample6

data_processing:
TOP 2000 variant genes of each sample were first identified for later integration analysis. In this experiment, the Harmony algorithm was used to integrate multiple samples of single cells. Since Harmony uses soft clustering, each single cell can be corrected linearly for the soft cluster assignment by a linear combination of multiple factors, repeating these steps until the cell cluster assignment is stable.The cell types were annotated by combining the single-cell sequencing cell type annotation software SingleR（version v1.0.0）and marker genes. SingleR selects the highly variable genes among different cell types in the reference database, and then calculates the correlation between the predicted cells and the reference database. By continuously eliminating the worst correlation type, SingleR calculates the correlation, and finally obtains the type annotation of cells.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Lung tissue

extract_protocol:
The Isolation Kit furnished by Shanghai Biotechnology Corporation was exploited. Tissue samples were homogenized and transformed into a liquid state with a tissue homogenizer, succeeded by thorough lysis on ice. The resultant tissue lysates were filtrated through a 40μm cell sieve to eliminate impurities, and the supernatant was meticulously aspirated by means of centrifugation while preserving the precipitate. Nuclear suspensions were obtained in accordance with the standard protocols of the kit. Ultimately, 5μL of each nuclear suspension was aliquoted and stained with trypan blue for the quantification of cell nuclei and microscopic examination.
The Gel Beads-in-emulsion was transferred to a PCR instrument for reverse transcription in Shanghai Biotechnology Corporation, and the cDNA strand with Barcode and UMI information was obtained according to the standard procedure of the system, followed by purification, amplification and detection of concentration. After passing the quality inspection, cluster generation and hybridization of the first sequencing primers were completed, and the flow cell with cluster was carried on the computer.

value: Lung tissue

tag: patient diagnosis

value: NSCLC

value: Wild type

value: 4 circles therapy of Camrelizumab combined with Anlotinib


title: RPE, Async, CUT&Tag, rep3

description: Library name: CUT_Tag_A3


title: ChIP-Seq_PAF1_Salivary_glands_NHS_rep1


title: ChIP-Seq_EcR-full_Salivary_glands_HS_rep2

value: EcR-full antibodies against full-length EcR-A isoform NM_165461 were obtained in our lab and described in this manuscript for the first time.


title: ChIP-Seq_PolII_Ser2P_Salivary_glands_NHS_rep1

value: Antibodies against RNA polymerase II CTD repeat (phospho S2) (Ab5095) were purchased from Abcam


title: ChIP-Seq_EcR-full_Salivary_glands_HS_rep1


title: Non-MPR-2

description: Library name: Sample5


title: RNA library from E18.5 IVF Testis 5

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: E18.5 Testis

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols.

treatment_protocol: E18.5 testis, 12 weeks testis, 39 weeks testis, F2 12 weeks testis, F2 12 weeks male livers, F2 12 weeks ovaries, F2 weeks female livers awere collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

value: E18.5 Testis

value: Male

tag: group

value: IVF


title: ChIP-Seq_EcR-full_Salivary_glands_NHS_rep2

value: hsp-GAL4 7-1,CyO/IF;10UAS-3xFLAG-E23,w+  stock (described in a current study)


title: Non-MPR-1

description: Library name: Sample4


title: RNA library from E18.5 IVF Testis 4


title: RNA library from E18.5 IVF Testis 6


title: RNA library from E18.5 IVF Testis 3


title: RNA-Seq_Brains_hsp-e23_HS_rep1

molecule: polyA RNA

source_name: Brains/eye-antennal discs dissected from Oregon-R wandering larvae 4-6 hours before puparium formation

value: Brains


title: ChIP-Seq_CBP_Nejire_Salivary_glands_HS_rep2

value: anti-CBP/p300/Neijre  (125–310 aa) antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: RNA library from E18.5 IVF Testis 2


title: RNA-Seq_Brains_hsp-e23_HS_rep2


title: MPR-3

description: Library name: Sample3


title: ChIP-Seq_EcR-full_Salivary_glands_NHS_rep1


title: ChIP-Seq_PolII_Ser5P_Salivary_glands_NHS_rep1

value: Antibodies against RNA polymerase II CTD repeat (phospho S5) (Ab5131) were purchased from Abcam


title: RNA-Seq_Salivary_glands_Oregon_HS_rep2

treatment_protocol:
Oregon-R larvae of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation.
For the RNA-Seq and ChIP-Seq experiments, hsp-e23 larvae (or Oregon-R larvae) of L3 stage 20-22h before puparium formation were subjected to double 1-hour heat shocks at 37°C with a 1-hour rest period between at RT. For dissection, wandering larvae were used approximately 4-6 hours before the puparium formation. Dissections were performed manually in PBS/0.1% NP-40. Tissues targeted for RNA-Seqs were collected directly into TRI-reagent. Dissected salivary glands and brains (brains were taken with eye/antennal discs) aimed for ChIP-Seqs and FAIRE-Seqs were accumulated in tubes containing PBS/0.1% NP-40 and placed on ice. Dissected tissues were stored on ice not more than 1 hour. After the dissection, tissues were warmed to room temperature and fixated by addition of FA up to 1% for 10 min. The fixation was stopped by addition of 1/20V 2.5M Gly to the reaction for 5 min. After the fixation, the Sonication buffer (ChIP lysis buffer) containing 0.1% SDS and PIC (Roche) was added to the tissues and they were stored at -70°C. The sonication step was performed after the thawing.

value: Oregon-R-modENCODE (Bloomington stock 25211)


title: MPR-2

description: Library name: Sample2


title: MPR-1

description: Library name: Sample1


title: RNA library from E18.5 IVF Testis 1


title: RNA-Seq_Brains_hsp-e23_NHS_rep1

value: wandering larvae 4-6 hours before puparium formation


title: RNA-Seq_Brains_hsp-e23_NHS_rep2

value: no treatment


title: RNA-Seq_Salivary_glands_Oregon_HS_rep1

value: heat shock


title: RNA-Seq_Salivary_glands_Oregon_NHS_rep2


title: RNA library from E18.5 Natural Testis 4

value: Natural


title: RNA-Seq_Salivary_glands_Oregon_NHS_rep1


title: RNA library from E18.5 Natural Testis 3


title: RNA-Seq_Salivary_glands_hsp-e23_HS_rep1


title: RNA library from E18.5 Natural Testis 2


title: RNA-Seq_Salivary_glands_hsp-e23_NHS_rep2


title: RNA-Seq_Salivary_glands_hsp-e23_HS_rep2


title: Hep3Bcells, shHYOU1-2

city: hefei

first: xiao

last: du

state: anhui

address: Anhui Medical University, 81 Meishan Road, Shushan District, Hefei City, Anhui Province

institute: first affiliated hospital of anhui medical university

description:
Library name: SAMPLES5
hep3b_KD_2

data_processing:
Using the Illumina NovaSeq 6000 sequencer with Paired-End sequencing.
Assembly: The tab-separated raw files contain the raw counts for each sample.
Supplementary files format and content: The CSV file includes the FPKM values for each sample

source_name: liver

extract_protocol:
RNA was extracted from Hep3B cells using a standard extraction method. The RNA samples were then subjected to strict quality control,  primarily using the Agilent 2100 Bioanalyzer to accurately assess RNA integrity.
mRNA was enriched from total RNA using Oligo dT magnetic beads. After fragmentation,  the first-strand cDNA was synthesized using random hexamer primers,  followed by the synthesis of the second-strand cDNA. After end repair,  A-tailing,  adapter ligation,  fragment selection,  amplification,  and purification,  the library was ready for use.

value: liver

value: liver cancer cell

value: HYOU1 knockdown


title: Hep3Bcells, shHYOU1-3

description:
Library name: SAMPLES6
hep3b_KD_3


title: Hep3Bcells, shHYOU1-1

description:
Library name: SAMPLES4
hep3b_KD_1


title: RNA-Seq_Salivary_glands_hsp-e23_NHS_rep1


title: Hep3Bcells, shControl-3

description:
Library name: SAMPLES3
hep3b_NC_3

value: control


title: RNA library from E18.5 Natural Testis 1


title: shNol10_2_9_NUP98-DDX10 leukemia cells

city: Toyoake

first: Yutaka

last: Shima

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake-cho

country: Japan

institute: Fujita Health University

data_processing:
All data analysis were performed in Galaxy Europe website (https://usegalaxy.eu).
Assembly: mm10
Supplementary files format and content: Text file includes raw gene counts for each sample

source_name: Bone marrow

growth_protocol: Leukemia cells were maintained in StemPro-34 SFM medium (Gibco) supplemented with 10 ng/ml IL3, 50 ng/ml SCF, 10 ng/ml Oncostatin M, 2.5% nutrients, 0.1% tylosin, and 1% L-glutamine-penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
Stranded library preparation with polyA selection for Illumina by AZENTA.

value: Bone marrow

value: NUP98-DDX10 leukemia cells

value: Nol10 knockdown


title: maize_leaf, U. myadis, S. reilianum rUSH_OE_Umdhp2,  3 dpi, rep1

city: Köln

first: Janina

last: Werner

state: NRW

address: Zülpicherstraße 47A

country: Germany

institute: University of Cologne, Terrestrial Microbiology

description: Library name: A10

data_processing:
alignment: HISAT2 (version 2.0.5)
featureCounts (version 1.5.0-p3)
R package DESeq2 (version 1.20.0)
Assembly: U. maydis (Kämper et al., 2006), S. reilianum (Schirawski et al., 2010), Z. mays (Hufford et al., 2021)
Supplementary files format and content: count files

organism: Zea mays

source_name: leaf

growth_protocol: fungal cells were grown in YEPSlight medium until reaching an OD of 1, prior infection of maize seedling.

extract_protocol:
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: The fungal culture of OD1 was supplemented with 0.1% of Tween.

value: leaf

value: infection

value: 3 dpi


title: maize_leaf, U. myadis, S. reilianum rUSH_OE_Umdhp2,  3 dpi, rep2

description: Library name: A11


title: maize_leaf, U. myadis, S. reilianum rUSH,  3 dpi, rep3

description: Library name: A9


title: Hep3Bcells, shControl-2

description:
Library name: SAMPLES2
hep3b_NC_2


title: maize_leaf, U. myadis, S. reilianum rUSH_OE_Umdhp2,  3 dpi, rep3

description: Library name: A12


title: maize_leaf, U. myadis, S. reilianum rUSH,  3 dpi, rep1

description: Library name: A7


title: maize_leaf, U. myadis, S. reilianum rUSH,  3 dpi, rep2

description: Library name: A8


title: Hep3Bcells, shControl-1

description:
Library name: SAMPLES1
hep3b_NC_1


title: shNol10_2_8_NUP98-DDX10 leukemia cells


title: shNol10_2_7_NUP98-DDX10 leukemia cells


title: maize_leaf, U. myadis, S. reilianum FB1+SRZ2,  3 dpi, rep2

description: Library name: A5


title: maize_leaf, U. myadis, S. reilianum FB1+SRZ2,  3 dpi, rep3

description: Library name: A6


title: U-2 OS cells, IR3

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

description: Library name: IR3

data_processing:
RNA-seq reads were pseudoaligned with Kallisto using the genome build GENCODE Homo sapiens GRCh38 Release 37
Assembly: Grch38
Supplementary files format and content: Kallisto transcript text files

source_name: U-2 OS

growth_protocol: All cell lines were grown at 37°C under standard cell culture conditions (humidified atmosphere, 5 % CO2) in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) containing 10% fetal bovine serum (Corning) and 1% penicillin-streptomycin antibiotics.

extract_protocol:
RNA was extracted using the TRIzol Isolation Kit following manufacturer’s protocol. Extracted RNA was prepared for sequencing using the Illumina Truseq mRNA Library assay following manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Before RNA extraction, cells were treated for 24 hours with 4 Gy of ionizing radiation, or left untreated

value: U-2 OS

value: cancer cells

value: IR


title: shNol10_1_6_NUP98-DDX10 leukemia cells


title: maize_leaf, U. myadis, S. reilianum FB1+SRZ2,  3 dpi, rep1

description: Library name: A4


title: shNol10_1_5_NUP98-DDX10 leukemia cells


title: U-2 OS cells, IR1

description: Library name: IR1


title: shNol10_1_4_NUP98-DDX10 leukemia cells


title: U-2 OS cells, UT3

description: Library name: UT3

value: Untreated


title: shCtrl_3_NUP98-DDX10 leukemia cells

value: WT


title: U-2 OS cells, UT2

description: Library name: UT2


title: maize_leaf, rUSH, 6 dpi, rep2

description:
Library name: C8
6 dpi, Hybrid, rep2

data_processing:
Trimmomatic (0.39) was used for quality filtering of the paired-end reads.
bowtie2 (2.3.5.1) was used for the mapping of the quality-filtered reads to the reference genome of maize.
samtools (1.9) were used to dort the BAM files.
Htseq-count (2.0.1) was used to count the mapped reads.
edgeR (3.36.0) was used for the differential gene expression analysis.
Assembly: Zea mays reference genome Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: Gzipped text files containing transcript counts for each sample.
Supplementary files format and content: csv files containing counts

tag: agent

value: hybrid

value: treatment

value: GB

value: rUSH


title: maize_leaf, rUSH, 6 dpi, rep1

description:
Library name: C7
6 dpi, Hybrid, rep1


title: maize_leaf, rUSH, 3 dpi, rep1

description:
Library name: C4
3 dpi, Hybrid, rep1


title: maize_leaf, rUSH, 3 dpi, rep3

description:
Library name: C6
3 dpi, Hybrid, rep3


title: maize_leaf, rUSH, 6 dpi, rep3

description:
Library name: C9
6 dpi, Hybrid, rep3


title: maize_leaf, rUSH, 3 dpi, rep2

description:
Library name: C5
3 dpi, Hybrid, rep2


title: maize_leaf, rUSH, 20 hpi, rep3

description:
Library name: C3
20 hpi, Hybrid, rep3


title: U-2 OS cells, UT1

description: Library name: UT1


title: shCtrl_2_NUP98-DDX10 leukemia cells


title: shCtrl_1_NUP98-DDX10 leukemia cells


title: maize_leaf, rUSH, 20 hpi, rep2

description:
Library name: C2
20 hpi, Hybrid, rep2


title: maize_leaf, rUSH, 20 hpi, rep1

description:
Library name: C1
20 hpi, Hybrid, rep1


title: minic3

city: jinan

first: shujuan

last: sun

state: jinan

address: jiyan road 440,jinan ,china

department: Shandong Cancer Hospital and Institute

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

description: Library name: Sample 6

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo sapiens.GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mimic


title: maize_leaf, S. reilianum SRZ1+SRZ2, 6 dpi, rep2

description:
Library name: B8
6 dpi, S. reilianum WT SRZ1+SRZ2, rep2

value: Sporisorium reilianum


title: maize_leaf, S. reilianum SRZ1+SRZ2, 6 dpi, rep3

description:
Library name: B9
6 dpi, S. reilianum WT SRZ1+SRZ2, rep3


title: maize_leaf, S. reilianum SRZ1+SRZ2, 3 dpi, rep3

description:
Library name: B6
3 dpi, S. reilianum WT SRZ1+SRZ2, rep3


title: 6 DIV primary mouse cortical neurons from 1 litter of P0 pups of C57BL/6J mice (Biological repeat 3)

city: Stanford

first: Mengting

last: Han

state: CA

address: 290 Jane Stanford Way  ChEM-H/Neuroscience Building W117

department: Bioengineering

institute: Stanford University

data_processing:
The reads were aligned to the GRCm39 mouse genome using STAR. Bedtools coverage was used to calculate the read abundance over each gRNA. The reads were normalized for each sample and target gene.
Assembly: GRCm39 mouse genome
Supplementary files format and content: Bed format files containing raw counts for the reads that cover each of the guides.

source_name: Cortex

growth_protocol: Primary mouse cortical neuron were cultued in PDL-treated 6-well plates with 500K cells per well in culture media (Neurobasal-A medium (Thermo Fisher Scientific, 10888022) supplemented with 2% B-27 (Thermo Fisher Scientific, 17504044) and 1% GlutaMAX (Thermo Fisher Scientific, 35050061)). Neurons were collected at 6 day in vitro (DIV) for RNA extraction.

extract_protocol:
Total RNA was extracted from 6 DIV primary mouse cortical neurons dissected from 3 litters of P0 pups of C57BL/6J mice using RNeasy Plus Mini Kit (Qiagen, 74136) for lncRNA-seq profiling through Novogene Corporation Inc.
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required.

treatment_protocol: Cells were treated with 16 µM Floxuridine (FUDR) at 3 DIV.

value: Cortex

value: Primary mouse cortical neuron

value: No treatment


title: U-2 OS cells, IR2

description: Library name: IR2


title: maize_leaf, S. reilianum SRZ1+SRZ2, 3 dpi, rep1

description:
Library name: B4
3 dpi, S. reilianum WT SRZ1+SRZ2, rep1

value: leaf


title: maize_leaf, S. reilianum SRZ1+SRZ2, 3 dpi, rep2

description:
Library name: B5
3 dpi, S. reilianum WT SRZ1+SRZ2, rep2


title: maize_leaf, S. reilianum SRZ1+SRZ2, 6 dpi, rep1

description:
Library name: B7
6 dpi, S. reilianum WT SRZ1+SRZ2, rep1


title: minic2

description: Library name: Sample 5


title: minic1

description: Library name: Sample 4


title: 6 DIV primary mouse cortical neurons from 1 litter of P0 pups of C57BL/6J mice (Biological repeat 1)


title: 6 DIV primary mouse cortical neurons from 1 litter of P0 pups of C57BL/6J mice (Biological repeat 2)


title: Reina SIRT1 KI-3 (S-KI3)

first: Brahim

last: Chaqour

state: PA

address: 422 Curie Blvd

department: Ophthalmology

data_processing:
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: mm10
Supplementary files format and content: tab delimited tex files contains RPKM for each sample

source_name: Retina

extract_protocol:
Total RNA was extracted from homogenized mixtures of retinas using RNeasy purification kit according to the manufacturer’s instructions (Qiagen).
RNA sequencing was performed with three biological replicates per group of mice by Genewiz/Azenta (New Jersey, USA) where the cDNA libraries were prepared and sequenced using Illumina Hiseq, 2×150bp paired-end chemistry.
Prior to cDNA library preparation, samples were treated for initial polyA selection, mRNA fragmentation and random priming with first and second strand cDNA synthesis. Thereafter, adaptor ligation, polymerase chain reaction (PCR) enrichment, and Illumina NovaSeq technology–based sequencing with 2× 150–base pair (bp) read length were performed. The library preparation was specific to each strand. Library quality was assessed on the Agilent Bioanalyzer 2100 system. To remove adaptor sequence and poor-quality nucleotide reads, the trimmomatic v.0.36 software was used.

treatment_protocol: Eight-week-old mice were immunized subcutaneously at two sites on the back, each with 150 μg myelin oligodendrocyte glycoprotein (MOG35–55) emulsified in complete Freund’s adjuvant  containing 2.5 mg/ml heat-killed Myobacterium tuberculosis. Mice were further injected intraperitoneally with 200 ng pertussis toxin  in 0.1 mL of PBS at 0 hours and 48 hours postimmunization with MOG35–55.  Both WT and SIRT1 KI mice showed typical features of EAE that worsened over time (4 weeks) including loss of tail tone, waddling gait, partial or total paralysis of one or two limbs, etc. For RSV treatment, WT mice were gavagged with RSV ( 100 mg/kg) on a daily basis. For AAV-SIRT1 treatment, two microliters of AAV vector preparation (1 × 10^10 vector genomes) were intravitreally injected into each eye of mice at six-week old of age. Vehicle-treated eyes were injected with an equivalent volume of vector dilution buffer (0.001% Pluronic F68 in PBS). Four weeks after MOG immunization, all treated  mice and their respective controls were sacrificed, and retinas were rapidly isolated and snap frozen in liquid nitrogen. Total RNA was extracted from homogenized mixtures of retinas using RNeasy purification kit according to the manufacturer’s instructions (Qiagen).

value: Retina

value: SIRT1 Knockin


title: maize_leaf, U. maydis FB1+FB2,  6 dpi, rep3

description:
Library name: A9
6 dpi, U. maydis WT FB1+FB2, rep3

value: Ustilago maydis


title: maize_leaf, S. reilianum SRZ1+SRZ2, 20 hpi, rep1

description:
Library name: B1
20 hpi, S. reilianum WT SRZ1+SRZ2, rep1


title: maize_leaf, S. reilianum SRZ1+SRZ2, 20 hpi, rep3

description:
Library name: B3
20 hpi, S. reilianum WT SRZ1+SRZ2, rep3


title: maize_leaf, U. myadis FB1+FB2,  6 dpi, rep1

description:
Library name: A7
6 dpi, U. maydis WT FB1+FB2, rep1


title: Reina SIRT1 KI-2 (S-KI2)


title: minic_nc1

description: Library name: Sample 1

value: control


title: maize_leaf, S. reilianum SRZ1+SRZ2, 20 hpi, rep2

description:
Library name: B2
20 hpi, S. reilianum WT SRZ1+SRZ2, rep2


title: Reina SIRT1 KI-1 (S-KI1)


title: Retina EAE SIRT1 KI-3 (E-S-KI3)

value: EAE


title: maize_leaf, U. myadis FB1+FB2,  3 dpi, rep1

description:
Library name: A4
3 dpi, U. maydis WT FB1+FB2, rep1


title: LUHMES cells, 24hours, Pb-acet,10 μM-2

city: Kanagawa

first: Tsunehiko

last: Hongen

address: Matanocho

institute: university

description: Library name: S12

data_processing:
RNA-seq raw data was processed using Salmon version (1.10.3) on macOS (Apple Inc.). The raw sequencing reads (FASTQ files) were aligned to the reference transcriptome using Salmon’s quasi-mapping algorithm, which provides a robust and efficient method for transcript quantification. Subsequently, RStudio version (2024.04.2+764) was used for further data analysis.
Assembly: hg38
Supplementary files format and content: comma delimited file includes raw counts for each Sample

source_name: Brain

growth_protocol: LUHMES cells were cultured at 37°C with 5% CO₂ on poly-L-ornithine/fibronectin-coated dishes. The proliferation medium comprised Advanced DMEM/F12, L-glutamine, N-2 supplement, and 40 ng/mL bFGF. After 24 hours, differentiation was induced with cAMP, tetracycline, and GDNF for 48 hours. Subsequently, cells were transferred to multi-well plates for exposure.

extract_protocol:
Total RNA was extracted using NucleoSpin RNA (Macherey-Nagel). The quantity and quality of the RNA were measured using a Nano-Drop Lite (Thermo Fisher Scientific). Total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on MGI DNBSEQ-T7 sequencing platforms, according to effective library concentration and data amount.

treatment_protocol: On day 2 of differentiation, LUHMES cells were passaged to coated 24 well plate. After 1 hr, cells were exposed to Lead (II) acetate at 1 and 10 uM for 3 and 24 hr.

value: Brain

value: Lund Human Mesencephalic cells

value: Neurons

value: 24 hr, Pb-acet, 10 μM


title: maize_leaf, U. myadis FB1+FB2,  6 dpi, rep2

description:
Library name: A8
6 dpi, U. maydis WT FB1+FB2, rep2

value: treatment

value: GB


title: LUHMES cells, 24hours, Pb-acet,1 μM-2

description: Library name: S11

value: 24 hr, Pb-acet, 1 μM


title: maize_leaf, U. myadis FB1+FB2,  3 dpi, rep2

description:
Library name: A5
3 dpi, U. maydis WT FB1+FB2, rep2


title: maize_leaf, U. maydis FB1+FB2,  3 dpi, rep3

description:
Library name: A6
3 dpi, U. maydis WT FB1+FB2, rep3


title: maize_leaf, U. maydis FB1+FB2, 20 hpi, rep3

description:
Library name: A3
20 hpi, U. maydis WT FB1+FB2, rep3


title: Retina EAE SIRT1 KI-2 (E-S-KI2)


title: maize_leaf, U. myadis FB1+FB2, 20 hpi, rep1

description:
Library name: A1
20 hpi, U. maydis WT FB1+FB2, rep1


title: LUHMES cells, 24hours, Control-2

description: Library name: S10

value: 24 hr, control


title: minic_nc3

description: Library name: Sample 3


title: maize_leaf, U. myadis FB1+FB2, 20 hpi, rep2

description:
Library name: A2
20 hpi, U. maydis WT FB1+FB2, rep2


title: LUHMES cells, 3hours, Pb-acet,10 μM-2

description: Library name: S9

value: 3 hr, Pb-acet, 10 μM


title: Retina EAE SIRT1 KI 1 (E-S-KI1)


title: Reina EAE RSV-3 (E-R3)

value: Wild-type (WT)

value: RSV


title: LUHMES cells, 3hours, Pb-acet,1 μM-2

description: Library name: S8

value: 3 hr, Pb-acet, 1 μM


title: C2C12_KO38-1 replicate 1

type: RNA

city: Illkirch

first: Françoise

last: DANTZER

address: 300 boulevard S. Brant

country: France

institute: CNRS

description: Gene expression data from differentiated Parp3KO-C2C12

hyb_protocol: Following fragmentation and end-labeling, 3 μg of cDNAs were hybridized for 16h at 45oC on GeneChip® Mouse Gene 2.0 ST arrays (Affymetrix) interrogating 35240 RefSeq transcripts and ~ 2000 LncRNAs represented by approximately 27 probes spread across the full length of the transcript.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2

data_processing:
CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 200 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: C2C12 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) at 4.5 g/L D-glucose, w/o sodium pyruvate (Gibco) and supplemented with 20% FBS (Dutscher), 1% P/S and incubated at 37 °C and 5% CO2. To induce differentiation, cells were grown to confluency and shifted to differentiation medium composed of DMEM 4.5 g/L D-glucose, w/o sodium pyruvate supplemented with 2% heat-inactivated horse serum (Hyclone), 1% P/S and 1 μM insulin (Sigma) for 72h.

extract_protocol: Total RNA was extracted using the RNeasy Mini-Kit (Qiagen) following the manufacturer’s instructions.

value: induced to differentiate for 72h


title: minic_nc2

description: Library name: Sample 2


title: C2C12_KO38-3 replicate 3


title: C2C12_KO38-2 replicate 2


title: Reina EAE RSV-2 (E-R2)

value: Retina


title: Reina EAE RSV-1 (E-R1)


title: LUHMES cells, 3hours, Control-2

description: Library name: S7

value: 3 hr, control


title: LUHMES cells, 24hours, Pb-acet,1 μM-1

description: Library name: S5


title: C2C12_KO19-2 replicate 2


title: LUHMES cells, 24hours, Control-1

description: Library name: S4


title: 2018-03-07-F-sagittal

city: Cambridge

first: Ayshwarya

last: Subramanian

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
cellranger-6.1.2, CellBender remove-background 0.2.0, scDblFinder_1.6.0
Samples raw base calls demultiplexing, barcoded processing, sequence alignment and gene counting  were made using the Cell Ranger software 6.1.2 function. Raw sequence reads were aligned to the latest mouse reference genome (mm10).
Counts were pre-processed for ambient RNA and doublet removal using CellBender remove-background 0.2.0
Doublet removal was performed using scDblFinder_1.6.0 in the R programing language
Downstream analysis were performed in R.
Assembly: mm10_v3.0.0
Supplementary files format and content: h5 files from CellRanger and CellBender, respectively.

source_name: Kidney

extract_protocol:
As each region was sampled, the tissue was chopped into 1mm x1mm cubes and placed in 0.25mg/ml liberase TH (Roche Diagnostics, Indianapolis, USA) dissociation medium. Following further dissection, the samples were incubated at 37°C for 1 hour at 600rpm. Samples were regularly triturated during the incubation period using a 1ml pipette, after which 10% heat- inactivated FBS RPMI was added to stop the digestion. Centrifugation at 500 g for 5 minutes at room temperature with the removal of the supernatant, was followed by the addition of ACK lysing buffer to remove erythrocytes (Thermo Fisher Scientific, Waltham, USA). Following centrifugation, the resulting cell pellet was incubated with Accumax at 37°C for 3 minutes (Innovative Cell Technologies Inc, San Diego, USA). 10% FBS RPMI was again used to neutralize the Accumax and centrifugation was followed by resuspension of the cell pellet in 0.4% BSA/PBS. The single cell suspension was filtered using a 30um CellTrics filter (Sysmex America Inc, Lincolnshire, USA) with cell viability and concentration determined using trypan blue and the Auto T4 cellometer (Nexcelom Bioscience LLC, Lawrence, USA).
17,500 cells were loaded into the 10x Genomics microfluidic system/onto the 10x Genomics platform to achieve a targeted recovery of 10,000 cells (10x Genomics, Pleasanton, USA).

tag: Sex

value: F

value: Kidney

tag: region

value: Sagittal

tag: age (weeks)


title: LUHMES cells, 24hours, Pb-acet,10 μM-1

description: Library name: S6

value: Brain

value: Lund Human Mesencephalic cells

tag: cell type


title: C2C12_WT_3 replicate 3

description: Gene expression data from differentiated WT-C2C12

source_name: C2C12 WT T72h

value: WT


title: C2C12_KO19-3 replicate 3


title: 2018-02-08-F-Pelvis

description: 10x Genomics

tag: strain

value: Pelvis


title: LUHMES cells, 3hours, Pb-acet,10 μM-1

description: Library name: S3

value: Neurons


title: C2C12_KO19-1 replicate 1

tag: genotype


title: C2C12_WT_2 replicate 2


title: Retina EAE AAV-SIRT-3 (E-A-S3)

tag: tissue


title: 2018-02-15-F-cortex

description: 10x Genomics

value: Cortex


title: 2018-02-15-F-medulla

description: 10x Genomics

value: Medulla


title: Retina EAE AAV-SIRT-2 (E-A-S2)


title: Retina EAE3 (EAE3)

value: EAE


title: 2018-02-16-F-cortex

description: 10x Genomics


title: Retina EAE2 (EAE2)

value: Wild-type (WT)


title: Retina EAE 1 (EAE1)


title: 2018-02-14-M-cortex

description: 10x Genomics

value: M


title: C2C12_WT_1 replicate 1

tag: cell line


title: siRNA targeted Capan-1 cells with B3GNT3 expression knocked down rep3

city: Shanghai

first: Shiqi

last: Yin

address: 上海市奉贤区南桥新城南奉公路6600号

institute: 奉贤区中心医院

description: Library name: capan1_siB3_4

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: cancer cell

tag: treatment


title: LUHMES cells, 3hours, Pb-acet,1 μM-1

description: Library name: S2

value: 3 hr, Pb-acet, 1 μM


title: ABC-1,CCS1477,24h,rep3

city: Sendai

first: KE

last: WANG

state: Miyagi

address: 仙台市青葉区星陵町2-1

department: Department of Biochemistry and Molecular Biology

institute: Tohoku University, Tohoku Medical Megabank Organization,

description:
Library name: Sample 18
CCS5uM_3

data_processing:
Sequencing data was processed on the Galaxy server (https://usegalaxy.org).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: lung

extract_protocol:
RNA was extracted using Sepasol-RNA I Super G (09379-97; Nacalai Tesque). RNA quantity and purity were assessed using NanoPhotometer® NP800 (Implen) and RNA integrity (RIN) was assessed using TapeStation®(Agilent).
Double-stranded DNA (dsDNA) libraries were then constructed using the MGIEasy RNA directional library prep kit® (MGI). These libraries were sequenced on the DNBSEQ-G400RS® (MGI) system, utilizing the DNBSEQ-G400RS high-throughput sequencing kit V1.0 (MGI), which produced 150 bp paired-end reads.

value: lung

value: lung adenocarcinoma


title: ABC-1,CCS1477,24h,rep2

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 17
CCS5uM_2


title: 2018-02-14-M-medulla

description: 10x Genomics


title: 2018-02-14-M-pelvis

description: 10x Genomics


title: 2018-02-13-M-Pelvis

description: 10x Genomics


title: 2018-02-13-M-Medulla

description: 10x Genomics


title: ABC-1,DMSO,24h,rep3

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 15
DMSO_3


title: siRNA targeted Capan-1 cells with B3GNT3 expression knocked down rep1

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: capan1_siB3_1


title: siRNA targeted Capan-1 cells with B3GNT3 expression knocked down rep2

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: capan1_siB3_2


title: Retina control1 (C1)

value: Retina


title: ABC-1,DMSO,24h,rep2

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 14
DMSO_2


title: LUHMES cells, 3hours, Control-1

description: Library name: S1

value: 3 hr, control


title: ABC-1,DMSO,24h,rep1

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 13
DMSO_1


title: si-NC sequence transfected Capan-1 cells as control rep3

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: capan1_NC_3


title: Retina EAE AAV-SIRT-1 (E-A-S1)


title: ABC-1,CCS1477,24h,rep1

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 16
CCS5uM_1


title: tdTomato+ cells, KO, 12wks, scRNA-seq

first: Yuanyuan

last: Wei

address: No. 130, Dong'an Road

institute: Fudan University

data_processing:
Raw sequencing reads were processed using CellRanger v.5.0.0.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: tdTomato+ cells FACS sorted from murine atherosclerotic plaques

extract_protocol:
LysMCre-RosatdTomato/Apoe−/−mice with or without floxed Srsf3 were fed a high-cholesterol diet for either 12 weeks or 30 weeks. The aortic roots, aortas, and carotid arteries were collected from these mice in RPMI1640 media containing 10% FBS on ice, followed by the digestion with aortic adventitia digestion enzyme solution containing 2.5 mg/ml collagenase II and 1.88 mg/ml Elastase for 5-6 min at 37 °C. After carefully peeling the adventitial layers away, the aortas were cut into 2-5 mm pieces and digested with aorta dissociation enzyme solution containing 0.24 mg/ml DNase I, 5.4 mg/ml collagenase I, 0.24 mg/ml collagenase XI, and 0.22 mg/ml hyaluronidase for 45 min at 37 °C. The resulting suspensions were passed through 70 μm cell strainers and subsequently centrifuged at 400g for 5 min at 4 °C. The pelleted cells were resuspended in pre-cold RPMI1640 media containing 10% FBS and kept on ice for further process. tdTomato+ cells were then FACS sorted using a MoFlo XDP cell sorter for single-cell RNA sequencing.
Single-cell RNA-seq libraries were prepared using Chromium Next GEM Single Cell 3' Reagent Kits v.3.1 (10 x Genomics) according to the manufacturer’s instructions.

value: LysMCre, Srsf3flox, RosatdTomato, Apoe-/-

value: High cholesterol diet, 12 weeks


title: si-NC sequence transfected Capan-1 cells as control rep2

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: capan1_NC_2


title: retina control 2 (C2)


title: 2018-02-12-M-Medulla

description: 10x Genomics

value: Kidney


title: 2018-02-08-F-Medulla

description: 10x Genomics

value: F


title: H2023,CCS1477,24h,rep3

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 12
CCS5uM_3

value: squamous cell lung carcinoma


title: tdTomato+ cells, WT, 30wks, scRNA-seq, bio rep 2

value: tdTomato+ cells FACS sorted from murine atherosclerotic plaques

value: LysMCre, Srsf3wt, RosatdTomato, Apoe-/-

value: High cholesterol diet, 30 weeks


title: tdTomato+ cells, WT, 30wks, scRNA-seq, bio rep 1


title: H2023,CCS1477,24h,rep2

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 11
CCS5uM_2


title: H2023,CCS1477,24h,rep1

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 10
CCS5uM_1


title: tdTomato+ cells, WT, 12wks, scRNA-seq, bio rep 2


title: 2018-03-08-F-sagittal

description: 10x Genomics

value: Sagittal


title: 2018-02-08-F-Cortex

description: 10x Genomics

value: Cortex


title: 2018-02-12-M-Pelvis

description: 10x Genomics

value: M

value: Pelvis


title: siRNA targeted AsPC-1 cells with B3GNT3 expression knocked down rep3

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_siB3-5

value: cancer cell


title: siRNA targeted AsPC-1 cells with B3GNT3 expression knocked down rep2

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_siB3-2


title: H2023,DMSO,24h,rep3

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 9
DMSO_3

value: lung


title: si-NC sequence transfected Capan-1 cells as control rep1

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: capan1_NC_1


title: siRNA targeted AsPC-1 cells with B3GNT3 expression knocked down rep1

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_siB3-1


title: 2018-03-06-F-sagittal

description: 10x Genomics


title: tdTomato+ cells, WT, 12wks, scRNA-seq, bio rep 1


title: High iron diet, DUX4 6

city: Chuo-ku, Kumamoto-shi

first: Kodai

last: Nakamura

state: Kumamoto-ken

address: 2-2-1 Honjo

department: Institute of molecular embryology and genetics

institute: Kumamoto university

data_processing:
StrandNGS software 3.4 (by Tomy digital biology) was used for base-calling.
Assembly: mm10
Supplementary files format and content: Sequenced reads were trimmed for low-quality sequences and then mapped to UCSC mm10 mouse reference transcript and genome.
Supplementary files format and content: TPM (transcripts per million) was used as a normalization procedure to quantify the gene expressions in each sample.

source_name: Skeletal muscle

extract_protocol:
Total RNA was obtained from the gastrocnemius and plantaris muscles of ND- and HID-fed mice using ISOGEN ll and the RNeasy kit.
Library preparation and RNA-Seq were performed by Novogene (Beijing, China)

value: Skeletal muscle

value: DUX4 knockin

value: High iron diet


title: H2023,DMSO,24h,rep2

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 8
DMSO_2


title: High iron diet, DUX4 5


title: 2018-03-05-F-sagittal

description: 10x Genomics


title: H2023,DMSO,24h,rep1

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 7
DMSO_1


title: H460,CCS1477,24h,rep3

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 6
CCS5uM_3

value: large cell lung carcinoma


title: siRNA targeted AsPC-1 cells with B4GALT5 expression knocked down rep2

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_siB4-3


title: 2018-03-02-F-sagittal

description: 10x Genomics


title: siRNA targeted AsPC-1 cells with B4GALT5 expression knocked down rep3

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_siB45


title: High iron diet, DUX4 4


title: siRNA targeted AsPC-1 cells with B4GALT5 expression knocked down rep1

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_siB4-1


title: H460,CCS1477,24h,rep2

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 5
CCS5uM_2


title: High iron diet, DUX4 3


title: si-NC sequence transfected AsPC-1 cells as control rep3

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_NC-4


title: 2018-03-01-M-sagittal

description: 10x Genomics


title: H460,CCS1477,24h,rep1

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 4
CCS5uM_1


title: 2018-02-28-M-sagittal

description: 10x Genomics


title: H460,DMSO,24h,rep3

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 3
DMSO_3


title: High iron diet, DUX4 1


title: High iron diet, DUX4 2


title: 2018-02-23-M-sagittal

description: 10x Genomics


title: H460,DMSO,24h,rep2

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 2
DMSO_2


title: High iron diet, control 5

value: wild type

value: Normal diet


title: si-NC sequence transfected AsPC-1 cells as control rep1

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_NC-2


title: 2018-02-16-F-pelvis

description: 10x Genomics

value: F

value: Kidney


title: High iron diet, control 4


title: 2018-02-26-M-sagittal

description: 10x Genomics


title: 4P_HepG2_rep2

city: New Haven

first: Michael

last: Mak

state: CT

address: 55 Prospect St

institute: Yale University

data_processing:
The raw reads were aligned by a read aligner STAR to the human GRCh38 release-86 transcriptome (https:// www.ensembl.org/). Data normalization and differential expression analysis were conducted with the R-package DESEQ2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with raw counts for all samples

source_name: Liver

extract_protocol:
Total RNA was extracted with an RNeasy mini kit (QIAGEN), following the manufacturer’s protocol.
The library was prepared and sequenced on the Illumina HiSeq or NovaSeq platforms (paired-end 100bp reads per sample) by Yale Center for Genome Analysis (YCGA).

treatment_protocol: Biological replicates of HepG2 cells cultured in isotonic and 4% PEG medium for 5 days were collected for bulk RNA sequencing.

value: Liver

value: Hepatoblastoma

value: WT


title: Responder 8

city: Rome

first: Francesca

last: Sacco

address: Via della Ricerca Scientifica, 1

country: Italy

institute: University of Rome Tor Vergata

data_processing:
llumina Nova Seq 6000 base call (BCL) files were converted in fastaq file through bcl2fastaq (v2.20.0.422).
nf-core/rnaseq  v3.14.0 in Nextflow 23.10.1
The pipeline performed quality control with FastQC (v0.12.1), trimming with Trim Galore (v0.6.7), alignment using STAR (v2.7.9), and quantification with Salmon (v1.10.1).
Gene expression was normalized using TPM.
Assembly: GRCh38.111
Supplementary files format and content: tab-delimited text files include raw counts for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Blood

extract_protocol:
RNA was prepared from PBMCs using the RNeasy Mini Kit (QIAGEN, Germany).  The pellets obtained from buffycoat were resuspended in the RLT buffer. We proceed with the addition of equal volume of 70% Ethanol (EtOH) to our already homogenized sample in RTL. It was spinned at ≥8000 x g (≥10,000 rpm) for 15sec. 700 µl of Buffer RW1 were added and the solution was spinned at ≥8000 x g (≥10,000 rpm) for 15sec. It was emptied carefully, and 500 μl of RPE Buffer were added and the solution was spinned ≥8000 x g (≥10,000 rpm) for 2 minutes. The column was emptied again and placed in a new tube and centrifuged at maximum power for 1 minute to dry.
NEGEDIA Digital mRNA-seq research grade sequencing service 2.0 (Next Generation Diagnostic srl)

value: Blood

value: PBMCs

tag: disease state

value: chronic myeloid leukemia

value: Untreated


title: Responder 16


title: High iron diet, control 3


title: H460,DMSO,24h,rep1

address: 仙台市青葉区星陵町2-1

description:
Library name: Sample 1
DMSO_1


title: Responder 12


title: 4P_HepG2_rep1


title: High iron diet, control 2


title: Non_Responder 9


title: si-NC sequence transfected AsPC-1 cells as control rep2

address: 上海市奉贤区南桥新城南奉公路6600号

description: Library name: AS_NC-3

value: cancer cell


title: PR-R-28N

city: Tampa

first: Manishkumar

middle: S

last: Patel

state: FL

address: 12902 USF Magnolia Drive

department: Tumor Microenvironment and Metastasis

institute: H. Lee Moffitt Cancer Center and Research Institute

description:
Library name: PR-R-28N
Normal

data_processing:
Initial quality control was performed on the sequenced files using fastqc, fastp and multiqc. The sequence reads were aligned to the human genome (hg38) using Bowtie 2 with the default settings and were further sorted and indexed using SAMtools. The duplicated reads were removed using Picard command line tool and, raw read counts per gene were generated using the feature Counts tool from package subread.
Differentially methylated genes were identified using the DESeq2 package. All samples were normalized using DESeq2 internal normalization and further compared in unpaired manner with multiple-hypothesis testing. Genes with |log2 fold-change| >0.4 and adjusted p-value<0.05 were considered differentially methylated.
Assembly: GRCh38
Supplementary files format and content: .txt
Supplementary files format and content: The processed data file contains normalized counts for 22 prostate tumors and 24 adjacent normal samples across different genes.

source_name: Prostate

extract_protocol:
Genomic DNA samples were obtained from the FFPE prostate tumor tissues as described in the manufacturer’s instructions (QIAamp DNA FFPE Tissue kit, Qiagen, Germantown, MD). We used 7-50 ng of genomic DNA as starting material.
DNA was enriched by labeling and capturing as described previously in Song et al., 2011 (https://www.nature.com/articles/nbt.1732). The 5hmC DNA was amplified using universal primer (New England Biolabs, USA), index primer (New England Biolabs, USA) and HiFi HotStart ReadyMix (KAPA/Roche). Single-end 75 bp sequencing was performed on an Illumina NextSeq 500. 22 prostate tumors and 24 adjacent normal FFPE samples were sequenced after 5hmC enrichment.

value: Prostate

value: FFPE Tissue


title: High iron diet, control 1

value: Skeletal muscle


title: PR-16N

description:
Library name: PR-16N
Normal


title: Retina control3 (C3)

institute: University of Pennsylvania

value: Retina

value: Wild-type (WT)


title: PR-51N

description:
Library name: PR-51N
Normal


title: Iso_HepG2_rep1


title: Non_Responder 14


title: 2018-02-22-M-sagittal

description: 10x Genomics

value: M

value: Sagittal


title: Non_Responder 13


title: Normal diet, DUX4 6

value: DUX4 knockin

value: High iron diet


title: Ponce-46N

description:
Library name: Ponce-46N
Normal


title: Iso_HepG2_rep2

value: Liver


title: Non_Responder 11


title: Ponce-16N

description:
Library name: Ponce-16N
Normal


title: 6-base-seq, H9, 8 day NPCdiff B

city: Nashville

first: Lindsey

last: Guerin

state: Tennessee

address: 2215 Garland Ave, 673B Light Hall

department: Biochemistry

institute: Vanderbilt University

data_processing:
trim and filter
align to reference
duplicate removal
epoigenetic quantification
variant associated methylation, allele-specific methylation
Assembly: hg38
Supplementary files format and content: .zarrz, all sample modC calculation

growth_protocol: STEMdiff™ SMADi Neural Induction Kit and mTeSR

extract_protocol:
phenol-chloroform
evoC 6-base

treatment_protocol: STEMdiff™ SMADi Neural Induction Kit

value: differentiated human embryonic stem cell/ neural progenitor cell


title: Normal diet, DUX4 3


title: Ponce-15N

description:
Library name: Ponce-15N
Normal


title: Normal diet, DUX4 4


title: 6-base-seq, H9, 4 day NPCdiff B


title: LuCaP_92

city: Vancouver

first: Ning

last: Shen

state: BC

address: 2875 Osoyoos Crescent, Apt 124

institute: University of British Columbia

description: Library name: 92

data_processing:
After sequencing, the quality and quantity of the raw reads were examined using FastQC version 0.11.5 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and MultiQC version 1.7. Raw reads were quality and adapter trimmed using Trim Galore! version 0.6.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default settings in paired-end mode. The trimmed reads then were aligned to hg19 using Bowtie2 version 2.3.5.1 in paired-end mode and all other settings default. The SAMtools version 1.10 software suite was used to convert SAM alignment files to BAM format, sort and index reads, and remove duplicates.
Assembly: hg19
Supplementary files format and content: Comma-separated text file

source_name: Prostate cancer

extract_protocol:
DNA from the LuCaP PDXs was extracted using the DNeasy Blood and Tissue Kit (Qiagen). Genomic DNA was sheared using a Covaris Sonicator E220 and AMPure XP beads (Beckman Coulter) were used to size select 150-250 bp DNA fragments.
Library preparation was performed using KAPA HyperPrep Kit (KAPA Biosystems) according to the manufacturer’s protocol. We then performed end-repair, A-tailing, and ligation of NEBNext adaptors (NEBNext Multiplex Oligos for Illumina kit, New England BioLabs). Libraries were digested using the USER enzyme (New England BioLabs). λ DNA, consisting of unmethylated and in vitro methylated DNA, was added to prepared libraries to achieve a total amount of 100 ng DNA. Methylated and unmethylated Arabidopsis thaliana DNA (Diagenode) was added for quality control. MeDIP was performed using the MagMeDIP kit (Diagenode) following the manufacturer’s protocol. Samples were purified using the iPure Kit v2 (Diagenode). Success of the immunoprecipitation was confirmed using qPCR to detect recovery of the spiked-in Arabidopsis thaliana methylated and unmethylated DNA. KAPA HiFi Hotstart ReadyMix (KAPA Biosystems) and NEBNext Multiplex Oligos for Illumina (New England Biolabs) were added to a final concentration of 0.3 uM and libraries were amplified as follows: activation at 95°C for 3 minutes, amplification cycles of 98°C for 20 seconds, 65°C for 15 seconds, 72°C for 30 seconds, and a final extension of 72°C for 1 minute. Samples were pooled and sequenced (Novogene Corporation, CA) on Illumina HiSeq 4000 to generate 150 bp paired-end reads.

value: Prostate cancer

value: PRAD


title: LuCaP_78CR

description: Library name: 78CR


title: LuCaP_136CR

description: Library name: 136CR


title: PR-45N

description:
Library name: PR-45N
Normal


title: Normal diet, DUX4 2


title: LuCaP_78

description: Library name: 78


title: 6-base-seq, H9, 0 day NPCdiff B

value: human embryonic stem cell


title: Ponce-35N

description:
Library name: Ponce-35N
Normal


title: Normal diet, DUX4 1


title: LuCaP_77

description: Library name: 77


title: Normal diet, control 6

value: wild type

value: Normal diet


title: LuCaP_70

description: Library name: 70


title: Normal diet, DUX4 5


title: Ponce-48N

description:
Library name: Ponce-48N
Normal


title: 6-base-seq, H9, 0 day NPCdiff A


title: LuCaP_35CR

description: Library name: 35CR


title: scRNA-seq, H9, 6 day NPCdiff A

data_processing:
https://github.com/Ken-Lau-Lab/STAR_Protocol
Assembly: hg38
Supplementary files format and content: .mtx, filtered cell matrix

extract_protocol:
inDrop
TruDrop protocol


title: LuCaP_136

description: Library name: 136


title: LuCaP_105

description: Library name: 105


title: Normal diet, control 3


title: LuCaP_96

description: Library name: 96


title: Ponce-36N

description:
Library name: Ponce-36N
Normal


title: Ponce-26N

description:
Library name: Ponce-26N
Normal


title: 6-base-seq, H9, 8 day NPCdiff A


title: Normal diet, control 5


title: LuCaP_86.2

description: Library name: 86.2


title: 6-base-seq, H9, 4 day NPCdiff A


title: LuCaP_81

description: Library name: 81


title: Ponce-34N

description:
Library name: Ponce-34N
Normal


title: RNA-seq, H9, 12 day NPCdiff B

data_processing:
alignment via STAR_2.6.1a_08-27
QC filtering via SAMtools/1.9
differential expression via DESeq2 v1.38.3
Assembly: hg38
Supplementary files format and content: bigWig, read signal for visualization

extract_protocol:
TRIzol
NEBNext®Ultra™II RNA Library Prep


title: RPE/choroid complex - ADQ 4

city: St. Louis

first: Ryo

last: Terao

state: MO

address: 517 S. Euclid Ave

department: Ophthalmology & Visual Sciences

institute: Washington University School of Medicine in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq2 software.  RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
To find the most critical genes, the Limma voomWithQualityWeights transformed log 2 counts-per-million expression data was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA. Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data. An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coefficients of the model matrix.  Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. These de-novo clustered genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler. Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module.  The information for all clustered genes for each module were then combined with their respective statistical significance results from Limma to determine whether or not those features were also found to be significantly differentially expressed.
Assembly: Mouse Ensembl GRCm38.76
Supplementary files format and content: all.gene_counts.tsv: Raw counts.
Supplementary files format and content: group_ADQ_Differential_Expression.tsv: Differential gene expression performed comparing control and the experimental group

source_name: RPE/choroid complex

extract_protocol:
Samples were collected in TRIzol reagent. mRNA was obtained using NucleoSpin RNA columns (Takara, 740955) according to the manufacturer’s instructions.
cDNA amplification for mRNA-Seq was performed by SMARTer

value: RPE/choroid complex

value: iDTR Adiponectin-Cre

value: Diphtheria toxin (i.p)


title: LuCaP_58

description: Library name: 58


title: PR-44N

description:
Library name: PR-44N
Normal

value: Prostate

value: FFPE Tissue


title: PR-5N

description:
Library name: PR-5N
Normal


title: Normal diet, control 4

value: Skeletal muscle


title: RPE/choroid complex - ADQ 5


title: scRNA-seq, H9, 2 day NPCdiff B


title: RNA-seq, H9, 12 day NPCdiff A


title: RNA-seq, H9, 6 day NPCdiff B


title: PR-31N

description:
Library name: PR-31N
Normal


title: RPE/choroid complex - ADQ 3


title: PR-34N

description:
Library name: PR-34N
Normal


title: scRNA-seq, H9, 0 day NPCdiff A


title: RNA-seq, H9, 6 day NPCdiff A


title: RPE/choroid complex - ADQ 2


title: Ponce-25N

description:
Library name: Ponce-25N
Normal


title: Normal diet, control 2


title: RNA-seq, H9, 4.5 day NPCdiff B


title: LuCaP_23.1

description: Library name: 23.1


title: RPE/choroid complex - ADQ 1


title: LuCaP_73

description: Library name: 73


title: PR-54N

description:
Library name: PR-54N
Normal


title: RNA-seq, H9, 4.5 day NPCdiff A


title: RPE/choroid complex - control 5

value: iDTR


title: PR-40N

description:
Library name: PR-40N
Normal


title: LuCaP_145.2

description: Library name: 145.2

value: NEPC


title: Ponce-27N

description:
Library name: Ponce-27N
Normal


title: RNA-seq, H9, 3 day NPCdiff B


title: Ponce-42N

description:
Library name: Ponce-42N
Normal


title: RNA-seq, H9, 3 day NPCdiff A


title: LuCaP_145.1

description: Library name: 145.1


title: LuCaP_35

description: Library name: 35


title: Ponce-39N

description:
Library name: Ponce-39N
Normal


title: RPE/choroid complex - control 3


title: RNA-seq, H9, 2 day NPCdiff B


title: LuCaP_93

description: Library name: 93


title: Ponce-37N

description:
Library name: Ponce-37N
Normal


title: RNA-seq, H9, 2 day NPCdiff A


title: Ponce-20T

description:
Library name: Ponce-20T
Tumor


title: LuCaP_49_2018

description: Library name: 49_2018


title: RNA-seq, H9, 1 day NPCdiff B


title: LuCaP_147

description: Library name: 147


title: Ponce-12T

description:
Library name: Ponce-12T
Tumor


title: CD73-MCD-3

city: beijing

first: xinjie

last: zhong

address: No. 95 Yong 'an Road

institute: Beijing Friendship Hospital

data_processing:
HISAT2 2.1.0 --dta -t -p 4
RNA samples were purified, fragmented, reverse transcribed, end-repaired. After sequenced adapters were added, the target fragments were recovered by magnetic bead screening, and PCR amplification was performed to complete the entire library preparation work.
After the library construction was completed, use Agilent2100 to detect the insert size of the library.
If insert size met the expectation, Bio-RAD CFX 96 fluorescent quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN were used to perform q-PCR to accurately quantify the effective concentration of the library (the effective concentration of the library was > 10nM) to ensure the quality of the library.
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: liver

extract_protocol:
C57BL/6 mice and CD73 KO mice were fed with NCD (normal control diet) and MCD(methionine/choline-deficient diet) for 4 weeks. Immune cells in liver samples were stained and detected by fluorescence activated cell sorting (FACS) cells Aria II (BD Biosciences, CA, USA), CD4+ CD25+ cells (Treg) were selected. Trizol reagent was used for collecting total RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: T cell

value: CD73 KO

tag: diet

value: methionine/choline-deficient diet


title: RNA-seq, H9, 1 day NPCdiff A

value: differentiated human embryonic stem cell/ neural progenitor cell


title: LuCaP_96CR

description: Library name: 96CR

value: Prostate cancer

value: PRAD


title: CD73-MCD-2


title: RNA-seq, H9, 12 hour NPCdiff B


title: CD73-MCD-1


title: RPE/choroid complex - control 4


title: PR-27T

description:
Library name: PR-27T
Tumor


title: LuCaP_86.2CR

description: Library name: 86.2CR


title: MCD-2

value: Wild type


title: RNA-seq, H9, 12 hour NPCdiff A


title: PR-R-24T

description:
Library name: PR-R-24T
Tumor


title: RPE/choroid complex - control 2


title: LuCaP_77CR

description: Library name: 77CR


title: RNA-seq, H9, 6 hour NPCdiff B


title: LuCaP_173.1

description: Library name: 173.1


title: PR-25T

description:
Library name: PR-25T
Tumor


title: MCD-1


title: LuCaP_73CR

description: Library name: 73CR


title: PR-R-23T

description:
Library name: PR-R-23T
Tumor


title: NCD-2

value: normal control


title: RNA-seq, H9, 6 hour NPCdiff A


title: LuCaP_23.1CR

description: Library name: 23.1CR


title: RNA-seq, H9, 0 day NPCdiff B

value: human embryonic stem cell


title: LuCaP_70CR

description: Library name: 70CR


title: RPE/choroid complex - control 1

value: RPE/choroid complex


title: Ponce-47T

description:
Library name: Ponce-47T
Tumor


title: Spleen Treg, ATF4KO 3

city: La Jolla

first: Chunyu

last: Jin

address: 9500 Gilman Dr. MC0648

institute: University of California, San Diego

data_processing:
The data were mapped using STAR with default parameters. The gene expression raw counts were quantified by HOMER’s analyzeRepeats command with the option ‘-condenseGenes -count exons -noadj’. Differential gene expression was calculated using the HOMER command ‘getDiffExpression.pl’. Transcript per kilobase million (TPM) was quantified for all genes matching accession number to raw counts.
Assembly: mm10
Supplementary files format and content: text (.txt) file for the TPM counts for each gene.
Supplementary files format and content: Excel file including up- and down-regulated genes in obese vs. normal.

source_name: spleen

extract_protocol:
Treg cells were sorted into Trizol LS and RNA was extracted using the Zymo Direct-zol RNA microprep kit.
Libraries were prepared using NEB Next Ultra II Directional RNA Library Prep Kit for Illumina.

value: spleen

value: Treg cells


title: NCD-1


title: Ponce-41T

description:
Library name: Ponce-41T
Tumor

value: Prostate

value: FFPE Tissue


title: Spleen Treg, ATF4KO 2


title: RNA-seq, H9, 0 day NPCdiff A


title: ATAC-Me, H9, 6 day NPCdiff B

data_processing:
trimming via trim_galore v0.6.2
alignment via WALT v1.0
QC filtering via SAMtools/1.9
methylation quantification via methpipe-5.0.1
peak calling via Genrich, version 0.6
Assembly: hg38
Supplementary files format and content: .meth for methylation quantification

extract_protocol:
Tn5 incubation on in-tact cells, part of ATAC-Me protocol
ATAC-Me as outlined in Nature Protocols paper (Guerin et al. Nat Protocol 2021), https://www.nature.com/articles/s41596-021-00608-z
ATAC-Me


title: Spleen Treg, ATF4KO 1


title: Ponce-57T

description:
Library name: Ponce-57T
Tumor


title: ATAC-Me, H9, 6 day NPCdiff A


title: LuCaP_147CR

description: Library name: 147CR


title: Ponce-51T

description:
Library name: Ponce-51T
Tumor


title: Spleen Treg, ATF4KO 4


title: Spleen Treg, control 4

value: control


title: Ponce-16T

description:
Library name: Ponce-16T
Tumor


title: ATAC-Me, H9, 12 day NPCdiff B