title: CD45+Ter119- cells from bone marrow of PyMT-N tumor-bearing mice

source_name: PyMT-N tumor-bearing

value: PyMT-N


title: CD45+Ter119- cells from bone marrow of Naïve C57BL/6 mice

status: Public on Nov 08 2023

type: SRA

city: Houston

first: Xiang

last: Zhang

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

library_source: transcriptomic single cell

data_processing:
The mm10 genome was used for reads mapping. Raw sequencing files were imported into 10x Genomics Cell Ranger toolkit (v3.1.0) with default settings for quantifications.
Assembly: mm10
Supplementary files format and content: Compressed .gz files contains the filtered_feature_bc_matrix output folder from Cellranger. Each .gz file contains a .mtx file which is the count matrix and two .tsv files that list the feature names and sample annotations.

molecule: total RNA

organism: Mus musculus

source_name: Tumor-free

extract_protocol:
PB was collected by retro-orbital sampling. To isolate the BM cells, the muscle tissue on the tibia and femur were completely removed, BM cells were flushed out with PBS(2%FBS) from long bone (tibia and femur) and filtered through a 70 µm strainer. red blood cells are depleted by resuspending BM cells in RBC lysis buffer (Tonbo). For each group, cells were sampled from five mice and pooled into one, then stained with DAPI, CD45-APC and TER-119-VF450. To get rid of erythroid cells, DAPI-CD45+TER119- singlet cells were purified by fluorescence-activated cell sorting (FACS)orted into single-cell suspension and immediately submitted to the Single Cell Genomics Core at Baylor College of Medicine.
The single-cell gene expression Library was prepared according to the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). In brief, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on the Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS are broken and cDNA from each single cell is pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification. The libraries that passed the quality control, were sequenced by the NovaSeq 6000 (Illumina).

tag: tissue

value: Bone marrow

tag: strain

tag: cell type

tag: inoculated tumor cell line


title: KDM5 JmjC 2

city: Bronx

first: Matanel

last: Yheskel

state: NY

address: 1300 Morris Park

department: Genetics

institute: Albert Einstein College of Medicine

description:
JmjC_2
counts.csv

library_source: transcriptomic

data_processing:
R
Reads were trimmed using fastp
Reads were aligned using Rsubread (RNA-Seq) or RNA-STAR (Ribo-Seq)
Counts were obtained using featureCounts (RNA-Seq) or ORFik (Ribo-Seq)
Differential expression analysis was performed with DESeq2
Assembly: dm6
Supplementary files format and content: RNA-Seq comma separated values (csv) of raw counts
Supplementary files format and content: Ribo-Seq differential expression analyses using the R package ORFik.

organism: Drosophila melanogaster

source_name: heads

growth_protocol: Flies were kept at 25℃ with a 12-hour light/dark cycle and 50% humidity. All flies were collected or harvested 1-5 days after eclosion from 9AM-12PM

extract_protocol:
Trizol/chloroform followed by precipitation using isopropanol
TruSeq Stranded mRNA Library Preparation Kit.

value: heads

tag: genotype

value: JmjC


title: 1_SKM1_AZA

city: Montréal

first: Claude

last: Perreault

state: Québec

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 0 mismatch in the index for paired-end samples, and 0 mismatch for the single read samples.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version 26 (based on Ensembl 88)
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned

molecule: polyA RNA

organism: Homo sapiens

source_name: cell line

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

value: cell line

tag: cell line

value: acute myeloid leukemia

tag: treatment

value: AZA


title: KDM5 JmjC 1

description:
JmjC_1
counts.csv


title: CD45+Ter119- cells from peripheral blood of PyMT-N tumor-bearing mice

value: Peripheral blood


title: KDM5 D234G 3

description:
D234G_3
counts.csv


title: CD45+Ter119- cells from peripheral blood of Naïve mice


title: 1_OCIAML3_AZA


title: 1_OCIAML3_CT

value: Untreated


title: WTNOR2

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description: WT 21%O2

data_processing:
Using STAR software [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/], FASTQ files were aligned to Genome data base (Mus musculus.GRCm38.mm10) and read counts obtained for each gene
For the detection of diﬀerentially expressed genes, the following method has been applied:  DESeq2 [https://www.ncbi.nlm.nih.gov/pubmed/25516281]: a shrinkage estimation has been applied for dispersions and calculation of expression fold changes, to improve stability and interpretability of estimates
Assembly: GRCm39.mm39
Supplementary files format and content: A matrix is generated as a plain text file (*.txt), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: WT Mouse Lewis Lung Carcinoma cell cultured under 21%O2

growth_protocol: Lewis Lung Carcinoma cells (LLC) (CRL-1642; ATCC) were maintained in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/ streptomycin.

extract_protocol:
NucleoSpin RNA kit (Macherey-Nagel Cat. No.740955.250), with Dnase treatment. Total RNA was eluted in RNase-free water
Sequencing libraries were prepared following the protocol "TruSeq Stranded mRNA Sample Preparation Guide (Part#15031047 Rev.E)" with the “TruSeq® Stranded mRNA Library Prep” kit  (Illumina Inc. Cat. # 20020594) and TruSeq RNA CD Index Plate (96 Indexes, 96 Samples) (Illumina Inc. Cat. # 20019792)

treatment_protocol: No treatment

value: Lewis Lung Carcinoma cell

value: WT


title: 2_OCIAML3_CT


title: 1_MOLM13_CT


title: KDM5 D234G 2

description:
D234G_2
counts.csv


title: 1_THP1_CT


title: WTNOR1

description: WT 21%O2


title: 1_MOLM13_AZA


title: KDM5 A224T 3

description:
A224T_3
counts.csv


title: WTHYP2

description: WT 1%O2

source_name: WT Mouse Lewis Lung Carcinoma cell cultured under 1%O2


title: WGBS_rWT_M_Striatum_44921

city: St. Louis

first: Diana

middle: Christian

last: Beard

state: Missouri

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

library_source: genomic

data_processing:
Reads were adaptor trimmed and mapped to the mm9 genome using bowtie2 alignment and subsequently deduplicated.
Reads were called for methylation using BS-seeker2
Methylation levels across regions were assessed using bedtools map -o sum, summing the number of reads mapping to Cs (supporting mC) and the number of reads mapping to Cs + Ts (supporting C) in the region, then dividing those two numbers (% mC/C in region)
Regions were adjusted for nonconversion rate by substracting % methylation in Lambda spike-ins per-sample from the calculated %mC/C value
di- to penta-nucleotide methylation were generated from each library and compiled into the .xlsx file
Supplementary files format and content: mm9

molecule: genomic DNA

source_name: Striatum

extract_protocol:
DNA was extracted using the Allprep DNA/RNA Mini Kit (Qiagen).
300ng of DNA was sonicated using the S220 Ultrasonicator (Covaris) and libraries were prepped using the Tecan Ovation Ultralow Methyl-Seq Kit (Tecan) with bisulfite conversion done with the Epitect Bisulfite Kit (Qiagen). Libraries were amplified using 11-13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt Beads. Libraries were validated using the Agilent DNA D1000 Screntape Assay Kit.

value: Striatum

tag: Sex

value: Male

tag: age


title: KDM5 JmjC 3

description:
JmjC_3
counts.csv


title: KDM5 A224T 2

description:
A224T_2
counts.csv


title: KDM5 A224T 1

description:
A224T_1
counts.csv


title: WGBS_rWT_M_Hippocampus_44921

source_name: Hippocampus

value: Hippocampus


title: KDM5 WT 5

description:
WT_5
counts.csv


title: WTHYP1

description: WT 1%O2


title: KONOR2

description: FIH-KO 21%O2

source_name: FIH-deficient Mouse Lewis Lung Carcinoma cell cultured under 21% O2

value: FIH-deficient


title: WGBS_rWT_F_Hippocampus_44930

value: Female


title: KONOR1

description: FIH-KO 21%O2


title: WGBS_rWT_M_Cortex_44921

source_name: Cortex

value: Cortex


title: KOHYP2

description: FIH-KO 1%O2

source_name: FIH-deficient Mouse Lewis Lung Carcinoma cell cultured under 1% O2


title: KDM5 D234G 1

description:
D234G_1
counts.csv


title: MDA-MB-468 cells, LSE rep2

city: Southampton

first: Hualong

last: Zhao

state: Not US or Canada

address: University Road

department: Biological Sciences

country: United Kingdom

institute: University of Southampton

data_processing:
Raw read counts were imported into RStudio (version 4.2.0) and analyzed by using R packages.
Transcripts with low abundance (under 10 counts across all samples) were removed.
Genes with Padj < 0.05 and |Log2FoldChange| >1 were considered as differentially expressed genes (DEGs).
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco® by Life Technology) with 10% FBS and 1% (v/v) penicillin/streptomycin, and were kept at 37 °C and 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen) according to manufacturer’s instructions and quantified using a Nanodrop Spectophotometer 2000c (Thermo Fisher Scientific). A total amount of 3 μg RNA per sample was used as input material for library construction.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, Massachusetts, USA) following manufacturer’s instruction. Libraries were pooled in equimolar and sequenced using the paired-end strategy (2 × 150) on the Illumina NovaSeq 6000 platform following the standard protocols (Novogene, UK).

treatment_protocol: MDA-MB-468 cells were treated with Limonium Sinense Ethanol extract (LSE) for 48 hours at 500 μg/mL

value: breast cancer cells

value: LSE, 500 ug/mL, 48 hours


title: MDA-MB-468 cells, Control rep3


title: MDA-MB-468 cells, LSE rep3


title: WGBS_rWT_F_Cortex_44930


title: MDA-MB-468 cells, LSE rep1


title: KDM5 WT 3

description:
WT_3
counts.csv

value: heads


title: HO site scRNAseq

city: Dallas

first: Robert

middle: J

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tendon injury

extract_protocol:
Bone marrow flushed and subjected to RBC lysis. Blood spun on ficoll gradient, then subjected to RBC lysis. HO site subjected to enzymatic digestion at 37C
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: unsorted

value: tendon injury

value: 10 weeks


title: WGBS_rWT_F_Striatum_44930


title: blood scRNAseq

description: 10x Genomics

source_name: blood

value: blood


title: MDA-MB-468 cells, Control rep1


title: KDM5 WT 2

description:
WT_2
counts.csv


title: MDA-MB-468 cells, Control rep2


title: WGBS_rWT_F_Cerebellum_44930

source_name: Cerebellum

value: Cerebellum


title: WGBS_R878H_M_Striatum_44922


title: hTSC-BL-Input, ChIP-seq, control

city: Beijing

first: Hongmei

last: Wang

address: 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R.China

country: China

institute: INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES

data_processing:
We used FastQC v0.11.9 to estimate the quality of fastq files and trim_galore v0.6.7 to filter low quality reads if necessary.
We applied bowtie2 (v2.4.2) with default parameters for raw fastq reads mapping to human (hg38) reference genome and used MACS2 to call peaks for CUT&Tag and ChIP-seq datasets. We used the ‘reduce’ function from the R package GenomicRanges for merge of peaks of each replications. Then we intersected and counted overlap peaks from CUT&Tag and previous eGRN  peaks which were assigned to nearby gene by peak to gene links. We quantitatively summarized the validation result by overlap percentage of these two peak sets. Finally we visualized the regulatory events with CUT&Tag, ChIPseq tracks and eGRN TF target peaks tracks for two genes (FLT1 and EGLN3) within the eGRN target gene list.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for IgG and input)

source_name: hTSC-BL

growth_protocol: The culture of human trophoblast stem cell lines was performed as previously described. Briefly, the plate was coated with 5 μg/ml Collagen I (Cat#354233, Corning) at 37℃ at least for 1 h. hTSCs were cultured in hTSCs medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 1.5 μg/ml L-ascorbic acid, 50 ng/ml EGF, 2 μM CHIR99021, 0.5 μM A83-01, 1 μM SB431542, 0.8 mM VPA and 5 μM Y27632). hTSCs were dissociated with TrypLE for 8 min at 37℃ and the cells were passaged to a new Collagen I-coated plate. hTSCs were routinely passaged every 4-5 days at a 1: 4-1: 6 ratio.

extract_protocol:
For ChIP-seq sample extraction, hTSCs-BL and STB-BL cells were dissociated with TrypLE for 8 min at 37℃ and washed with phosphate buffer solution for 3 times. About 5 × 106 cells were used for cross-linking by 1% formaldehyde. After rotating at room temperature for 10 min, the crosslinking was quenched by 125 mM Glycine and rotated for 10 min at room temperature. The crosslinked cells were quick-froze with liquid N2.
For CUT&Tag sample extraction, STB-BL cells were dissociated with TrypLE for 8 min at 37℃ and washed with phosphate buffer solution. About 5 × 104 cells were resuspend with wash buffer.
The experiment of ChIP-seq was performed as previously described (A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models). Briefly, about 5 × 106 hTSCs-BL and STB-BL were used for cross-linking by 1% formaldehyde and quenched by 125 mM glycine. Cells were lysed and nuclei were sonicated and diluted to a final concentration of 0.1% by SDS. Protein A/G magnetic beads were added and incubated at 4°C for 1 h. Pre-cleared chromatin was incubated with CEBPB antibody (Cat#23431-1-AP, Proteintech) or monoclonal rabbit isotype control (Cat#ab172730, Abcam) overnight at 4°C. Then Protein A/G magnetic beads were added to capture the specific chromatin complexes. The supernatants were collected with 500 mM NaCl and incubated at 65 °C overnight for reverse crosslinking. Sample was incubated at 37°C for 1 h with RNase A, and was incubated at 50°C for 1 h with proteinase-K. The released DNA was purified by the QIAquick PCR purification Kit and processed to sequencing library preparation. Multiplexed ChIP-seq libraries were prepared by NEBNext Ultra II DNA Library Prep Kit (Cat#E7645S, NEB). The final libraries and multiplexed libraries were subjected to Illumina Sequencing 2500 platforms.For CUT&Tag,the experiment was conducted according to the instructions provided by Vazyme (Cat#TD904). In brief, approximately 5 × 104 cells were harvested and counted, then mixed with activated ConA Beads and incubated overnight with primary antibodies (CEBPB, Cat#23431-1-AP, Proteintech and FOSL2, Cat#351814, USBiological). The secondary antibody (Cat#Ab207, Vazyme) was incubated at room temperature (RT) with rotation for 1 hour. After removing the supernatant, pA/G-Tnp Pro and TTBL were separately incubated with rotation at RT and 37℃ for 1 hour. The supernatant was then mixed with DNA Extract Beads Pro to dissolve DNA with ddH2O and used directly for PCR amplification. Subsequently, VAHTS DNA Clean Beads were added to purify the DNA, which was then subjected to next-generation sequencing using the Illumina NovaSeq 6000 platform.

treatment_protocol: hTSCs were grown to 80% confluence in the hTSCs medium and dissociated with TrypLE for 8 min at 37°C. For the induction of STB, hTSCs were seeded in a 6-well plate pre-coated with 2.5 μg/ml Collagen I at a density of 1 × 105 cells per well and cultured in STB medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X supplement, 2.5 μM Y27632, 2 μM forskolin, and 4% KSR). The medium was replaced every 2 days and analyzed on day 6.

value: hTSC-BL

value: human trophoblast stem cell


title: KDM5 WT 1

description:
WT_1
counts.csv

value: WT


title: hTSC-BL-IgG, ChIP-seq, control


title: PMA_J_input

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low-quality reads using trim-galore (v0.6.4). Then FastQC (v0.11.9) and Multiqc (v1.8) is used to ensure high reads quality. The clean reads were mapped to the human genome (assembly human genome hg38, primary genome) using the Burrow-Wheeler Aligner (BWA v0.7.17) software. The clean reads were mapped to the Drosophila genome (assembly Drosophila genome dm6, spike-in genome) using the Burrow-Wheeler Aligner (BWA v0.7.17) software.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: human cell line

extract_protocol:
In brief, chromatin was isolated by adding lysis buffer and fragmented by sonication. DNA was sheared to an average length of 200-500 bp with EpiShear probe sonicator (Active Motif, 53051). The same amount of Drosophila chromatin (Active Motif, 53083) was incubated with sheared chromatins from THP-1 cells and PMA-treated PMA cells, respectively for ChIP normalization. Genomic DNA (Input) was prepared by de-crosslinking at 65°C for 4 hours followed by RNase A and Proteinase K digestion. The Input DNA was purified with PCR Purification Kit (Qiagen, 28004) and quantified (Onedrop, Wins).Fragmented chromatin mix (for IP) was incubated with 5 μl of anti-C/EBPα (Cell Signaling Technology, 8178) and 1 μg of Drosophila H2A.v antibody (Active Motif, 61686) at 4°C for overnight. 25 μl of rProtein G Magarose Beads (Smart-Lifesciences, SM004005) were added to the samples and incubated at 4°C for 2 hours. Complexes were washed, eluted from the beads with SDS buffer, then de-crosslinked at 65°C for overnight. The de-crosslinked chromatin was subjected to RNase A and proteinase K treatment.
ChIP DNA was purified with PCR Purification Kit (Qiagen, 28004) and quantified (Thermo Fisher, Qubit). Illumina sequencing libraries were prepared from the ChIP-DNA and input DNAs with VAHTS Universal DNA Library Prep Kit for Illumina V4.

value: human cell line

tag: chip antibody

value: none (input)

value: PMA


title: WGBS_R878H_F_Striatum_44931

value: Striatum


title: LPS-CKO3

city: Changsha

first: Shuang

last: Yang

address: No.139，Renmin Road Central Changsha-Hunan-China

institute: The Second Xiangya Hospital of central south university

data_processing:
The Skewer software was used for dynamically remove the joint sequence and poor-quality fragment.
The STAR software was used to compare the preprocessed sequence with the reference genome sequence of the sequenced species.
The StringTie software was used to count the original sequence of known genes, and FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) was used to calculate the expression.
Using DESeq2 software to screen differently expressed genes between two groups according to the experimental design
Assembly: mm10 or hg38
Supplementary files format and content: h_RFX1_RNA-seq worksheet: counts for RNA-seq of ontrol and Rfx1-overexpressed hMDMs
Supplementary files format and content: m_Rfx1_RNA-seq worksheet:counts.txt for RNA-seq of ontrol and Rfx1-overexpressed PMAs
Supplementary files format and content: m_CKO_RNA-seq worksheet:counts.txt for RNA-seq of WT and CKO PMAs

source_name: PMAs

growth_protocol: PMAs and hMDMs maintained in DMEM  supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kit for Illumina

treatment_protocol: Macrophage with RFX1 overexpression or Rfx1 deficiency were treated by LPS  for 24h.

value: PMAs

value: macrophage

value: Rfx1 knockout

value: LPS treatment

tag: time

value: 24 hours


title: KDM5 WT 4

description:
WT_4
counts.csv

value: heads


title: PMA_J

value: anti-C/EBPa


title: KOHYP1

description: FIH-KO 1%O2

value: Lewis Lung Carcinoma cell

value: FIH-deficient


title: LPS-CKO2


title: WGBS_R878H_M_Hippocampus_44922

value: Hippocampus

value: Male


title: THP-J_input


title: hTSC-BL-CEBPB, ChIP-seq, rep2

value: hTSC-BL

value: human trophoblast stem cell


title: THP-J

value: human cell line

value: WT


title: LPS-CKO1


title: WGBS_rWT_M_Cerebellum_44921

value: Cerebellum


title: hTSC-BL-CEBPB, ChIP-seq, rep1


title: LPS_WT3


title: STB-Input, ChIP-seq, control

source_name: STB-BL

value: STB-BL

value: hTSC derived syncytiotrophoblast cell


title: bone marrow scRNAseq

description: 10x Genomics

source_name: bone marrow

value: unsorted

value: bone marrow

value: 10 weeks


title: THP1-PMA3

data_processing:
The expression analysis of genes was performed by DESeq2 software.
Assembly: hg38
Supplementary files format and content: FPKM values for each sample

extract_protocol:
RNA-seq assay was performed on THP-1 and PMA-treated THP-1 by LC SCIENCES (Hangzhou, China). Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure.
After total RNA was extracted, mRNA was purified from total RNA (5 μg) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA)

value: PMA


title: STB-IgG, ChIP-seq, control


title: LPS_WT2

value: PMAs

value: macrophage

value: LPS treatment

value: 24 hours


title: WGBS_R878H_M_Cortex_44922

value: Cortex


title: STB-CEBPB, ChIP-seq, rep2


title: THP1-PMA1


title: THP1-PMA2


title: WGBS_R878H_M_Cerebellum_44922

value: Male


title: PVAX85_Baseline

city: Farmington

first: Duygu

last: Ucar

state: CT

address: 10 Discovery Dr

institute: The Jackson laboratory for Genomic Medicine

data_processing:
Raw BCL files generated by the sequencer were converted to FASTQ files. CASAVA was used to generate FASTQ files for RNAseq data. Trimmomatic (version 0.33) was used to remove adapters, leading and trailing low-quality bases.  Reads less than 36 bases long were dropped. Reads with more than 50% low-quality bases overall were filtered out. The remaining high-quality reads were then used for expression estimation. Alignment estimation of gene expression levels using the EM algorithm for paired-end read data was performed using RSEM (package version 1.2.12); default settings were used for alignment. RSEM uses bowtie2 as aligner to align the mapped reads against the hg38 reference genome. Data quality control was performed using Picard (version 1.95) and bamtools to obtain general alignment statistics from the bam file.
Gene expression values from PBMC RNA-seq data were converted into count-per-million (cpm) using edgeR R package (version 3.28.1)113. Genes with cpm values less than 0.5 across all samples were filtered out from the rest of the analyses. Differential gene expression analyses were conducted using generalized linear models (as implemented in the edgeR package) using the default TMM normalization.
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes counts per million (in log2) for each sample

source_name: Blood

extract_protocol:
Total RNA was isolated from PBMCs using the Qiagen RNeasy Mini Kit (Qiagen) or  Arcturus PicoPure (Life Technologies) kits following manufacturer’s protocols.
RNA-seq libraries were prepared with KAPA mRNA HyperPrep kit (Roche) according to manufacturer’s instruction.

tag: figureid

value: Blood

value: PBMCs

value: Baseline

value: Pneumovax -23

tag: age (in years)


title: RPTC_NEW_PAHPROB_3_8_A

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

data_processing:
The gene count matrices were generated from single-end reads with four lanes per sample with ~75 base pairs (bp).
Reads were quality trimmed using fastp (version 0.20.0 or 0.20.1) using the default settings with the exceptions of adapter trimming being excluded and the reads being trimmed to 50 bp (Chen et al., 2018).
The reads from the four lanes for each sample were combined to generate a single fastq file.
These files were used as input to the TempO-seq analysis pipeline (House et al., 2017) with the human S1500+ probe manifest file to generate a gene count matrix.
Transcripts with fewer than 25 mean counts across the entire sample space were removed as non-expressed except for the genes listed. For further analyses, a total of 1,497 transcripts were evaluated. The Bioconductor's DESeq2 package (Love et al., 2014) was utilized to perform differential expression analysis and generate the complete normalized count matrix for all experimental conditions.
Assembly: S1500+ Gene Set
Supplementary files format and content: normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: hash.csv file with meta data of the samples

extract_protocol:
Cell lysates were prepared from OrganoPlate® 3-lane 40 devices through injection lysis buffer into the RPTEC channel. Following 10 minutes of incubation at room temperature, the cell lysate was flushed out by addition lysis buffer. For 384 well plates, media was aspirated and lysis buffer was added and cells were incubated for 10 minutes at room temperature after which the lysates were collected from each well. All lysates were stored at −80 °C until further processing. The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022)
TempO-seq libraries were prepared using the S1500+ targeted transcriptome panel (Mav et al., 2018) consisting of 2,982 transcripts according to the manufacturer’s instructions.

value: TERT1-immortalized cells

tag: cell source

tag: platform

value: OrganoPlate® 3-lane 45

value: Probenecid

tag: ID


title: LPS_m_pLV_Rfx1_3

value: Rfx1 overexpression


title: WGBS_R878H_F_Hippocampus_44931

value: Hippocampus

value: Female


title: THP1-3

value: human cell line

value: WT


title: STB-CEBPB, ChIP-seq, rep1

value: STB-BL

value: hTSC derived syncytiotrophoblast cell


title: THP1-2


title: LPS_m_pLV_Rfx1_1

value: PMAs

value: macrophage

value: LPS treatment

value: 24 hours


title: RPTC_NEW_PAHPROB_2_8_A

value: OrganoPlate® 3-lane 44


title: WGBS_pWT_F_Striatum_306-1

value: Striatum


title: LPS_m_pLV_Rfx1_2


title: RPTC_NEW_PAHPROB_1_8_A

value: OrganoPlate® 3-lane 43


title: RPTC_NEW_PAH0000_2_8_A

value: TERT1-immortalized cells

value: OrganoPlate® 3-lane 41

value: Untreated


title: WGBS_pWT_F_Hippocampus_306-1


title: THP1-1


title: LPS_WT1


title: WGBS_R878H_F_Cortex_44931

value: Cortex


title: WGBS_pWT_M_Cortex_602-2

value: Male


title: LPS_m_pLV_NC3

value: Negetive control


title: LPS_m_pLV_NC2


title: WGBS_pWT_M_Hippocampus_602-2

value: Hippocampus


title: Mature adipocyte cells, Day 14, Treat with LPS at Day 10 6

city: Salt

first: Núria

last: Oliveras Cañellas

address: Dr Castany s/n

institute: IdiBGi

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh37 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2.
Raw read count and normalized values were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -e for each sample
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw read count and normalized values for each sample.

growth_protocol: SP-F-1 preadipocyte cells were maintained with PM-1 medium in humidified atmosphere with 5% CO2 at 37ºC

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 0.5ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded Total RNA Library Prep Gold Kit following manufacturer's protocols

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells with DM-2 and AM-1 mediums, over 14 days.
Treatment with 1ug/ml of LPS were done 96h before differentiation were finished (at day 10) in LPS group, for controls 1ug/ml of PBS was added.

value: subcutaneous preadipocytes

value: WT

value: adipogenic differentiation + LPS 1ug/ml


title: RPTC_NEW_PAH0000_3_8_A

value: OrganoPlate® 3-lane 42


title: Mature adipocyte cells, Day 14, Treat with LPS at Day 10 3


title: WGBS_pWT_F_Cortex_306-1

value: Female


title: Mature adipocyte cells, Day 14, Treat with LPS at Day 10 5


title: RNA-seq_p10_wt_rep3

city: Saint Louis

first: Shiming

last: Chen

address: 517 South Euclid Avenue

department: Department of Ophthalmology & Visual Sciences

institute: Washington University in St Louis

data_processing:
Sequencing reads were first run through Trim Galore (v0.6.1) to remove adapter sequences.
Trimmed reads were then mapped to the mm10 genome and quantified with kallisto (v0.46.2).
Kallisto output transcript-level abundance matrices were then imported and summarized into gene-level matrices with R package tximport (v1.18.0).
Assembly: mm10
Supplementary files format and content: Tsv file with raw counts by gene

source_name: Retina

extract_protocol:
For each genotype, three biological replicates, two retinas per replicate from one male and one female mouse were harvested and flash frozen in Trizol reagent. All retinas were processed for RNA simultaneously using TRIzol™ Reagent following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Retina

tag: developmental stage

value: Post-natal day 10


title: LPS_m_pLV_NC1

value: PMAs

value: macrophage

value: LPS treatment

value: 24 hours


title: WGBS_R878H_F_Cerebellum_44931

tag: tissue

value: Cerebellum


title: Mature adipocyte cells, Day 14, Treat with LPS at Day 10 2


title: RPTC_384_NONE000_4_0_N

value: TERT1-immortalized cells

value: 384-well plate

value: Untreated


title: WGBS_pWT_F_Cerebellum_306-1

tag: strain


title: Mature adipocyte cells, Day 14, Treat with LPS at Day 10 1

tag: cell type


title: Mature adipocyte cells, Day 14, Treat with LPS at Day 10 4


title: RPTC_NEW_PAH0000_1_8_A

value: OrganoPlate® 3-lane 40


title: Amygdala, opioid withdrawal, rep3

city: Miami

first: Sabita

last: Roy

state: Florida

address: 1501 NW 10th Ave

department: Surgery

institute: University of Miami

description: 10x Genomics

data_processing:
Cell Ranger (v.6.1) (10X Genomics) was used to perform de-multiplexing, barcode processing and generate the single cell gene expression matrix with the default parameters.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Amygdala

extract_protocol:
Three batches of experiments were conducted, and each batch included one Naive, Dep and With group. Thus, nine independent biological samples were processed. Amygdala dissection and tissue dissociation were performed at the same time period (10am–12pm) for all the samples to limit circadian variation. The widely used Papain Dissociation System was modified based on other published protocols so that single cell solutions with high cell viability (~90%) could be acquired within 2 hours. Briefly, after mice were sacrificed brains were immediately dissected and transferred into ice-cold HBSS. The amygdalae were dissected from 4~5 mice according to the previous protocol and were pooled together. The tissues were cut into small pieces and incubated in 2ml pre-warmed papain solution (EBSS containing approximately 20 units/ml papain and 0.005% DNase) at 30°C for 45 min with gentle constant agitation. After the incubation, all the following procedures were performed on ice. The mixture was triturated gently with a fire polished 2ml Pasteur glass pipette and the supernatant were transferred carefully to a fresh tube. 2ml of EBSS containing the albumin ovomucoid inhibitor was added to the remaining tissues, which was triturated gently with another fire polished 2ml Pasteur glass pipette and the supernatant was transferred. This step was repeated one more time. The resulted 6ml supernatant containing single cells were pooled together and the cell clusters/tissue debris were removed by serial filtration through prewetted 70μm and 40μm cell strainers. The single cell suspension was centrifuged at 220g for 7 min at 4°C. The cells were then washed in 10ml PBS containing 0.04% BSA twice, after which the cells were resuspended in PBS containing 0.04% BSA. 10μl aliquots were stained with Trypan Blue and cell numbers were counted three times for each sample. During the whole procedure, 5% (w/v) trehalose was added in the buffers to ensure higher cell viability.
For every sample, 16,500 cells were loaded into a Chromium Single Cell 3’ Chip (10X Genomics) and processed according to the manufacturer’s protocol. scRNA-seq libraries were prepared with the Chromium Single Cell 3’ GEM, Library & Gel Bead kits v3.1 (10X Genomics). Libraries were pooled and sequenced on the NovaSeq 6000 instrument (Illumina).

value: Amygdala

value: brain cells

value: Male

value: 24 hours after morphine withdrawal

value: 8-10 weeks old


title: Amygdala, opioid withdrawal, rep1

description: 10x Genomics


title: WGBS_pWT_M_Striatum_602-2

value: Striatum


title: RPTC_384_NONE000_5_0_N


title: Amygdala, opioid withdrawal, rep2

description: 10x Genomics


title: WGBS_pWT_M_Cerebellum_602-2


title: Amygdala, opioid dependent, rep3

description: 10x Genomics

value: mice were treated with morphine sulphate for 8 days


title: RPTC_384_NONE000_2_0_N


title: WGBS_P900L_F_Striatum_306-2

value: Female


title: RPTC_384_NONE000_1_0_N


title: RPTC_384_NONE000_3_0_N


title: Mature adipocyte cells, Day 14, Control 6

value: subcutaneous preadipocytes

value: WT

value: adipogenic differentiation


title: WGBS_P900L_M_Hippocampus_602-1

value: Hippocampus


title: Amygdala, opioid dependent, rep2

description: 10x Genomics


title: WGBS_P900L_M_Striatum_602-1


title: Amygdala, opioid dependent, rep1

description: 10x Genomics


title: Mature adipocyte cells, Day 14, Control 5


title: WGBS_P900L_M_Cortex_602-1

value: Cortex


title: Mature adipocyte cells, Day 14, Control 3


title: Mature adipocyte cells, Day 14, Control 4


title: OCT2_NEW_PAHPROB_3_8_C

value: TERT1-immortalized cells

value: OrganoPlate® 3-lane 45

value: Probenecid


title: Amygdala, naive, rep2

description: 10x Genomics

value: naïve mice


title: OCT2_NEW_PAHPROB_2_8_C

value: OrganoPlate® 3-lane 44


title: Amygdala, naive, rep3

description: 10x Genomics

value: Amygdala

value: brain cells


title: Mature adipocyte cells, Day 14, Control 1


title: Amygdala, naive, rep1

description: 10x Genomics

value: Male


title: Mature adipocyte cells, Day 14, Control 2


title: OCT2_NEW_PAH0000_3_8_C

value: OrganoPlate® 3-lane 42

value: Untreated


title: WGBS_P900L_M_Cerebellum_602-1

value: Cerebellum


title: B18

city: Greenville

first: Akshaya

middle: K

last: Meher

state: North Carolina

address: MICROBIOLOGY AND IMMUNOLOGY, BRODY SCHOOL OF MEDICINE

institute: East Carolina University

source_name: B cells

growth_protocol: The B cells are grown at 37 °C in a humidified incubator

extract_protocol: Total RNA was extracted from the samples using QIAGEN RNeasy Mini Kit (included a DNase treatment step) and were sent to Novogene Corporation (Wilmingtom, DE, USA) for RNA sequencing and to determine the gene expression levels in FPKM.

treatment_protocol: B cells were pre-treated with 1000 ng/ml of the control Ab or the mBaffR-mFc for 1 h, and then treated with 100 ng/ml of BAFF 3mer, 60mer or left untreated for next 4 h

value: Pan B cells isolated from spleen

value: mBaffR-mFc, BAFF 60mer


title: OCT2_NEW_PAH0000_2_8_C

value: OrganoPlate® 3-lane 41


title: B17

data_processing: Novogene Corporation (Wilmingtom, DE, USA) for RNA sequencing and to determine the gene expression levels in FPKM


title: WGBS_P900L_F_Cortex_306-2

value: Female


title: WGBS_P900L_F_Cerebellum_306-2


title: HCV29, RMC-6272, 3nM, Rep2

city: Boston

first: Heng

last: Du

address: 45 Francis St

institute: Brigham and Women's Hospital

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp.
clean data (clean reads) were obtained by removing reads containing adapter and poly-N. Q20, Q30 and GC content of the clean data were calculated
sequences and reads with low quality from raw data
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene.
Assembly: mm10/hg38
Supplementary files format and content: tab-delimited text file including raw counts
Supplementary files format and content: tab-delimited text file including RPKM values

growth_protocol: Cells were maintained in DMEM medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml of penicillin and streptomycin, and incubated at 37℃ in 5% CO2.

extract_protocol:
Total RNA was extracted using a RNeasy mini kit (Qiagen, #74104).
1 μg RNA per sample was used for cDNA library preparation using the NEBNextÒ UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Cells were treated with DMSO, Rapamycin (10 nM), or RMC-6272 (3 nM) for 24h (triplicates per condition).

value: Bladder cancer

value: TSC1 null

tag: concentration

value: 3 nM


title: HCV29, RMC-6272, 3nM, Rep3

tag: genotype


title: OCT2_NEW_PAH0000_1_8_C

tag: cell line

value: TERT1-immortalized cells

value: OrganoPlate® 3-lane 40


title: B16

tag: treatment


title: WGBS_P900L_F_Hippocampus_306-2

value: Hippocampus

tag: Sex


title: HCV29, RMC-6272, 3nM, Rep1


title: OCT2_384_NONE000_6_0_N

value: 384-well plate


title: B15

value: Control antibody, BAFF 60mer


title: OCT2_384_NONE000_5_0_N


title: B14


title: OCT2_NEW_PAHPROB_1_8_C

value: OrganoPlate® 3-lane 43

value: Probenecid


title: HCV29, Rapamycin, 10nM, Rep2

value: Rapamycin

value: 10 nM


title: OCT2_384_NONE000_4_0_N

value: Untreated


title: HCV29, Rapamycin, 10nM, Rep3


title: OCT2_384_NONE000_2_0_N


title: B12

value: Pan B cells isolated from spleen

value: mBaffR-mFc, BAFF 3mer


title: HCV29, Rapamycin, 10nM, Rep1


title: B13


title: B11


title: HCV29, Ctrl, Rep3

value: DMSO


title: OCT2_384_NONE000_1_0_N


title: HCV29, Ctrl, Rep2


title: B9

value: Control antibody, BAFF 3mer


title: B10


title: HCV29, Ctrl, Rep1

value: Bladder cancer


title: OAT3_NEW_PAHPROB_3_8_D

value: OrganoPlate® 3-lane 45


title: RNAseq_E6_7_rep4

city: Milano

first: Susanna

last: Chiocca

address: Via Adamello 16

country: Italy

institute: European Institute of Oncology, IEO

data_processing:
Read filtering with fastx toolkit 0.0.13.2: fastq_masker -Q33 -q 20 -r N -v
alignment with tophat version 2.0.8: tophat -r 170 -p 8 --no-novel-juncs --no-novel-indels --library-type fr-unstranded --transcriptome-index transcriptome_index reffile fastq_file_R1 fastq_file_R2
Removing duplicate reads: samtools rmdup -sS bamfile
Quantifying read counts over features with featureCounts v. 1.4.5-p1: featureCounts -T 2 -p -P -a gtffile
Idendifying Differentially Expressed Genes (DEG) using DESeq2 R Bioconductor package
Assembly: hg38
Supplementary files format and content: diff_gene_expr_paired.txt =  tab-delimited text file containing differential gene expression results form DESeq2

source_name: primary keratinocytes

extract_protocol:
Quick-RNA MiniPrep (Zymo Research)
TruSeq Stranded Total RNA

value: primary keratinocytes

value: HPV16 E6/E7


title: OCT2_384_NONE000_3_0_N

value: TERT1-immortalized cells


title: OAT3_NEW_PAHPROB_2_8_D

value: OrganoPlate® 3-lane 44


title: B8


title: RNAseq_E6_7_rep3


title: intestine_infected_antiTNF_4d_rep4

type: RNA

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: Before hybridization, 600 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: Scanning of microarrays was performed with 5µm resolution using an Agilent G2505C DNA microarray laser scanner (Agilent Technologies).

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200 ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript MT -RT. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was extracted.

value: intestine

tag: infection

value: infected with DENV-3 P12/08

value: anti-TNF

tag: duration


title: intestine_infected_antiTNF_4d_rep3


title: intestine_infected_antiTNF_4d_rep2


title: intestine_infected_IgG_4d_rep3

value: IgG


title: intestine_infected_antiTNF_4d_rep1


title: intestine_infected_IgG_4d_rep5


title: intestine_infected_IgG_4d_rep4


title: B7


title: RNAseq_E6_7_rep2


title: intestine_infected_IgG_4d_rep2


title: B6

value: mBaffR-mFc


title: OAT3_NEW_PAHPROB_1_8_D

value: OrganoPlate® 3-lane 43

value: Probenecid


title: OAT3_NEW_PAH0000_3_8_D

value: OrganoPlate® 3-lane 42

value: Untreated


title: OAT3_NEW_PAH0000_2_8_D

value: OrganoPlate® 3-lane 41


title: RNAseq_E6_7_rep1


title: B5

value: Pan B cells isolated from spleen


title: intestine_infected_IgG_4d_rep1


title: OAT3_NEW_PAH0000_1_8_D

value: OrganoPlate® 3-lane 40


title: B4


title: RNAseq_E7_rep3

value: HPV16 E7


title: B3

value: Control antibody


title: intestine_infected_antiTNF_3d_rep4


title: B2


title: OAT3_384_NONE000_4_0_N

value: 384-well plate


title: RNAseq_E7_rep2

value: primary keratinocytes


title: intestine_infected_antiTNF_3d_rep2


title: OAT3_384_NONE000_5_0_N

value: TERT1-immortalized cells


title: RNAseq_E7_rep1


title: intestine_infected_antiTNF_3d_rep3

value: intestine


title: B1


title: RNAseq_E6_rep4

value: HPV16 E6


title: intestine_infected_antiTNF_3d_rep1

value: infected with DENV-3 P12/08

value: anti-TNF


title: intestine_infected_IgG_3d_rep3

value: IgG


title: RNAseq_E7_rep4


title: OAT3_384_NONE000_6_0_N


title: OAT3_384_NONE000_3_0_N


title: OAT3_384_NONE000_1_0_N


title: RNAseq_E6_rep3


title: splenic NK cells, with primary antibody [AIOLOS CnR]

city: Monash University

first: Harrison

last: Sudholz

state: VIC

address: 15 Innovation walk

department: Biochemistry and Molecular Biology

country: Australia

institute: Monash University

data_processing:
Data was demultiplexed using splitBarcode and trimmed to 100b using bbduk. Fastq files were aligned to mm10 using Bowtie2 and peaks were called using MACS2 over the control sample (without primary antibody). Data was visualized using IGV
FASTQ files were aligned to mm10 using bowtie2 (v. 1.3.0).
Duplicate reads in the resulting BAM files were marked using picard tools (v ≥ 2.18). The aligned reads were sorted and indexed in samtools (v ≥ 1.9).
MACS2 (v ≥ 2.1.1) was used to perform peak calling. De-novo bindings were detected using csaw using a window-based strategy.
BigWig files were generated using Galaxy.
Assembly: mm10
Supplementary files format and content: narrow peak calls
Supplementary files format and content: bigwig
Library strategy: CUT&Run

source_name: spleen

growth_protocol: NK cells were expanded in culture (complete IMDM + 50 ng/ml IL-15) to obtain at least 500,000 cells per sample

extract_protocol: Libraries were constructed using MGIEasy DNA FS library prep set 2 (MGITech)

value: spleen

value: NK


title: RNAseq_E6_rep2


title: sorted splenic WT NK cells, rep 2

data_processing:
Read quality was assessed using FASTQC.
Reads were aligned to mm10 (Bowtie2).
Bigwig files were generated using bamCoverage for visualisation in IGV
Assembly: mm10
Supplementary files format and content: read coverage
Supplementary files format and content: bigwig

extract_protocol:
Nuclei were first extracted for 2 min on ice using nuclei buffer (10 mM Tris-HCl (pH 7.4), 10mM NaCl, 3 mM MgCl2 0.1% Tween-20, 0.1% 755 Nonidet P40 substitute, 0.01% Digitonin, 1% BSA). Nuclei were washed and accessible DNA was tagmented using the Tn5 transposition reaction mix (Illumina Nextera DNA 757 sample preparation kit, FC121-1030; 30 min at 37°C). Tagmented DNA isolated using the MinElute PCR Purification kit (Qiagen, Cat #28004).
Following 5 PCR cycles on the thermocycler using a combination of a PCR primer (Ad1_noMX) and an indexed PCR primer, an aliquot was used to assess the number of PCR cycles required for library amplification. The amplified DNA library was subsequently purified using the MinElute PCR Purification kit (Qiagen). Quality and concentration of the library was assessed using Bioanalyser (Agilent).

value: WT (Ikzf floxed, Cre negative)

value: Viable splenic NK (NK1.1+ NKp46+ CD3- TCRβ- 7AAD-) cells were directly sorted from the spleens of mice prior to processing for ATAC-seq.


title: RNAseq_E6_rep1


title: splenic NK cells, no primary antibody [input]


title: OAT3_384_NONE000_2_0_N

value: Untreated


title: intestine_infected_IgG_3d_rep2


title: sorted splenic WT NK cells, rep 1


title: RNAseq_NT_rep4

value: empty vector


title: OAT1_NEW_PAHPROB_3_8_B

value: OrganoPlate® 3-lane 45

value: Probenecid


title: intestine_noninfected_IgG_3d_rep3

value: non-infected


title: intestine_noninfected_IgG_3d_rep2


title: intestine_infected_IgG_3d_rep1


title: RNAseq_NT_rep3


title: sorted splenic Ikzf1 KO NK cells, rep 2

value: Ikzf1 KO


title: OAT1_NEW_PAH0000_3_8_B

value: OrganoPlate® 3-lane 42


title: intestine_noninfected_IgG_3d_rep1


title: OAT1_NEW_PAHPROB_2_8_B

value: TERT1-immortalized cells

value: OrganoPlate® 3-lane 44


title: OAT1_NEW_PAHPROB_1_8_B

value: OrganoPlate® 3-lane 43


title: RNAseq_NT_rep2

value: primary keratinocytes


title: OAT1_NEW_PAH0000_2_8_B

value: OrganoPlate® 3-lane 41


title: VEH_4_1

city: Henan

first: Wenhao

last: Zhang

address: 开封

institute: Henan University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows: 1) Remove the reads containing the adaptor(adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
The filtered "Clean Reads" are saved in FASTQ format. SOAPnuke(Version v1.5.2)  Official Websitehttps://github.com/BGI-flexlab/SOAPnuke
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads.HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these
Supplementary files format and content: gene_expression of fpkm

source_name: skin

extract_protocol:
RNA was harvested using Trizol reagent.The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

value: skin

value: vehicle


title: liver_infected_antiTNF_3d_rep3

value: liver

value: infected with DENV-3 P12/08

value: anti-TNF


title: RNAseq_NT_rep1


title: OAT1_NEW_PAH0000_1_8_B

value: OrganoPlate® 3-lane 40

value: Untreated


title: VEH_2_1


title: TF1 RNA, IDH2-MUT

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description:
10x Genomics
Raw data deposited at EGA; accession number:

data_processing:
Demultiplexing, barcode processing, genome mapping, gene counting (including introns) and aggregation were conducted using the Cell Ranger ARC software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc).
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell count matrix of RNA genes and ATAC peaks, comma-separated cell barcode info file

molecule: nuclear RNA

source_name: Bone marrow

growth_protocol: TF1-IDH2 wildtype and mutant cell lines were acquired form ATCC (order numbers CRL-2003 and CRL-2003I). They were cultured following the providers instructions.

extract_protocol:
Cells were harvested using accutase, washed once in PBS and 1x106 cells fixed with 1 ml 0.2 % PFA for five minutes at room temperature. Fixation was stopped with glycine for 5 min followed by one wash with PBS. Cells were then resuspended in 500 µl ice cold nuclei buffer and incubated for 10 min on ice. Cells were pelleted and resuspended in 500 µl antibody buffer (2 mM EDTA, 0.1 % BSA, 0.04 % digitonin, 20 mM HEPES pH 7.5, 150 mM NaCl and 0.5 mM spermidine).
Libraries were prepared according to the Chromium single-cell Multiome ATAC +Gene Expression protocol v1 (10x Genomics).

value: Erythroblasts

value: Bone marrow

tag: disease state

value: Erythroleukemia


title: OAT1_384_NONE000_5_0_N

value: 384-well plate


title: liver_infected_antiTNF_4d_rep3


title: CCR3_4_1


title: TF1, IDH2-MUT

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ARC software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc).
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell count matrix of RNA genes and H3K27me3 peaks, tab-separated fragment file, comma-separated cell barcode info file

extract_protocol:
Cells were harvested using accutase, washed once in PBS and 1x106 cells fixed with 1 ml 0.2 % PFA for five minutes at room temperature. Fixation was stopped with glycine for 5 min followed by one wash with PBS. Cells were then resuspended in 500 µl ice cold nuclei buffer and incubated for 10 min on ice. Cells were pelleted and resuspended in 500 µl antibody buffer (2 mM EDTA, 0.1 % BSA, 0.04 % digitonin, 20 mM HEPES pH 7.5, 150 mM NaCl and 0.5 mM spermidine).
10 µl of H3K27me3 (cell signalling, #9733) and 1 U/µl RNase Inhibitor final concentration was added and incubated over night at 4 °C. Cells were washed with wash buffer (0.04 % digitonin, 20 mM HEPES pH 7.5, 150 mM NaCl and 0.5 mM spermidine), resuspended in 500 µl wash buffer containing 10 µl 1 µg/µl anti-rabbit secondary antibody made in guinea pig () and 1 U/µl RNase Inhibitor. After 30 min at room temperature cells were washed three times with wash buffer with five minutes incubation time per wash and resuspended in Tn5 buffer (0.01 % digitonin, 20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and 1X protease inhibitor).
Cells were counted and 500,000 cells were used from this point forward. 10 µl of loaded proteinA-Tn5 was added and incubated at room temperature for 30 minutes. After three washes with wash buffer, cells were resuspended in tagmentation buffer (10 mM Tris pH 7.5, 10 mM MgCl, 5 mM HEPES, 50 mM NaCl, 25 % DMF, 0.01 % Digitonin, 1 U/µl Rnase inhibitor), transferred to a PCR tube and incubated for one hour at 37 °C. 15 µl were then used for GEM formation according to the Chromium single-cell Multiome ATAC +Gene Expression protocol v1 (10x Genomics).
scChIP-seq (H3K27me3)


title: liver_infected_antiTNF_3d_rep2


title: TF1 RNA, IDH2-WT


title: TF1, IDH2-WT


title: OAT1_384_NONE000_2_0_N


title: sorted splenic Ikzf1 KO NK cells, rep 1

value: spleen

value: Ikzf1 KO

value: Viable splenic NK (NK1.1+ NKp46+ CD3- TCRβ- 7AAD-) cells were directly sorted from the spleens of mice prior to processing for ATAC-seq.


title: CCR3_1_1


title: liver_infected_antiTNF_4d_rep2


title: CCR3_2_1


title: V7_FLOX_MC_5

value: basophils VAMP7 Flox

value: WT


title: liver_infected_IgG_3d_rep3

value: IgG


title: VEH_1_1

value: skin


title: OAT1_384_NONE000_3_0_N

value: TERT1-immortalized cells


title: B11_S82

value: primary RPTECs

value: OrganoPlate® 3-lane 59


title: liver_infected_antiTNF_4d_rep1

value: liver

value: infected with DENV-3 P12/08

value: anti-TNF


title: liver_infected_IgG_3d_rep2


title: liver_infected_antiTNF_3d_rep1


title: PBMC RNA, Multiome, Tn5hc

data_processing:
Demultiplexing, barcode processing, genome mapping, gene counting (including introns) and aggregation were conducted using the Cell Ranger ARC software v2.0.2 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell count matrix of RNA genes and ATAC peaks, comma-separated cell barcode info file

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated as previously described and stored viably frozen in serum containing DMSO (JP Mallm et al. 2019, Mol Sys Bio; doi:10.15252/msb.20188339). Prior to the experiments they were thawed in a water bath and immediately processed.
Libraries were prepared according to the Chromium single-cell Multiome ATAC + Gene Expression v1 protocol (10x Genomics) using the provided Tn5 (10xTn5), an in-house loaded Tn5 at high concentration (Tn5hc) or a dilution of Tn5hc to 50 % activity (Tn5hc 50 %) for ATAC.

value: Peripheral blood mononuclear cells

value: Peripheral blood

value: Healthy


title: V7_FLOX_MC_4


title: V7_FLOX_MC_3


title: liver_infected_IgG_3d_rep1


title: PBMC, 10xTn5

library_source: genomic single cell

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.1.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file

extract_protocol:
PBMCs were isolated as previously described and stored viably frozen in serum containing DMSO (JP Mallm et al. 2019, Mol Sys Bio; doi:10.15252/msb.20188339). Prior to the experiments they were thawed in a water bath and immediately processed.
Libraries were prepared according to the Chromium single-cell ATAC v2 protocol (10x Genomics) using the provided Tn5 (10xTn5) or an in-house loaded Tn5 at high concentration (Tn5hc).


title: OAT1_384_NONE000_4_0_N

value: 384-well plate

value: Untreated


title: PBMC RNA, Multiome, Tn5hc (50 %)


title: B10_S74

value: OrganoPlate® 3-lane 58


title: PBMC, Tn5hc


title: V7_FLOX_MC_2


title: PBMC RNA, Multiome, 10xTn5


title: B09_S66

value: OrganoPlate® 3-lane 57


title: V7_FLOX_MC_1

value: basophils VAMP7 Flox


title: PBMC, Multiome, Tn5hc

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ARC software v2.0.2 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc).
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: h5 single cell peak count matrix of RNA genes and ATAC peaks, tab-separated fragment file, comma-separated cell barcode info file

extract_protocol:
PBMCs were isolated as previously described and stored viably frozen in serum containing DMSO (JP Mallm et al. 2019, Mol Sys Bio; doi:10.15252/msb.20188339). Prior to the experiments they were thawed in a water bath and immediately processed.
Libraries were prepared according to the Chromium single-cell Multiome ATAC + Gene Expression v1 protocol (10x Genomics) using the provided Tn5 (10xTn5), an in-house loaded Tn5 at high concentration (Tn5hc) or a dilution of Tn5hc to 50 % activity (Tn5hc 50 %).


title: OAT1_384_NONE000_1_0_N


title: liver_infected_IgG_4d_rep3


title: V7_CKO_MC_5

value: basophils VAMP7 CKO

value: CKO


title: PBMC, Multiome, Tn5hc (50 %)


title: liver_infected_IgG_4d_rep1

value: IgG


title: B08_S58

value: OrganoPlate® 3-lane 56


title: liver_infected_IgG_4d_rep2


title: V7_CKO_MC_4

value: skin


title: PBMC, Multiome, 10xTn5


title: V7_CKO_MC_3


title: B07_S50

value: primary RPTECs

value: OrganoPlate® 3-lane 55

value: PFOA


title: Bovine placenta, day 50 of gestation, rep3

city: Pullman

first: Kimberly

middle: M

last: Davenport

state: WA

address: 100 Dairy Rd

department: Animal Science

institute: Washington State University

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)
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

source_name: Placenta

extract_protocol:
Nuclei were isolated from fresh tissue following the 10X Genomics protocol
Libraries were consructed according to the 10X Genomics manufacterer's instructions

value: Placenta


title: B05_S34

data_processing:
The gene count matrices were generated from single-end reads with four lanes per sample with ~75 base pairs (bp).
Reads were quality trimmed using fastp (version 0.20.0 or 0.20.1) using the default settings with the exceptions of adapter trimming being excluded and the reads being trimmed to 50 bp (Chen et al., 2018).
The reads from the four lanes for each sample were combined to generate a single fastq file.
These files were used as input to the TempO-seq analysis pipeline (House et al., 2017) with the human S1500+ probe manifest file to generate a gene count matrix.
Transcripts with fewer than 25 mean counts across the entire sample space were removed as non-expressed except for the genes listed. For further analyses, a total of 1,497 transcripts were evaluated. The Bioconductor's DESeq2 package (Love et al., 2014) was utilized to perform differential expression analysis and generate the complete normalized count matrix for all experimental conditions.
Assembly: S1500+ Gene Set
Supplementary files format and content: normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: hash.csv file with meta data of the samples

extract_protocol:
Cell lysates were prepared from OrganoPlate® 3-lane 40 devices through injection lysis buffer into the RPTEC channel. Following 10 minutes of incubation at room temperature, the cell lysate was flushed out by addition lysis buffer. For 384 well plates, media was aspirated and lysis buffer was added and cells were incubated for 10 minutes at room temperature after which the lysates were collected from each well. All lysates were stored at −80 °C until further processing. The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022)
TempO-seq libraries were prepared using the S1500+ targeted transcriptome panel (Mav et al., 2018) consisting of 2,982 transcripts according to the manufacturer’s instructions.

value: OrganoPlate® 3-lane 53


title: V7_CKO_MC_2


title: liver_noninfected_IgG_4d_rep2

value: liver

value: non-infected


title: Bovine placenta, day 50 of gestation, rep2

description: 10X Genomics


title: B04_S26

value: OrganoPlate® 3-lane 52

value: Cisplatin


title: Bovine placenta, day 50 of gestation, rep1

description: 10X Genomics


title: liver_noninfected_IgG_4d_rep1


title: Bovine placenta, day 30 of gestation, rep4

description: 10X Genomics


title: RNAseq T24R2 Rep4

city: Los Angeles

first: Emmanuelle

last: Hodara

state: CA

address: 1450 Biggy Street

institute: Keck School of Medicine of USC

data_processing:
Samples were aligned to the hg38 with reference annotation GENCODE v39 using STAR (2.7.0).
Only uniquely mapped reads without duplicates were selected usign samtools (version 1.10)
Read counts were assigned to genes using Subread featureCounts.
Assembly: GRCh38/hg38
Supplementary files format and content: Tab delimited files containing gene names and featurecounts

source_name: cell line

growth_protocol: RPMI, 10% fetal bovine serum, 1% Penicillin/Streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
RNA Extraction using Zymo RNA MiniPrep Kit followed by library preparation
NEBNExt Ultra II RNA Library Prep Kit for Illumina (Catalog# E7420, NEB)

treatment_protocol: Grown to 3 days confluence

value: Human bladder cancer

tag: time

value: Day 3


title: B03_S18

value: OrganoPlate® 3-lane 51


title: V7_CKO_MC_1

value: basophils VAMP7 CKO


title: Bovine placenta, day 30 of gestation, rep3

description: 10X Genomics


title: RNAseq T24R2 Rep2


title: FLOX_3

value: wildtype


title: RNAseq T24R2 Rep3


title: Bovine placenta, day 30 of gestation, rep2

description: 10X Genomics


title: RNAseq T24R2 Rep1


title: B01_S2

value: OrganoPlate® 3-lane 49

value: Untreated


title: B06_S42

value: OrganoPlate® 3-lane 54


title: B02_S10

value: primary RPTECs

value: OrganoPlate® 3-lane 50


title: FLOX_2

value: skin


title: RNAseq T24R2 Rep5


title: liver_noninfected_IgG_4d_rep3

value: IgG


title: Bovine placenta, day 30 of gestation, rep1

description: 10X Genomics

value: Placenta


title: A12_S89

value: OrganoPlate® 3-lane 48


title: Bovine placenta, day 24 of gestation, rep3

description: 10X Genomics


title: RNAseq T24 Rep4


title: CKO_5


title: CKO_2


title: A10_S73

value: OrganoPlate® 3-lane 46


title: RNAseq T24 Rep3


title: CKO_1


title: Bovine placenta, day 24 of gestation, rep2

description: 10X Genomics


title: FLOX_5


title: RNAseq T24 Rep2


title: A09_S65

value: OrganoPlate® 3-lane 45

value: PFOA


title: Bovine placenta, day 24 of gestation, rep1

description: 10X Genomics


title: P1AM25 [Subarray 61]

type: protein

city: Bronx

first: Jacqueline

middle: M.

last: Achkar

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: IgG

hyb_protocol: Arrays were blocked with 3% BSA overnight, and diluted mAb was incubated on the array for 4 hours at 37 C and gentle agitation (100 RPM).  Slides were then washed with PBS contain 0.05% Tween (PBST).  After washing, bound antibodies were detected by goat anti-human biotin-labeled IgG (Jackson Immunoresearch), followed by a Streptavidin probe tagged with SureLight®P3 Cy5 (Cayman Chemicals). Slides were then washed with PBST, spun dry in a centrifuge, and scanned.

scan_protocol: The GenePix 4000 Microarray scanner system (Molecular Devices, CA) was used for scanning.

data_processing:
We analyzed images using GenePix Pro 7.3.0.0 to measure median pixel intensity (MPI) and neighboring background pixel intensity (BPI) of individual spots. The median fluorescence intensity (MFI), representing AM-epitope specific mAb reactivity, was calculated using the MPI minus the BPI and averaged from the triplicate spots.
average (background-subtracted median pixel intensity for technical triplicates)

label: SureLight®P3 Cy5

molecule: protein

source_name: monoclonal antibody

label_protocol: SureLight®P3 Cy5

extract_protocol: MAb expressed in HEK293 cell

treatment_protocol: Diluted to 5 µg/mL

tag: antibody

value: monoclonal antibody


title: Bovine placenta, day 17 of gestation, rep3

description: 10X Genomics


title: RNAseq T24 Rep1

value: Human bladder cancer

value: Day 3


title: A08_S57

tag: cell source

value: OrganoPlate® 3-lane 44


title: P1AM25 [Subarray 30]

description: IgG


title: MeRIP T24R2 Rep 5 RIP

data_processing:
Samples were aligned to the hg38 with reference annotation GENCODE v39 using STAR (2.7.0).
Only uniquely mapped reads without duplicates were selected usign samtools (version 1.10)
Unique read files were used for peak calling using MACS2 (3.0.0a6) using the callpeaks with the options “-nomodel -extsize100 -gsize300e6”
Assembly: GRCh38/hg38
Supplementary files format and content: Bigwig files for visualization
Supplementary files format and content: MACS2 called peaks

extract_protocol:
RNA Extraction using Zymo RNA MiniPrep Kit followed by low-input MeRIP protocol
SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian (Catalog # 634413, Takara-Clontech, Japan)
MeRIP-seq

value: WT

tag: merip antibody

value: anti m6A antibody (NEB, E1610)


title: Bovine placenta, day 17 of gestation, rep2

description: 10X Genomics


title: MeRIP T24R2 Rep 4 RIP


title: A07_S49

tag: platform

value: OrganoPlate® 3-lane 43

tag: ID


title: Bovine placenta, day 17 of gestation, rep1

description: 10X Genomics

tag: tissue

tag: developmental stage


title: DI2

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

data_processing:
The paired-end sequencing was done  using Illumina HiSeqTM 2500
FastQC (v 0.11.7) was used to assess sequence quality for all samples
Quality trimmed reads were aligned to the reference genome of common bean (v 2.1) using Bowtie2 (v 2.3.5.1)
Quality of FAIRE-seq data was assessed using  DeepTools (v 3.1.1)
The ChIPseeker (v 1.26.2)  was used to characterize peaks.
Genome_build: v2.1
Supplementary_files_format_and_content: tdf

organism: Phaseolus vulgaris

source_name: Leaf

growth_protocol: Red Hawk dark red kidney bean (Phaseolus vulgaris L.) was procured from Central Bean Co. Inc . The plants were maintained at 28/20°C in a greenhouse at Delaware State University, Dover, Delaware, with a 14/10 h photoperiod.

extract_protocol:
The nuclei were sonicated and purified using Phenol chloroform isoamyl alcohol. A library was prepared from purified FAIRE and input DNA to be sequenced with the  Illumina HiSeqTM 2500
Illumina compatible FAIRE-Seq libraries were prepared using NEBNext Ultra  DNA Library Preparation

treatment_protocol: At the R2 stage, when at least 50% of the flower buds had opened, the plants were subjected to drought stress

tag: plant

value: Red Hawk dark red kidney bean

tag: sample group

value: DI

value: Leaf Tissue


title: A06_S41

tag: cell type

value: primary RPTECs

value: OrganoPlate® 3-lane 42

value: Cisplatin


title: A11_S81

tag: cell line

value: OrganoPlate® 3-lane 47

value: Untreated


title: Whole_MeRIP_IP_DD25-3

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description: Parental photoperiod: White-light: darkness = 12 h: 12h; Parental age after eclosion: 3 days

data_processing:
After removing adaptors and low-quality bases by fastp (version 0.20.1), the resulting reads no less than 50 bp were mapped to the Drosophila melanogaster reference genome (FB2021_02) released by FlyBase database (http://flybase.org/).
The featureCounts program within SourceForge Subread package (version 2.0.2) was used for counting the reads that mapped to genes.
The genes with an average read count less than 10 in any group or lacking read count in any replicate were primarily filtered.
R package DESeq2 (version 1.30.0) was used for the identification of differentially expressed genes (DEGs) by setting false discovery rate corrected P-value (FDR) < 0.05 and fold change >= 2 as the thresholds of significance (Supplementary Table S2), and the read count normalization across samples by size factors.
t-SNE dimension reduction analysis was performed using R (version 4.0.3) package Rtsne (version 0.15); heatmap was generated using R package pheatmap (version 1.0.12); common and unique DEGs were visualized in a Venn diagram generated using R package VennDiagram; volcano plot was generated using R package ggplot2; GO (Gene Ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for the DEGs were performed using either Metascape (version 3.5) (https://metascape.org/) or R package clusterProfiler (version 3.18.1);  Gene set enrichment analysis (GSEA) software (version 4.2.0) was used for determining the statistical significance of priori defined gene sets.
Mapping results of both the IP and Input libraries of MeRIP-seq were provided for calling the m6A peaks of each replicate and group and the differential m6A peaks of the single factor comparisons between groups using R package exomePeak2 (version 0.99.92) with Poisson generalized linear model (GLM) as the quantitative method.
To reduce false positives, the called m6A peaks were regarded as significant and reserved for subsequent analyses under the following thresholds: sequencing coverage of Input library >= 50 reads, peak width <= 1500 bp, fold change >= 2, P < 0.01, and FDR < 0.01. Similarly, the called differential m6A peaks were regarded as significant under the following thresholds: sequencing coverage of both IP and Input libraries >= 50 reads, peak width <= 1500 bp, fold change >= 1.5, P < 0.01, and FDR < 0.01.
HOMER (version 4.11) was used for de novo motif searching around the called significant (differential) peaks. R packages ChIPseeker (version 1.18.0) and Guitar (version 2.8.0) were used for the annotation and the representation of distribution characteristics of the called significant (differential) m6A peaks. IGV software (version 2.11.9) was employed for displaying the read coverage tracks of targeted genes using the mapping results of both the IP and Input libraries in bigwig format.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text files (.txt) include: (1) the identification results of both positive and negative ions of untargeted metabolome quantification by LC-MS/MS of w1118 male adult whole flies; (2) the raw read counts for the Input and m6A IP data of MeRIP-seq of w1118 male adult whole flies.

source_name: Male adult whole flies

growth_protocol: We collected the eggs oviposited by 3-day-old Drosophila melanogaster w1118 adults which were colonized under the photoperiodic cycles of 12 h white fluorescent light: 12 h darkness (LD) after eclosion. These eggs were grown on standard mediums (comprised of 80 g cornmeal, 125 g sucrose, 16 g yeast, and 5 g agar/L) under the photoperiodic cycles of LD until one day after eclosion.

extract_protocol:
Total RNAs were isolated and dissolved in RNase-free water after the bulk samples had been homogenized in 0.5–1 mL TRIzol AG RNAex Pro Reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) with glass beads using a homogenizer.
Extracted total RNAs were subjected to poly-A selection utilizing VAHTS® mRNA Capture Beads (#N401-02, Vazyme Biotech. Co., Ltd., Jiangsu, China). These purified poly-A RNAs were fragmented as ~100 nt fragments for the preparation of both m6A IP and untreated Input control sequencing libraries of MeRIP-seq. VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina (#NR604-02, Vazyme Biotech. Co., Ltd.) and VAHTS® RNA Adapters set6 for Illumina (#N812, Vazyme Biotech. Co., Ltd.) provided necessary reagents for the fragmentation of poly-A RNAs, first- and second-strand cDNA synthesis, adaptor ligation, and library amplification with index sequences. For the m6A IP sequencing libraries, we carried out m6A IP with poly-A RNA fragments with EpiMark® N6-Methyladenosine Enrichment Kit (#E1610S, New England Biolabs, MA, USA). Then the m6A-enriched poly-A RNA fragments and un-enriched poly-A RNA fragments were employed for the construction of strand-specific IP and Input libraries of MeRIP-seq, respectively.

treatment_protocol: We transferred these 1-day-old adults to a climatic chamber under the photoperiodic cycles of BD and DD, respectively. We collected the bulk 10- and 25-day-old male adult whole flies (BD10, BD25, DD10, and DD25) for poly-A MeRIP-seq.

tag: strain

tag: photoperiod

value: Consistent darkness

tag: age after eclosion

value: 25 days

tag: replicate


title: DI1


title: RNAseq T24 Rep5


title: MeRIP T24R2 Rep 2 RIP

tag: genotype


title: Whole_MeRIP_IP_DD25-2


title: MeRIP T24R2 Rep 3 RIP

tag: time


title: DDW3

value: DDW


title: A04_S25

value: OrganoPlate® 3-lane 40

tag: treatment


title: Whole_MeRIP_IP_DD25-1


title: DDW2


title: MeRIP T24R2 Rep 1 RIP

value: Human bladder cancer

value: Day 3


title: Whole_MeRIP_IP_DD10-3

value: 10 days


title: DDW1


title: A03_S17

source_name: Blank

value: Blank

tag: cell source


title: A02_S9


title: MeRIP T24R2 Rep 5 Input

value: WT

tag: merip antibody

value: Input Ctrl - no antibody


title: DD3

value: Red Hawk dark red kidney bean

value: DD


title: A01_S1

value: primary RPTECs

tag: platform


title: DD2

value: Leaf Tissue


title: MeRIP T24R2 Rep 4 Input


title: Whole_MeRIP_IP_DD10-1


title: Whole_MeRIP_IP_BD25-3

value: Blue-light:darkness = 12 h:12h


title: MeRIP T24R2 Rep 2 Input


title: MeRIP T24R2 Rep 3 Input


title: CI2

value: CI


title: mig1glu30min+A 3

city: beijing

first: lei

last: chen

address: NO.1 Beichen West  Road, Chaoyang District, Beijing 100101, China

institute: the institute of microbiology chinese academy of sciences

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to H99 whole genome using STAR 2.7.7a with parameters  STAR --runMode genomeGenerate --runThreadN 8  --genomeDir index/  --genomeFastaFiles $king/1_data/fa/H99.fasta  --sjdbGTFfile $king/1_data/gtf/H99.gtf  --sjdbOverhang 134  --genomeSAindexNbases 11;  STAR --runThreadN 8  --genomeDir index/   --outFileNamePrefix ./ --readFilesIn $king/${a}_R1.paired.fq.gz $king/${a}_R2.paired.fq.gz --readFilesCommand zcat    --outFilterTy --alignMatesGapMax 1000000pe BySJout  --outFilterMultimapNmax 10  --alignSJoverhangMin 5 --alignSJDBoverhangMin 3  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --outSAMtype SAM --outSAMattributes NH HI AS nM NM XS --quantMode GeneCounts; STAR --runThreadN 8   --genomeDir index/ --outFileNamePrefix ./ --readFilesIn $king/${a}_R1.paired.fq.gz $king/${a}_R2.paired.fq.gz --readFilesCommand zcat  --sjdbFileChrStartEnd $sjFileList  --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 5  --alignSJDBoverhangMin 3  --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04  --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical --outSAMtype SAM --outSAMattributes NH HI AS nM NM XS --quantMode GeneCounts
Gene  were calculated using htseq 0.6.0 with parameters htseq-count -s reverse ./${a}_filtered.sam  ../1_data/gtf/H99.gtf > ./${a}_2.count
Assembly: H99

organism: Cryptococcus neoformans H99

growth_protocol: 50 ODs of cells from overnight YPD cultures were washed twice in water and resuspended in water at a final concentration of 1 OD600, transferred into YPD, YPG liquid medium with or without AmB treatment (10xMIC), cultured in 37℃ 5% CO2 for 10, 20 30min.

extract_protocol:
Total RNA was purified using the Ultrapure RNA Kit. Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit.
Frozen pellets were ground in liquid nitrogen and total RNA was purified using the Ultrapure RNA Kit (Kangweishiji, CW0581S) according to the manufacturer's instructions, and then reverse-transcribed with the Fastquant RT Kit (Tiangen KR106-02, with gDNase).
Illumina cDNA libraries were generated using VAHTSTM mRNA-seq v2 Library Prep Kit (Vazyme Biotech Co., Ltd, Nanjing, China) as described by the manufacture. Samples were clustered using VAHRS RNA adapters set1/set2 and then sequenced using Illunima Hiseq 4000 platform in a 2x150 pair-ended manner.

tag: age

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: MeRIP T24R2 Rep 1 Input


title: A05_S33

city: College Station

first: Ivan

last: Rusyn

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

institute: Texas A&M University

value: OrganoPlate® 3-lane 41

value: Cisplatin

tag: ID


title: DD1

tag: tissue


title: mig1gal30min+A 3

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C


title: Whole_MeRIP_IP_BD25-2

value: 25 days


title: CI1

tag: plant


title: MeRIP T24 Rep 5 RIP

value: Human bladder cancer

value: anti m6A antibody (NEB, E1610)


title: Whole_MeRIP_IP_DD10-2

value: Consistent darkness

value: 10 days


title: MeRIP T24 Rep 4 RIP

value: WT

value: Day 3


title: mig1glu30min+A 2


title: Whole_MeRIP_IP_BD10-3


title: Whole_MeRIP_IP_BD10-1


title: MeRIP T24 Rep 3 RIP


title: Whole_MeRIP_IP_BD10-2


title: CDW3

value: Red Hawk dark red kidney bean

tag: sample group

value: CDW


title: mig1gal30min+A 2


title: CDW1


title: mig1gal30min-A 3


title: CDW2


title: Whole_MeRIP_Input_DD25-3


title: Whole_MeRIP_IP_BD25-1


title: MeRIP T24 Rep 1 RIP

tag: cell type


title: Whole_MeRIP_Input_DD25-2


title: MeRIP T24 Rep 5 Input

tag: cell line

value: Input Ctrl - no antibody


title: wtgal30min+A 3

source_name: wild type

tag: strain

value: wild type


title: mig1gal30min+A 1


title: CD1

value: CD

value: Leaf tissue


title: Whole_MeRIP_Input_DD25-1

tag: photoperiod


title: wtgal30min+A 2


title: MeRIP T24 Rep 4 Input


title: wtgal30min+A 1


title: MeRIP T24 Rep 3 Input


title: Whole_MeRIP_Input_DD10-3

tag: age after eclosion


title: wtglu30min+A 3

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: MeRIP T24 Rep 2 RIP


title: shoot+N_K9me2_Rep6

city: West Lafayette

first: Ryan

last: Patrick

address: 625 Agriculture Mall Dr

data_processing:
ChIP-Seq data was trimmed using CutAdapt and aligned using Bowtie2. Paired reads were convereted to fragments and dynamic islands were called using SICER-df.
Assembly: SL4.0

organism: Solanum lycopersicum

source_name: shoot

growth_protocol: Plants were germinated on 1/2 strength MS plates and then transferred to a hydroponic system under greenhouse conditions.

extract_protocol:
Two grams of tissues were fixed with 1% formaldehyde by applying vacuum at 700 mmHg for 25 min. Fixation was terminated by adding 2M glycine to a final concentration of 0.125M and vacuum application for 5 minutes. Formaldehyde-fixed tissues were ground in liquid nitrogen and nuclei were isolated. Isolated nuclei were sonicated using Bioruptor to prepare chromatin samples with single nucleosomes.
Chromatin immunoprecipitated using Protein A dynabeads with antibodies against histone marks or input chromatin was recovered and reverse-crosslinked. Libraries were prepared using NEBNext dual index library kit.

treatment_protocol: Twenty-two day old plants were transferred to nitrogen free media for four days and then either replenished with fresh nitrogen free media (-N condition) or resupply of media containing nitrate (+N condition). After 6 hours of treatment, -N and +N samples were harvested.

tag: cultivar

value: shoot

value: shoot+N

tag: chip antibody


title: shoot+N_K9me2_Rep5


title: mig1glu30min+A 1

tag: genotype


title: MeRIP T24 Rep 1 Input

tag: time


title: CD3

value: Leaf Tissue


title: shoot+N_K9me2_Rep4

tag: treatment


title: shoot-N_K9me2_Rep6

value: shoot-N


title: wtglu30min+A 1


title: wtglu30min+A 2


title: Whole_MeRIP_Input_BD25-3

value: Blue-light:darkness = 12 h:12h

value: 25 days

tag: replicate


title: CD2


title: K562, Treatment, rep3

city: Helsinki

first: Alisa

last: Olkinuora

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Results_TPM_counts_K562_Untreated_vs_Treatment.xlsx
Results_TPM_counts_K562_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_K562_Positive_ctrl_vs_Treatment.xlsx
K562_DHX40_3_S36

data_processing:
RNAseq data was quantified and aligned by using Salmon and STAR.
Differential transcript and gene expression data generated using the Fishpond R pacakge.
Novel splice events were called using ASGAL.
Assembly: GRCh38
Supplementary files format and content: Fishpond-generated differential experssion analysis results are given in accompanying tab-delimited Excel-tables.

source_name: bone marrow from chronic myeloid leukemia

extract_protocol:
RNA was extracted using NucleoSpin® RNA extraction kit with DNAse(Macherey-Nagel, Düren, Germany). 300ng of RNA was used for library prep.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit

value: leukemic

value: DHX40 knockdown

value: Treatment


title: K562, Treatment, rep2

description:
Results_TPM_counts_K562_Untreated_vs_Treatment.xlsx
Results_TPM_counts_K562_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_K562_Positive_ctrl_vs_Treatment.xlsx
K562_DHX40_2_S35

value: bone marrow from chronic myeloid leukemia


title: shoot-N_K9me2_Rep5


title: Whole_MeRIP_Input_BD25-2


title: mig1gal30min-A 1

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C


title: mig1gal30min-A 2


title: shoot-N_K9me2_Rep4


title: K562, Treatment, rep1

description:
Results_TPM_counts_K562_Untreated_vs_Treatment.xlsx
Results_TPM_counts_K562_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_K562_Positive_ctrl_vs_Treatment.xlsx
K562_DHX40_1_S34


title: shoot+N_INPUT_Rep6


title: Whole_MeRIP_Input_BD25-1


title: mig1glu30min-A 3


title: Whole_MeRIP_Input_BD10-3

value: 10 days


title: K562, Negative_ctrl, rep3

description:
Results_TPM_counts_K562_Negative_ctrl_vs_Positive_ctrl.xlsx
K562_nonT3_S33

value: Non-Target knockdown


title: Whole_MeRIP_Input_DD10-2

value: Consistent darkness


title: MeRIP T24 Rep 2 Input

value: Human bladder cancer

value: WT

tag: merip antibody

value: Input Ctrl - no antibody

value: Day 3


title: Whole_MeRIP_Input_DD10-1


title: mig1glu30min-A 2

tag: age

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: shoot+N_INPUT_Rep4

value: shoot

value: shoot+N


title: shoot+N_INPUT_Rep5


title: Whole_MeRIP_Input_BD10-2

value: Blue-light:darkness = 12 h:12h


title: K562, Negative_ctrl, rep2

description:
Results_TPM_counts_K562_Negative_ctrl_vs_Positive_ctrl.xlsx
K562_nonT2_S32


title: mig1glu30min-A 1


title: Whole_MeRIP_Input_BD10-1


title: Whole_RNA_DD23F1-3

description: Photoperiod: Consistent darkness; Parental age after eclosion: 3 days

data_processing:
After removing adaptors and low-quality bases by fastp (version 0.20.1), the resulting reads no less than 50 bp were mapped to the Drosophila melanogaster reference genome (FB2021_02) released by FlyBase database (http://flybase.org/).
The featureCounts program within SourceForge Subread package (version 2.0.2) was used for counting the reads that mapped to genes.
The genes with an average read count less than 10 in any group or lacking read count in any replicate were primarily filtered.
R package DESeq2 (version 1.30.0) was used for the identification of differentially expressed genes (DEGs) by setting false discovery rate corrected P-value (FDR) < 0.05 and fold change >= 2 as the thresholds of significance (Supplementary Table S2), and the read count normalization across samples by size factors.
t-SNE dimension reduction analysis was performed using R (version 4.0.3) package Rtsne (version 0.15); heatmap was generated using R package pheatmap (version 1.0.12); common and unique DEGs were visualized in a Venn diagram generated using R package VennDiagram; volcano plot was generated using R package ggplot2; GO (Gene Ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for the DEGs were performed using either Metascape (version 3.5) (https://metascape.org/) or R package clusterProfiler (version 3.18.1);  Gene set enrichment analysis (GSEA) software (version 4.2.0) was used for determining the statistical significance of priori defined gene sets.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data of w1118 F1 generation male adult whole flies.

extract_protocol:
Total RNAs were isolated and dissolved in RNase-free water after the bulk samples had been homogenized in 0.5–1 mL TRIzol AG RNAex Pro Reagent (#AG21102, Accurate Bioeng. Co., Ltd., Hunan, China) with glass beads using a homogenizer.
Poly-A RNAs were purified from the extracted total RNAs using Dynabeads™ Oligo(dT)25 (#61002, Invitrogen, CA, USA) and were further fragmented as ~350 nt fragments using NEBNext® Second Strand Synthesis (dNTP-Free) Reaction Buffer (#B6117S, New England BioLabs, MA, USA). Strand-specific sequencing libraries were conducted using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, New England BioLabs) according to the manufacturer's protocols including first- and second-strand cDNA synthesis, adaptor ligation, and library amplification with index sequences.

treatment_protocol: To investigate the mRNA profiles of w1118 F1 generation under the influences of parental photoperiods and natural aging, we collected the eggs from 8- and 23-day-old flies, colonized them under DD until 3 days after eclosion, and sampled these bulk 3-day-old male adult whole flies for poly-A RNA-seq (BD8F1, BD23F1, DD8F1, and DD23F1).

tag: parental photoperiod

tag: parental age after eclosion

value: 23 days


title: shoot-N_INPUT_Rep6

tag: tissue

value: shoot-N


title: wtgal30min-A 3

value: wild type


title: K562, Negative_ctrl, rep1

description:
Results_TPM_counts_K562_Negative_ctrl_vs_Positive_ctrl.xlsx
K562_nonT1_S31

value: leukemic


title: K562, Positive_ctrl, rep3

description:
Results_TPM_counts_K562_Untreated_vs_Positive_ctrl.xlsx
K562_GAPDH3_S30

value: bone marrow from chronic myeloid leukemia

value: GAPDH knockdown


title: wtgal30min-A 2

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C


title: wtgal30min-A 1


title: shoot-N_INPUT_Rep4


title: K562, Positive_ctrl, rep2

description:
Results_TPM_counts_K562_Untreated_vs_Positive_ctrl.xlsx
K562_GAPDH2_S29


title: shoot-N_INPUT_Rep5


title: Whole_RNA_DD23F1-2


title: Whole_RNA_DD23F1-1


title: wtglu30min-A 2


title: wtglu30min-A 3


title: K562, Positive_ctrl, rep1

description:
Results_TPM_counts_K562_Untreated_vs_Positive_ctrl.xlsx
K562_GAPDH1_S28


title: shoot+N_mRNA, Rep2

data_processing:
ChIP-Seq data was trimmed using CutAdapt and aligned using Bowtie2. Paired reads were converted to fragments and dynamic islands were called using SICER-df.
RNA-Seq data was trimmed using CutAdapt and aligned using TopHat2. The gene counts were generated from mapped reads using htseq and counts were normalized with EDAseq, while differentially expressed genes were determined using DESeq2.
Genome_build: SL4.0
Supplementary_files_format_and_content: raw_counts.txt, SICER-df output files

extract_protocol:
Tomato root and shoot tissue was ground in liquid nitrogen and total RNA was extracted using mirVana kit following the manufacturer’s protocol for total RNA extraction. Turbo DNase was used to remove contaminating DNA and then the quality of extract total RNA was analyzed using Bioanalyzer in Purdue Genomics Core.
Poly(A) RNA was prepared for sequencing using standard Illumina protocols

value: +N


title: Whole_RNA_DD8F1-3

value: Consistent darkness

value: 8 days


title: shoot+N_mRNA, Rep3


title: K562, Untreated, rep3

description:
Results_TPM_counts_K562_Untreated_vs_Negative_ctrl.xlsx
K562_UT3_S27

value: WT

value: Untreated


title: Whole_RNA_DD8F1-2


title: shoot+N_mRNA, Rep1


title: K562, Untreated, rep2

description:
Results_TPM_counts_K562_Untreated_vs_Negative_ctrl.xlsx
K562_UT2_S26


title: Whole_RNA_DD8F1-1


title: K562, Untreated, rep1

description:
Results_TPM_counts_K562_Untreated_vs_Negative_ctrl.xlsx
K562_UT1_S25


title: shoot-N_mRNA, Rep3

value: -N


title: mig1gal20min+A 3


title: Whole_RNA_BD23F1-3


title: wtglu30min-A 1

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: CCD841, Treatment, rep3

description:
Results_TPM_counts_CCD841_Untreated_vs_Treatment.xlsx
Results_TPM_counts_CCD841_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_CCD841_Positive_ctrl_vs_Treatment.xlsx
CCD841CoN_DHX40_3_S24

source_name: normal colon epithelium from fetus

value: normal colon epithelium from fetus

value: CCD841 CoN

value: normal

value: DHX40 knockdown

value: Treatment


title: mig1gal20min+A 2


title: shoot-N_mRNA, Rep2

value: shoot


title: Whole_RNA_BD23F1-2

value: Blue-light:darkness = 12 h:12h

value: 23 days


title: mig1gal20min+A 1


title: CCD841, Treatment, rep2

description:
Results_TPM_counts_CCD841_Untreated_vs_Treatment.xlsx
Results_TPM_counts_CCD841_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_CCD841_Positive_ctrl_vs_Treatment.xlsx
CCD841CoN_DHX40_2_S23


title: Whole_RNA_BD23F1-1


title: shoot-N_mRNA, Rep1


title: mig1glu20min+A 3


title: CCD841, Treatment, rep1

description:
Results_TPM_counts_CCD841_Untreated_vs_Treatment.xlsx
Results_TPM_counts_CCD841_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_CCD841_Positive_ctrl_vs_Treatment.xlsx
CCD841CoN_DHX40_1_S22


title: Whole_RNA_BD8F1-3


title: root+N_mRNA, Rep3

source_name: root

value: root


title: root+N_mRNA, Rep2


title: CCD841, Negative_ctrl, rep2

description:
Results_TPM_counts_CCD841_Negative_ctrl_vs_Positive_ctrl.xlsx
CCD841CoN_nonT2_S20

value: Non-Target knockdown


title: Whole_RNA_BD8F1-2


title: CCD841, Negative_ctrl, rep1

description:
Results_TPM_counts_CCD841_Negative_ctrl_vs_Positive_ctrl.xlsx
CCD841CoN_nonT1_S19


title: root+N_mRNA, Rep1

value: +N


title: mig1glu20min+A 1


title: wtgal20min+A 3

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C

value: wild type


title: Head_RNA_DD25-3

description: Parental photoperiod: White-light: darkness = 12 h: 12h; Parental age after eclosion: 3 days

data_processing:
After removing adaptors and low-quality bases by fastp (version 0.20.1), the resulting reads no less than 50 bp were mapped to the Drosophila melanogaster reference genome (FB2021_02) released by FlyBase database (http://flybase.org/).
The featureCounts program within SourceForge Subread package (version 2.0.2) was used for counting the reads that mapped to genes.
The genes with an average read count less than 10 in any group or lacking read count in any replicate were primarily filtered.
R package DESeq2 (version 1.30.0) was used for the identification of differentially expressed genes (DEGs) by setting false discovery rate corrected P-value (FDR) < 0.05 and fold change >= 2 as the thresholds of significance (Supplementary Table S2), and the read count normalization across samples by size factors.
t-SNE dimension reduction analysis was performed using R (version 4.0.3) package Rtsne (version 0.15); heatmap was generated using R package pheatmap (version 1.0.12); common and unique DEGs were visualized in a Venn diagram generated using R package VennDiagram; volcano plot was generated using R package ggplot2; GO (Gene Ontology) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses for the DEGs were performed using either Metascape (version 3.5) (https://metascape.org/) or R package clusterProfiler (version 3.18.1);  Gene set enrichment analysis (GSEA) software (version 4.2.0) was used for determining the statistical significance of priori defined gene sets.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text file (.txt) includes raw read counts for the RNA-seq data of w1118 male adult heads.

source_name: Male adult heads

treatment_protocol: We transferred these 1-day-old adults to a climatic chamber under the photoperiodic cycles of BD and DD, respectively. We collected the bulk 10- and 25-day-old male adult heads (BD10, BD25, DD10, and DD25) for poly-A RNA-seq.

value: Consistent darkness

value: 25 days


title: wtgal20min+A 2


title: wtgal20min+A 1


title: root-N_mRNA, Rep3

value: -N


title: root-N_mRNA, Rep2


title: CCD841, Positive_ctrl, rep3

description:
Results_TPM_counts_HEK_Untreated_vs_Positive_ctrl.xlsx
CCD841CoN_GAPDH3_S18

value: GAPDH knockdown


title: Head_RNA_DD25-2


title: CCD841, Positive_ctrl, rep1

description:
Results_TPM_counts_HEK_Untreated_vs_Positive_ctrl.xlsx
CCD841CoN_GAPDH1_S16

value: normal colon epithelium from fetus


title: wtglu20min+A 3

value: YPD liquid medium (10g/l glucose, 20g/l peptone, 10g/l yeast extract) at 30C


title: Head_RNA_DD25-1


title: Head_RNA_DD10-3

value: 10 days


title: CCD841, Untreated, rep3

description:
Results_TPM_counts_CCD841_Untreated_vs_Negative_ctrl.xlsx
CCD841CoN_UT3_S15

value: CCD841 CoN

value: normal

value: WT

value: Untreated


title: CCD841, Positive_ctrl, rep2

description:
Results_TPM_counts_HEK_Untreated_vs_Positive_ctrl.xlsx
CCD841CoN_GAPDH2_S17


title: shoot+N_K4me3, Rep3

value: shoot


title: CCD841, Negative_ctrl, rep3

description:
Results_TPM_counts_CCD841_Negative_ctrl_vs_Positive_ctrl.xlsx
CCD841CoN_nonT3_S21


title: mig1glu20min+A 2


title: wtglu20min+A 2


title: CCD841, Untreated, rep2

description:
Results_TPM_counts_CCD841_Untreated_vs_Negative_ctrl.xlsx
CCD841CoN_UT2_S14


title: Head_RNA_DD10-2


title: Whole_RNA_BD8F1-1

description: Photoperiod: Consistent darkness; Parental age after eclosion: 3 days

value: Blue-light:darkness = 12 h:12h

value: 8 days


title: Head_RNA_DD10-1


title: shoot+N_K4me3, Rep1

value: +N


title: CCD841, Untreated, rep1

description:
Results_TPM_counts_CCD841_Untreated_vs_Negative_ctrl.xlsx
CCD841CoN_UT1_S13


title: shoot-N_K4me3, Rep3


title: Head_RNA_BD25-3


title: shoot+N_K4me3, Rep2


title: mig1gal20min-A 3

value: YPG liquid medium (10g/l galactose, 20g/l peptone, 10g/l yeast extract) at 30C


title: HEK293, Treatment, rep3

description:
Results_TPM_counts_CCD841_Untreated_vs_Treatment.xlsx
Results_TPM_counts_HEK_Negative_ctrl_vs_Treatment.xlsx
Results_TPM_counts_HEK_Positive_ctrl_vs_Treatment.xlsx
HEK293_DHX40_3_S12

source_name: immortalized human embryonic kidney cells

value: DHX40 knockdown

value: Treatment


title: root-N_mRNA, Rep1

value: root


title: shoot-N_K4me3, Rep2

value: -N


title: mig1gal20min-A 2


title: Head_RNA_BD25-2

value: 25 days