title: Liver_AT3_2

first: Guoyin

last: Kai

address: No. 548 Binwen Road, Binjiang District

institute: Zhejiang Chinese Medical University

description: Library name: Liver_AT3_2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

tag: strain

value: BALB/c

tag: Sex

value: male

value: cisplatin-induced acute liver injury


title: PBMC; SeqWell; Animal T627; Timepoint ART2; Array A2

status: Public on Aug 01 2026

type: SRA

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Massachusetts Ave

country: USA

institute: Massachusetts Institute of Technology

description:
Library name: T627_ART2_A2
T627_ART2_A2

library_source: transcriptomic single cell

data_processing:
BCL files were converted to fastQs via Terra cumulus/bcl2fastq/5
For processed data: A custom genome combining  mmul10 and SIVmac251 was created using jgould/dropseq_bundle/10 (Terra). Alignment was performed using cumulus/dropseq_workflow/11 (Terra).
Assembly: custom mmul10 + SIVmac251
Supplementary files format and content: RDS, a seurat object of all cells combined from all samples directly following alignment (untrimmed, filtered)

molecule: polyA RNA

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
PBMC samples from rhesus macaque were processed for single-cell analysis using SeqWellS3 as described in Hughes, et al; Immunity 2020.
scRNAseq libraries were prepared via NexteraXT as described in Hughes, et al; Immunity 2020

tag: tissue

value: PBMC

tag: animalid

tag: timepoint

tag: array

tag: assay

value: SeqWell

tag: hassiv

value: yes

tag: onart

tag: weekssinceinfection

tag: weeksonart


title: RPM, 2h post CLP, replicate 4

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description: Library name: CLP-4

library_source: transcriptomic

data_processing:
Reads were quality checked with fastQC and no further processing was required
Reads were mapped to the mm39 reference genome with STAR (2.7.10b) and the gencode M30. Read counts were directly obtained using the the featurecounts package
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: tab delimited count matrix with the raw counts per sample

molecule: total RNA

organism: Mus musculus

source_name: spleen

growth_protocol: All mice were housed in individually ventilated cages at conventional housing conditions (22°C, 14/10h light/dark cycle, dark phase starting at 9 p.m.) in a specific pathogen-free facility. Food (chow diet consisting of 18% proteins, 4.5% fibers, 4.5% fat and 6.3% ashes, Provimi Kliba SA) and water were given at libitum

extract_protocol:
Total RNA was isolated with Aurum Total RNA mini Kit (Bio-Rad) following the manufacturer’s instructions
Library preparation was done using the illumina truseq stranded library kit for sequencing with a Cloudbreak sequencing kit on the element AVITI according the the manufacturer's instructions

treatment_protocol: Mice were subject to CLP or sam surgery and 2 hours later spleend were isolated and prepared for FACS to isoate RPMs

value: spleen

tag: cell type

value: red pulp macrophage

tag: genotype

value: WT C57BL/6J

tag: treatment

value: CLP


title: Leaves, PIP2-7 OE, Rep2

city: Bengaluru

first: Shivaprasad

last: Padubidri V.

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Centre for Biological Sciences, TIFR

description: Indica Rice, Pusa Basmati-1 (PB-1)

data_processing:
The raw reads were quality and adapter trimmed using TrimGalore (-q 20 -length 30)
Single-end RNA-seq reads were aligned to the rice IRGSP-1.0 genome using Hisat2 (--dta-cufflinks --max-intronlen 20000 --secondary --phred33 -k 20 -q -U).
Differetial expression analysis was performed using Cuffdiff (v2.2.1) as mentioned in Cole Trapnell et al, 2012.
Raw read counts per gene was calculated using featureCounts (Liao Y et al., 2013)
Supplementary files format and content: FPKM values of the genes obtained using Cuffdiff and featureCounts output are provided in tsv format

organism: Oryza sativa

source_name: 2.5-month-old PIP2-7 OE Leaves

growth_protocol: Regenerated and rooted transgenics were transferred to soil and kept for acclimatization for 3-5 days in plant growth chamber (16/8 hr light /Dark cycle, 70% RH, 24°C Temperature). The plants were then transferred to bigger pots in transgenic green house with the same conditions.

extract_protocol:
Total RNA from vegetative leaves were extracted using Trizol (Invitrogen) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Samples were collected equally at 2.5 months post transfer to Green house.

tag: variety

value: Pusa Basmati-1 (PB-1)

value: PIP2-7 OE

value: Leaves


title: Liver_AT3_1

city: Hangzhou

country: China

description: Library name: Liver_AT3_1

source_name: liver


title: PBMC; SeqWell; Animal T627; Timepoint ART1; Array A2

description:
Library name: T627_ART1_A2
T627_ART1_A2


title: Leaves, PIP2-7 OE, Rep1

description: Indica Rice, Pusa Basmati-1 (PB-1)


title: RPM, 2h post CLP, replicate 3

description: Library name: CLP-3


title: Liver_CPT_3

description: Library name: Liver_CPT_3


title: PBMC; SeqWell; Animal T627; Timepoint ART1; Array A1

description:
Library name: T627_ART1_A1
T627_ART1_A1


title: Leaves, WT, control for OsPIP2-7,  Rep2

description: Indica Rice, Pusa Basmati-1 (PB-1)

source_name: 2.5-month-old WT Pusa Basmati-1 Leaves

value: WT


title: Liver_CPT_2

description: Library name: Liver_CPT_2


title: PBMC; SeqWell; Animal T623; Timepoint chronic; Array A4

description:
Library name: T623_chronic_A4
T623_chronic_A4

value: chronic

value: no


title: RPM, 2h post CLP, replicate 2

description: Library name: CLP-2


title: RPM, 2h post CLP, replicate 1

description: Library name: CLP-1


title: Liver_CPT_1

description: Library name: Liver_CPT_1

value: liver


title: Leaves, WT, control for OsPIP2-7,  Rep1

description: Indica Rice, Pusa Basmati-1 (PB-1)


title: PBMC; SeqWell; Animal T623; Timepoint chronic; Array A3

description:
Library name: T623_chronic_A3
T623_chronic_A3


title: Leaves, pip2-1 KO, Rep2

description: Indica Rice, Pusa Basmati-1 (PB-1)

source_name: 2.5-month-old PIP2-1 KO Leaves

value: pip2-1 KO


title: PBMC; SeqWell; Animal T623; Timepoint chronic; Array A2

description:
Library name: T623_chronic_A2
T623_chronic_A2


title: Leaves, pip2-1 KO, Rep1

description: Indica Rice, Pusa Basmati-1 (PB-1)


title: Mouse_Liver_4W_B2_minus_RNA_4

city: Palo Alto

first: Yohei

last: Abe

state: California

address: 3181 Porter Dr

institute: Arc Institute

description: Library name: Sample 161

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
RNA sequencing reads were aligned to the hg38 human or mm10 mouse reference genome using STAR using default parameters.  Gene expression levels were calculated using HOMER by counting all strand specific reads within exons.  Only the most abundant transcripts, including multiple alternative variants, were selected for each gene, and the genes with a length smaller than 250 bp were removed.  Transcripts per million (TPM) were used to evaluate the correlation among replicates.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters.
Assembly: hg38 or mm10
Supplementary files format and content: TPM expression matrices

source_name: Liver

extract_protocol:
For RNA-seq, total RNA was isolated from culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) as described by the manufacturer.
RNA-seq library preparation was performed according to the manufacturer’s instructions of the QuantSeq 3’ mRNA-Seq V2 Library Prep Kit (Lexogen Inc). In detail, RNA-seq libraries were prepared from 500 ng of total RNA using a reverse transcription–based workflow incorporating Illumina-compatible adapter sequences. First-strand cDNA synthesis was performed using an oligo(dT) primer containing an Illumina-compatible sequence at its 5′ end. The primer was annealed to polyadenylated RNA, and reverse transcription was carried out according to the manufacturer’s instructions to generate first-strand cDNA. Following first-strand synthesis, the RNA template was enzymatically degraded to enable efficient second-strand synthesis. Reaction plates were briefly centrifuged prior to removal of the sealing film to ensure complete recovery of reaction volume. Second-strand synthesis was initiated using a random primer harboring an Illumina-compatible linker sequence at its 5′ end, resulting in double-stranded cDNA (dsDNA) libraries. Double-stranded cDNA libraries were purified using magnetic beads to remove residual enzymes, primers, nucleotides, and buffer components. Beads were equilibrated to room temperature for 30 min prior to use and thoroughly resuspended before addition to samples. Libraries were washed and eluted in an elution buffer according to the manufacturer’s protocol. Purified dsDNA libraries were PCR-amplified (14–16 cycles) to introduce full-length Illumina adapter sequences required for cluster generation, as well as unique dual indices for multiplexed sequencing. Amplified libraries were purified using magnetic beads to remove residual PCR components that may interfere with downstream applications. Final libraries were quantified using a QubitTM 1× dsDNA HS Assay Kit (Thermo Fisher Scientific) and subjected to quality control prior to sequencing.

treatment_protocol: Control vs. Vitamin B2 deficiency

value: Liver


title: Liver_CON_2

description: Library name: Liver_CON_2

value: BALB/c

value: male


title: PBMC; SeqWell; Animal T623; Timepoint chronic; Array A1

description:
Library name: T623_chronic_A1
T623_chronic_A1

value: PBMC

value: SeqWell


title: Mouse_Liver_4W_B2_minus_RNA_3

description: Library name: Sample 160


title: Leaves, PIP2-1 OE, Rep2

description: Indica Rice, Pusa Basmati-1 (PB-1)

source_name: 2.5-month-old PIP2-1 OE Leaves

value: PIP2-1 OE


title: Liver_CON_1

description: Library name: Liver_CON_1


title: PBMC; SeqWell; Animal T623; Timepoint acute; Array A4

description:
Library name: T623_acute_A4
T623_acute_A4

value: acute

value: yes


title: Mouse_Liver_4W_B2_minus_RNA_2

description: Library name: Sample 159


title: Leaves, PIP2-1 OE, Rep1

description: Indica Rice, Pusa Basmati-1 (PB-1)


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_ATAC_rep3

description: Library name: Sample 116

library_source: genomic

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters. Alignment files were processed using HOMER. Peaks were called by combining replicate conditions and using HOMER (findPeaks) using parameters “-style factor -size 200”.
Assembly: hg38 or mm10
Supplementary files format and content: peak files (BED format)

molecule: genomic DNA

source_name: Hepatocyte

extract_protocol:
For ATAC-seq, cultured cells were collected and centrifuged at 500 × g for 5 min at 4°C. Cells were washed once with 100 µL ice-cold PBS and centrifuged at 500 × g for 5 min at 4°C. The supernatant was carefully removed, and the cell pellet was resuspended in 100 µL ice-cold ATAC lysis buffer.
ATAC-seq library preparation was performed according to the manufacturer’s instructions of the ATAC-Seq Kit (Active Motif). In detail, 75,000 cultured cells were collected and centrifuged at 500 × g for 5 min at 4°C. Cells were washed once with 100 µL ice-cold PBS and centrifuged at 500 × g for 5 min at 4°C. The supernatant was carefully removed, and the cell pellet was resuspended in 100 µL ice-cold ATAC lysis buffer. Nuclei were pelleted by centrifugation at 500 × g for 10 min at 4°C, and the supernatant was carefully aspirated without disturbing the nuclei pellet. Nuclei were resuspended in 50 µL of Tagmentation Master Mix and incubated at 37°C for 30 min with shaking at 800 rpm. Immediately following transposition, DNA was purified by adding 250 µL DNA Purification Binding Buffer and 5 µL of 3 M sodium acetate, followed by column-based purification according to the kit protocol. Columns were washed with Wash Buffer containing 80% ethanol and DNA was eluted in 35 µL Elution Buffer. Purified DNA was amplified using indexed primers under the following PCR conditions: 72°C for 5 min; 98°C for 30 sec; 10 cycles of 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min; followed by a hold at 10°C. Amplified libraries were purified using SPRI beads at a 1.2× sample volume ratio. Beads were washed twice with freshly prepared 80% ethanol, air-dried, and DNA was eluted in 20 µL Elution Buffer.

tag: cell line

value: Hepatocyte


title: PBMC; SeqWell; Animal T623; Timepoint acute; Array A3

description:
Library name: T623_acute_A3
T623_acute_A3


title: Leaves, WT, control for OsPIP2-1,  Rep2

description: Indica Rice, Pusa Basmati-1 (PB-1)

value: Pusa Basmati-1 (PB-1)


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_ATAC_rep2

description: Library name: Sample 115


title: Mouse_Liver_4W_B2_minus_RNA_1

description: Library name: Sample 158


title: PBMC; SeqWell; Animal T623; Timepoint acute; Array A2

description:
Library name: T623_acute_A2
T623_acute_A2


title: Leaves, WT, control for OsPIP2-1,  Rep1

description: Indica Rice, Pusa Basmati-1 (PB-1)


title: Mouse_Liver_4W_B2_minus_RNA_5

description: Library name: Sample 162


title: kidney,no HPC,renal ischemia–reperfusion injury,rep3

city: Xining

first: Drolma

last: Gomchok

address: No. 16 Kunlun Road

institute: Qinghai university

description: Library name: NR3

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences, low-quality reads, and reads containing ambiguous bases. Clean reads were then mapped to the mouse reference genome using a standard RNA-seq alignment pipeline.
Gene-level read counts were generated using HTSeq-count, and gene expression abundance was calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Principal component analysis (PCA) was performed to evaluate sample clustering and biological reproducibility among groups. Differential gene expression analysis was conducted using DESeq2. Genes with an adjusted P value (q value) < 0.05 and a fold change > 2.0 or < 0.5 were considered differentially expressed genes.
Hierarchical clustering was performed to visualize expression patterns of differentially expressed genes across experimental groups.
Functional enrichment analysis of differentially expressed genes was performed using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, and WikiPathways databases. Gene set enrichment analysis (GSEA) was further performed to evaluate coordinated pathway-level changes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA was extracted from frozen renal tissues using TRIzol reagent according to the manufacturer's instructions. RNA purity and concentration were assessed using a NanoDrop 2000 spectrophotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. Only RNA samples meeting the quality-control criteria were used for library construction.
RNA-seq libraries were prepared using the VAHTS Universal V10 RNA-seq Library Prep Kit according to the manufacturer's protocol. Sequencing was performed on a DNBSEQ-T7 platform.

value: kidney

value: renal ischemia–reperfusion injury

tag: batch


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_ATAC_rep1

description: Library name: Sample 114


title: Mouse_Liver_4W_Control_RNA_5

description: Library name: Sample 157

value: Control


title: Liver_CON_3

description: Library name: Liver_CON_3

tag: strain


title: PBMC; SeqWell; Animal T623; Timepoint acute; Array A1

description:
Library name: T623_acute_A1
T623_acute_A1


title: Kupffer cells, 2h post CLP, replicate 4

description: Library name: CLP-4

treatment_protocol: Mice were subject to CLP or sham surgery and 2 hours later livers were isolated and prepared for FACS to isolate KCs

value: Kupffer cell

value: WT C57BL/6J

value: CLP


title: THP-1, Lenti-Vsir,V3

city: Shanghai

first: Lifei

last: Liang

address: 180 Fenglin Road

institute: Zhongshan Hospital, Fudan University

description:
Library name: Sample6
Column name in genes_fpkm_expression.xlsx:V3

data_processing:
Raw sequencing reads were trimmed for adapters and low-quality sequences in CLC Genomics Workbench v11.0.1 with a quality limit of 0.05. Clean reads were aligned to mouse reference genome GRCm38/mm10 using preset mapping parameters (mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8). Gene read count extraction and expression normalization were completed within the same software.
Assembly: hg38
Supplementary files format and content: xlsx file includes genes and FPKM values for each Sample

organism: Homo sapiens

extract_protocol:
Total RNA was extracted from samples using the RNeasy Mini Plus Kit (Qiagen) following the manufacturer’s instructions, and 1.3 μg qualified total RNA was reserved for subsequent library construction.
mRNA enrichment and RNA-seq library construction were performed with the SMARTER mRNA-Seq Library Prep Kit strictly in accordance with the manufacturer’s standard protocols.

value: Lenti-Vsir


title: Mouse_Liver_4W_Control_RNA_4

description: Library name: Sample 156

value: Liver


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_ATAC_rep3

description: Library name: Sample 113


title: THP-1, Lenti-Vsir,V2

description:
Library name: Sample5
Column name in genes_fpkm_expression.xlsx:V2


title: PBMC; SeqWell; Animal T623; Timepoint ART3; Array 5E; techrep2; NextSeq500

description:
Library name: T623_ART3_5E_techrep2
T623_ART3_5E


title: Mouse_Liver_4W_Control_RNA_3

description: Library name: Sample 155


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_ATAC_rep2

description: Library name: Sample 112


title: PBMC; SeqWell; Animal T623; Timepoint ART3; Array 3C; techrep2; NextSeq500

description:
Library name: T623_ART3_3C_techrep2
T623_ART3_3C


title: THP-1, Lenti-Vsir,V1

description:
Library name: Sample4
Column name in genes_fpkm_expression.xlsx:V1


title: Mouse_Liver_4W_Control_RNA_2

description: Library name: Sample 154


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_ATAC_rep1

description: Library name: Sample 111


title: PBMC; SeqWell; Animal T623; Timepoint ART2; Array A2

description:
Library name: T623_ART2_A2
T623_ART2_A2


title: THP-1, Lenti-Con,C3

description:
Library name: Sample3
Column name in genes_fpkm_expression.xlsx:C3

value: Lenti-Con


title: Mouse_Liver_4W_Control_RNA_1

description: Library name: Sample 153


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_ATAC_rep3

description: Library name: Sample 110


title: THP-1, Lenti-Con,C2

description:
Library name: Sample2
Column name in genes_fpkm_expression.xlsx:C2


title: PBMC; SeqWell; Animal T623; Timepoint ART2; Array A1

description:
Library name: T623_ART2_A1
T623_ART2_A1


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_RNA_rep3

description: Library name: Sample 104


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_ATAC_rep2

description: Library name: Sample 109


title: PBMC; SeqWell; Animal T623; Timepoint ART1; Array A2

description:
Library name: T623_ART1_A2
T623_ART1_A2


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_RNA_rep2

description: Library name: Sample 103


title: THP-1, Lenti-Con,C1

description:
Library name: Sample1
Column name in genes_fpkm_expression.xlsx:C1


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_ATAC_rep1

description: Library name: Sample 108


title: PBMC; SeqWell; Animal T537; Timepoint chronic; Array A4

description:
Library name: T537_chronic_A4
T537_chronic_A4

value: chronic

value: no


title: Mouse NKT1 CD4 positive, thymocytes, rep3

city: Bethesda

first: Jung-Hyun

last: Park

state: MD

address: 10 Center Drive

department: NCI/CCR/EIB

institute: National Institutes of Health

description: Library name: Sample_R4NKT1_4P

data_processing:
Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing
Samples have 104 to 131 million pass filter reads with more than 91% of bases above the quality score of Q30.
Reads were aligned to the mm10 genome using STAR.
The mapping statistics are calculated using Picard software.
Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility.
Gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw count for each samples

source_name: Thymus

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
Samples were sequenced on HiSeq4000 using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing.

value: Thymus

value: iNKT cells

value: WT BALB/c


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_RNA_rep1

description: Library name: Sample 102


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_ATAC_rep3

description: Library name: Sample 107


title: PBMC; SeqWell; Animal T537; Timepoint chronic; Array A3

description:
Library name: T537_chronic_A3
T537_chronic_A3

value: PBMC

value: SeqWell

value: yes


title: Mouse NKT1 CD4 negative, thymocytes, rep3

description: Library name: Sample_R4NKT1_4N


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_RNA_rep3

description: Library name: Sample 101

value: Hepatocyte


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_ATAC_rep2

description: Library name: Sample 106


title: PBMC; SeqWell; Animal T537; Timepoint acute; Array all

description:
Library name: T537_acute_undetermined
T537_acute_undetermined

value: acute

value: all


title: PBMC; SeqWell; Animal T627; Timepoint acute; Array A3

description:
Library name: T627_acute_A3
T627_acute_A3


title: Mouse NKT1 CD4 negative, thymocytes, rep2

description: Library name: Sample_6_NKT1_pt4N_3


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_RNA_rep2

description: Library name: Sample 100

value: Control


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_ATAC_rep1

description: Library name: Sample 105


title: PBMC; SeqWell; Animal T537; Timepoint ART3; Array 2B; techrep2; NextSeq500

description:
Library name: T537_ART3_B1_2B_techrep2
T537_ART3_B1_2B


title: Mouse NKT1 CD4 negative, thymocytes, rep1

description: Library name: Sample_4_NKT1_pt4N_1


title: Gpt2 WT mice sample3 (H3K9me3 ChIP)

city: Dallas

first: Samuel

last: McBrayer

state: Texas

address: 5901 Forest Park Road

department: Children’s Research Institute

institute: University of Texas Southwestern Medical Center

description: Library name: K9me3-WT-3

data_processing:
Fastq files were trimmed with TrimGalore (v.0.6.10), and quality control was performed both before and after trimming using FastQC (v.0.12.1). ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2 (v.2.5.1). The sam files were converted to bam files by Samtools (v.1.6). PCR duplicates were removed with PicardTools (v.3.0). The signal is normalized by the spike in values of the ChIP and Input samples. We chose Macs2 (v.2.2.9.1) to call the peaks using the broad peaks setting for H3K9me3 and H3K27me3 (FDR < 0.1); we used the narrow peaks for H3K4me3 (FDR < 0.1) in the analysis. ChIP-seq peaks that were significantly increased or decreased in the Gpt2 KO mice were then identified using the DiffBind (v.3.16.0) package in R (v.4.2). Bigwig files for heatmap generation were created from bam files using the bamCoverage function in deepTools. For visualization, representative track diagrams were generated using the Integrated Genomics Viewer (IGV) (v.2.9.4).
Assembly: mm10
Supplementary files format and content: bigWig (except input samples)

source_name: Brain

extract_protocol:
About 20 mg brain tissue for each sample and histone mark were lysed by TissueLyser (Qiagen), then cross-linked with 1% formaldehyde in PBS for 10 minutes at room temperature. Cross-linking reactions were quenched with glycine for 5 minutes, followed by washes in cold PBS. The crosslinked tissue was homogenized using a cooled blade homogenizer in homogenization buffer (50 mM Tris-HCl pH 7.5, 1% Nonidet P-40, 0.25% deoxycholic acid, 1 mM EDTA). Then, cells were lysed with Farnham Buffer (5 mM PIPES, pH 8.0, 85 mM KCl, 0.5% Nonidet P-40, 1 mM DTT, 0.1 mM PMSF) and followed by SDS Lysis Buffer (50 mM Tris-HCl pH 7.9, 10 mM EDTA, 1% SDS, 1 mM DTT) to obtain soluble chromatin. Chromatin was sheared using a Covaris M220 Focused-ultrasonicator to generate DNA fragments approximately 200 to 400 bp in size, as verified by gel electrophoresis. The sonicated chromatin was centrifuged at maximum speed in a microcentrifuge for 1 minute at 4°C to remove insoluble debris. The soluble chromatin supernatant was diluted 1:9 with Dilution Buffer (20 mM Tris-HCl pH 7.9, 300 mM NaCl, 2 mM EDTA, 0.5% Triton X-100, 1 mM DTT, 0.2 mM PMSF) supplemented with a protease inhibitor cocktail (Roche). The diluted chromatin was precleared with 20 μL/mL protein A-agarose beads (ThermoFisher Scientific) on a nutator for 1 hour at 4°C. After centrifugation at 1000g for 3 minutes at 4°C, the supernatant was reserved for immunoprecipitation and 24 ng of spike-in chromatin (Active Motif 53083) was added per sample, with 2% set aside as input DNA. For immunoprecipitation, antibodies used included 5 µl H3K9me3 (Abcam; AB8898; 1063771-1), 5 µl H3K4me3 (Active Motif; 39159) or 15 µl H3K27me3 (Cell Signaling; 9733), along with 2 μg of spike-in antibody (Active Motif 61686), which were bound to 50 μl protein G Dynabeads (Invitrogen). The mixture was incubated with precleared supernatant overnight at 4°C with rotation. The Dynabeads were washed sequentially with the following buffers: low-salt wash buffer (10 mM Tris-HCl, pH 8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl), high-salt wash buffer (10 mM Tris-HCl, pH 8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), LiCl wash buffer (10 mM Tris-HCl, pH 8, 1 mM EDTA, 1% NP-40, 1% Na-Deoxycholate, 250 mM LiCl), and a final wash with TE buffer containing 50 mM NaCl. Chromatin was eluted, incubated overnight at 65°C, and treated with RNase A and proteinase K. DNA was purified using the QIAquick PCR Purification Kit (Qiagen).
For library preparation, 3 ng of H3K4me3 ChIP DNA, 10 ng of H3K9me3 ChIP DNA, and 10 ng of H3K27me3 ChIP DNA were used with the NEBNext Ultra II DNA Library Preparation Kit for Illumina (New England Biolabs; NEB). Library quality was assessed using a High Sensitivity D5000 ScreenTape on an Agilent 2200 TapeStation and quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher). Libraries with unique adaptor barcodes were multiplexed and sequenced on an Illumina NextSeq 2000 platform (paired-end, 100 base pair reads), with a sequencing depth of 30 million reads per sample for H3K4me3 ChIP, 50 million reads for H3K9me3 ChIP, and 40 million reads per sample for H3K27me3 ChIP.

value: Brain

tag: chip antibody


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_RNA_rep1

description: Library name: Sample 99


title: kidney, no HPC, sham control, rep1

description: Library name: NS1

tag: tissue

value: kidney

value: WT

value: sham control


title: A549 cells, shRAD21, rep1

city: Beijing

first: Chu

last: Xiao

state: Beijing

address: Nanli panjiayuan, Chaoyang District, Beijing

department: Thoracic Surgery

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description:
Library name: RAD21 knockdown in A549, rep1
column name in raw_counts_shRAD21_shNC_samples.xls: A549_SH_4

data_processing:
Raw data of fastq format was processed by fastp to remove low quality reads and adaptor reads. The clean data was mapped to the hg38 reference genome by HISAT2 (v2.0.5). Then the read counts of genes were obtained by featureCounts (v1.5.0-p3).
Assembly: hg38
Supplementary files format and content: xls files include raw count values for each sample

growth_protocol: A549 and H358 lung adenocarcinoma cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 ℃.

extract_protocol:
The total RNA of cells was extracted with TRIzol regent (Invitrogen) and the qualities of RNA were evaluated with Qubit3.0 and Agilent 2100 bioanalyzer.
RNA libraries for RNA-seq were constructed using a VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme) following manufacturer's protocols.

value: lung adenocarcinoma cells

value: RAD21 knockdown

value: April, 2024


title: Mouse NKT1 CD4 positive, thymocytes, rep2

description: Library name: Sample_3_NKT1_pt4P_3

value: Thymus


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_RNA_rep3

description: Library name: Sample 98


title: PBMC; SeqWell; Animal T627; Timepoint ART2; Array A3

description:
Library name: T627_ART2_A3
T627_ART2_A3

tag: animalid


title: Gpt2 WT mice sample2 (H3K9me3 ChIP)

description: Library name: K9me3-WT-2


title: PBMC; SeqWell; Animal T537; Timepoint ART3; Array 1A; techrep 2; NextSeq500

description:
Library name: T537_ART3_B1_1A_techrep2
T537_ART3_B1_1A

tag: timepoint


title: PBMC; SeqWell; Animal T537; Timepoint ART2; Array A4

description:
Library name: T537_ART2_A4
T537_ART2_A4

tag: array


title: Mouse NKT1 CD4 positive, thymocytes, rep1

description: Library name: Sample_1_NKT1_pt4P_1

value: iNKT cells


title: Liver_AT3_3

description: Library name: Liver_AT3_3

value: liver

value: BALB/c

tag: Sex

value: male

value: cisplatin-induced acute liver injury


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_RNA_rep2

description: Library name: Sample 97

value: Hepatocyte


title: Gpt2 WT mice sample1 (H3K9me3 ChIP)

description: Library name: K9me3-WT-1


title: PBMC; SeqWell; Animal T537; Timepoint ART2; Array A3

description:
Library name: T537_ART2_A3
T537_ART2_A3

value: PBMC

tag: assay

value: SeqWell

tag: hassiv

value: yes


title: Ventricle, TAB, Rep3

city: Iowa City

first: Chad

middle: E

last: Grueter

state: IA

address: 169 Newton Rd, 4332 PBDB

department: Internal Medicine

institute: University of Iowa

description:
Library name: Sample 7
TAB-B322FPKM

data_processing:
Raw sequence reads were analyzed with BaseSpace (Illumina) by trimming to 125bp and aligning reads to the mus musculus mm10 genome using the TopHat Alignment app.
Alignments were uploaded into the Cufflinks Assembly and DE  (BaseSpace, Illumina)
Assembly: UCSC mm10
Supplementary files format and content: FPKMs for all samples in xlsx

source_name: Ventricular Lysate

extract_protocol:
Total RNA was isolated using Tri-zol (invitrogen) according to the manufacturer's protocol.
PolyA-Enriched stranded RNA libraries were generated by the University of Iowa Institute of Human Genetics.

treatment_protocol: Eight-week-old male mice were anesthetized with isoflurane. The aorta was exposed, and constriction was performed using a 7-0 nylon suture tied against a 27-gauge needle. Sham operated animals underwent anesthesia and aorta exposure, but the suture was not ligated.

value: Ventricular Lysate

value: Trans-aortic Banding

value: Male

tag: age

value: 12 Weeks


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_RNA_rep1

description: Library name: Sample 96


title: Gpt2 KO mice sample3 (H3K9me3 ChIP)

description: Library name: K9me3-KO-3

value: Brain


title: PBMC; SeqWell; Animal T537; Timepoint ART2; Array A2

description:
Library name: T537_ART2_A2
T537_ART2_A2

tag: onart

tag: weekssinceinfection

tag: weeksonart


title: PBMC; SeqWell; Animal T627; Timepoint ART2; Array A1

description:
Library name: T627_ART2_A1
T627_ART2_A1


title: Ventricle, TAB, Rep2

description:
Library name: Sample 6
TAB-B321FPKM

tag: treatment


title: Gpt2 KO mice sample2 (H3K9me3 ChIP)

description: Library name: K9me3-KO-2

tag: genotype


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_RNA_rep3

description: Library name: Sample 95

tag: cell line

tag: cell type

value: Control


title: PBMC; SeqWell; Animal T537; Timepoint ART2; Array A1

description:
Library name: T537_ART2_A1
T537_ART2_A1


title: Ventricle, TAB, Rep1

description:
Library name: Sample 5
TAB-B319FPKM


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_RNA_rep2

description: Library name: Sample 94


title: Gpt2 KO mice sample1 (H3K9me3 ChIP)

description: Library name: K9me3-KO-1


title: Ventricle, Sham, Rep4

description:
Library name: Sample 4
Sham-B328FPKM

value: Sham


title: PBMC; SeqWell; Animal T537; Timepoint ART1; Array A1

description:
Library name: T537_ART1_A1
T537_ART1_A1


title: Gpt2 WT mice sample3 (H3K4me3 ChIP)

description: Library name: K4me3-WT-3


title: Mouse_Liver_4W_B2_minus_AhR_ChIP_Input_3

description: Library name: Sample 152

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.
FASTQ files were mapped to the hg38 human or mm10 mouse reference genome with Bowtie2 using default parameters. Alignment files were processed using HOMER. Peaks were called by combining replicate conditions and using HOMER (findPeaks) using parameters “-style factor -size 200”.
Assembly: hg38 or mm10
Supplementary files format and content: Peak files (BED format)

extract_protocol:
For ChIP-seq, crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1× protease inhibitor cocktail), and centrifuged at 1,000 × g for 5 min at 4°C to obtain a nuclear fraction.
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described58 with modifications as follows. For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde in PBS for 10 min at room temperature. For AhR and C/EBPα ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min. The crosslinking reaction was quenched by 0.125 M glycine (Sigma-Aldrich). Cells were washed once with ice-cold PBS and pelleted at 1,000 × g for 5 min at 4°C. Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1× protease inhibitor cocktail), and centrifuged at 1,000 × g for 5 min at 4°C to obtain a nuclear fraction. Nuclear pellets were resuspended in 100 µl of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1× protease inhibitor cocktail, for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1× protease inhibitor cocktail, for AhR and C/EBPα ChIPs). Chromatin DNA was sonicated in a 0.2 ml microtube (Diagenode) using a Bioruptor® Pico sonication device (30 sec ON / 30 sec OFF cycles) for 10 min at 4°C. Samples were centrifuged at 15,000 rpm for 10 min at 4C, and the supernatant was used for immunoprecipitation. LB3 lysate was diluted 1.1-fold with 10% Triton X-100. 1% of the lysate was kept as ChIP input. The lysates were rotated with each antibody pre-bound to 20 µl of beads (10 µl of Dynabeads protein A (Thermo Fisher Scientific) + 10 µl of Dynabeads protein G (Thermo Fisher Scientific)) overnight at 4°C. After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1× protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1× protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1× protease inhibitor cocktail), and then resuspended in 25 µl of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20). The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions. DNA in 46.5 µl of NEB reactions was revers crosslinked by adding 4 µl of 10% SDS, 4.5 µl of 5 M NaCl, 3 µl of 500 mM EDTA, 1 µl of 20 mg/ml proteinase K and 20 µl of water by incubation for 1 hr at 55°C, and then 30 min at 65°C. DNA was purified with 2 µl of SpeedBeads in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 µl of TT. The eluted DNA was amplified for 14 cycles in 50 µl of PCR reactions using NEBNext High-Fidelity 2× PCR Master Mix (NEB) and 0.5 mM each of primers Solexa 1GA and Solexa 1GB. The amplified libraries were purified with 2 µl of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 µl of TT, size selected using PAGE/TBE gel for 225-325 bp fragments by gel extraction, and single-end sequenced on NextSeq 2000 or NovaSeq X Plus (Illumina). ChIP input material (1% of sheared DNA) in 46.5 µl of TE was revers crosslinked by adding 4 µl of 10% SDS, 4.5 µl of 5 M NaCl, 3 µl of 500 mM EDTA, 1 µl of 20 mg/ml proteinase K and 20 µl of water by incubation for 1 hr at 55°C, and then 30 min at 65°C. The input DNA was purified with SpeedBeads as described above, and eluted with 25 µl of TT. The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.

value: Liver

tag: batch


title: PBMC; SeqWell; Animal T530; Timepoint chronic; Array A4

description:
Library name: T530_chronic_A4
T530_chronic_A4

value: chronic

value: no


title: Ventricle, Sham, Rep3

description:
Library name: Sample 3
Sham-B327FPKM


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_RNA_rep1

description: Library name: Sample 93


title: Ventricle, Sham, Rep2

description:
Library name: Sample 2
Sham-B325FPKM


title: PBMC; SeqWell; Animal T530; Timepoint chronic; Array A3

description:
Library name: T530_chronic_A3
T530_chronic_A3


title: Gpt2 WT mice sample2 (H3K4me3 ChIP)

description: Library name: K4me3-WT-2

tag: chip antibody


title: Mouse_Liver_4W_B2_minus_AhR_ChIP_Input_2

description: Library name: Sample 151

tag: tissue


title: PBMC; SeqWell; Animal T530; Timepoint acute; Array A3

description:
Library name: T530_acute_A3
T530_acute_A3

tag: animalid

value: acute


title: Gpt2 WT mice sample1 (H3K4me3 ChIP)

description: Library name: K4me3-WT-1


title: Ventricle, Sham, Rep1

description:
Library name: Sample 1
Sham-B324FPKM


title: Mouse_Liver_4W_B2_minus_AhR_ChIP_Input_1

description: Library name: Sample 150


title: Gpt2 KO mice sample2 (H3K4me3 ChIP)

description: Library name: K4me3-KO-2


title: PBMC; SeqWell; Animal T530; Timepoint acute; Array A2

description:
Library name: T530_acute_A2
T530_acute_A2

tag: timepoint


title: D30 Cl13 YFP- rep1

first: Zixuan

last: Zhao

address: Shuangqing road 30

institute: Tsinghua University

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4.
The clean reads were aligned to mm10 by bowtie2 with default parameter, and uniquely mapping reads were summarized by featureCounts (from Subread package).
FPKM (Fragments Per Kilobase of exon model per Million mapped reads) were calculated using RSEM
Differentially expressed genes (DEGs) were identified by at least two-fold changes and a false discovery rate (FDR) adjusted P value of 0.05 by using DESeq2.
Assembly: mm10
Supplementary files format and content: txt file for storing FPKM values for RNA-seq data

source_name: Spleen

growth_protocol: VFP+ and VFP-, YFP+ and YFP- activated (CD44+) CD8+ T cells were isolated at D5 and D30 post LCMV-Armstrong or LCMV-Cl13 infections using flow cytometry followed by RNA extraction and sequencing.

extract_protocol:
Total RNA was extracted from sorted cells using TRIzol (Invitrogen, cat#15596018) according to the manufacturer’s protocol.
RNA-seq library was constructed for deep sequencing by BGI Genomics

treatment_protocol: 2×10^5 plaque-forming units (p.f.u.) of LCMV Armstrong viruses were injected intraperitoneally, and 2×10^6 p.f.u. of LCMV Cl13 were injected intravenously into 6-8-week-old IL-21-VFP mice and IL-21cre-RosaYFP mice, respectively. Cells were sorted out on day 5 and day 30 post-infections for RNA extraction and sequencing

value: Spleen

value: CD8 T cells


title: Gpt2 KO mice sample1 (H3K4me3 ChIP)

description: Library name: K4me3-KO-1


title: Mouse_Liver_4W_Control_AhR_ChIP_Input_3

description: Library name: Sample 149


title: D30 Cl13 YFP+ rep1


title: Mouse_Liver_4W_Control_AhR_ChIP_Input_2

description: Library name: Sample 148


title: Gpt2 WT mice sample2 (H3K27me3 ChIP)

description: Library name: K27me3-WT-2


title: PBMC; SeqWell; Animal T530; Timepoint ART2; Array A4

description:
Library name: T530_ART2_A4
T530_ART2_A4

tag: array


title: PBMC; SeqWell; Animal T530; Timepoint ART2; Array A1

description:
Library name: T530_ART2_A1
T530_ART2_A1


title: Mouse_Liver_4W_Control_AhR_ChIP_Input_1

description: Library name: Sample 147


title: Gpt2 WT mice sample1 (H3K27me3 ChIP)

description: Library name: K27me3-WT-1


title: D30 Armstrong YFP- rep1

value: LCMV-Armstrong


title: D30 Armstrong YFP+ rep1


title: PBMC; SeqWell; Animal T530; Timepoint ART1; Array A4

description:
Library name: T530_ART1_A4
T530_ART1_A4

value: PBMC


title: Mouse_Liver_4W_B2_minus_AhR_ChIP_3

description: Library name: Sample 146

value: AhR


title: D5 Cl13 YFP- rep2


title: Gpt2 KO mice sample2 (H3K27me3 ChIP)

description: Library name: K27me3-KO-2


title: PBMC; SeqWell; Animal T530; Timepoint ART1; Array A3

description:
Library name: T530_ART1_A3
T530_ART1_A3

value: SeqWell

value: yes


title: Mouse_Liver_4W_B2_minus_AhR_ChIP_2

description: Library name: Sample 145


title: PBMC; SeqWell; Animal K237; Timepoint baseline; Array A4

description:
Library name: K237_baseline_A4
K237_baseline_A4

value: baseline


title: D5 Cl13 YFP- rep1


title: Gpt2 KO mice sample1 (H3K27me3 ChIP)

description: Library name: K27me3-KO-1


title: Mouse_Liver_4W_B2_minus_AhR_ChIP_1

description: Library name: Sample 144


title: PBMC; SeqWell; Animal K237; Timepoint baseline; Array A2

description:
Library name: K237_baseline_A2
K237_baseline_A2


title: Gpt2 WT mice sample3 (Input)

description: Library name: Input-WT-3

value: Input


title: Mouse_Liver_4W_Control_AhR_ChIP_3

description: Library name: Sample 143


title: D5 Cl13 YFP+ rep2


title: Gpt2 WT mice sample2 (Input)

description: Library name: Input-WT-2


title: PBMC; SeqWell; Animal J400; Timepoint baseline; Array A3

description:
Library name: J400_baseline_A3
J400_baseline_A3


title: Mouse_Liver_4W_Control_AhR_ChIP_2

description: Library name: Sample 142


title: Gpt2 WT mice sample1 (Input)

description: Library name: Input-WT-1


title: D5 Armstrong YFP- rep2


title: D5 Cl13 YFP+ rep1


title: PBMC; SeqWell; Animal J400; Timepoint baseline; Array A2

description:
Library name: J400_baseline_A2
J400_baseline_A2


title: Mouse_Liver_4W_Control_AhR_ChIP_1

description: Library name: Sample 141


title: Gpt2 KO mice sample3 (Input)

description: Library name: Input-KO-3


title: D5 Armstrong YFP- rep1


title: PBMC; SeqWell; Animal GCC6; Timepoint baseline; Array A4

description:
Library name: GCC6_baseline_A4
GCC6_baseline_A4


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_H3K27ac_ChIP_rep3

description: Library name: Sample 128

value: Hepatocyte


title: Gpt2 KO mice sample2 (Input)

description: Library name: Input-KO-2

value: Brain


title: PBMC; SeqWell; Animal GCC6; Timepoint baseline; Array A3

description:
Library name: GCC6_baseline_A3
GCC6_baseline_A3


title: D5 Armstrong YFP+ rep2


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_H3K27ac_ChIP_rep2

description: Library name: Sample 127


title: Gpt2 KO mice sample1 (Input)

description: Library name: Input-KO-1


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cre_H3K27ac_ChIP_rep1

description: Library name: Sample 126


title: Respiratory Sample RS30 - ENDS users

city: Beirut

first: AUB

last: Submission

address: Bliss street

country: Lebanon

institute: American University of Beirut

description: Library name: RS30

data_processing:
Adapters trimmed using TrimGalore.
Reads denoised and ASVs generated using DADA2 in QIIME2.
Taxonomy assigned using Greengenes 2024.09 in QIIME2.
Diversity metrics computed with QIIME2 core-metrics workflow.
Plots generated using R and GraphPad
Assembly: Greengenes 2024.09
Supplementary files format and content: TSV files with ASVs, taxonomy, and diversity data

Library strategy: 16S rRNA-seq

source_name: Sputum sample

extract_protocol:
Sputum Samples were extracted using the Pathogen DNA kit
16S V3–V4 region amplified and indexed using Zymo Quick-16S™ kit; sequenced on Illumina MiSeq.

value: Sputum sample

tag: sample group

value: ENDS users


title: D5 Armstrong YFP+ rep1


title: D5 Cl13 VFP- rep2


title: bulk RNAseq ES TET-TKO

city: Jerusalem

first: Shlomtzion

last: Lahav

address: Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: cells lacking all three TET proteins (TET-TKO)

data_processing:
Basecalls were performed using illumina nextseq and bcl2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using Bismark and bowtie
Data were aligned paired ended (PE)
Single CpGs were extracted using Bismark_methylation_extractor program.
We applied HOMER to find peaks and used bedtools to intersect peaks with reads
We counted the number of methylated vs. non methylated CpGs within 200-bp bins.
Single cell RNA-Seq aligned to mm10 followed by in-house perl pipeline to produce single cell matrix
Assembly: mm9 (ChIP) and mm10 (RNA)
Supplementary files format and content: peaks
Supplementary files format and content: segements of 200bp
Supplementary files format and content: segements of 200bp relative to TSS
Supplementary files format and content: segements of 200bp with methylated vs. non methylated CpGs
Supplementary files format and content: matirx files

growth_protocol: ESCs were grown on 0.1% gelatin-coated dishes and maintained in DMEM with 15% ESC-grade fetal calf serum, 50 μg/mL penicillin, 50 μg/mL streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1000 U/ml LIF, supplemented with 1 μM PD0325901, an inhibitor of the MEK/ERK pathway, and 3 μMCHIR99021, an inhibitor of GSK3. For retinoic acid-induced differentiation, cells were grown on 0.1% gelatin-coated dishes for 2/5 days in DMEM with 10% ESC-grade fetal calf serum, 50 μg/mL penicillin, 50 μg/mL streptomycin, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1 μM retinoic acid. For XEN differentiation, cells were grown on 0.1% gelatin-coated dishes for 9 days in RPMI 1640 with 15% ESC-grade fetal calf serum, 0.1 mM β-mercaptoethanol, Penicillin/Streptomycin 100 U/mL, 2 mM L-glutamine, 1 mM sodium pyruvate, 0.1 mM nonessential amino acids, 10 ng/mL Activin A and 0.1 μM retinoic acid.

extract_protocol:
For ChIP and ChIP-BS: cells were lysed, treated with MNAse, and histone-DNA complexes were isolated with antibody. For bulk RNA:mRNA extraction was performed using Invitrogen Dynabeads mRNA DIRECT Purification Kit (61011) according to the manufacturer’s protocol. For scRNA: cells were collected into  reverse transcription/lysis buffer mix.
For ChIP-BS libraries: DNA samples were converted to blunt-ended, phosphorylated DNA using End-It™ DNA End-Repair Kit. DNA was purified using ratio of 1:1.8 sample: AMPure XP beads. An adenosine was added to the 3’ end of the DNA fragments using Klenow (3’-5’ exo-) (New England Biolabs, M0212L). DNA was purified using ratio of 1:1.8 sample:AMPure XP beads. Methylated adapters were added by ligation using DNA ligase (New England Biolabs, M2200S). DNA was purified using ratio of 1:1.2 sample:AMPure XP beads. Next the DNA was subjected to bisulfite conversion using the EZ DNA Methylation Gold kit (Zymo Research) according to the manufacturer’s instructions. The bisulfite-converted DNA samples were amplified using KAPA HiFi HotStart Uracil (KK2801) with 25 μM full-length primer mix containing Illumina library indices for multiplexing. Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads and eluted in 10 mM Tris-HCl [pH 8]. Library fragments were selected and isolated using the PureLink DNA gel extraction kit (Invitrogen). The resulting libraries had an average size of 350-550 bp. For ChIP libraries: 10ng DNA samples were converted to blunt ended, phosphorylated DNA using the End-It DNA End-Repair Kit (Lucigen). DNA was purified using ratio of 1:1.8 sample to AMPure XP beads. Adenosine was added to the 3’ end of the DNA fragments using Klenow (3’-5’ exo-) (New England Biolabs). DNA was purified using ratio of 1:1.6 sample to AMPure XP beads. Adapters containing Illumina library indices for multiplexing were 20 Article Title added (P7-index-PE2 and P5-PE1 long primers) by ligation using DNA ligase (New England Biolabs). DNA was purified using ratio of 1:1.2 sample to AMPure XP beads. DNA samples were amplified using KAPA HiFi HotStart (Roche) with 25μM primers (P7 and P5-PE1 short primers). Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads and eluted in 22μℓ 10mM Tris-HCl [pH 8]. Resulting libraries were run in a 2% agarose gel, and the desired 250–600 bp DNA library fragments were selected and isolated using the PureLink DNA gel extraction kit (Invitrogen). For bulk RNA libraries:  500ng mRNA samples were fragmented using RNA Fragmentation Reagents (Thermo, AM8740) by combining 9μl of sample with 1μl of RNA fragmentation reagent and incubating at 70 °C for 2 min. The sample was transferred to ice, and 40μl fragmentation stop mix containing 5μl fragmentation stop solution and 35μl 10mM Tris- HCl [pH 8] was added. Fragmented RNA was purified with 1.5x reaction volume of AMPure XP beads and eluted in 10μl 10mM Tris- HCl [pH 8]. The fragmented RNA was reverse transcribed using an oligo dT Primer as follows: First, 10μl RNA was mixed with 2μl of 50μM oligo dT primer (IDT) and 1μl of 25mM dNTP mix (NEB). The sample was incubated for 5 min at 65 °C and transferred to ice. The following components were added to the reaction to a total volume of 20μl: 4μl of 5x First-Strand SuperScript III buffer (Thermo), 2μl of 0.1M DTT (Thermo), 1μl murine RNase inhibitor (NEB), and 1μl of 200 U/μl Super-Script III reverse transcriptase (Thermo) and the sample was incubated for 1 hour at 50 °C 15 minutes at 70 °C. cDNA was purified with 1.5x reaction volume of AMPure XP beads and eluted in 17μl 10mM Tris- HCl [pH 8]. For second-strand synthesis, 17μl were combined with 2μl second-strand synthesis (SSS) buffer and 1μl of SSS enzyme mix from the NEBNext mRNA Second Strand Synthesis Module (NEB) and incubated at 16 °C for 2.5 h, followed by 20 min at 65 °C. cDNA was purified with 1.2x reaction volume of AMPure XP beads and eluted in 14μl 10mM Tris- HCl [pH 8]. DNA samples were converted to blunt-ended, phosphorylated DNA using the End-It DNA End-Repair Kit (Lucigen). DNA was purified using 1.8x reaction volume of AMPure XP beads.  Adenosine was added to the 3’ end of the DNA fragments using Klenow (3’-5’ exo-) (New England Biolabs). DNA was purified using 1.6x reaction volume of AMPure XP beads. Adapters containing Illumina library indices for multiplexing (P7-index-PE2 and P5-PE1 long primers) were added by ligation using DNA ligase (New England Biolabs). DNA was purified using 0.7x reaction volume of AMPure XP beads. The DNA samples were amplified using KAPA HiFi HotStart (Roche) with 25μM primers (P7 and P5-PE1 short primers). Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads and eluted in 22μl 10mM Tris-HCl [pH 8]. Resulting libraries were run in a 2% agarose gel, and the desired 250–600 bp DNA library fragments were selected and isolated using a PureLink DNA gel extraction kit (Invitrogen). For scRNA libraries: The reverse transcription/lysis mix consisted of 180 μL of 5X First-Strand buffer (Invitrogen), 27 μL 10% (v/v) IGEPAL CA-630 (Sigma), 18 μL 25 mM dNTPs (NEB), 30 μL 0.1 M DTT (Invitrogen), 45 μL 1 M Tris-HCl [pH 8.0] (Biological Industries), 30 μL murine RNase inhibitor (NEB), 45 μL SuperScript III reverse transcriptase (200 U/μL, Invitrogen), and 75 μL nuclease-free water (Biological Industries) in a total volume 450 μL. The carrier oil was HFE-7500 with 3% (w/w) fluorosurfactant (RAN Biotechnologies. The collection tubes were exposed to 6.5 J/cm2of 365-nm UV light for 10 min to release photocleavable barcoding primers from the barcoding beads. Next, the collection tubes containing the UV-exposed emulsions were transferred to a reverse transcription reaction at 50°C for 2 h followed by 15 min at 70°C. Each sample was demulsified by addition of 50 μL perfluoro-1-octanol (Sigma) to release the barcoded cDNA from the droplets. To remove unused primers and primer dimers, the upper, aqueous phase containing the barcoded cDNA (~50 μL) was combined with 50 μL digestion mix containing 5 μL ExoI enzyme (NEB), 5 μL HinFI enzyme (NEB), 5 μL ExoI buffer (NEB), 5 μL CutSmart buffer (NEB), and 30 μL of nuclease-free water and incubated for 1 h at 37°C and 10 min at 80°C. The reaction product was purified with 1.5x reaction volume of AMPure XP beads and eluted in 13.5 μL TE buffer (10 mM Tris–HCl [pH 8.0], 0.1 mM EDTA). For second-strand synthesis, 13.5 μL digestion reaction product was combined with 1.5 μL second-strand synthesis (SSS) buffer and 1 μL of SSS enzyme mix from the NEBNext mRNA Second Strand Synthesis Module (NEB) and incubated at 16°C for 2.5 h, followed by 20 min at 65°C. For in vitro transcription, SSS reaction products (16 μL) were combined with 24 μL HiScribe T7 High Yield RNA Synthesis Kit (NEB) reagent mix containing 4 μL T7 Buffer, 4 μL ATP, 4 μL CTP, 4 μL GTP, 4 μL UTP, and 4 μL T7 enzyme mix. The reaction was incubated at 37°C for 13 h, and the resulting RNA was purified with 1.3x reaction volume of AMPure XP beads and eluted with 20 μL TE buffer. RNA was fragmented using RNA fragmentation kit (Ambion), and 9 μL of this sample was combined with 1 μL of RNA fragmentation reagent and incubated at 70°C for 2 min. The sample was transferred to ice, and 40 μL fragmentation stop mix containing 5 μL fragmentation stop solution and 35 μL TE buffer was added. Fragmented RNA was purified with 1.3x reaction volume of AMPure XP beads and eluted in 10 μL TE buffer. The resulting amplified and fragmented RNA was reverse transcribed using a random hexamer primer as follows: First, 10 μL RNA was mixed with 2 μL of 100 μM PvG748-SBS12-RT random hexamer primer (IDT) and 1 μL of 10 mM dNTP mix (NEB). The sample was incubated for 3 min at 65°C and transferred to ice. The following components were added to the reaction to a total volume of 20 μL: 4 μL of 5x First-Strand SuperScript III buffer (Invitrogen), 1 μL of 0.1 M DTT (Invitrogen), 1 μL murine RNase inhibitor (NEB), and 1 μL of 200 U/μL SuperScript III reverse transcriptase (Invitrogen). The resulting cDNA was purified with 1.2x reaction volume of AMPure XP beads and eluted in 11.5 μL TE buffer. The resulting libraries were PCR amplified using standard PE1/PE2 full-length primer mix containing Illumina library indices for multiplexing. Each PCR reaction contained 11.5 μL post-RT cDNA library, 12.5 μL 2x KAPA HiFi HotStart PCR mix (Kapa Biosystems), and 1 μL of 25 μM PE1/PE2 index primer mix. Amplification was performed in 14 cycles. Amplified libraries were purified using 0.7x reaction volume of AMPure XP beads and eluted in 30 μL nuclease-free water. Aliquots of 15 μL of each resulting library were run in 2% agarose gels, and 200–700 bp DNA library fragments were isolated using PureLink DNA gel extraction kit (Invitrogen).  For all libraries quality was confirmed using an Agilent 2200 TapeStation nucleic acids system and an Agilent High Sensitivity D1000 DS DNA kit. Size-selected libraries were diluted to 4nM concentration and combined for paired-end, single index sequencing on the Illumina NextSeq 550 and 2000 instrument using an Illumina 550 High Output v2 (75 cycles) kit or NextSeq 1000/2000 P2 Reagents (100 Cycles) v3 kit. Cycle distribution was 45 cycles for Read 1, 35 cycles for Read 2, and 8 cycles for the library index read or 50 cycles for Read 1, 70 cycles for Read 2, and 8 cycles for the library indexes reads for Illumina 2000.

value: embryonic stem cells (ESCs)

tag: agent

value: 2i LIF


title: Respiratory Sample RS29 - Non-ENDS users

description: Library name: RS29

value: Non-ENDS users


title: bulk RNAseq ES WT

value: WT


title: Respiratory Sample RS28 - ENDS users

description: Library name: RS28


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_H3K27ac_ChIP_rep3

description: Library name: Sample 125

value: Control


title: D5 Cl13 VFP- rep1

value: Spleen

value: CD8 T cells


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_H3K27ac_ChIP_rep2

description: Library name: Sample 124


title: scRNAseq day5 TET-TKO Mix rep2

description: TET-TKO cells co-cultured with WT ESCs for 3 days

value: TET-TKOMix

value: RA based Differntiated ESCs

value: RA

tag: time point

value: 5 days


title: Respiratory Sample RS27 - ENDS users

description: Library name: RS27


title: D5 Cl13 VFP+ rep2


title: Respiratory Sample RS26 - ENDS users

description: Library name: RS26


title: scRNAseq day5 TET-TKO Mix rep1


title: A549 cells, EV, rep1

description:
Library name: Control A549 cells of OE, rep1
column name in raw_counts_RAD21OE_EV_samples.xls: A549_Ctrl_1

value: lung adenocarcinoma cells

value: wild type


title: AhR_flox_Hepatocyte_Cont_Ad_Cre_H3K27ac_ChIP_rep1

description: Library name: Sample 123

value: Hepatocyte


title: D5 Cl13 VFP+ rep1


title: scRNAseq day5 TET-TKO rep2

value: TET-TKO


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_H3K27ac_ChIP_rep3

description: Library name: Sample 122


title: Respiratory Sample RS25 - Non-ENDS users

description: Library name: RS25

value: Sputum sample


title: D5 Armstrong VFP- rep2

value: LCMV-Armstrong


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_H3K27ac_ChIP_rep2

description: Library name: Sample 121


title: Respiratory Sample RS24 - Non-ENDS users

description: Library name: RS24


title: D5 Armstrong VFP- rep1


title: scRNAseq day5 TET-TKO rep1


title: scRNAseq day5 WT rep2


title: D5 Armstrong VFP+ rep2


title: AhR_flox_Hepatocyte_B2_minus_Ad_Cont_H3K27ac_ChIP_rep1

description: Library name: Sample 120


title: Respiratory Sample RS23 - Non-ENDS users

description: Library name: RS23


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_H3K27ac_ChIP_rep3

description: Library name: Sample 119


title: scRNAseq day5 WT rep1


title: Respiratory Sample RS22 - Non-ENDS users

description: Library name: RS22


title: D5 Armstrong VFP+ rep1


title: scRNAseq day2 TET-TKO rep2

value: 2 days


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_H3K27ac_ChIP_rep2

description: Library name: Sample 118


title: AhR_flox_Hepatocyte_Cont_Ad_Cont_H3K27ac_ChIP_rep1

description: Library name: Sample 117


title: Respiratory Sample RS21 - Non-ENDS users

description: Library name: RS21


title: Respiratory Sample RS20 - Non-ENDS users

description: Library name: RS20


title: scRNAseq day2 TET-TKO rep1


title: TRI_H2228_3

city: Lexington

first: Andrew

last: Conery

address: 1050 Waltham St. Suite 301

institute: Triana Biomedicines

description:
Library name: 18
column name in TPM_values.csv:X18

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1. UMI-based de-duplication was performed using fastp v.0.23.1 simultaneously. Trimmed and de-duplicated reads were then mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the customer-defined groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison. Below are the results of the number of significantly differentially expressed genes for all comparisons provided.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: csv file containing TPM values for each sample.

growth_protocol: RPMI 1640+10%FBS+1x antibiotic/antimycotic, 5% humidified CO2 incubator

extract_protocol:
Qiagen RNEasy mini kit with poly-A enrichment.
Twist NGS UMI Library Preparation Kit with mechanical fragmentation.

treatment_protocol: 0.8E06 cells were plated in 10 cm plates and incubated overnight. DMSO or 3 uM TRI-611 was added for 3 h and cells were pelleted and frozen.

value: NSCLC


title: TRI_H2228_2

description:
Library name: 17
column name in TPM_values.csv:X17


title: scRNAseq day2 WT rep2


title: Respiratory Sample RS19 - ENDS users

description: Library name: RS19

value: ENDS users


title: TRI_H2228_1

description:
Library name: 16
column name in TPM_values.csv:X16

value: WT


title: NRCMs cells, conditioned medium of ALOX5-/--BMMCs treated with TNF-a，repeat3

city: Chengdu

first: lingyu

last: li

address: Sichuan University West China Hospital

institute: Sichuan University

description: Library name: Sample 6

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: NRCMs

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: NRCMs

value: Neonatal Rat Cardiomyocytes


title: NRCMs cells, conditioned medium of ALOX5-/--BMMCs treated with TNF-a，repeat2

description: Library name: Sample 5


title: scRNAseq day2 WT rep1


title: Respiratory Sample RS18 - Non-ENDS users

description: Library name: RS18

value: Non-ENDS users


title: NRCMs cells, conditioned medium of ALOX5-/--BMMCs treated with TNF-a，repeat1

description: Library name: Sample 4


title: DMSO_H2228_3

description:
Library name: 15
column name in TPM_values.csv:X15

value: DMSO


title: H3K4me3 ESC TET-TKO Mix

value: TET-TKOMix

value: embryonic stem cells (ESCs)

value: 2i LIF


title: Respiratory Sample RS17 - ENDS users

description: Library name: RS17


title: DMSO_H2228_2

description:
Library name: 14
column name in TPM_values.csv:X14


title: NRCMs cells, conditioned medium of WT-BMMCs treated with TNF-a，repeat3

description: Library name: Sample 3


title: Respiratory Sample RS16 - ENDS users

description: Library name: RS16


title: H3K4me3 ESC TET-TKO


title: DMSO_H2228_1

description:
Library name: 13
column name in TPM_values.csv:X13


title: NRCMs cells, conditioned medium of WT-BMMCs treated with TNF-a，repeat2

description: Library name: Sample 2


title: H3K4me3 ESC WT


title: Respiratory Sample RS15 - Non-ENDS users

description: Library name: RS15


title: TRI_H3122_3

description:
Library name: 12
column name in TPM_values.csv:X12


title: NRCMs cells, conditioned medium of WT-BMMCs treated with TNF-a，repeat1

description: Library name: Sample 1


title: H3K27me3 ESC TET-TKO Mix


title: Respiratory Sample RS14 - Non-ENDS users

description: Library name: RS14


title: TRI_H3122_2

description:
Library name: 11
column name in TPM_values.csv:X11


title: WT_3

city: La Jolla

first: Stephanie

last: Cherqui

address: 9500 Gilman Drive

department: Department of Pediatrics

institute: University of California San Diego

description:
Library name: FJ140-C
Column name in raw_counts.xslx: FJ140-C

data_processing:
FASTQ files were aligned to the GRCm39 mouse genome supplemented with the human FXN sequence using STAR in quantification mode to generate gene-level counts
Assembly: GRCm39 + hFXN
Supplementary files format and content: Raw data counts per gene aligned to the genome

source_name: Cerebellum

extract_protocol:
mRNA was isolated from flash frozen cerebellum samples with PureLink RNA Mini Kit (Cat. #12-183-018A, ThermoFisher Scientific) according to manufacturer’s protocol.
RNA quality was assessed using Agilent Tapestation 4200 and 50ng of ribodepleted RNA with RNA Integrity Number (RIN) greater than 7.0 were used to generate RNA sequencing libraries using the Illumina stranded mRNA prep kit (Illumina) following manufacturer’s instructions. The resulting libraries were multiplexed and sequenced with paired end reads (PE150) to a depth of approximately 25 million reads per sample on NovaSeq X Plus and demultiplexed using bcl2fastaq conversion software.

treatment_protocol: HSPC Isolation: Bone marrow cells were flushed from the femurs and tibias of 8 – 12-week-old YG8JR mice. Sca1+ HSPCs were isolated by immunomagnetic separation HSPCs were electroporated using the Neon transfection system. mPPL-001 was generated by electroporating 1.1x10^6 cells in 90µL Buffer T, 1.8µM Alt R Cas9 electroporation enhancer and 10µL pre-prepared Ribonucleic Protein (RNP) solution. RNP complex contains 3µL SpyFi Cas9 Nuclease, 11µM each of sgRNA UP4 and sgRNA DN4 and 2µL Buffer T. Mock HSPCs were generated by electroporating 1.1x10^6 cells with 1.8µM Alt R Cas9 electroporation enhancer, 11µM sgRNA UP4 and DN4 in Buffer T without Cas9. 2.5 – 3.0-month-old recipient YG8JR mice were lethally irradiated (7Gy; X-Rad 320, PXi) 24-hours prior to stem cell infusion. Mice were injected with Mock HSPCs or mPPL-001 cells at a density of 1.5 – 1.75x10^6 cells per mouse via tail vein injection. A subset of Mock HSPCs and mPPL-001 were retained in culture in the post-electroporation Stemspan medium for 7-days to evaluate the on-target hFXN gene editing efficiency in the drug product delivered to YG8JR mice. Mice were maintained on antibiotic water containing Sulphamethoxazole and Trimethoprom (oral suspension) for 1-month post-transplant to prevent post-myeloablation infection.

value: Cerebellum

tag: age

value: 6 months post-transplant

value: A


title: H3K27me3 ESC TET-TKO


title: TRI_H3122_1

description:
Library name: 10
column name in TPM_values.csv:X10


title: Respiratory Sample RS13 - Non-ENDS users

description: Library name: RS13


title: WT_2

description:
Library name: FA354-C
Column name in raw_counts.xslx: FA354-C

value: B


title: H3K27me3 ESC WT


title: WT_1

description:
Library name: FA383-C
Column name in raw_counts.xslx: FA383-C


title: H3K27Ac day5 TET-TKO rep2

tag: antibody

value: TET-TKO

value: RA based Differntiated ESCs

value: RA

value: 5 days


title: DMSO_H3122_3

description:
Library name: 9
column name in TPM_values.csv:X9

value: NSCLC


title: Respiratory Sample RS12 - Non-ENDS users

description: Library name: RS12

value: Sputum sample


title: Respiratory Sample RS11 - Non-ENDS users

description: Library name: RS11


title: DMSO_H3122_2

description:
Library name: 8
column name in TPM_values.csv:X8

value: WT


title: YG8JR_3

description:
Library name: FA112-C
Column name in raw_counts.xslx: FA112-C

value: Untreated


title: Respiratory Sample RS10 - Non-ENDS users

description: Library name: RS10

value: Non-ENDS users


title: H3K27Ac day5 TET-TKO rep1

description: cells lacking all three TET proteins (TET-TKO)


title: DMSO_H3122_1

description:
Library name: 7
column name in TPM_values.csv:X7

value: DMSO


title: YG8JR_2

description:
Library name: FA281-C
Column name in raw_counts.xslx: FA281-C


title: Respiratory Sample RS9 - ENDS users

description: Library name: RS9

value: ENDS users


title: H3K27Ac day5 WT rep2


title: YG8JR_1

description:
Library name: FA491-C
Column name in raw_counts.xslx: FA491-C


title: TRI_SNU_3

description:
Library name: 6
column name in TPM_values.csv:X6


title: H3K27Ac day5 WT rep1


title: TRI_SNU_2

description:
Library name: 5
column name in TPM_values.csv:X5


title: YG8JR/Mock HSPC_4

description:
Library name: FA424-C
Column name in raw_counts.xslx: FA424-C

value: Mock


title: Respiratory Sample RS7 - ENDS users

description: Library name: RS7


title: H3K27Ac day2 TET-TKO rep2

value: 2 days


title: Respiratory Sample RS8 - ENDS users

description: Library name: RS8


title: TRI_SNU_1

description:
Library name: 4
column name in TPM_values.csv:X4


title: YG8JR/Mock HSPC_3

description:
Library name: FA585-C
Column name in raw_counts.xslx: FA585-C

value: Cerebellum


title: Respiratory Sample RS6 - ENDS users

description: Library name: RS6


title: H3K27Ac day2 TET-TKO rep1


title: YG8JR/Mock HSPC_2

description:
Library name: FA583-C
Column name in raw_counts.xslx: FA583-C

value: 6 months post-transplant


title: DMSO_SNU_3

description:
Library name: 3
column name in TPM_values.csv:X3


title: DMSO_SNU_2

description:
Library name: 2
column name in TPM_values.csv:X2


title: H3K27Ac day2 WT rep2


title: Respiratory Sample RS5 - ENDS users

description: Library name: RS5


title: YG8JR/Mock HSPC_1

description:
Library name: FA465-C
Column name in raw_counts.xslx: FA465-C


title: H3K27Ac day2 WT rep1


title: DMSO_SNU_1

description:
Library name: 1
column name in TPM_values.csv: X1


title: Tomato root, OE-CRP1-2, rep3

city: nanjing

first: hai

last: zhu

address: xiaolingwei Street 50th

institute: nanjing agricultural university

description: Library name: g6-root_3

data_processing:
Illumina Casava1.7 software used for basecalling. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.The clean paired-end reads were mapped to the Solanum lycopersicum reference genome assembly SL3.1 using HISAT2 (version 2.1.0). Gene expression levels were also quantified as fragments per kilobase of transcript per million mapped reads (FPKM). FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: Solanum lycopersicum reference genome assembly SL3.1.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample.

organism: Solanum lycopersicum

source_name: Root

extract_protocol:
Total RNA was extracted using the TRlzol reagent (Invitrogen, CA, USA) according to themanufacturer' s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer's instructions.

value: Root


title: Respiratory Sample RS3 - ENDS users

description: Library name: RS3


title: GB3

first: Chen

last: fei

address: Xiangyin road

institute: The Second Military Medical University

data_processing:
Perform quality assessment on the raw sequencing data through FastQC, align the valid data of samples to the reference genome using HISAT2, evaluate gene expression levels using StringTie and known gene models, conduct differential gene expression analysis using DESeq2, and visualize the results of differential expression analysis
Assembly: hg18
Supplementary files format and content: counts of genes

source_name: gallbladder

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA quality was measured by Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA) .
samples with an RNA integrity number over than 8 were used for subsequent experiments. The total RNA was further purified by digesting the double-stranded and single-stranded DNA with DNase I and remove of rRNA using Ribo-Zero method (human, mouse, plants) (Illumina, USA). The library construction and RNA sequencing were performed on a Illumina HiSeq 4000.

value: gallbladder

value: human gallbladder epithelial cells

value: chemical defined medium


title: YG8JR/mPPL-001_4

description:
Library name: FA586-C
Column name in raw_counts.xslx: FA586-C

value: Edited

value: A


title: YG8JR/mPPL-001_5

description:
Library name: FA584-C
Column name in raw_counts.xslx: FA584-C

value: B


title: Tomato root, OE-CRP1-2, rep2

description: Library name: g6-root_2


title: Respiratory Sample RS2 - ENDS users

description: Library name: RS2

value: Sputum sample


title: GB2

value: WT


title: Respiratory Sample RS1 - ENDS users

description: Library name: RS1


title: YG8JR/mPPL-001_3

description:
Library name: FA581-C
Column name in raw_counts.xslx: FA581-C


title: Tomato root, OE-CRP1-2, rep1

description: Library name: g6-root_1


title: GB1


title: YG8JR/mPPL-001_2

description:
Library name: FA379-C
Column name in raw_counts.xslx: FA379-C


title: Tomato root, WT, rep3

description: Library name: WT-root_3


title: K562 cells, early S-Phase (S2)

city: Boston

first: Annalisa

last: Di Ruscio

state: Massachusetts

address: 3 Blackfan Circle

institute: Harvard Medical School Initiative for RNA Medicine

description:
K562_S2
Cuff_Gene_Counts_S1_S2.csv

data_processing:
Visualization Pipeline for RNA-seq (VIPER) was used to analyze RNA-seq reads. Fastq files were aligned to hg19 reference genome using STAR aligner (2.7.0f) with default parameters
cufflinks v2.2.1 was used to generate FPKM values
bedtools (v2.27.1) genomecov and bedGraphToBigWig v 4 were used to convert Bam to bigwig
Assembly: hg19
Supplementary files format and content: comma-separated values file includes FPKM vaues for each sample
Supplementary files format and content: bigwig files contain genome-wide signal data for each sample

source_name: Blood

growth_protocol: K562 cells were cultured in DMEM (10% FBS).

extract_protocol:
RNA was extracted with TRI Reagent® (MRC). RNA samples were treated with DNase I: 10 U of DNase I (Roche) per 3 mg of total RNA; 37ºC for 1 hr in the presence of RNase A inhibitor. Nascent RNA capture was performed using Click-iT® Nascent RNA Capture Kit (ThermoFisher) according to the manufacturer’s instructions with minor modifications.
Transcriptome library construction (with BGI Genomics)

treatment_protocol: K562 cells were grown overnight to 70-80% confluence, washed twice with 1xPBS, and then cultured in DMEM (10% FBS) supplemented with 2.5 mM Thymidine for 18 hours (first block). Subsequently, Thymidine was washed out with 1xPBS, and the cells were cultured in DMEM (10% FBS). After 8 hours, the cells were treated with Thymidine again for 18 hours (second block). Cells were then released from the block. Synchrony was assessed by flow cytometry analysis of propidium iodide-stained cells using a LSRII flow cytometer (BD Biosciences). EU (5-ethynyl uridine) was used to label nasRNA at final concentration of 0.5mM (EU). Then cells were collected in 2hours (S1) and 5 hours (S2).

value: Blood

value: myelogenousleukemiacell

value: Cell Synchronization

tag: phase

value: early S-Phase (S2)

tag: fraction

value: nasRNA


title: Primary astrocytes, BHB treated 3

city: Xi'an

first: Sen

last: Shang

address: West Xianning Road

institute: Xi'an Jiaotong University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean in DESeq2 package
Differential gene expression by DEseq2 was performed on normalized gene counts
Assembly: Genome_build: rn6
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

organism: Rattus norvegicus

extract_protocol:
The cells were havested using RNeasy Micro Kit(QIAGEN), and the RNA was pufify by oligo-dT beads
RNA libraries were constructed by TruSeq RNA Library Preparation Kit v2 (Illumina)

value: Brain

value: Primary astrocytes

value: Astrocytes

tag: treatment

value: BHB


title: YG8JR/mPPL-001_1

description:
Library name: FA124-C
Column name in raw_counts.xslx: FA124-C

value: Cerebellum

value: 6 months post-transplant

tag: genotype


title: Tomato root, WT, rep2

description: Library name: WT-root_2

value: Root


title: K562 cells, early S-Phase (S1)

description:
K562_S1
Cuff_Gene_Counts_S1_S2.csv

tag: cell line

value: early S-Phase (S1)


title: Primary astrocytes, BHB treated 2

tag: cell type


title: FTO_OE_CS_rep3

city: nanning

first: Hai-Guang

last: Xu

address: shuangyong

institute: The First Affiliated Hospital of Guangxi Medical University

description:
Library name: Sample 6
Column name in gene.counts.matrix.txt: OE_CS3

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2
Assembly: The mapped reads of each sample were assembled by StringTie in a reference-based approach
Supplementary files format and content: tab-delimited text file includes raw counts for each samples

source_name: lung

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RQN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
librariy was prepared following Illumina® Stranded mRNA Prep, Ligation

value: lung

value: exposure to cigarette smoke


title: Tomato root, WT, rep1

description: Library name: WT-root_1


title: Primary astrocytes, BHB treated 1


title: FTO_OE_CS_rep2

description:
Library name: Sample 5
Column name in gene.counts.matrix.txt: OE_CS2


title: K562 cells, DRB, Input for RIP

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke software filter parameters：-n 0.001 -l 20 -q 0.4 -A 0.25 --cutAdaptor -Q 2 -G --minLen 100
CHromatin enrIchment ProceSsor (CHIPS) an analysis pipelinewas used to analyze RIP-seq reads. Fastq files were aligned to hg19 reference genome using bwa mem aligner (0.7.15-r1140) with default parameters
MACS2 (2.2.7.1) was used to call peaks
MACS2 (2.2.7.1) and bedGraphToBigWig (v 4) were used to generate bigwig files
Assembly: hg19
Supplementary files format and content: bigwig files contain genome-wide signal data for each sample, narrowPeak files contain genomic regions for each sample

molecule: nuclear RNA

extract_protocol:
K562 cells (1.6x10^6) were crosslinked with 1% freshly made formaldehyde solution for 10 min at room temperature. Crosslinking was stopped by adding 1/10th volume of 2.66 M Glycine, kept for 5 min at room temperature and 10 min on ice. Cell pellets were washed twice with ice-cold PBS (freshly supplemented with 1 mM PMSF). Nuclei were extracted. DNase I treatment (250 U/ml) was performed for 30 min at 37°C, and EDTA (final concentration 20 mM) added to stop the reaction. Resuspended Nuclei were sonicated once for 20s (1 pulse every 3 seconds) at 30% amplitude (Branson Digital Sonifer, Danbury, CT). 5. 5 μg antibody or preimmune serum was used for IP - ORC1 (Abcam, ab85830), preimmune serum: IgG (ab171870) or no antibody, no serum (input).
BGISEQ platform library preparation

treatment_protocol: K562 cells were grown overnight to 70-80% confluence, washed twice with 1xPBS, and then cultured in DMEM (10% FBS) supplemented with 2.5 mM Thymidine for 18 hours (first block). Subsequently, Thymidine was washed out with 1xPBS, and the cells were cultured in DMEM (10% FBS). After 8 hours, the cells were treated with Thymidine again for 18 hours (second block). Cells were then released from the block. Synchrony was assessed by flow cytometry analysis of propidium iodide-stained cells using a LSRII flow cytometer (BD Biosciences). After release from double thymidine block, cells were treated with 100 μM of 5,6-Dichlorobenzimidazole 1-β–D-ribofuranoside (DRB; Sigma Aldrich) or DMSO.

value: DRB

tag: rip antibody


title: Tomato leaf, OE-CRP1-2, rep3

description: Library name: g6-leaf_3

source_name: Leaf

value: Leaf


title: Primary astrocytes, Control3

value: Control


title: K562 cells, DMSO, Input for RIP

value: Blood

value: myelogenousleukemiacell

value: WT

value: DMSO


title: Tomato leaf, OE-CRP1-2, rep2

description: Library name: g6-leaf_2


title: FTO_OE_CS_rep1

description:
Library name: Sample 4
Column name in gene.counts.matrix.txt: OE_CS1


title: Primary astrocytes, Control2

value: Brain


title: K562 cells, IgG, DRB, RIP

value: IgG (Abcam ab171870)


title: CS_rep3

description:
Library name: Sample 3
Column name in gene.counts.matrix.txt: CS3


title: Primary astrocytes, Control1

value: Primary astrocytes

value: Astrocytes


title: K562 cells, IgG, DMSO, RIP


title: Tomato leaf, WT, rep3

description: Library name: WT-leaf_3


title: DNA from K562 treated with non AW1-51 [K562_SA_2]

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to human Infinium MethylationEPIC BeadChip (illumina) using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan and standard recommended Illumina scanner setting

data_processing:
A cross-package Bioconductor workflow for analysing methylation array data in R environment (https://dockflow.org/workflow/methylation-array-analysis/#abstract)
processed value definition: Average beta values

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

growth_protocol: K562 and A549 cell lines were grown in RPMI medium supplemented with 10% fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific) in humidified incubator at 37ºC with 5% CO2

extract_protocol: Genomic DNA was isolated using a homemade Lysis buffer (10 mM Tris pH 8, 25 mM EDTA pH 8, 0.5% SDS, 200 mM NaCl) followed by RNase A treatment (25μg/mL, Roche) for 30 minutes at 37°C and then Proteinase K (0.44mg/mL, Roche) overnight at 65°C. DNA was then recovered by basic phenol:chloroform:isoamyl alcohol 25:24:1 pH 8.0 (Sigma) extraction and 1:1 isopropanol precipitation. DNA was resuspended in TE pH 8.0 overnight

treatment_protocol: saRNAs (50 nM) were transfected into K562 cells with Kit V program T-016 by Amaxa Nucleofector Device II (Lonza). In A549, saRNAs (50 nM) were transfected using DharmaFECT 1 (DF1, Horizon Discovery). Following Voutila et al protocol, cells were first reverse transfected and then forward transfected 24h later

value: Chronic Myeloid Leukemia

value: AW1-51 saRNA

tag: time


title: K562 cells, ORC1, DRB, RIP

tag: tissue

value: ORC1 (Abcam, ab85830)


title: CS_rep1

description:
Library name: Sample 1
Column name in gene.counts.matrix.txt: CS1


title: K562 cells, ORC1, DMSO, RIP


title: lateral septum of mice brain,CFA,day3-6

city: Hangzhou

first: Furui

last: Liu

address: Yuhangtang

institute: Hangzhou Normal University

description: Library name: Sample 12

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rat whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain tissue

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 0.2 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306） following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

value: brain tissue

value: CFA


title: DNA from K562 treated with non targetting saRNA [K562_NC_2]

value: non targetting saRNA


title: lateral septum of mice brain,CFA,day3-5

description: Library name: Sample 11


title: ba70, intracellular to qs9

city: Waterville

first: Suegene

last: Noh

state: ME

address: 5717 Mayflower Hill

department: Biology

institute: Colby College

description:
Library name: b70_qs9
rRNA depleted

data_processing:
D. discoideum reads were aligned to the D. discoideum reference genome and GTF annotation file (downloaded Jan 2023 from dictybase). The segmental duplication in this reference genome (2: 3016083-3768654) was masked using bedtools v2.28.0 (Quinlan and Hall 2010). Paraburkholderia reads were aligned to draft genome assemblies (Noh et al 2022) and Prokka GFF annotation files. Host alignments were performed with STAR v2.7.5c and symbiont alignments were performed with Bowtie2 v2.4.2. Samtools v1.3.1 was used to sort and filter alignments, Picard v2.17.10 (downloaded from broadinstitute.github.io/picard) was used to assign read groups. Read counts were extracted from primary alignments with correct strand orientation using HTSeq v0.11.2 (Anders et al. 2015).
Assembly: The D. discdoideum reference genome was downloaded Jan 2023 from http://dictybase.org. Paraburkholderia draft genome assemblies are available from NCBI and https://github.com/noh-lab/clade_infection/tree/main/genome_files
Supplementary files format and content: Tab-delimited file of raw counts per gene for each sample

organism: Paraburkholderia agricolaris

source_name: whole organism

extract_protocol:
For uninfected host samples, cells were removed from RNAlater® and processed following a standard RNA extraction protocol using Qiagen RNeasy Mini kits. For free-living symbiont samples, cells were disrupted with a lysozyme treatment prior to RNeasy extraction, then treated with illumina Ribozero according to its product protocol. Symbiont-associated (infected) host samples were obtained by taking the supernatant of the first RLN buffer treatment of associated amoebas in the RNeasy protocol. Host-associated (intracellular) symbiont samples were obtained by taking the spun-down pellet of this same RLN buffer treatment step that contains amoeba nuclei as well as intracellular Paraburkholderia. This pellet was treated with lysozyme, then the RNeasy protocol and illumina Ribozero protocol as with the free-living symbiont samples.
All samples were then prepared with the illumina TruSeq Stranded mRNA library preparation protocol but only D. discoideum samples were subjected to the polyA enrichment step.

value: whole organism

tag: strain

value: intracellular

tag: batch


title: DNA from K562 treated with non targetting saRNA [K562_NC_1]


title: Respiratory Sample RS4 - Non-ENDS users

description: Library name: RS4

value: Sputum sample

value: Non-ENDS users


title: K562 cells, DMSO, Input

data_processing:
Raw data with adapter sequences or low-quality sequences was filtered using SOAPnuke software filter parameters：-n 0.01 -l 20 -q 0.4 --cutAdaptor -Q 2 -G --polyX 50 --minLen 100
CHromatin enrIchment ProceSsor (CHIPS) an analysis pipelinewas used to analyze ChIP-seq reads. Fastq files were aligned to hg19 reference genome using bwa mem aligner (0.7.15-r1140) with default parameters
MACS2 (2.2.7.1) was used to call peaks
MACS2 (2.2.7.1) and bedGraphToBigWig (v 4) were used to generate bigwig files
Assembly: hg19
Supplementary files format and content: bigwig files contain genome-wide signal data for each sample, narrowPeak files contain genomic regions for each sample

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Pellets of 1x106 cells were used for immunoprecipitation, lysed for 10 min on ice. Chromatin was fragmented using a Branson 250 digital sonicator. Each ChIP was performed with 4ug of antibody (H2A.Z (Abcam ab4174, lot GR3176820-1), and IgG (Abcam ab171870)), incubated overnight at 4°C. A 50/50 slurry of protein A and protein G Dynabeads was used to capture enriched chromatin, which was then washed before reverse-crosslinking and proteinase K digestion at 65C.
BGISEQ platform Chip-seq library preparation

value: Blood

value: myelogenousleukemiacell

tag: chip antibody


title: lateral septum of mice brain,CFA,day3-4

description: Library name: Sample 10

value: WT


title: DNA from A549 treated with non AW1-51 [A549_SA_2]

value: lung adenocarinoma


title: lateral septum of mice brain,CFA,day3-3

description: Library name: Sample 9


title: K562 cells, IgG, DRB, ChIP

value: DRB

value: IgG (Abcam ab171870)


title: ba70, intracellular to qs18

description:
Library name: b70_qs18
rRNA depleted


title: DNA from A549 treated with non AW1-51 [A549_SA_1]


title: K562 cells, IgG, DMSO, ChIP

value: DMSO


title: ba70, freeliving, sample c

description:
Library name: b70_c
rRNA depleted

value: freeliving


title: DNA from A549 treated with non targetting saRNA [A549_NC_2]


title: lateral septum of mice brain,CFA,day3-1

description: Library name: Sample 7


title: K562 cells, H2AZ, DRB, ChIP

value: H2A.Z (Abcam ab4174)


title: ba70, freeliving, sample b

description:
Library name: b70_b
rRNA depleted


title: DNA from A549 treated with non targetting saRNA [A549_NC_1]


title: K562 cells, H2AZ, DMSO, ChIP


title: lateral septum of mice brain,saline,day3-6

description: Library name: Sample 6

value: Saline


title: ba70, freeliving, sample a

description:
Library name: b70_a
rRNA depleted


title: Tnfr1-/- mouse 6 (Tnfr1ko6)

city: Nanchang

first: Pan

last: Zheng

address: 17 of Yongwaizhengjie Street

institute: The Affiliated Hospital of Nanchang University

description: Library name: sample12

data_processing:
Paired-end sequencing (150 bp) was performed on an Illumina NovaSeq 6000 platform (∼40 million reads/sample)
Raw reads were quality-trimmed (Fastp) and aligned to the mouse reference genome (GRCm38) using STAR
Gene-level counts were generated with featureCounts and normalized for differential expression analysis (DESeq2, FDR < 0.05).
Assembly: mm10
Supplementary files format and content: csv files including counts values for each sample

source_name: pancreas

extract_protocol:
Total RNA of pancreas from Tnfr1-/- mice and wide type mice were depleted (NEBNext rRNA Depletion Kit)
Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit.

value: pancreas

value: acinar cells, ductal cells, myeloid cells, neutrophil cells

value: Tnfr1 knockout


title: Bio Rep3_hda9_ABA treat

city: Seoul

first: Zein Eddin

last: Bader

state: Seoul

address: 서울특별시 광진구 광나루로22나길 3

department: Biomedical Science and Engineering

country: South Korea

institute: Konkuk University

description: High Output, 75bp

data_processing:
Sequencing reads were trimmed for adaptor sequecning/low-quality sequence using bowtie2 with defautl-sensitive parameter
Trimmed sequence reads were mapped to TAIR10 genome reference using Salmon tool to calculate transcript level expression
Read counts and transcripts per million generated by Salmon is processed using Tximport (version 1.10.0 R package with lenghScaledTPM method
For the quality control, genes with low expression were filtered and batch effecs were estimated and corrected using RUVSeq (version 1.16.0)
The data of visualization performed using IGV on bigwig files generated from normalized bedgraph using bedools genomecov package with inputs from the aligned BAM files
DEG analysis si performed using LIMMA R package (version 3.56)
Assembly: TAIR10
Supplementary files format and content: tsv read counts

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis (Col-0) Wild type and hda9-1 plants were used in this study. All plants were grown in MS media contain 1% Sucrose under the condition (16 hr light/8hr dark, 20°C)

extract_protocol:
Total RNA was extracted from ABA-treated seedling including control sample (no ABA-treated) using Directzol RNA miniprep (Zymo Research, USA)
1µg of DNA-free total RNA for Isolate mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) and followed the procedure by NEBNext UltraII Directional RNA library Prep Kit for Illumina (NEB, E7765) with slightly modified condition such diluted adaptor (1:5), extended incubation of ligation for 2 hours at room temperature, and 7 PCR cycles.

treatment_protocol: 2-3 week-old seedings (8 buds) were sprayed with 50 uM ABA for 4hr.

value: Seedling

value: mutant

value: ABA


title: lateral septum of mice brain,saline,day3-5

description: Library name: Sample 5

value: brain tissue


title: ba159, intracellular to qs9

description:
Library name: b159_qs9
rRNA depleted

value: whole organism

value: intracellular


title: Bio Rep2_hda9_ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: Tomato leaf, OE-CRP1-2, rep1

description: Library name: g6-leaf_1

value: Leaf


title: Tnfr1-/- mouse 5 (Tnfr1ko5)

description: Library name: sample11


title: lateral septum of mice brain,saline,day3-4

description: Library name: Sample 4

value: WT


title: Bio Rep1_hda9_ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: ba159, intracellular to qs864

description:
Library name: b159_864
rRNA depleted


title: Tnfr1-/- mouse 4 (Tnfr1ko4)

description: Library name: sample10


title: CS_rep2

description:
Library name: Sample 2
Column name in gene.counts.matrix.txt: CS2

value: lung

value: exposure to cigarette smoke


title: lateral septum of mice brain,saline,day3-3

description: Library name: Sample 3


title: ba159, intracellular to qs18

description:
Library name: b159_qs18
rRNA depleted


title: DNA from K562 treated with non AW1-51 [K562_SA_1]

value: Chronic Myeloid Leukemia

value: AW1-51 saRNA


title: lateral septum of mice brain,saline,day3-2

description: Library name: Sample 2


title: Tnfr1-/- mouse 3 (Tnfr1ko3)

description: Library name: sample9


title: Bio Rep3_hda9_No ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: Tomato leaf, WT, rep1

description: Library name: WT-leaf_1


title: K562 cells, DRB, Input

value: Blood

value: myelogenousleukemiacell

value: DRB


title: ba159, freeliving, sample c

description:
Library name: b159_c
rRNA depleted

value: freeliving


title: Tnfr1-/- mouse 2 (Tnfr1ko2)

description: Library name: sample8

value: pancreas

value: acinar cells, ductal cells, myeloid cells, neutrophil cells

value: Tnfr1 knockout


title: lateral septum of mice brain,saline,day3-1

description: Library name: Sample 1

value: Saline


title: Bio Rep2_hda9_No ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp

value: Seedling

value: mutant

value: ABA


title: ba159, freeliving, sample b

description:
Library name: b159_b
rRNA depleted

value: whole organism


title: Bio Rep1_hda9_No ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp


title: Tnfr1-/- mouse 1 (Tnfr1ko1)

description: Library name: sample7


title: ba70, intracellular to qs864

description:
Library name: b70_864
rRNA depleted

value: intracellular


title: ba159, freeliving, sample a

description:
Library name: b159_a
rRNA depleted


title: Bio Rep3_Wildtype1_ABA treat

address: 서울특별시 광진구 광나루로22나길 3

description: High Output, 75bp

value: Wild Type

value: No