title: HepG2_Kyn_AhRinh_Day12_RNA_EX4_rep3

city: Palo Alto

first: Yohei

last: Abe

state: California

address: 3181 Porter Dr

institute: Arc Institute

description: Library name: Sample 140

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

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


title: P. promelas larvae, EFP, biological replicate EFP_FIELD37, lane 1, time step = NA, analyzed on 20161011

status: Public on Aug 01 2026

type: SRA

city: Durham

first: Steven

middle: Thomas

last: Purucker

state: NC

address: 109 TW Alexander Dr

country: USA

institute: US EPA

description: Library name: 20161011_ EFP_FIELD_37_AGTCAA_L001_R1_001

library_source: transcriptomic

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

molecule: total RNA

organism: Pimephales promelas

source_name: whole larvae

growth_protocol: Lab-reared individual fathead minnow larvae (Pimephales promelas) 2 days post-fertilization.

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.

treatment_protocol: 48 hour lab exposures to moderately hard reconstituted water or river water grab samples collected in August 15 for 6 locations in the vicinity of a wastewater treatment plant (WWTP): upstream of WWTP, WWTP effluent discharging point, proximal location downstream WWTP outfall, distal location downstream of WWTP outfall, a downstream drinking water intake, and treated drinking water collected prior to discharge to the distribution system. Other exposures included 48 hour field fish deployments in exposure vessels secured to a minnow trap at 2 locations (upstream of a WWTP, WWTP effluent discharging point).

tag: tissue

value: whole larvae

tag: age

value: 2 dpf

tag: treatment-replicate id

tag: treatment-time

tag: treatment-location

value: EFP

tag: batch


title: Control_rep1

city: Beijing

first: jun

last: Huang

address: No.16, Nanxiao Street, Dongzhimen, Dongcheng District, Beijing, China.

country: China

institute: Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing

description: Library name: Control1

data_processing:
Step 1: Quality Control and Preprocessing Raw sequencing reads in FASTQ format were first processed through FastQC (v0.11.9) to assess read quality. Low-quality reads, adapter sequences, and poly-N sequences were trimmed using Trimmomatic (v0.39) (or Cutadapt/fastp) to obtain clean reads.  Step 2: Read Alignment The cleaned reads were mapped to the mouse reference genome (Mus musculus, e.g., GRCm39/mm10) using STAR (v2.7.9a) (or HISAT2) with default parameters. The alignment files (BAM format) were generated for downstream quantification.  Step 3: Quantification of Gene Expression The number of reads mapped to each gene was counted using featureCounts (v2.0.1) (or HTSeq-count) based on the corresponding GTF annotation file.  Step 4: Normalization and Differential Expression Analysis Differential expression analysis between groups (Control, Model, and HBG doses L/M/G) was performed using the DESeq2 (v1.34.0) R package. Read counts were normalized using the median-of-ratios method. Genes with an adjusted p-value < 0.05 and |log2FoldChange| > 1 were identified as differentially expressed genes (DEGs).  Step 5: Functional Enrichment Analysis Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted using the clusterProfiler R package to explore the biological functions and signaling pathways (e.g., TGF-β/Smad, PI3K-Akt) associated with the therapeutic effects of HBG.
Assembly: mm10
Supplementary files format and content: The processed data file (e.g., all_counts_matrix.txt) is a tab-delimited text file containing raw read counts and FPKM/TPM values for each sample. Each row represents a gene and each column represents a sample.
Supplementary files format and content: The processed data file (expression_matrix.xls) contains normalized expression values for all samples. Rows represent Ensembl gene IDs and columns represent biological replicates.

molecule: polyA RNA

organism: Mus musculus

source_name: Lung tissue

growth_protocol: Male C57BL/6 mice (6-8 weeks old) were housed under standard pathogen-free conditions with a 12h light/dark cycle and free access to food and water. Pulmonary fibrosis was induced by a single intratracheal instillation of bleomycin

extract_protocol:
Total RNA was extracted from fresh lung tissues using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity and concentration were assessed using the Agilent 2100 Bioanalyzer.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Libraries were constructed using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit. Sequencing was performed on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

treatment_protocol: Starting from day 7 post-modeling, mice in the HBG groups were orally administered HBG daily at doses of L, M, or G (specify doses, e.g., 7g/kg for G) for 14 consecutive days. The control and model groups received an equal volume of distilled water.

value: Lung tissue


title: HepG2_Kyn_AhRinh_Day12_RNA_EX4_rep2

description: Library name: Sample 139

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: P. promelas larvae, MHW, biological replicate MHW_B13, lane 2, time step = NA, analyzed on 20161011

description: Library name: 20161011_ 15-07_B13_AGTTCC_L002_R1_001

value: MHW


title: anti-CD3 antibody stimulated, day1, rep3

first: Qi

last: Tang

address: Chengfu Road #292

institute: Peking University

description:
Library name: CD3_day1_rep3
polyA RNA

data_processing:
Raw FASTQ data were filtered by TrimGalore v0.6.5 (https://www.bioinformatics.babraham-.ac.uk/projects/trim_galore/). Reads with a mapping quality score Q < 30 were removed. Reference mouse genome (GRCm38) and gene annotation files were downloaded from Gencode. Paired-end clean reads were aligned to the reference genome using STAR v2.7.6a with default parameters. The mapped reads were then counted to different genes by featureCounts v1.6.3.
Assembly: GRCm38
Supplementary files format and content: featureCounts output txt file

source_name: CD8+T cells

extract_protocol:
Total RNA was extracted using TRIzol™ (Thermo), according to the manufacturer’s instructions. For input cells less than 100,000, the aqueous phase of the TRIZol/chloroform extraction was carefully transferred into a new tube and the RNAs were cleaned and concentrated by using the ZYMO RNA Clean & Concentrator following the manufacturers’ instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library was sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: For in vitro stimulated CD8+ T cells, naïve splenic CD8+ T cells form OT-1 mice were either left unstimulated (considered naïve) or stimulated under various conditions: treated with antigen peptides for 24 or 48 hours, activated with immobilized anti-CD3 antibody, or anti-CD3/CD28-coated microbeads for 24 hours.

value: CD8+T cells

tag: genotype

value: Anti-CD3 antibody stimulation for 1 day

tag: library type

value: mRNA


title: SAMPLE 63

city: Little Rock

first: Roopa

last: Siddaiah

state: AR

address: 1 Children's way

department: Pediatrics

institute: Arkansas Children's Hospital

description:
Library name: G984-4
Small RNA library prepared using QIAseq miRNA kit with UMI

data_processing:
The libraries were pooled and diluted to 3 nM using 10 mM Tris-HCl, pH 8.5 and denatured. The denatured libraries were then loaded onto an SP flow cell on an Illumina® NovaSeq 6000 instrument and run for 68 cycles according to the manufacturer’s instructions.
Assembly: Fitlered reads were aligned to the human reference genome (GRCh38 using HISAT2 (version 2.1.0) and the resulting ded-duplicated reads were summarized to each gene using HTSeq.
Supplementary files format and content: XLS

source_name: Tracheal Aspirate

extract_protocol:
Frozen tracheal aspirate (TA) samples were thawed on ice, and mixed by pipetting. For each sample, 300 uL of the aspirate was transferred to a 1.5 ml tube and 75 ul of ExoQuick Exosome Precipitation Solution (System biosciences, cat # EXOQ5A-1) was added. Sample and solution were mixed well by inverting, incubated upright and undisturbed at 4 C overnight. Sample mixture was then centrifuged at 1550 x g for 30 min at 4 C. After centrifugation, supernatant was discarded without disturbing the pellet. Pellet was then resuspended in 100 uL 1x PBS. All 100 uL of the sample was used for RNA extraction. RNA was extracted using Zymo Research Quick-RNA Micro Prep Kit following manufacturer's protocol. The typical size distribution for the small RNA ranged between 13.14 and 283.50 ng. Frozen saliva (SA) samples were thawed on ice. RNA was extracted using Quick-RNA Microprep purification kits (Zymo Research). RNA Pico BioAnalyzer (Agilent technologies) was used to determine the RNA quality and quantity. The typical size distribution for the small RNA and quantities for saliva ranged between 33.90 and 922.50 ng
Small RNA libraries were prepared from 5–250 ng total RNA using the QIAseq miRNA Library Kit (QIAGEN) as per the manufacturer’s instructions.

value: Tracheal Aspirate

value: PH

tag: Sex

value: F


title: anti-CD3 antibody stimulated, day1, rep2

description:
Library name: CD3_day1_rep2
polyA RNA


title: HepG2_DMSO_AhRinh_Day12_RNA_EX4_rep3

description: Library name: Sample 137


title: P. promelas larvae, UP, biological replicate UP_FIELD21, lane 2, time step = NA, analyzed on 20161010

description: Library name: 20161010_ UP_FIELD_21_GTCCGC_L002_R1_001

value: UP


title: SAMPLE 61

description:
Library name: G984-1
Small RNA library prepared using QIAseq miRNA kit with UMI


title: HepG2_DMSO_AhRinh_Day12_RNA_EX4_rep2

description: Library name: Sample 136


title: P. promelas larvae, UP, biological replicate UP_FIELD21, lane 1, time step = NA, analyzed on 20161010

description: Library name: 20161010_ UP_FIELD_21_GTCCGC_L001_R1_001


title: CD3/CD28 Dynabeads stimulated, day1, rep3

description:
Library name: beads_day1_rep3
polyA RNA

value: CD3/CD28 Dynabeads stimulation for 1 day


title: SAMPLE 62

description:
Library name: G984-2
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD

value: M


title: HepG2_DMSO_AhRinh_Day12_RNA_EX4_rep1

description: Library name: Sample 135


title: SAMPLE 60

description:
Library name: G778-14
Small RNA library prepared using QIAseq miRNA kit with UMI

source_name: Saliva

value: Saliva


title: CD3/CD28 Dynabeads stimulated, day1, rep2

description:
Library name: beads_day1_rep2
polyA RNA


title: HepG2_Kyn_Day12_RNA_EX4_rep3

description: Library name: Sample 134

value: Kyn


title: P. promelas larvae, UP, biological replicate UP_B08, lane 1, time step = 4, analyzed on 20161010

description: Library name: 20161010_ UP_4_B08_ATCACG_L001_R1_001

value: whole larvae


title: CD3/CD28 Dynabeads stimulated, day1, rep1

description:
Library name: beads_day1_rep1
polyA RNA


title: SAMPLE 58

description:
Library name: G778-12
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_FIELD26, lane 2, time step = NA, analyzed on 20161010

description: Library name: 20161010_ EFP_FIELD_26_GAGTGG_L002_R1_001

value: 2 dpf


title: p53_6__normal_Stroma_sample16

city: Chicago

first: CRI

last: Bioinformatics

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

description: Library name: DSP-1001660008418-D-B06

data_processing:
Sequencing files were processed into DCC format using the GeoMx NGS Pipeline software v1.0. GeoMx counts were log2 transformed in preparation for statistic data analysis.
Assembly: GRCh38.p13
Supplementary files format and content: DCC files include raw read counts along with RTS_IDs for each ROI
Supplementary files format and content: PKC file includes probe metadata describing the targets and is needed to interpret RTS_IDs in the DCC files

source_name: Fallopian tube, dysplastic lesion or invasive cancer

extract_protocol:
Tissue processing began with sectioning FFPE samples to a 5 μm thickness following the Nanostring GeoMx user manual (MAN-10132-04). After deparaffinization and rehydration, protein target retrieval was performed using Tris-EDTA antigen retrieval buffer for 20 minutes in a pressure cooker. RNA targets were retrieved through proteinase K digestion for 15 minutes at 37 °C. Tissues were then post-fixed in 10% NBF and hybridized overnight at 37 °C with RNA probes (Human Whole Transcriptome Atlas, containing 18,000 protein-coding genes coupled to UV-cleavable oligonucleotide barcodes). Following hybridization, excess probes were removed by stringent washing at 37 °C and incubated in blocking buffer W (Nanostring LOT#:2-23020032). The tissue sections were subsequently stained with conjugated primary antibodies targeting pan-cytokeratin (mouse monoclonal antibody, Novus NBP2-33200AF488) and p53 (Dako primary and secondary antibodies), along with CAPS (primary and secondary antibodies) and SYTO13 nuclear stain (ThermoFisher Scientific, S7575) for one hour at room temperature. For transcriptomic data acquisition, slides were analyzed on the GeoMx Digital Spatial Profiler (DSP) at 20× magnification. Regions of interest (ROIs) were identified based on immunofluorescence images with a pathologist's (AB) supervision and matched to regions selected in DVP. Following ROI selection, RNA probes were photocleaved using UV illumination within each ROI, and oligonucleotide barcodes were collected into a 96-well plate, allowing precise separation of tissue compartments.
Sequencing libraries were prepared using Illumina TruSeq technology for adaptor ligation and amplification. The amplified libraries underwent two rounds of Ampure XP magnetic bead cleanup (1.2:1 beads ratio) (HighPrep PCR from MAGBIO, Cat#: AC-60500). Purified libraries were sequenced on an Illumina NovaSeq flowcell PE50 at a depth of 100× per μm².

value: Stroma

tag: cohort

value: normal


title: p53_6__normal_Stroma_sample17

description: Library name: DSP-1001660008418-D-B08

value: Fallopian tube, dysplastic lesion or invasive cancer


title: p53_6__FOXJ1pos_Epithelium_sample15

description: Library name: DSP-1001660008418-D-B05

value: Epithelium


title: p53_6__FOXJ1pos_Epithelium_sample18

description: Library name: DSP-1001660008418-D-B09


title: P. promelas larvae, UP, biological replicate UP_FIELD49, lane 2, time step = NA, analyzed on 20161108

description: Library name: 20161108_ UP_FIELD_49_ATCACG_L002_R1_001


title: V4 stimulated, day1, rep3

description:
Library name: V4_day1_rep3
polyA RNA

value: CD8+T cells

value: V4 peptide stimulation for 1 day


title: HepG2_Kyn_Day12_RNA_EX4_rep1

description: Library name: Sample 132


title: HepG2_DMSO_Day12_RNA_EX4_rep3

description: Library name: Sample 131

value: DMSO


title: P. promelas larvae, EFP, biological replicate EFP_FIELD26, lane 1, time step = NA, analyzed on 20161010

description: Library name: 20161010_ EFP_FIELD_26_GAGTGG_L001_R1_001

value: EFP


title: V4 stimulated, day1, rep2

description:
Library name: V4_day1_rep2
polyA RNA

value: mRNA


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 1, time step = 4, analyzed on 20161010

description: Library name: 20161010_ EFP_4_B07_ACTGAT_L001_R1_001


title: SAMPLE 55

description:
Library name: G778-09
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH


title: HepG2_DMSO_Day12_RNA_EX4_rep2

description: Library name: Sample 130


title: P. promelas larvae, UP, biological replicate UP_B22, lane 1, time step = 1, analyzed on 20161108

description: Library name: 20161108_ UP_1_B22_GAGTGG_L001_R1_001

value: UP


title: Q4 stimulated, day1, rep3

description:
Library name: Q4_day1_rep3
polyA RNA

value: Q4 peptide stimulation for 1 day


title: HepG2_DMSO_Day12_RNA_EX4_rep1

description: Library name: Sample 129


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 2, time step = 3, analyzed on 20161010

description: Library name: 20161010_ EFP_3_B11_ACTTGA_L002_R1_001


title: HepG2_B2_minus_Day12_RNA_EX2_rep3

description: Library name: Sample 74


title: Q4 stimulated, day1, rep2

description:
Library name: Q4_day1_rep2
polyA RNA


title: SAMPLE 53

description:
Library name: G778-07
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD

value: F


title: Q4 stimulated, day1, rep1

description:
Library name: Q4_day1_rep1
polyA RNA


title: HepG2_B2_minus_Day12_RNA_EX2_rep2

description: Library name: Sample 73


title: SAMPLE 52

description:
Library name: G778-06
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Saliva


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 2, time step = 2, analyzed on 20161010

description: Library name: 20161010_ EFP_2_B03_GTGGCC_L002_R1_001

value: whole larvae


title: OVA stimulated, day1, rep3

description:
Library name: OVA_day1_rep3
polyA RNA

value: OVA peptide stimulation for 1 day


title: HepG2_B2_minus_Day12_RNA_EX2_rep1

description: Library name: Sample 72


title: SAMPLE 51

description:
Library name: G778-05
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 1, time step = 2, analyzed on 20161010

description: Library name: 20161010_ EFP_2_B03_GTGGCC_L001_R1_001

value: 2 dpf


title: OVA stimulated, day1, rep2

description:
Library name: OVA_day1_rep2
polyA RNA


title: HepG2_Cont_Day12_RNA_EX2_rep3

description: Library name: Sample 71

value: Control


title: P. promelas larvae, EFP, biological replicate EFP_B09, lane 2, time step = 1, analyzed on 20161010

description: Library name: 20161010_ EFP_1_B09_TAGCTT_L002_R1_001


title: P. promelas larvae, UP, biological replicate UP_B08, lane 2, time step = 4, analyzed on 20161010

description: Library name: 20161010_ UP_4_B08_ATCACG_L002_R1_001


title: OVA stimulated, day1, rep1

description:
Library name: OVA_day1_rep1
polyA RNA


title: HepG2_Cont_Day12_RNA_EX2_rep2

description: Library name: Sample 70


title: SAMPLE 49

description:
Library name: G778-03
Small RNA library prepared using QIAseq miRNA kit with UMI


title: HepG2_Kyn_Day12_RNA_EX4_rep2

description: Library name: Sample 133

value: Kyn


title: P. promelas larvae, EFP, biological replicate EFP_B09, lane 1, time step = 1, analyzed on 20161010

description: Library name: 20161010_ EFP_1_B09_TAGCTT_L001_R1_001


title: V4 stimulated, day2, rep3

description:
Library name: V4_day2_rep3
polyA RNA

value: V4 peptide stimulation for 2 day


title: HepG2_Cont_Day12_RNA_EX2_rep1

description: Library name: Sample 69


title: LPS Male Biological Rep 3, Technical Replicate

city: New York

first: Gordana

last: Vunjak-Novakovic

state: NY

institute: Columbia University

description: Library name: GR036

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) was used for converting BCL to fastq format, coupled with adaptor trimming.
Pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96, Human: GRCh38.12) was performed using kallisto (0.44.0).
Estimated counts and tpm values for each gene were computed from tximport R package.
Assembly: GRCh38.p12
Supplementary files format and content: tpm_values_transcripts_kallisto.txt: tab delimited file includes transcripts per million (tpm) values for each transcript for all samples
Supplementary files format and content: est_counts_transcripts_kallisto.txt: tab delimited file includes estimated counts for each transcript for all samples
Supplementary files format and content: tpm_values_genes_kallisto.txt: tab delimited file includes tpm values for each gene for all samples
Supplementary files format and content: est_counts_genes_kallisto.txt: tab delimited file includes estimated counts for each gene for all samples

growth_protocol: All iPSC lines were expanded and cultured in mTeSR Plus medium on tissue culture treated plates coated with 1:100 Matrigel in RPMI 1640. Cells were passaged every 3-4 days, and passaged upon reaching 70% confluency using 0.5 mM EDTA in PBS. iPSCs were replated on tissue culture plates coated with 1:175 Matrigel with low agitation to enable cell clusters to attach at approximately 8-16 clusters/cm2. Cells were first differentiated into hematopoietic stem and progenitors using a STEMdiff Hematopoietic Kit, according to the manufacturer’s instructions. At day 12, cells in suspension were removed and the adherent hemogenic endothelial cell fraction was cultured in X-VIVO 15 Serum-free Hematopoietic Cell Medium supplemented with 1:100 GlutaMAX, 1:100 2-mercaptoethanol, 100 ng/mL recombinant human macrophage colony stimulating factor (M-CSF), and 25 ng/mL recombinant human interleukin 3 (IL-3). Hemogenic endothelial cells were maintained for over 8 weeks with weekly media exchange, with cells in the suspension fraction discarded during week 1. Myeloid- and monocytic-specific lineage cells subsequently collected in the suspension fraction were replated onto 6-well ultra-low attachment plasticin X-VIVO 15 media containing 100 ng/mL M-CSF for at least 5 days to achieve macrophage differentiation. CD14+ macrophages were positively selected prior to use via CD14 microbeads, according to the manufacturer’s protocol.

extract_protocol:
Following treatment, iMacs were lysed in Buffer RLT and stored at –20°C. Samples were thawed on ice and total RNA was isolated using a Qiagen RNeasy Micro Kit, according to the manufacturer's instructions. The quality and quantity of total RNA was assessed using an Agilent 2100 Bioanalyzer with an RNA Pico Chip at Columbia's Molecular Pathology core. All samples had an RNA integrity number (RIN) ≥ 9.6 and were considered acceptable for further analysis. Total RNA samples were submitted to the JP Sulzberger Columbia Genome Center for sequencing.
A poly-A pulldown was used to enrich mRNAs from total RNA samples, then a library was constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s protocol.

treatment_protocol: Human iPSC-derived macrophages were cultured in X-VIVO 15 media supplemented with 100 ng/mL M-CSF in the absence (control) or presence of 100 ng/mL LPS for 48 h.

value: iPSC-derived macrophage

value: LPS


title: SAMPLE 50

description:
Library name: G778-04
Small RNA library prepared using QIAseq miRNA kit with UMI


title: p53_6__FOXJ1pos_Epithelium_sample10

description: Library name: DSP-1001660008418-D-A12

value: Fallopian tube, dysplastic lesion or invasive cancer

value: Epithelium


title: SAMPLE 48

description:
Library name: G778-02
Small RNA library prepared using QIAseq miRNA kit with UMI

value: M


title: SAMPLE 57

description:
Library name: G778-11
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, DSP, biological replicate DSP_B07, lane 2, time step = NA, analyzed on 20161010

description: Library name: 20161010_ DSP_B07_GGCTAC_L002_R1_001

value: DSP


title: SAMPLE 56

description:
Library name: G778-10
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH


title: V4 stimulated, day2, rep2

description:
Library name: V4_day2_rep2
polyA RNA

value: CD8+T cells

value: mRNA


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 2, time step = 4, analyzed on 20161010

description: Library name: 20161010_ EFP_4_B07_ACTGAT_L002_R1_001

value: EFP


title: Caco2_Day9_B2_minus_RNA_rep3

description: Library name: Sample 30


title: SAMPLE 47

description:
Library name: G778-01
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Saliva


title: P. promelas larvae, DSP, biological replicate DSP_B07, lane 1, time step = NA, analyzed on 20161010

description: Library name: 20161010_ DSP_B07_GGCTAC_L001_R1_001

value: whole larvae


title: V4 stimulated, day2, rep1

description:
Library name: V4_day2_rep1
polyA RNA


title: V4 stimulated, day1, rep1

description:
Library name: V4_day1_rep1
polyA RNA

value: V4 peptide stimulation for 1 day


title: p53_6__FOXJ1neg_Epithelium_sample9

description: Library name: DSP-1001660008418-D-A11


title: Caco2_Day9_B2_minus_RNA_rep2

description: Library name: Sample 29


title: SAMPLE 46

description:
Library name: G923-33
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, UP, biological replicate UP_FIELD53, lane 2, time step = NA, analyzed on 20161010

description: Library name: 20161010_ UP_FIELD_53_GTCCGC_L002_R1_001

value: 2 dpf

value: UP


title: Caco2_Day9_B2_minus_RNA_rep1

description: Library name: Sample 28


title: Q4 stimulated, day2, rep3

description:
Library name: Q4_day2_rep3
polyA RNA

value: Q4 peptide stimulation for 2 day


title: SAMPLE 45

description:
Library name: G923-32
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD


title: P. promelas larvae, UP, biological replicate UP_FIELD53, lane 1, time step = NA, analyzed on 20161010

description: Library name: 20161010_ UP_FIELD_53_GTCCGC_L001_R1_001


title: Q4 stimulated, day2, rep2

description:
Library name: Q4_day2_rep2
polyA RNA


title: Caco2_Day9_Cont_RNA_rep3

description: Library name: Sample 27

value: Control


title: P. promelas larvae, UP, biological replicate UP_B26, lane 2, time step = 4, analyzed on 20161010

description: Library name: 20161010_ UP_4_B26_TAGCTT_L002_R1_001


title: SAMPLE 44

description:
Library name: G923-31
Small RNA library prepared using QIAseq miRNA kit with UMI


title: Q4 stimulated, day2, rep1

description:
Library name: Q4_day2_rep1
polyA RNA


title: Caco2_Day9_Cont_RNA_rep2

description: Library name: Sample 26


title: SAMPLE 43

description:
Library name: G923-30
Small RNA library prepared using QIAseq miRNA kit with UMI


title: SAMPLE 54

description:
Library name: G778-08
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, UP, biological replicate UP_B26, lane 1, time step = 4, analyzed on 20161010

description: Library name: 20161010_ UP_4_B26_TAGCTT_L001_R1_001


title: Caco2_Day9_Cont_RNA_rep1

description: Library name: Sample 25


title: SAMPLE 42

description:
Library name: G923-29
Small RNA library prepared using QIAseq miRNA kit with UMI


title: OVA stimulated, day2, rep3

description:
Library name: OVA_day2_rep3
polyA RNA

value: OVA peptide stimulation for 2 day


title: P. promelas larvae, UP, biological replicate UP_B22, lane 2, time step = 3, analyzed on 20161010

description: Library name: 20161010_ UP_3_B22_ATCACG_L002_R1_001


title: OVA stimulated, day2, rep2

description:
Library name: OVA_day2_rep2
polyA RNA


title: HepG2_Day12_B2_minus_H3K27ac_ChIP_rep3

description: Library name: Sample 44

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

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.


title: SAMPLE 41

description:
Library name: G923-28
Small RNA library prepared using QIAseq miRNA kit with UMI

value: F


title: P. promelas larvae, UP, biological replicate UP_B22, lane 1, time step = 3, analyzed on 20161010

description: Library name: 20161010_ UP_3_B22_ATCACG_L001_R1_001


title: OVA stimulated, day2, rep1

description:
Library name: OVA_day2_rep1
polyA RNA


title: HepG2_Day12_B2_minus_H3K27ac_ChIP_rep2

description: Library name: Sample 43


title: SAMPLE 40

description:
Library name: G923-27
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_FIELD54, lane 1, time step = NA, analyzed on 20161010

description: Library name: 20161010_ EFP_FIELD_54_GAGTGG_L001_R1_001


title: HepG2_Day12_B2_minus_H3K27ac_ChIP_rep1

description: Library name: Sample 42


title: P. promelas larvae, EFP, biological replicate EFP_FIELD54, lane 2, time step = NA, analyzed on 20161010

description: Library name: 20161010_ EFP_FIELD_54_GAGTGG_L002_R1_001


title: SAMPLE 39

description:
Library name: G923-26
Small RNA library prepared using QIAseq miRNA kit with UMI


title: OT1 CD8+T, day0, rep2

description:
Library name: CD8T_day0_rep2
polyA RNA

value: No treatment


title: OT1 CD8+T, day0, rep3

description:
Library name: CD8T_day0_rep3
polyA RNA


title: HepG2_Day12_Cont_H3K27ac_ChIP_rep3

description: Library name: Sample 41


title: SAMPLE 38

description:
Library name: G923-25
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 2, time step = 4, analyzed on 20161010

description: Library name: 20161010_ EFP_4_B27_GGCTAC_L002_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B11, lane 1, time step = 3, analyzed on 20161010

description: Library name: 20161010_ EFP_3_B11_ACTTGA_L001_R1_001


title: OT1 CD8+T, day0, rep1

description:
Library name: CD8T_day0_rep1
polyA RNA


title: SAMPLE 37

description:
Library name: G923-24
Small RNA library prepared using QIAseq miRNA kit with UMI


title: HepG2_Day12_Cont_H3K27ac_ChIP_rep2

description: Library name: Sample 40


title: RNA-seq, Sia2,6loPD-1+CD8+ T, replication 3

description:
Library name: Sia2,6loPD-1+CD8+ T_rep3
Sia_lo-3

source_name: B16-OVA syngeneic tumor

extract_protocol:
CD8+T subsets were subjected to total RNA extraction. Total RNAs was extracted from FACS-isolated cells by using TRIzolTM (Thermo) following the manufacturers’ instructions. For input cells less than 100,000, the aqueous phase of the TRIZol/chloroform extraction was carefully transferred into a new tube and the RNAs were cleaned and concentrated by using the ZYMO RNA Clean & Concentrator following the manufacturers’ instructions. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers, and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library was sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: B16-OVA syngeneic tumor

value: WT


title: HepG2_Day12_Cont_H3K27ac_ChIP_rep1

description: Library name: Sample 39


title: SAMPLE 36

description:
Library name: G923-23
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 1, time step = 4, analyzed on 20161010

description: Library name: 20161010_ EFP_4_B27_GGCTAC_L001_R1_001


title: RNA-seq, Sia2,6loPD-1+CD8+ T, replication 2

description:
Library name: Sia2,6loPD-1+CD8+ T_rep2
Sia_lo-2


title: SAMPLE 35

description:
Library name: G923-22
Small RNA library prepared using QIAseq miRNA kit with UMI


title: HepG2_Day12_Cont_ATAC_rep4

description: Library name: Sample 38

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 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.


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 1, time step = 3, analyzed on 20161010

description: Library name: 20161010_ EFP_3_B27_ACTGAT_L001_R1_001


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 2, time step = 3, analyzed on 20161010

description: Library name: 20161010_ EFP_3_B27_ACTGAT_L002_R1_001


title: RNA-seq, Sia2,6loPD-1+CD8+ T, replication 1

description:
Library name: Sia2,6loPD-1+CD8+ T_rep1
Sia_lo-1


title: HepG2_Day12_Cont_ATAC_rep3

description: Library name: Sample 37


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 2, time step = 2, analyzed on 20161010

description: Library name: 20161010_ EFP_2_B26_ACTTGA_L002_R1_001


title: RNA-seq, Sia2,6hiPD-1+CD8+ T, replication 3

description:
Library name: Sia2,6hiPD-1+CD8+ T_rep3
PD1_hi-3


title: SAMPLE 33

description:
Library name: G923-19
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH

value: M


title: HepG2_Day12_Cont_ATAC_rep2

description: Library name: Sample 36


title: P. promelas larvae, EFP, biological replicate EFP_B26, lane 1, time step = 2, analyzed on 20161010

description: Library name: 20161010_ EFP_2_B26_ACTTGA_L001_R1_001


title: RNA-seq, Sia2,6hiPD-1+CD8+ T, replication 2

description:
Library name: Sia2,6hiPD-1+CD8+ T_rep2
PD1_hi-2

value: CD8+T cells

value: mRNA


title: HepG2_Day12_Cont_ATAC_rep1

description: Library name: Sample 35


title: SAMPLE 32

description:
Library name: G923-18
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Saliva


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 2, time step = 1, analyzed on 20161010

description: Library name: 20161010_ EFP_1_B27_GTGGCC_L002_R1_001

value: whole larvae

value: EFP


title: HFD/KL-2_preventive_n2

city: Leipzig

first: Jes-Niels

last: Boeckel

address: Johannisalle 30

department: Klinik und Poliklinik für Kardiologie

country: Germany

institute: Universitätsklinikum Leipzig

description:
Library name: KK_28
bulk-seq

data_processing:
After demultiplexing with the bcl2fastq software (Illumina, version 2.20), the fastq files underwent trimming and adapter removal using Trim Galore. On average, 18.2 million reads (therapeutic mouse model liver bulk RNA-seq) and 27.9 million reads (preventive mouse model liver bulk RNA-seq) per sample passed quality control and were retained for downstream analysis. Read mapping was performed against the respective reference genome (mouse mm39) using Hisat2. Gene expression quantification was achieved by read counting using FeatureCounts (R package). The resulting counts were then converted to transcripts per million (TPM) for normalization in R. Differential expression analysis was performed using the R package edgeR. Differences in mean expression between conditions were assessed using a negative binomial exact test.
Assembly: Reference transcriptome consisting of: mouse mm39
Supplementary files format and content: Tab-separated values files

source_name: liver

growth_protocol: C57BL/6NTac (Charles River) male mice were maintained in a room under pathogen-free conditions with controlled 21 ± 1°C on a 12:12 h light/dark cycle (6 a.m./6 p.m.). Two different treatment models were analyzed: preventive and therapeutical treatment with KL-2. In both models, mice were randomly divided into two groups: hypercholesterolemia-induced atherosclerosis and control group. At 8 weeks, the first group received a vector containing a Pcsk9-D377Y gain-of-function variant with liver-specific promoter packed in an AAV8 virus was injected in the tail vein of mice, which were subsequently fed ad libitum with a modified, cholesterol (Chol)-enriched semisynthetic Clinton/Cybulsky diet (Sniff, Soest, Germany) starting at the age of 9 weeks.

extract_protocol:
RNA from mouse liver tissue was homogenized with BD Microlances (22G and 18G, 304100, BD). RNA from homogenized mouse tissue was extracted using the miRNeasy mini Kit.
Quality control and quantification of the isolated RNA were performed using Fragment Analyzer 5200 (Agilent) using the High Sensitivity RNA quantification kit and Fragment Analyzer Controller Software (Agilent v3.1.0.12). Random primed library preparation was started with 150 ng of total RNA using the Watchmaker RNA library prep kit with Polaris depletion (Watchmaker Genomics) according to the instructions of the manufacturer. The barcoded libraries were purified and quantified using Qubit Fluorometric Quantification (ThermoFisher Scientific). Size distribution of the library DNA was analyzed using the Fragment Analyzer 5200 (Agilent). Sequencing of 2x150 bp was performed with an Illumina NovaSeq 6000 sequencer (Illumina, San Diego, CA, USA).

treatment_protocol: Preventive treatment: PCSK9-AAV8 was injected into the tail vein of C57BL/6NTac mice, after 1-week mice were subjected to a high fat diet (HFD). After four weeks, the levels of cholesterol in the serum were analysed and the mice were randomly and blindly selected for injection with either KL-2 (10 mg/kg BW) or the corresponding volume of DMSO, at fortnightly intervals until the end of the 20-week experiment. Therapeutic treatment: PCSK9-AAV8 was injected into the tail vein of C57BL/6NTac mice, after 1-week mice were subjected to a high fat diet (HFD). After four weeks, the levels of cholesterol in the serum were analysed and the mice were randomly and blindly selected for injection with either KL-2 (10 mg/kg BW) or the corresponding volume of DMSO, at weekly intervals until the end of the 24-week experiment.

value: liver


title: RNA-seq, Sia2,6hiPD-1+CD8+ T, replication 1

description:
Library name: Sia2,6hiPD-1+CD8+ T_rep1
PD1_hi-1


title: HepG2_Day12_B2_minus_ATAC_rep4

description: Library name: Sample 34


title: SAMPLE 31

description:
Library name: G923-17
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 1, time step = 1, analyzed on 20161010

description: Library name: 20161010_ EFP_1_B27_GTGGCC_L001_R1_001

value: 2 dpf


title: RNA-seq, Sia2,6hiPD-1−CD8+ T, replication 3

description:
Library name: Sia2,6hiPD-1−CD8+ T_rep3
PD1_low-3


title: SAMPLE 30

description:
Library name: G923-16
Small RNA library prepared using QIAseq miRNA kit with UMI


title: HepG2_Day12_B2_minus_ATAC_rep3

description: Library name: Sample 33


title: HepG2_Day12_B2_minus_ATAC_rep2

description: Library name: Sample 32


title: RNA-seq, Sia2,6hiPD-1−CD8+ T, replication 2

description:
Library name: Sia2,6hiPD-1−CD8+ T_rep2
PD1_low-2


title: P. promelas larvae, UP, biological replicate UP_B12, lane 2, time step = 4, analyzed on 20161007

description: Library name: 20161007_ UP_4_B12_ACTTGA_L002_R1_001

value: UP


title: SAMPLE 29

description:
Library name: G923-15
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD


title: P. promelas larvae, UP, biological replicate UP_B12, lane 1, time step = 4, analyzed on 20161007

description: Library name: 20161007_ UP_4_B12_ACTTGA_L001_R1_001


title: SAMPLE 28

description:
Library name: G923-12
Small RNA library prepared using QIAseq miRNA kit with UMI


title: RNA-seq, Sia2,6hiPD-1−CD8+ T, replication 1

description:
Library name: Sia2,6hiPD-1−CD8+ T_rep1
PD1_low-1


title: P. promelas larvae, UP, biological replicate UP_B03, lane 2, time step = 3, analyzed on 20161007

description: Library name: 20161007_ UP_3_B03_GTGGCC_L002_R1_001


title: HepG2_Day12_B2_minus_ATAC_rep1

description: Library name: Sample 31


title: Cis Stat6 KO2

city: Albuquerque

first: Dandan

last: Wu

state: NM

address: 915 CAMINO DE SALUD  NE room 360

department: Molecular Genetics and Microbiology

institute: University of New Mexico

description:
Library name: Sample 6
raw_count.txt

data_processing:
Sequence and filtering of Clean Reads
Alignment with Reference Genome
Quantification of Gene Abundance
Differentially expressed genes (DEGs) Analysis
GO Enrichment Analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RKPM values for each sample

source_name: Lung

growth_protocol: Balf cells were took from lung

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent,CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing

treatment_protocol: No treatment

value: Lung

value: BALF cell

value: Immune cell

value: Double KO


title: SAMPLE 27

description:
Library name: G923-11
Small RNA library prepared using QIAseq miRNA kit with UMI

value: F


title: SAMPLE 79

description:
Library name: G778-23
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Tracheal Aspirate


title: Week5_CIS_scMulti_ATAC_2022_05_17

city: Seattle

first: Kevin

middle: Z.

last: Lin

state: Washington

address: 3980 15th Avenue NE

department: Biostatistics

institute: University of Washington

description:
Library name: Sample42
10X Multiome

library_source: genomic single cell

data_processing:
Cell Ranger ARC (version 2.0.1) was used for demultiplexing cell barcodes and aligning reads.
SAVER was used to recover gene expression signal
FastTopics was used to perform dimensionality reduction on RNA data
Seurat was used to normalize data, perform dimensionality reduction and UMAP visalization
MAC2 was used to identify peaks
PeakVI was used to generate a bin-by-cell matrix, perform dimensionality reduction and UMAP visualization on ATAC data
Assembly: hg38
Supplementary files format and content: metadata.csv: contains information on treatment, time point, cell barcode metadata, lineage barcode assignment
Supplementary files format and content: cells_rna.tsv: cell barcodes used in analysis
Supplementary files format and content: features_rna.csv: genes used in analysis
Supplementary files format and content: counts_rna.mtx: transcript count per gene per cell used in analysis
Supplementary files format and content: features_atac.csv: genomic peaks called in analysis
Supplementary files format and content: counts_atac.mtx: Tn5 insertion count per peak per cell used in analysis
Supplementary files format and content: features_lineage.csv: lineage barcodes present in study
Supplementary files format and content: counts_lineage.mtx: : lineage barcode read count per cell
Supplementary files format and content: umap_rna.csv: UMAP coordinates based on RNA modality
Supplementary files format and content: umap_atac.csv: UMAP coordinates based on ATAC modality
Supplementary files format and content: umap_wnn.csv: UMAP coordinates based on both RNA and ATAC modality
Supplementary files format and content: dimred_fasttopic.csv: FastTopics dimensionality reduction embedding based on RNA data
Supplementary files format and content: dimred_peakvi.csv: PeakVI dimensionality redicution embedding based on ATAC data

source_name: WM989 A6-G3 cells

extract_protocol:
Single nuclei were pooled and loaded onto a 10X Genomics Chromium controller for generation of 10X scMultiome libraries.
Single cell library preparation was performed following the 10X Multiome kit

value: WM989 A6-G3 cells

value: Cisplatin 5 weeks post treatment


title: P. promelas larvae, UP, biological replicate UP_B03, lane 1, time step = 3, analyzed on 20161007

description: Library name: 20161007_ UP_3_B03_GTGGCC_L001_R1_001


title: Week5_CIS_scMulti_ATAC_2022_05_16

description:
Library name: Sample41
10X Multiome


title: Cis KO2

description:
Library name: Sample 4
raw_count.txt

value: KO


title: Cis Stat6 KO1

description:
Library name: Sample 5
raw_count.txt


title: P. promelas larvae, UP, biological replicate UP_B06, lane 2, time step = 2, analyzed on 20161007

description: Library name: 20161007_ UP_2_B06_TAGCTT_L002_R1_001


title: SAMPLE 26

description:
Library name: G923-10
Small RNA library prepared using QIAseq miRNA kit with UMI

value: M


title: P. promelas larvae, UP, biological replicate UP_B06, lane 1, time step = 2, analyzed on 20161007

description: Library name: 20161007_ UP_2_B06_TAGCTT_L001_R1_001


title: Cis KO1

description:
Library name: Sample 3
raw_count.txt


title: Week5_COCL2_scMulti_ATAC_2022_05_16

description:
Library name: Sample39
10X Multiome

value: CoCl2 for 5 weeks


title: Week5_COCL2_scMulti_ATAC_2022_05_17

description:
Library name: Sample40
10X Multiome


title: SAMPLE 24

description:
Library name: G923-07
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Saliva


title: P. promelas larvae, UP, biological replicate UP_B01, lane 2, time step = 1, analyzed on 20161007

description: Library name: 20161007_ UP_1_B01_ATCACG_L002_R1_001

value: whole larvae


title: Cis WT2

description:
Library name: Sample 2
raw_count.txt

value: WT


title: SAMPLE 23

description:
Library name: G923-06
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH


title: Week5_DABTRAM_scMulti_ATAC_2022_05_17

description:
Library name: Sample38
10X Multiome

value: Dabrafenib and Trametinib for 5 weeks


title: Cis WT1

description:
Library name: Sample 1
raw_count.txt


title: Week5_DABTRAM_scMulti_ATAC_2022_05_16

description:
Library name: Sample37
10X Multiome


title: SAMPLE 22

description:
Library name: G923-04
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Control


title: P. promelas larvae, UP, biological replicate UP_B01, lane 1, time step = 1, analyzed on 20161007

description: Library name: 20161007_ UP_1_B01_ATCACG_L001_R1_001

value: 2 dpf

value: UP


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 2, time step = 4, analyzed on 20161007

description: Library name: 20161007_ EFP_4_B03_GAGTGG_L002_R1_001

value: EFP


title: 0914_HP1BP3_IGG

first: Bosong

last: Wang

address: No.19, Xinjiekouwai Street, Haidian District, Beijing, P.R.China

institute: Beijing Normal University

description: Library name: 0914_HP1BP3_IGG

data_processing:
Raw sequences were first processed for quality control using FastQC v0.11.9. Adapter sequences and low-quality reads were removed using fastp v1.01.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Brain cortex

extract_protocol:
Samples were minced into pieces <5 mm and then homogenized using a glass dounce tissue grinder in 2 mL of Nuclei EZ lysis buffer on ice. After two incubations on ice (with 4 mL of lysis buffer and 5 min each time), the homogenate was filtered through a 70 mm strainer, and then we used Debris Removal Solution to perform density gradient centrifugation to clean the nuclear suspension according to the manufacturer’s protocol. Isolated nuclei were resuspended and washed with nuclei suspension buffer (NSB, consisting of 13 mL PBS, 0.1% mL BSA and 0.4 U/mL Ambion RNase inhibitor and filtered through a 35 mm cell strainer.Nuclei were counted using a hemocytometer and diluted to 1000 nuclei/mL for optimal 10X loading.
For library amplification in PCR tube format, 21 µL DNA was combined with 2 µL of universal i5 and uniquely barcoded i7 primer where a different barcode was used for each sample that was intended to be pooled together. 25 µL NEBNext HiFi 2× PCR Master mix was added, and then the sample was gently mixed through and spun down. The sample was placed in a Thermocycler with heated lid following these conditions: 72 °C for 3 min (gap filling); 95 °C for 3 min; 10 cycles of 98 °C for 10 s and 60 °C for 5 s; final extension at 72 °C for 1 min; and hold at 4 °C. Following PCR, bead cleanup was conducted by the addition of 1.1x Ampure XP beads. Library and beads were mixed thoroughly, then spun down and incubated at RT for 10–15 min. Beads were gently washed twice with freshly prepared 80% ethanol using a magnetic rack, then the library was eluted with 20 µL 10 mM Tris-HCl pH 8.0 at RT.(Illumina novaseq6000，PE150)

value: Brain cortex


title: Day10_CIS_scMulti_ATAC_2022_05_17

description:
Library name: Sample36
10X Multiome

value: Cisplatin 10 days post treatment


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 1, time step = 4, analyzed on 20161007

description: Library name: 20161007_ EFP_4_B03_GAGTGG_L001_R1_001


title: SAMPLE 21

description:
Library name: G923-03
Small RNA library prepared using QIAseq miRNA kit with UMI


title: 0914_HP1BP3_CUTTAG

description: Library name: 0914_HP1BP3_CUTTAG


title: SAMPLE 20

description:
Library name: G923-02
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD


title: Day10_CIS_scMulti_ATAC_2022_05_16

description:
Library name: Sample35
10X Multiome

value: WM989 A6-G3 cells


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 2, time step = 3, analyzed on 20161007

description: Library name: 20161007_ EFP_3_B02_GTCCGC_L002_R1_001


title: Mouse macrophages, Donor M5, IFNy stimulated and Mtb infected

city: Greifswald - Insel Riems

first: Björn

last: Corleis

state: Mecklenburg-Western Pomerania

address: Südufer 10

department: Institute of immunology

institute: Friedrich-Loeffler-Institut

description: Library name: M5_IFNyMtb

data_processing:
STAR (version 2.7.9a) read alignment
Subread featureCounts (version 2.0.3) read counting
Assembly: GRCh38.p14, GRCm39
Supplementary files format and content: tab delimeted .txt file containing raw read counts for each gene

source_name: bone marrow derived macrophages

growth_protocol: For transcriptomic analysis, macrophages were differentiated in 48-well plates at a density of 1 × 10⁶ cells per well in RPMI 1640 supplemented with 10% FCS, 2 mM L-glutamine, and 1 mM sodium pyruvate.

extract_protocol:
RNA was extracted from 1 ml Trizol™ using PhaseMaker tubes and chloroform. After phase separation by centrifugation (12,000 × g, 15 min, 4°C), the aqueous phase was precipitated with glycogen and isopropanol (–20°C, 60 min), pelleted, washed with 75% ethanol, and air-dried. RNA was resuspended in 20 µl nuclease-free water and incubated at 60°C for 15 min.
TotTotal RNA was purified with RNA-SPRI beads and ethanol washes. Whole-transcriptome amplification was performed using Smart-seq2. cDNA was synthesized, amplified, and purified with DNA-SPRI beads. Quality was assessed via Qubit and Bioanalyzer. Libraries were prepared using Nextera XT for tagmentation and adapter ligation, PCR-amplified, bead-purified, and stored at –20 °C

treatment_protocol: Cells were pre-treated with 500 ng/ml recombinant IFNγ for 24 hours, followed by infection with M. tuberculosis (Mtb) at a multiplicity of infection (MOI) of 1 for an additional 24 hours

value: bone marrow derived macrophages

value: IFNy stimulated and Mtb infected


title: Day10_COCL2_scMulti_ATAC_2022_05_17

description:
Library name: Sample34
10X Multiome

value: CoCl2 for 10 days


title: SAMPLE 19

description:
Library name: G923-01
Small RNA library prepared using QIAseq miRNA kit with UMI

value: F


title: P. promelas larvae, EFP, biological replicate EFP_B02, lane 1, time step = 3, analyzed on 20161007

description: Library name: 20161007_ EFP_3_B02_GTCCGC_L001_R1_001


title: Mouse macrophages, Donor M5, Mtb infected

description: Library name: M5_Mtb

value: Mtb infected


title: Day10_COCL2_scMulti_ATAC_2022_05_16

description:
Library name: Sample33
10X Multiome


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 2, time step = 2, analyzed on 20161007

description: Library name: 20161007_ EFP_2_B07_GGCTAC_L002_R1_001

value: whole larvae


title: SAMPLE 18

description:
Library name: G984-31
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Saliva

value: M


title: Mouse macrophages, Donor M5, IFNy stimulated

description: Library name: M5_IFNy

value: IFNy stimulated


title: Day10_DABTRAM_scMulti_ATAC_2022_05_17

description:
Library name: Sample32
10X Multiome

value: Dabrafenib and Trametinib for 10 days


title: SAMPLE 17

description:
Library name: G984-30
Small RNA library prepared using QIAseq miRNA kit with UMI


title: Mouse macrophages, Donor M5, untreated control

description: Library name: M5_CTR

value: untreated control


title: P. promelas larvae, EFP, biological replicate EFP_B07, lane 1, time step = 2, analyzed on 20161007

description: Library name: 20161007_ EFP_2_B07_GGCTAC_L001_R1_001

value: 2 dpf


title: Day10_DABTRAM_scMulti_ATAC_2022_05_16

description:
Library name: Sample31
10X Multiome


title: SAMPLE 16

description:
Library name: G984-28
Small RNA library prepared using QIAseq miRNA kit with UMI


title: Mouse macrophages, Donor M4, IFNy stimulated and Mtb infected

description: Library name: M4_IFNyMtb


title: Day0_scMulti_ATAC_2022_05_17

description:
Library name: Sample30
10X Multiome

value: No Treatment


title: SAMPLE 15

description:
Library name: G984-27
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 2, time step = 1, analyzed on 20161007

description: Library name: 20161007_ EFP_1_B03_ACTGAT_L002_R1_001

value: EFP


title: P. promelas larvae, EFP, biological replicate EFP_B03, lane 1, time step = 1, analyzed on 20161007

description: Library name: 20161007_ EFP_1_B03_ACTGAT_L001_R1_001


title: Day0_scMulti_ATAC_2022_05_16

description:
Library name: Sample29
10X Multiome


title: Mouse macrophages, Donor M4, Mtb infected

description: Library name: M4_Mtb


title: SAMPLE 14

description:
Library name: G984-26
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, UP, biological replicate UP_FIELD20, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ UP_FIELD_20_ATGTCA_L002_R1_001

value: UP


title: Mouse macrophages, Donor M4, IFNy stimulated

description: Library name: M4_IFNy


title: SAMPLE 25

description:
Library name: G923-09
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD


title: SAMPLE 13

description:
Library name: G984-25
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH


title: MALE_PDT_D6

city: Bryan

first: Irtisha

last: Singh

state: Texas

address: 8447 Riverside Pkwy

department: Cell Biology and Genetics

institute: Texas A&M University Health Science Center

data_processing:
The RNA quality was evaluated on the TapeStation 4200 using High sensitivity RNA screen tape and RNA was diluted to 100 pg/ul for a 1 ng input.
QC on the libraries were done on the TapeStation 4200 and concentrations were done on the ThermoFisher Qubit.
Libraries were diluted to 4nM and pooled for sequencing on the Nova Seq.
The sequenced reads of RNA-seq experiments were aligned to the drosophila melanogaster reference genome dm6 using STAR aligner
Gene expression was determined as reads per kilobase million (RPKM) by counting the number of uniquely mapping reads and normalizing it by gene length
Assembly: dm6
Supplementary files format and content: tab-delimited text file includes RPKM content for all RNA-seq samples

organism: Drosophila melanogaster

source_name: brain cells

extract_protocol:
The RNA was extracted using the Maxwell RSC simplyRNA tissue kit using the Maxwell 16 instrument from D. melanogaster brain samples
The SMART-Seq mRNA LP kit from Takara Bio USA, INC was used to prepare the libraries for the samples.

value: brain cells

tag: gender

value: male

value: photodynamic therapy


title: Mouse macrophages, Donor M4, untreated control

description: Library name: M4_CTR

value: bone marrow derived macrophages


title: P. promelas larvae, UP, biological replicate UP_FIELD20, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ UP_FIELD_20_ATGTCA_L001_R1_001


title: MALE_PDT_D5


title: SAMPLE 12

description:
Library name: G984-24
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, UP, biological replicate UP_FIELD06, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ UP_FIELD_06_GCCAAT_L002_R1_001


title: Mouse macrophages, Donor M3, IFNy stimulated and Mtb infected

description: Library name: M3_IFNyMtb

value: IFNy stimulated and Mtb infected


title: MALE_PDT_D4


title: SAMPLE 11

description:
Library name: G984-23
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, UP, biological replicate UP_FIELD06, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ UP_FIELD_06_GCCAAT_L001_R1_001

value: whole larvae


title: MALE_PDT_D3


title: Mouse macrophages, Donor M3, Mtb infected

description: Library name: M3_Mtb

value: Mtb infected


title: SAMPLE 10

description:
Library name: G984-22
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Saliva

value: F


title: P. promelas larvae, EFP, biological replicate EFP_FIELD24, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ EFP_FIELD_24_AGTTCC_L002_R1_001


title: MALE_PDT_D2


title: Mouse macrophages, Donor M3, IFNy stimulated

description: Library name: M3_IFNy

value: IFNy stimulated


title: P. promelas larvae, EFP, biological replicate EFP_FIELD24, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ EFP_FIELD_24_AGTTCC_L001_R1_001


title: Mouse macrophages, Donor M3, untreated control

description: Library name: M3_CTR

value: untreated control


title: SAMPLE 9

description:
Library name: G984-21
Small RNA library prepared using QIAseq miRNA kit with UMI

value: M


title: SAMPLE 8

description:
Library name: G984-20
Small RNA library prepared using QIAseq miRNA kit with UMI


title: MALE_PDT_D1


title: P. promelas larvae, EFP, biological replicate EFP_FIELD06, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ EFP_FIELD_06_AGTCAA_L002_R1_001

value: 2 dpf


title: Mouse macrophages, Donor M2, IFNy stimulated and Mtb infected

description: Library name: M2_IFNyMtb


title: FEM_PDT_C7

value: female


title: P. promelas larvae, MHW, biological replicate MHW_B13, lane 1, time step = NA, analyzed on 20161011

description: Library name: 20161011_ 15-07_B13_AGTTCC_L001_R1_001

value: MHW


title: P. promelas larvae, EFP, biological replicate EFP_FIELD06, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ EFP_FIELD_06_AGTCAA_L001_R1_001

value: EFP


title: SAMPLE 7

description:
Library name: G984-19
Small RNA library prepared using QIAseq miRNA kit with UMI

value: BPD


title: Mouse macrophages, Donor M2, Mtb infected

description: Library name: M2_Mtb


title: FEM_PDT_C6

value: brain cells


title: Mouse macrophages, Donor M2, IFNy stimulated

description: Library name: M2_IFNy


title: P. promelas larvae, DWIP, biological replicate DWIP_B07, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ DWIP_B07_CTTGTA_L002_R1_001

value: DWIP


title: SAMPLE 6

description:
Library name: G984-18
Small RNA library prepared using QIAseq miRNA kit with UMI


title: SAMPLE 5

description:
Library name: G984-17
Small RNA library prepared using QIAseq miRNA kit with UMI


title: P. promelas larvae, DWIP, biological replicate DWIP_B07, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ DWIP_B07_CTTGTA_L001_R1_001


title: FEM_PDT_C5

value: photodynamic therapy


title: Mouse macrophages, Donor M1, IFNy stimulated and Mtb infected

description: Library name: M1_IFNyMtb

value: bone marrow derived macrophages


title: FEM_PDT_C4


title: P. promelas larvae, DSP, biological replicate DSP_B19, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ DSP_B19_ACAGTG_L002_R1_001

value: DSP


title: SAMPLE 4

description:
Library name: G984-16
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH


title: Mouse macrophages, Donor M1, Mtb infected

description: Library name: M1_Mtb

value: Mtb infected


title: SAMPLE 3

description:
Library name: G984-15
Small RNA library prepared using QIAseq miRNA kit with UMI

value: Saliva


title: FEM_PDT_C3


title: P. promelas larvae, DSP, biological replicate DSP_B19, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ DSP_B19_ACAGTG_L001_R1_001

value: whole larvae


title: Mouse macrophages, Donor M1, untreated control

description: Library name: M1_CTR


title: FEM_PDT_C2


title: SAMPLE 2

description:
Library name: G984-14
Small RNA library prepared using QIAseq miRNA kit with UMI

value: F


title: P. promelas larvae, MHW, biological replicate MHW_B02, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ 15-08_B02_GTGAAA_L002_R1_001


title: FEM_PDT_C1


title: Treg depleted, replicate 5

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 1800 Orleans St

institute: Johns Hopkins

description: Library name: DTR_PCL5

data_processing:
Fastq files were aligned and gene expression was quantified using STAR aligner with counting.
Assembly: GRCm38 genome with GENCODE vM23 annotations
Supplementary files format and content: Processed data include raw counts files for each sample.

source_name: quadricep and fibrosis

extract_protocol:
RNAlater for storage to Trizol with chloroform extraction and RNA purification with Qiagen Rneasy PLUS Mini Kit
cDNA synthesis and library preparation was performed with the Stranded mRNA Prep, Ligation kit (Illumina). QC testing used Qubit and Agilent Fragment Analyzer, after which the libraries were pooled and sequenced with the NovaSeq platform (Illumina) using a SP100 flow cell with targeted rea₫ depth of 50 million/sample.

treatment_protocol: 50ng/g of DT on days -1 and -3 to harvest

value: quadricep and fibrosis

value: 50ng/g DT -1 and -3 days before harvest


title: P. promelas larvae, MHW, biological replicate MHW_B02, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ 15-08_B02_GTGAAA_L001_R1_001

value: 2 dpf


title: SAMPLE 1

description:
Library name: G984-13
Small RNA library prepared using QIAseq miRNA kit with UMI

value: M


title: Treg depleted, replicate 4

description: Library name: DTR_PCL4


title: MALE_CONTROL_B7

value: male

value: control


title: P. promelas larvae, MHW, biological replicate MHW_B07, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ 15-07_B07_GTTTCG_L002_R1_001

value: MHW


title: MALE_CONTROL_B6

value: brain cells


title: LUSC_2_3

first: Xiao

last: Yu

address: No. 17, Panjiayuan Nanli, Chaoyang District, Beijing

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

description: Library name: 27#

data_processing:
Utilize magnetic beads with oligo-dT to isolate mRNA from total RNA, and fragment the captured mRNA. Then, utilize reverse transcriptase to synthesize the first and second strands of cDNA, perform end repair on the reverse transcription products, and add A bases at the 3' end.
Subsequently, connect the fragment with sequencing adapters. After purifying the connection product, remove the products with incomplete connections and empty adapter self-ligation products, and then perform PCR amplification using primers complementary to the adapter sequence.
Finally, purify with magnetic beads to obtain the sequencing library
Assembly: h19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: tumor tissue

growth_protocol: Cells were cltured with RPMI-1640 supplemented with 10% FBS and 1% P/S in humidified atmosphere with 5%CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol Regant
The libiary were prepared using SAMRTER mRNA-seq library Prep Kit following manufacturer's protocols

value: tumor tissue

value: Patient-derived organoids

tag: tissue type

value: LUSC


title: LUSC_2_2

description: Library name: 26#


title: P. promelas larvae, MHW, biological replicate MHW_B07, lane 1, time step = NA, analyzed on 20161006

description: Library name: 20161006_ 15-07_B07_GTTTCG_L001_R1_001

extract_protocol:
Total RNA was isolated from individual FHM using the MagMAX-96 Total RNA Isolation Kit (ThermoFisher Scientific) following manufacturer's protocols. RNA was quantified by spectrophotometric analysis with a Synergy HTX multi-mode plate reader (BioTek).
Neoprep Library Prep System (Illumina) and the TruSeq Stranded mRNA Library Prep for NeoPrep (Illumina). Library concentrations were determined using either the KAPA Library Quantification Kit (Kapa Biosystems) or Qubit dsDNA HS Assay (ThermoFisher Scientific), normalized to equimolar amounts, and then combined into pools of eight samples each. Sequencing was performed at Michigan State University’s RTSF Genomics Core on the Illumina HiSeq 2500 Rapid Run flow cell (v2) for 1x50 bp single-end reads with Rapid SBS reagents.


title: Treg depleted, replicate 3

description: Library name: DTR_PCL3


title: Treg depleted, replicate 2

description: Library name: DTR_PCL2


title: MALE_CONTROL_B5


title: LUSC_2_1

description: Library name: 25#


title: Treg depleted, replicate 1

description: Library name: DTR_PCL1


title: P. promelas larvae, UP, biological replicate UP_B23, lane 2, time step = 4, analyzed on 20161006

description: Library name: 20161006_ UP_4_B23_ACTGAT_L002_R1_001

value: UP


title: MALE_CONTROL_B4


title: LUSC_1_3

description: Library name: 24#


title: SAMPLE 59

description:
Library name: G778-13
Small RNA library prepared using QIAseq miRNA kit with UMI

value: PH


title: MALE_CONTROL_B3


title: WT control, replicate 5

description: Library name: WT_PCL5

value: WT


title: P. promelas larvae, UP, biological replicate UP_B23, lane 1, time step = 4, analyzed on 20161006

description: Library name: 20161006_ UP_4_B23_ACTGAT_L001_R1_001


title: LUSC_1_2

description: Library name: 23#


title: WT control, replicate 4

description: Library name: WT_PCL4


title: P. promelas larvae, UP, biological replicate UP_B30, lane 2, time step = 3, analyzed on 20161006

description: Library name: 20161006_ UP_3_B30_ACTTGA_L002_R1_001


title: LUSC_1_1

description: Library name: 22#


title: P. promelas larvae, UP, biological replicate UP_B30, lane 1, time step = 3, analyzed on 20161006

description: Library name: 20161006_ UP_3_B30_ACTTGA_L001_R1_001


title: WT control, replicate 3

description: Library name: WT_PCL3


title: MALE_CONTROL_B2


title: MALE_CONTROL_B1


title: ESCC_3_3

description: Library name: 21#

value: ESCC


title: P. promelas larvae, UP, biological replicate UP_B27, lane 2, time step = 2, analyzed on 20161006

description: Library name: 20161006_ UP_2_B27_GTGGCC_L002_R1_001

value: whole larvae


title: FEMALE_CONTROL_A5

value: female


title: ESCC_3_2

description: Library name: 20#


title: WT control, replicate 1

description: Library name: WT_PCL1

value: quadricep and fibrosis


title: P. promelas larvae, UP, biological replicate UP_B27, lane 1, time step = 2, analyzed on 20161006

description: Library name: 20161006_ UP_2_B27_GTGGCC_L001_R1_001


title: WT control, replicate 2

description: Library name: WT_PCL2

value: 50ng/g DT -1 and -3 days before harvest


title: FEMALE_CONTROL_A4


title: ESCC_3_1

description: Library name: 19#


title: TNFR2 positive Treg-3

city: Nantong

first: Liwen

last: Zhao

address: 9 Seyuan Road

institute: Nantong University

description:
Library name: TNFR2 positive Treg-3
Column name in all_expression_raw_counts.txt: TNFR2 positive Treg-3

data_processing:
In order to better process this junction sequence, we used HISAT2 (v2.1.0) (Kim, D., Paggi, J.M., Park, C. et al., 2019) to align RNA sequencing data to the reference genome using HISAT2 (v2.1.0) that supports split read alignment
Integrate the original read count of gene expression from multiple samples.
Assembly: GRCm39
Supplementary files format and content: tab-delimited txt file includes raw counts values for each Sample

source_name: TNFR2 positive Treg

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. 2ug of total RNA was used for the construction of sequencing libraries.
Magnetic beads with oligo-dT were used to isolate mRNA from total RNA and the captured mRNA was fragmented. The first and second strands of cDNA were then synthesized using reverse transcriptase and the reverse transcription product was end-repaired, followed by the addition of a base A at the 3' end. The fragment is then connected to the sequencing adapter. The ligation product is purified, the product with incomplete ligation and the empty linker self-ligation product are removed, and PCR amplification is performed using primers that complement the linker sequence. Finally, the sequencing library was purified by magnetic beads.

value: TNFR2 positive Treg


title: P. promelas larvae, UP, biological replicate UP_B27, lane 2, time step = 1, analyzed on 20161006

description: Library name: 20161006_ UP_1_B27_TAGCTT_L002_R1_001

data_processing:
Raw read quality assessment with FastQC 0.11.9 & MultiQC 1.12
Reads were processed with fastp 0.23.2 trimming with quality, length, and adapter trimming all enabled by default, and polyX trimming (flag: -x) enabled manually
Alignment with STAR 2.7.10a (--outSAMattributes NH HI AS NM MD --outSAMtype BAM SortedByCoordinate --outSAMheaderHD @HD VN 1.4 SO:sorted --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outSAMunmapped Within --outFilterType BySJout)
Quantification with STAR 2.7.10a (--quantMode GeneCounts TranscriptomeSAM)
Assembly: P. promelas, GCF_016745375.1_EPA_FHM_2.0
Supplementary files format and content: Tab delimited text file with gene counts: all_counts_20220629.txt uploaded separately.

value: 2 dpf


title: FEMALE_CONTROL_A3


title: ESCC_2_3

description: Library name: 18#


title: P. promelas larvae, UP, biological replicate UP_B27, lane 1, time step = 1, analyzed on 20161006

description: Library name: 20161006_ UP_1_B27_TAGCTT_L001_R1_001


title: FEMALE_CONTROL_A2


title: ESCC_2_2

description: Library name: 17#


title: TNFR2 positive Treg-2

description:
Library name: TNFR2 positive Treg-2
Column name in all_expression_raw_counts.txt: TNFR2 positive Treg-2


title: TNFR2 positive Treg-1

description:
Library name: TNFR2 positive Treg-1
Column name in all_expression_raw_counts.txt: TNFR2 positive Treg-1


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 2, time step = 3, analyzed on 20161006

description: Library name: 20161006_ EFP_3_B22_GAGTGG_L002_R1_001

value: EFP


title: FEMALE_CONTROL_A1

value: control


title: TNFR2-deficient Treg-3

description:
Library name: TNFR2-deficient Treg-3
Column name in all_expression_raw_counts.txt: TNFR2-deficient Treg-3

source_name: TNFR2-deficient Treg

value: TNFR2-deficient Treg


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 1, time step = 3, analyzed on 20161006

description: Library name: 20161006_ EFP_3_B22_GAGTGG_L001_R1_001

source_name: whole larvae


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 2, time step = 2, analyzed on 20161006

description: Library name: 20161006_ EFP_2_B27_GTCCGC_L002_R1_001


title: ESCC_2_1

description: Library name: 16#


title: Library_12

city: Québec

first: Aldcejam

last: Martins da Fonseca Junior

state: QC

address: Services Pavilion, 2440 Bd Hochelaga Suite 1710

department: Animal Sciences

country: Canada

institute: Laval University

description: Library name: Library_12

data_processing:
Adapter trimming and quality filtering were performed using fastp (version 0.23.1) (Chen et al., 2018).  Reads with Phred scores < 30 were discarded, and only sequences ≥ 50 bp were retained. Read conversion, alignment to the Bos taurus reference genome (ARS-UCD1.2.104), and methylation calling were performed using Bismark (Krueger and Andrews, 2011). These steps were implemented within the DRAGEN Methylation Pipeline, which was executed on an Illumina DRAGEN server using default parameters. Lambda DNA spike-in was used to calculate conversion efficiency, and only samples with conversion rates >98% were included in downstream analyses
Adapter sequences and low-quality bases were trimmed using fastp (v0.23.1), applying default quality thresholds. Reads were aligned to the ARS-UCD1.2 (bosTau9) reference genome using Bismark (v0.23.0), with Bowtie2 as the underlying aligner.
Quality control metrics were compiled for each sample, including alignment rates, duplication levels, and conversion efficiency.
Only samples meeting stringent QC thresholds were retained for downstream analyses.
Methylation Extraction: PCR duplicates were removed, and single-nucleotide methylation extraction was strictly executed within the CpG context using Bismark's methylation extractor to generate the final context reports.
Assembly: Alignment to the Bos taurus reference genome (ARS-UCD1.2.104)
Supplementary files format and content: The submitted *.CX_report.txt processed files represent the base-resolution single-nucleotide methylation status generated by Bismark. These tab-delimited files contain the following structured columns for user interpretation:
Supplementary files format and content: 1. Chromosome (Bovine ARS-UCD1.2 scaffolds)
Supplementary files format and content: 2. Position (1-based genomic coordinate)
Supplementary files format and content: 3. Strand (+ or -)
Supplementary files format and content: 4. Count of methylated cytosines (coverage count supporting methylation)
Supplementary files format and content: 5. Count of unmethylated cytosines (coverage count supporting unmethylated status)
Supplementary files format and content: 6. Cytosine context (explicitly categorized into CG, CHG, or CHH contexts)
Supplementary files format and content: 7. Trinucleotide context
Library strategy: EM-seq

organism: Bos taurus

source_name: blood

extract_protocol:
Genomic DNA was extracted from whole-blood samples, and libraries were prepared with the NEBNext Enzymatic Methyl-seq Kit (New England Biolabs, Ipswich, MA) according to the manufacturer’s instructions. This protocol utilizes TET2 oxidation and APOBEC deamination to achieve base-resolution methylation calls while minimizing DNA degradation
Libraries were sequenced on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads at the Génome Québec Innovation Centre (Montreal, QC, Canada). Each sample generated hundreds of millions of reads, providing deep coverage for CpG-resolution analysis.

treatment_protocol: forty-eight female Holstein calves were selected in the Canadian province of Quebec as part of a longitudinal health surveillance program. All animals were sampled at approximately 40 days of age, representing the preweaning window of susceptibility. Calves were stratified into three phenotypically defined groups based on clinical veterinary records: low body mass index (BMI), respiratory disease (RESP), and diarrhea (DIAR), using established indicators for morbidity and growth in dairy calves [30]. A fourth group of resilient calves, showing no signs of these conditions, was used as a control.

value: blood

value: Holstein

value: Respiratory Disease and Diarrhea vs Resilient Control Contrast


title: ESCC_1_3

description: Library name: 15#

value: tumor tissue

value: Patient-derived organoids


title: TNFR2-deficient Treg-2

description:
Library name: TNFR2-deficient Treg-2
Column name in all_expression_raw_counts.txt: TNFR2-deficient Treg-2


title: Library_11

description: Library name: Library_11


title: ESCC_1_2

description: Library name: 14#


title: P. promelas larvae, EFP, biological replicate EFP_B27, lane 1, time step = 2, analyzed on 20161006

description: Library name: 20161006_ EFP_2_B27_GTCCGC_L001_R1_001


title: TNFR2-deficient Treg-1

description:
Library name: TNFR2-deficient Treg-1
Column name in all_expression_raw_counts.txt: TNFR2-deficient Treg-1


title: ESCC_1_1

description: Library name: 13#


title: Library_10

description: Library name: Library_10


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 2, time step = 1, analyzed on 20161006

description: Library name: 20161006_ EFP_1_B22_GGCTAC_L002_R1_001


title: 510L013-3

description: Library name: 12#


title: Islet cells,CDS group

city: Shenzhen

first: 丰

last: 洪

address: Shenzhen Institute of Advanced Technology

description:
Library name: CDS
10x Genomics

library_source: transcriptomic single cell

data_processing:
All single-cell analyses were performed using Cell Ranger and Seurat, as described previously37,38. Raw reads were first demultiplexed and mapped to the reference genome using the 10X Genomics Cell Ranger pipeline. Digital expression matrices were generated by counting unique molecule identifiers for each gene and cell barcode (filtered by Cell Ranger V7.1). Genes expressed in more than 3 cells were considered as expressed, and each cell was required at least 200 expressed genes. Subsequent analyses included secondary gene expression analysis, global analysis between samples, and enrichment analysis of cell type-specific markers. Data were normalized, clustered, and subjected to differential expression analysis using the Seurat V4 package. Canonical correlation analysis (CCA) was performed for integrated analysis of datasets. Clustering was performed using highly variable genes, and principal components were calculated to build a graph, which was segmented with a resolution of 0.6. Differential expression analysis between samples was performed using the edgeR package to identify zone-specific marker gene. Cell types were annotated based on marker genes for each cluster, and Gene Ontology (GO) enrichment analysis was conducted using clusterProfiler R package. Go terms with adjusted P-values less than 0.05 were considered significantly enriched.
Assembly: Mouse mm10
Supplementary files format and content: Helicobacter pylori ASM2599845v1
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreas

extract_protocol:
The isolated single islet-cell suspensions were barcoded with a 10x Chromium Controller (10X Genomics) according to the manufacturer's instructions. RNA from the barcoded cells was reverse-transcribed, and sequencing libraries were constructed using the Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry, 10X Genomics). Sequencing was performed on an Illumina NovaSeq 6000 platform.
Library was performed according to the manufacter's instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, Islets were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in- emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRlselect reagent for subsequent library construction. During the library construction llumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: the DIO mice treatmented with 10 mg/kg CDS or Saline for 2 weeks and then isolated the islets

value: Pancreas

value: islet b cell

value: CDS


title: Islet cells, saline group

institute: Shenzhen Institute of Advanced Technology

description:
Library name: Saline
10x Genomics

value: saline


title: 510L013-2

description: Library name: 11#

value: WT


title: Library_08

description: Library name: Library_08


title: Library_09

description: Library name: Library_09


title: P. promelas larvae, EFP, biological replicate EFP_B22, lane 1, time step = 1, analyzed on 20161006

first: Steven

last: Purucker

institute: US EPA

description: Library name: 20161006_ EFP_1_B22_GGCTAC_L001_R1_001

value: whole larvae


title: P. promelas larvae, MHW, biological replicate MHW_B27, lane 2, time step = NA, analyzed on 20161006

description: Library name: 20161006_ 15-07_B27_ATCACG_L002_R1_001

value: MHW


title: NAIO3-spatial

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

description: Library name: Sample1

data_processing:
Space Ranger (10x Genomics, version 1.2.0) for spatial transcriptomics
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: features.tsv.gz. list of genes
Library strategy: Spatial Transcriptomics

source_name: eyeball

extract_protocol:
For spatial transcriptomics sample preparation, eyeballs from NaIO3 mouse and PBS mouse were placed together in the same  embedding mold. Specifically, the eyeball from NaIO3 mouse was positioned in the upper left corner of the embedding mold, while the eyeball from PBS mouse was placed in the lower right corner. It was ensured that the maximum diameters of the two eyeballs were on the same horizontal plane. After sample positioning was completed, the entire embedding space was quickly filled with OCT (Optimal Cutting Temperature compound), and then the sample was immediately placed in liquid nitrogen for rapid freezing. After the rapid freezing process was finished, the samples awaited subsequent sectioning operations. Cryosections of eyeballs were cut at a thickness of 10 μm and mounted onto GEX arrays.Spatial gene expression profiling was performed using the Visium Spatial Gene Expression Slide and Reagent Kit (10x Genomics).
RNA libraries of  spatial transcriptomics were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were injected intravenously with 20 mg/kg of NaIO3 (Sigma-Aldrich Corp., St. Louis, MO, USA), which was dissolved in phosphate-buffered saline (PBS). The mice receiving the same volume of PBS worked as controls.Seven days later, the mice were sacrificed by carbon dioxide euthanasia and the eyes were collected for further investigation.

value: eyeball


title: Library_07

description: Library name: Library_07


title: 510L013-1

description: Library name: 10#


title: P. promelas larvae, MHW, biological replicate MHW_B27, lane 1, time step = NA, analyzed on 20161006

address: 109 TW Alexander Dr

description: Library name: 20161006_ 15-07_B27_ATCACG_L001_R1_001

value: 2 dpf


title: Control-1, NestinCre-Ai14, Cut&tag, H3K4me3

city: Xiamen

first: shuzhong

last: wang

state: Fujian

address: Xiangan South Road

department: School of Medicine

institute: Xiamen University

description: Library name: Control-H3K4me3-1

data_processing:
Neurons were performed using Bcl2Fastq for Novaseq output
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: cortex

extract_protocol:
The dorsal pallium was isolated from embryonic brains by micro-dissecting, and the tissue was transferred into ice-cold HBSS (no Ca2+, Mg2+) (Gibco) supplemented with B27 (Gibco) on a 24-well plate. After identification of Nestin-Cre; Ai14 (Control) and Nestin-Cre; Men1flox/flox; Ai14 (NCKO) genotypes, the cortices were digested in the solution containing 2 mg/mL Papain (Sigma) and 200 units/mL DNase (Sigma), followed by incubation for 20 minutes at 37°C. Subsequently, gently manual trituration of the tissue in the plate. The cell suspension was dropped across a 70 μm filter and then washed twice. The cells were incubated with 2-(4-Amidinophenyl)-6-indolecarbamidine dihydrochloride (DAPI) before sorting, Flash-tag+ Ai14+ cells were isolated using Beckman MoFlo Astrios EQS. Singlet cells were first sorted by forward and Side scattering properties (FSC and SSC), then the thresholds for FITC and PE sorting gates were set labeling cells. The negativity for DAPI to collect approximately 5×104 living cells in every biological replicate. The solution collected sorted cells kept at room temperature without Ca2+ and Mg2+
Cut&tag-seq was performed as previously described, using Hyperactive Universal CUT&Tag Assay Kit for Illumina. The positive cell enrichment was performed essentially using the ATAC-seq protocol. The cells were bound to Concanavalin A beads in wash buffer added complete protease inhibitors (Roche), then the cells were incubated with primary antibody in antibody buffer at 4°C overnight, followed by incubation with secondary antibodies goat anti-rabbit IgG H&L or goat anti-mouse IgG H&L for 1h at room temperature. Subsequently, the cells were incubated with pA/G-Tn5 adapter complex in Dig-300 buffer for 1h at room temperature after washing with Dig-Wash buffer. The cells were washed with Dig-300 buffer for three times and performed tagmentation in Dig-300 Wash buffer with Mg2+ for 1h at 37°C, then stop tagmentation with 0.1% SDS and digested with Proteinase K for 10 min at 55°C. The tagmented DNA was purified by DNA Extract Beads and amplified by PCR connecting sequencing adapters. The libraries were purified, using VAHTS DNA Clean Beads (N411, Vazyme Biotech). After library quality, the sequencing was performed, using PE150 reads on Illumina NovaSeq3000 (Novogene, Beijing, China).

value: cortex

value: neurons

value: Men1-WT (Ai14)


title: Library_06

description: Library name: Library_06

value: blood

value: Low BMI and Diarrhea vs Resilient Control Contrast


title: P. promelas larvae, UP, biological replicate UP_FIELD52, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ UP_FIELD_52_ATGTCA_L002_R1_001

value: UP


title: NCKO, NestinCre-Ai14-MEN1-KO, Cut&tag, RNA POLII

description: Library name: NCKO-RNA POLII

value: Men1-NCKO (Ai14)


title: 510DMSO-3

description: Library name: 9#

value: DMSO


title: Library_05

description: Library name: Library_05

value: Holstein


title: P. promelas larvae, UP, biological replicate UP_FIELD52, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ UP_FIELD_52_ATGTCA_L001_R1_001


title: 510DMSO-2

description: Library name: 8#


title: P. promelas larvae, UP, biological replicate UP_FIELD51, lane 2, time step = NA, analyzed on 20161005

description: Library name: 20161005_ UP_FIELD_51_AGTTCC_L002_R1_001


title: 510DMSO-1

description: Library name: 7#


title: Control, NestinCre-Ai14, Cut&tag, RNA POLII

description: Library name: Control-RNA POLII


title: Library_04

description: Library name: Library_04


title: NCKO, NestinCre-Ai14-MEN1-KO, Cut&tag, H3K9ac

description: Library name: NCKO-H3K9ac


title: 150L013-3

description: Library name: 6#


title: Library_03

description: Library name: Library_03


title: P. promelas larvae, UP, biological replicate UP_FIELD51, lane 1, time step = NA, analyzed on 20161005

description: Library name: 20161005_ UP_FIELD_51_AGTTCC_L001_R1_001


title: Library_02

description: Library name: Library_02


title: 150L013-2

description: Library name: 5#