title: Sertraline hydrochloride exposure, replicate C, concentration 12249

description: Library name: sertraline_C_12249


title: NK, fresh condition, wild type, replicate 3

status: Public on Aug 18 2025

type: SRA

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

country: USA

institute: Washington University in St Louis

description:
Library name: Fresh_WT_rep3
Fresh_WT_rep3

library_source: transcriptomic

data_processing:
Basecalls and demultiplexing were performed with Illumina's bcl2fastq2 software.
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: mm10
Supplementary files format and content: csv file including differential expression result
Supplementary files format and content: all.genes_counts_raw.tsv

molecule: total RNA

organism: Mus musculus

source_name: Spleen

growth_protocol: Rosa YFP/YFP Ncr1 CRE-ERT2 or Acly fl/fl Rosa YFP/YFP Ncr1 CRE-ERT2 mice were treated with tamoxifen diet for 48 hours. 5 days after withdrawal of tamoxifen diet, YFP+ cells from splenic NK cells were sorted.

extract_protocol:
RNA was harvested with Rneasy kit (Qiagen)
Takara-Clontech SMARTer

treatment_protocol: Priming was induced by IL-15 (100ng/ml) for 72 hours. Primed NK cells were washed and stimulated with plate-bound NKG2D (20ug/ml) for 6 hours.

tag: tissue

value: Spleen

tag: cell type

value: NK cell

tag: treatment

value: Fresh


title: Wildtype mouse 2, no doxycycline, eye cup (RPE, choroid, sclera)

city: Dallas

first: Katherine

middle: J.

last: Wert

state: TX

address: 5323 Harry Hines Blvd. E7.138

department: Ophthalmology and Molecular Biology

institute: University of Texas Southwestern Medical Center

description:
WTnoDx_RPE2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

data_processing:
Samples were processed by Novogene Inc.
Original image data file is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Remove reads with adapter contamination. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).  Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Perform alignments with HISAT2 to the reference. Gene expression level is calculated by the number of mapped reads.
Assembly: GRCm39/mm39
Supplementary files format and content: file includes: Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

molecule: polyA RNA

source_name: Eye cup (RPE, choroid, sclera)

growth_protocol: Animals were kept on a light–dark cycle (12 hour–12 hour). Food and water were available ad libitum throughout the experiment.

extract_protocol:
Eyes were dissected to harvest the neural retina and remaining eye cup (RPE, sclera, choroid), which were then flash frozen using liquid nitrogen. RNA was extracted from tissue samples following the standard protocol of the Qiagen RNeasy Mini Kit (Qiagen, 74106).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Mice were provided 2mg/mL doxycycline (Sigma-Aldrich, #D9891-100G) with 10% sucrose (Sigma-Aldrich, S0389-1KG) orally via drinking water. Doxycycline and sucrose treated water was provided ad libitum in red tinted water bottles for 72 hours.

value: Eye cup (RPE, choroid, sclera)

tag: genotype

value: Wildtype


title: Preterm microbiome, 2 wks old, mouse 2

city: Chicago

first: Jing

last: Lu

state: Illinois

address: 900 E 57th St

institute: University of Chicago

description: Library name: ECZ-16

library_source: transcriptomic single cell

data_processing:
The processed data files were created using Cell Ranger’s (10x Genomics) count function to align sequencing reads to the GRCm38 (mm10) mouse reference genome. The uploaded files originate from the raw_feature_bc_matrix folder created by running the function for each sample.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz - Contains a sparse gene expression matrix (UMI counts). Each non-zero entry indicates the number of UMIs detected for a specific gene in a specific cell. Cells and genes are referenced by indices that correspond to entries in barcodes.tsv.gz and features.tsv.gz.
Supplementary files format and content: barcodes.tsv.gz - Provides cell barcode identifiers
Supplementary files format and content: features.tsv.gz - Provides gene names/IDs

source_name: brain

growth_protocol: All mice in this study were allowed ad libitum access to NIH-31 germ-free chow and water. We maintained germ-free C57BL/6J mice (Jackson Laboratory, ME, USA) at the Gnotobiotic Research Animal Facility at the University of Chicago, where animals are routinely tested for microbes and parasites to ensure they remain germ-free.

extract_protocol:
When the pups reached two weeks of age, we collected whole-brain samples from four of the full-term microbiome mice (three female, one male) and four of the preterm microbiome mice (two female, two male). To isolate brain cells, we used the Neural Tissue Dissociation Kit - Postnatal Neurons created by Miltenyi Biotec. We followed the protocol established by Miltenyi Biotec for use of the kit without small modifications: using a 40 µm strainer instead of a 70 µm one, incubation after addition of enzyme mix 1 for eight minutes instead of fifteen, and incubation after dissociation of tissue for six minutes instead of ten. The change in filter size was necessary to remove debris, and we shortened the incubation times to reduce potential cell stress and RNA degradation.
We prepared scRNA-seq libraries using Chromium Next GEM Single Cell 3′ v.3.1 reagent kit (10x Genomics, CA, USA). We barcoded cells using the Chromium Controller (10x Genomics). Eleven polymerase chain reaction cycles were applied to generate cDNA and thirteen cycles for final library generation. The final scRNA-seq libraries were sequenced with the Illumina NovaSeq X (Illumina, CA, USA).

treatment_protocol: We obtained patient fecal samples from 2015 to 2023 from the Center for the Science of Early Trajectories biorepository at the University of Chicago Comer Children’s Hospital, which operates a level IV NICU in Chicago, IL, USA. All infants enrolled were delivered between 24 and 40 weeks of gestation age (GA) and had no congenital anomalies. We thawed 100-mg aliquots of fecal samples from two full-term, healthy infants at GAs of 39 weeks and 40 weeks (MTerm) and a sample from an infant born from a mother with confirmed chorioamnionitis with GA of 24 weeks (MPreterm). Under anaerobic conditions, we resuspended the fecal samples in PBS, clarified the homogenates through 100 µm nylon filters (BD Falcon, NJ, USA), and stored them in in PBS containing glycerol (concentration of 15% v/v) at -80°C in 600 µL aliquots. We colonized germ-free mice by gavaging eight- to nine-week-old pregnant females (estimated embryonic day 15-17) with 250 µL aliquots of the prepared MTerm or MPreterm fecal supernatant. Pups were delivered spontaneously and kept with their mothers until weaning, allowing them to naturally acquire the transplanted patient-derived microbiota.

value: brain

tag: strain

tag: Sex

value: male

value: preterm microbiome

tag: batch


title: Sertraline hydrochloride exposure, replicate B, concentration 12249

city: Duluth

first: Phillip

last: Ankley

state: MN

address: 6201 Congdon Blvd

institute: U.S. EPA

description: Library name: sertraline_B_12249

data_processing:
Sequencing was performed in a 1x100bp single read format using Illumina NovaSeq SP flow cells (Illumina, Inc., San Diego, CA, USA). Base calling was done by Illumina Real Time Analysis (RTA) v3.4.4 and the output of the RTA was demultiplexed and converted to FASTQ format with Illumina Bcl2fastq v2.20.0. The R. subcapitata reference genome (GCA_003203535.1) was indexed using STAR v2.7.10a (Dobin et al., 2012) using the following parameters: genomeSAindexNbases = 11, sjdbOverhang = 99, and sjdbGTFfeatureExon = gene. The raw, 1x100bp single end FASTQ sequence files were trimmed, quality filtered (Phred score <15), and had UMIs and adapter sequences removed after deduplication using fastp v0.23.2 (Chen 2023, Chen et al., 2018). Quality reads were aligned and mapped to the indexed reference genome using STAR. The resulting alignment files were sorted by coordinates and indexed by sample using Samtools v1.15.1 (Danecek et al., 2021). Aligned reads were quantified with respect to gene features using the “featureCounts” program (v2.0.6) of the subread package (Liao et al., 2014). A 1,400 bp extension was added to each read at the 5’ end as most reads aligned at unannotated 3’ untranslated regions (UTR) of the genome and gene features with the largest overlap were counted. The quantified reads were organized into a count matrix file where columns represented samples and rows represented genes.
Assembly: Raphidocelis subcapitata reference genome (GCA_003203535.1)
Supplementary files format and content: Three samples with low alignment (< 35 %) and assignment (< 10 %) rates were removed including an additional outlier sample, removing two samples from both treatment 12249 and 30623 (i.e. total 41 data columns in the Normalized_Sertraline_Microalgae_RNAseq.tsv). For additional quality control, genes that had 0 abundance in any of the controls or a mean count < 10 in treatment samples were removed prior to concentration-response modeling with DRomics. Data was then normalized with respect to library size and transfromed using the "rlog" method from DESeq2.

organism: Raphidocelis subcapitata

source_name: whole cell

growth_protocol: Reared in Woods Hole MBL media at 24°C with constant light (~250 µmol/m2/s)

extract_protocol:
RNA was extracted from pooled homogenates (Plant/Fungi Total RNA Purification kits, #31900, Norgen Biotek, Ontario, Canada) with a protocol slightly modified from the manufacturer’s instructions. First, the algae were centrifuged, and the supernatant was aspirated. Glass beads (0.5 mm) were added to each well and the plate went through five cycles of freezing with liquid nitrogen and bead milling for 2 minutes. Next, 400 µl of kit Buffer C was added to each well and then the manufacturer’s procedure was followed.
Libraries were prepared using the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit with UDI (Unique Dual Index) and QuantSeq UMI (Unique Molecular Identifier) module with PhiX spike-in making up ~5% of the total reads in each lane. The UMI module (https://faqs.lexogen.com/faq/quantseq-umi-module) added a random, 6nt sequence to the start of each read 1 (R1), followed by a constant, 4nt (TATA) spacer. Preparation followed manufacturer’s recommendations. Completed libraries were quality checked and quantified using Qubit dsDNA HS and Agilent 4200 TapeStation HS DNA1000 assays. Libraries were pooled in equimolar amounts and quantified using the Invitrogen Collibri Quantification qPCR kit.

treatment_protocol: Using 96-well plates, sertraline exposure was serially diluted in algae media (Woods Hole MBL media) with a Biomek i5 liquid handler to final nominal exposure concentrations of 100, 40, 16, 6.4, 2.56, 1.024, 0.410, and 0.164 uM with five replicates per concentration. There were also five control replicates and two concentrations of CuSO4 (0.75 and 1.5 mM) with three replicates each as positive controls. All sertraline and control replicates were arranged on a 96-well plate in a predetermined systematic layout such that each concentration was distributed to equal numbers of edge and interior wells. All wells contained 0.33% solvent. Prior to exposure, the cells per ml of a R. subcapitata culture in exponential growth was adjusted to approximately 5 x 10^6 cells/ml. Each well of exposure plates was loaded with 800 µl of algal suspension. All assays were conducted in four replicate, 96-well plates using deep-well plates sealed with optically clear adhesive covers. Three of the replicate plates were randomly designated for transcriptomic analysis while the fourth plate was used for phenotypic measurements. Algae were kept in suspension during incubation by shaking using a temperature controlled orbital shaker.

value: whole cell

value: Carolina Biological

value: Sertraline (DTXSID6023577)

tag: concentration

tag: concentration units

value: µg/L

tag: exposure duration

value: 24 hour

tag: growth stage

value: Exponential Growth Stage


title: Wildtype mouse 1, no doxycycline, eye cup (RPE, choroid, sclera)

description:
WTnoDx_RPE1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)


title: TBM1_PBMCs

city: Ho Chi Minh

first: HongThai

last: LeNguyen

address: 764, Vo Van Kiet

department: Tuberculosis Group

country: Viet Nam

institute: Oxford University Clinical Research Unit

description:
Library name: Sc002
10x Genomics

data_processing:
Sequencing data was processed using Cell Ranger v7.1.0 (10x Genomics). Namely, reads were aligned to a GRCh38 reference genome (v3.0.0) and gene expression matrices generated using cellranger count. SoupX (v1.6.2) was used to remove ambient RNA contamination [38]. Doublets were removed using Scrublet (v0.0.4) with default parameters [39]. The data from all samples were combined using the merge function in Seurat v4.3.1 [40]. Low quality cells with < 500 genes detected or > 10% of reads aligned to the mitochondrial genome were removed. Genes expressed in fewer than five cells were removed. After quality control, data was analyzed using Seurat v4.3.1 [40]. Raw count data was normalized using sctransform [41] with percent mitochondrial reads and the number of unique molecular identifier (UMI) counts regressed out. Variance stabilizing transformation was performed to identify the 3,000 most variable genes, which were used for principal component analysis (PCA). Batch effects from different donors were removed using Harmony [42]. A shared nearest neighbor graph was constructed using the top 30 Harmony components, and clustering was performed with the Louvain algorithm (resolution 1.9). Data was visualized using UMAP of the top 30 Harmony PCs.
Assembly: 10x human reference (GRCh38)
Supplementary files format and content: h5: Matrix files

organism: Homo sapiens

source_name: blood

extract_protocol:
As part of routine hospital procedure, 5-10 ml of CSF and 1 ml heparinized blood were collected. 2-3 ml of CSF were sent to the hospital laboratory for routine tests for viral, bacterial, or fungal infection. The remaining CSF was concentrated by centrifugation at 300 × g for 10 min and re-suspended in 700 µl of CSF supernatant. This CSF deposit was used for TB diagnostic tests, including 100 μl for Ziehl-Neelsen smear, 200 μl for Xpert MTB/RIF, and 200 μl was stored at -80°C for future use. The remaining 200 μl of CSF was used for scRNA-seq if processed within four hours of collection, with ≥ 75 cells/µl deposit, and no artificial blood contamination (evidenced by > 200 RBCs/μl CSF total) [15]. After re-centrifugation (300 × g, 5 min), CSF pellets were resuspended in 50 μl PBS containing 0.04% bovine serum albumin (BSA, Sigma) and counted. Blood was processed alongside CSF, with PBMCs isolated using density gradient centrifugation with Histopaque 1077 (Sigma) following the manufacturer’s instructions.
Single-cell suspensions were loaded onto a 10x Genomics Chromium Controller. One patient sample was loaded per channel with a target capture rate of 4,000 cells, while the healthy control PBMCs had a target capture rate of 1,000 cells. Libraries were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 according to the manufacturer’s instructions. The library from the healthy control PBMCs was sequenced internally on an Illumina MiSeq to a mean depth of 20,922 reads per cell, with a sequencing saturation of 66.1%. Patient libraries were sequenced on an Illumina NovaSeq 6000 (BGI, Hong Kong) to a mean depth of 33,072-163,448 reads per cell, with a sequencing saturation of 54.0-91.6%.

value: blood

value: PBMCs

tag: disease

value: tuberculous meningitis

value: baseline


title: TBM2_CSF

description:
Library name: Sc003
10x Genomics

source_name: CSF

value: CSF

value: CSF cells


title: Sertraline hydrochloride exposure, replicate E, concentration 4900

description: Library name: sertraline_E_4900


title: Wildtype mouse 2, no doxycycline, neural retina

description:
WTnoDx_Ret2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

source_name: retina

value: retina


title: Healthy microbiome, 2 wks old, mouse 4

description: Library name: ECZ-12

value: healthy microbiome


title: Sertraline hydrochloride exposure, replicate A, concentration 12249

description: Library name: sertraline_A_12249


title: Wildtype mouse 1, no doxycycline, neural retina

description:
WTnoDx_Ret1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: Wildtype


title: Preterm microbiome, 2 wks old, mouse 1

description: Library name: ECZ-15

value: brain

value: male


title: Sertraline hydrochloride exposure, replicate D, concentration 4900

description: Library name: sertraline_D_4900

value: whole cell


title: Healthy microbiome, 2 wks old, mouse 3

description: Library name: ECZ-11

value: female


title: TBM1_CSF

description:
Library name: Sc001
10x Genomics


title: CD8_Urea_3

city: Bonn

first: Sibylle

last: von Vietinghoff

address: Venusbergcampus 1

country: Germany

institute: University Clinic Bonn

data_processing:
Data was processed using nf-core/rnaseq v3.14.0
The pipeline was executed with Nextflow v24.04.243 with the following command: nextflow run nf-core/rnaseq -profile docker -params-file params_human.yaml
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contains raw-counts for each sample

source_name: primary blood CD8 T cells

growth_protocol: Primary adhesion depleted human PBMC obtained from blood donations were co-cultured with human kidney cells (HK2 cell line) in a 50:50 mix of RPMI1640 and DMEM-F12.

extract_protocol:
RNA was isolated using the NucleoSpin RNA kit (Macherey-Nagel)
RNA libraries for RNA-seq were prepared using the Lexogen QuantSeq 3'mRNA FWD Library Prep Kit

treatment_protocol: co-culure was treated with addition of 80mM NaCl or 160mM Urea or control medium for 72h. After this non-adherent cells were transferred onto fresh HK2 cells in the same culture conditions for 16h. RNA was isolated from CD11b-, LD-, CD3+ CD8+ sorted cells.

value: primary blood CD8 T cells

value: elevated Urea concentration


title: CD8_Urea_4


title: Sertraline hydrochloride exposure, replicate C, concentration 4900

description: Library name: sertraline_C_4900

value: Carolina Biological

value: Sertraline (DTXSID6023577)

value: µg/L

value: 24 hour


title: Healthy microbiome, 2 wks old, mouse 1

description: Library name: ECZ-1


title: Wildtype mouse 3, 72 hours doxycycline, eye cup (RPE, choroid, sclera)

description:
WT72Dx_RPE3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: Eye cup (RPE, choroid, sclera)

value: 72 hours doxycycline


title: CD8_Urea_2


title: Wildtype mouse 3, 72 hours doxycycline, neural retina

description:
WT72Dx_Ret3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)


title: Sertraline hydrochloride exposure, replicate B, concentration 4900

description: Library name: sertraline_B_4900

value: Exponential Growth Stage


title: Healthy microbiome, 2 wks old, mouse 2

description: Library name: ECZ-2


title: 21046X23_Islet_KD_replicate4

city: Salt Lake City

first: Amandine

middle: H

last: Chaix

state: Utah

department: NUIP

institute: University of Utah

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 110
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.9a in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.40.2
Assembly: mm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: islets

extract_protocol:
Trizol Chloroform
Intact poly(A) RNA was purified from total RNA samples (10-500 ng) using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.

treatment_protocol: 15 week old c57bl6j male mice were placed on one of 3 diets for 9 months, a 10% LFD, a 60% fat high fat diet, and an 89.9% fat ketogenic diet.

value: islets

value: WT

value: KD


title: TBM2_PBMCs

description:
Library name: Sc004
10x Genomics

value: blood

value: PBMCs

value: tuberculous meningitis

value: baseline


title: Wildtype mouse 2, 72 hours doxycycline, eye cup (RPE, choroid, sclera)

description:
WT72Dx_RPE2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: Wildtype


title: CD8_Urea_1

value: primary blood CD8 T cells


title: Sertraline hydrochloride exposure, replicate A, concentration 4900

description: Library name: sertraline_A_4900

value: whole cell


title: 21046X22_Islet_KD_replicate3


title: Wildtype mouse 2, 72 hours doxycycline, neural retina

description:
WT72Dx_Ret2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: retina


title: CD8_NaCl_4

value: elevated NaCl concentration


title: 21046X21_Islet_KD_replicate2


title: Sertraline hydrochloride exposure, replicate E, concentration 1960

description: Library name: sertraline_E_1960

value: Carolina Biological

value: Sertraline (DTXSID6023577)

value: µg/L


title: CD8_NaCl_3


title: Wildtype mouse 1, 72 hours doxycycline, neural retina

description:
WT72Dx_Ret1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: 72 hours doxycycline


title: CD8_NaCl_2


title: Sertraline hydrochloride exposure, replicate D, concentration 1960

description: Library name: sertraline_D_1960

value: 24 hour

value: Exponential Growth Stage


title: 21046X19_Islet_HFD_replicate2

value: islets

value: WT

value: HFD


title: Sertraline hydrochloride exposure, replicate C, concentration 1960

description: Library name: sertraline_C_1960


title: PRDM13-OE mouse 3, no doxycycline, eye cup (RPE, choroid, sclera)

description:
HetnoDx_RPE3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: Eye cup (RPE, choroid, sclera)

value: PRDM13-OE (heterozygous)


title: Wildtype mouse 1, 72 hours doxycycline, eye cup (RPE, choroid, sclera)

description:
WT72Dx_RPE1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)


title: CD8_NaCl_1


title: 21046X18_Islet_HFD_replicate1


title: PRDM13-OE mouse 3, no doxycycline, neural retina

description:
HetnoDx_Ret3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)


title: 21046X17_Islet_LFD_replicate3

value: LFD


title: CD8_Ctr_4

value: control


title: Sertraline hydrochloride exposure, replicate B, concentration 1960

description: Library name: sertraline_B_1960


title: PRDM13-OE mouse 2, no doxycycline, eye cup (RPE, choroid, sclera)

description:
HetnoDx_RPE2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)


title: CD8_Ctr_3

value: primary blood CD8 T cells


title: Sertraline hydrochloride exposure, replicate A, concentration 1960

description: Library name: sertraline_A_1960

value: whole cell


title: PRDM13-OE mouse 2, no doxycycline, neural retina

description:
HetnoDx_Ret2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: retina


title: 21046X16_Islet_LFD_replicate2


title: CD8_Ctr_2


title: Sertraline hydrochloride exposure, replicate D, concentration 784

description: Library name: sertraline_D_784


title: Sertraline hydrochloride exposure, replicate E, concentration 784

description: Library name: sertraline_E_784


title: 21046X15_Islet_LFD_replicate1


title: CD8_Ctr_1


title: Sertraline hydrochloride exposure, replicate C, concentration 784

description: Library name: sertraline_C_784


title: PRDM13-OE mouse 1, no doxycycline, neural retina

description:
HetnoDx_Ret1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)


title: 21046X20_Islet_KD_replicate1

value: KD


title: Sertraline hydrochloride exposure, replicate B, concentration 784

description: Library name: sertraline_B_784

value: Carolina Biological


title: HS + 0.5 µM TSA (sorted with FACS)_rep3

city: Amsterdam

first: Charlotte

last: Siemons

address: tt. Vasumweg, 40W7

department: Molecular Biology

country: Netherlands

institute: Wageningen University & Research

description: read length 150

data_processing:
For all samples, quality control on fastq files was performed using Fastp (v0.19.6). Fastp was also used to filter low-quality reads with default parameters (Chen et al., 2018). Filtered reads were then mapped to the Brassica napus Darmor-bzh genome using STAR 2.7.10a with default parameters. Then the featureCounts function of the subread package (version 1.5.2) was used to count the number of reads that mapped to the reference gene (Liao et al., 2014). DESeq2 (Love et al., 2014) was used to obtain normalized count values and to identify differentially expressed genes. Transcripts with counts levels greater than 10 across all libraries were retained.
Assembly: Brassica napus Darmor-bzh genome (version 10; https://www.genoscope.cns.fr/externe/plants/chromosomes.html)
Supplementary files format and content: processed_data.xlsx: contains log2FC values of pairwise comparisons, normalized expression values and raw counts

organism: Brassica napus

source_name: microspore culture

growth_protocol: Microspore isolation was performed according to the protocol described by (Custers, 2003).

extract_protocol:
Prior to FACS, the microspore density was increased to 2.0 × 106 - 4.0 × 106 microspores/ml. Cultures were then filtered through 70-µm cell strainers to remove cell debris and kept on ice prior to FACS. FACS was performed with the FACSAria II (BD Biosciences, San Jose, CA, USA) flow cytometer with a 100 µm nozzle. Cells were sorted in PBS (pH 7.4) as sheath fluid at an event rate of ~5000 to 10,000 events per second and a fluid pressure of 20 p.s.i. Upon excitation at 488 nm, GFP-expressing embryogenic structures were selected based on fluorescence emission in the green channel (530 nm with a band width of 30 nm) compared with wild-type negative controls. In the corresponding FACSDiva™ software, the emission signal of populations was visualized by PE-TEXAS RED-A set against GFP+YFP-A in a dot plot. An overlay was set before sorting with the wild-type line as a negative control to set GFP negative (P1 and P3) and GFP positive (P1) fields in dot plot for sort layout. We sorted both the GFP negative population of cells (pollen and dead cells) and the embryogenic population of cells. However, due to low RNA yields obtained from the GFP negative populations, we only sorted the GFP positive population of embryogenic cells directly into RNA Extraction Buffer (10,000 cells/100 uL buffer) of the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher) and these cells were flash frozen instantly in liquid N2 and stored at -80°C for no longer than one month.
RNA was purified using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher). For RNA isolation, FACS-sorted GFP positive samples (from LEC1:LEC1-GFP cultures treated with either HS + 0.05 μM TSA or HS + 0.5 μM TSA) were pooled over one column to obtain a total of 150,000 sorted cells per biological replicate. We collected four biological replicates for the HS + 0.05 μM TSA treatment and three biological replicates for the HS + 0.5 μM TSA treatment. In addition to the FACS-sorted samples, we collected three replicates of 150,000 pollen each from non-sorted pollen cultures, as described above. For each sample, ~10 ng of RNA was converted to cDNA and amplified for 12 cycles using SMART-seq v4 Ultra Low input RNA kit for sequencing (Takara Bio USA, Inc.) according to manufacturer’s instructions. Amplified cDNA was then purified by immobilization on AMPure XP beads (Beckman Coulter) and the cDNA concentration was measured with the Qubit Fluorometer and the dsDNA HS Assay Kit. The cDNA size distribution was checked using the 2100 Bioanalyzer and high sensitivity DNA kit following the manufacturer’s directions.
The Nextera XT DNA Library Preparation Kit and the Nextera Index Kit (Illumina, 24 indexes, 96 samples, FC-131-1001) were used to prepare cDNA libraries according to the manufacturer’s instructions. As input, we used 0.125 ng amplified cDNA for the tagmentation reaction and we applied 12 cycles for the enrichment PCR of adapter-ligated fragments. To clean up the cDNA libraries, we used a ratio of 0.6:1 of AMPure XP beads (Beckman Coulter). The cDNA library quality was checked as described above (typical libraries showed a broad size distribution of ~250-1000 bp). When needed, we used a second round of purification using a 0.8: 1 ratio with SPRIselect beads (Beckman Coulter) for size selection. Libraries were diluted and sequenced with paired-end 150 base mode on a Novaseq S4 (Novogene Corporation Inc.).

treatment_protocol: The RNA sequencing data comprises three different transcriptomes: 1) three-day old unsorted pollen (three biological replicates, pollen stage at the start of the culture: 95% late unicellular: 5% early bicellular); 2) three-day old FACS sorted embryogenic structures from the HS + 0.05 µM TSA treated LEC1-GFP cultures (four biological replicates); 3) three-day old FACS sorted embryogenic structures from the HS + 0.5 µM TSA treated LEC1-GFP cultures (three biological replicates).

value: microspore culture

value: embryogenic cells

value: pLEC1:LEC1-GFP reporter in DH12075 background

tag: developmental stage_used

value: late unicellular microspores

value: heat shock (HS) + 0.5 uM TSA, then sorted LEC1-GFP-expressing cells with FACS


title: PBMC-PBS

city: Guangzhou

first: Ling

last: Wang

address: zhongshan road No.74

country: China

institute: Sun Yat-sen University

data_processing:
Cellranger (10x Genomics, v6.1.2) was used for demultiplexing and generation of barcodes and count matrices.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by using Ficoll (Solarbio, #P8900) gradient centrifugation. PBMC DCs were sorted as Lin- (CD3/CD19/CD14/) CD123- CD11C+ HLA-DR+ from freshly isolated PBMCs (purity>93%).
The scRNA-seq libraries were constructed using the Chromium Single Cell 3ʹ Library, Gel Bead & Multiplex Kit (10x Genomics, V3.1) following the manufacturer’s instructions.

value: PBMC

value: DCs

value: PBS


title: PRDM13-OE mouse 3, 72 hours doxycycline, eye cup (RPE, choroid, sclera)

description:
Het72Dx_RPE3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: Eye cup (RPE, choroid, sclera)

value: 72 hours doxycycline


title: Sertraline hydrochloride exposure, replicate A, concentration 784

description: Library name: sertraline_A_784

value: Sertraline (DTXSID6023577)

value: µg/L

value: 24 hour

value: Exponential Growth Stage


title: HS + 0.5 µM TSA (sorted with FACS)_rep2

description: read length 150


title: PRDM13-OE mouse 3, 72 hours doxycycline, neural retina

description:
Het72Dx_Ret3
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: retina

value: PRDM13-OE (heterozygous)


title: Tx-PHH-D1-5

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
All sequencing reads from RNA-seq were mapped to the porcine reference genome sequence (Sscrofa11.1) using hisat2-2.104. FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks v.2.2.15 using default parameters for gene expression levels. We used htseq-count6 to count reads on genes. Differential expression analysis was performed using DESeq27. Genes were considered differentially expressed if FPKM>1 in all sample and | log2(fold changes) | >= 1, q-value<=0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Transplanted human hepatocytes harvested from FRG mice at day 1 after transplantation

extract_protocol:
To gain transcriptome profiling of Tx-Heps, the low-cell number RNA-seq was applied. Briefly, approximately 1,000-3,000 Tx-Heps from per FR mouse liver after transplantation at 1, 3 and 7 days were harvested by FACS, respectively. Cell samples were lysed in 50 μl of 4 M guanidine isothiocyanate solution (GuSCN, Invitrogen, 15577-018) at 45 °C for 15 min. Total RNA was precipitated and concentrated by adding 150 μl of nuclease-free water, 600 μl of ethanol, 20 μl of acetate sodium (pH 5.7, 3 M, Ambion) and 1.5 μl of carrier glycogen (20 mg/ml, Roche).
Total RNA pellets were dissolved in lysis solution and reverse-transcribed and amplified with a modified Smart-seq2 PCR technique, followed by sequencing on Illumina NovaSeq 6000

value: Liver

tag: cell line

value: hepatocyte

value: WT


title: Sertraline hydrochloride exposure, replicate E, concentration 314

description: Library name: sertraline_E_314

value: whole cell

value: Carolina Biological


title: Tx-PHH-D1-4


title: HS + 0.05 µM TSA (sorted with FACS)_rep4

description: read length 150

value: microspore culture

value: embryogenic cells

value: pLEC1:LEC1-GFP reporter in DH12075 background

value: late unicellular microspores

value: heat shock (HS) + 0.05 uM TSA, then sorted LEC1-GFP-expressing cells with FACS


title: PRDM13-OE mouse 2, 72 hours doxycycline, neural retina

description:
Het72Dx_Ret2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: 72 hours doxycycline


title: PRDM13-OE mouse 2, 72 hours doxycycline, eye cup (RPE, choroid, sclera)

description:
Het72Dx_RPE2
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: Eye cup (RPE, choroid, sclera)


title: Tx-PHH-D1-2


title: Tx-PHH-D1-3


title: Tx-PHH-D1-1


title: Sertraline hydrochloride exposure, replicate B, concentration 314

description: Library name: sertraline_B_314

value: Sertraline (DTXSID6023577)

value: µg/L


title: Sertraline hydrochloride exposure, replicate C, concentration 314

description: Library name: sertraline_C_314

value: 24 hour

value: Exponential Growth Stage


title: Sertraline hydrochloride exposure, replicate D, concentration 314

description: Library name: sertraline_D_314


title: PRDM13-OE mouse 1, 72 hours doxycycline, eye cup (RPE, choroid, sclera)

description:
Het72Dx_RPE1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: PRDM13-OE (heterozygous)


title: HS + 0.05 µM TSA (sorted with FACS)_rep3

description: read length 150


title: HS + 0.05 µM TSA (sorted with FACS)_rep1

description: read length 150


title: PHH-2

source_name: Human hepatocytes harvested from infant(11 months，male)

value: Liver


title: PRDM13-OE mouse 1, no doxycycline, eye cup (RPE, choroid, sclera)

description:
HetnoDx_RPE1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)


title: PRDM13-OE mouse 1, 72 hours doxycycline, neural retina

description:
Het72Dx_Ret1
Column 1: gene_id (gene ID); column 2: sample_count (the readcount of genes of sample); column 3: sample_fpkm (the FPKM of genes of sample); column 4: compare_treat (the mean value of normalised readcounts in treat group); column 5: compare_control (the mean value of normalised readcounts in control group); column 6: compare_log2FoldChange (log2FoldChange value of a comparison group); column 7: compare_pvalue (pvalue value of a comparison group); column 8: compare_padj (padj value of a comparison group); column 9: gene_name (gene symbol); column 10: gene_chr (the chromosome of gene); column 11: gene_start (the start site of gene); column 12: gene_end (the end site of gene); column 13: gene_strand (the direction of gene chain); column 14: gene_length (the length of the gene); column 15: gene_biotype (the biotype of gene); column 16: gene_description (the description of gene); column 17: tf_family (the transcription factor of gene)

value: retina


title: HS + 0.05 µM TSA (sorted with FACS)_rep2

description: read length 150


title: Sertraline hydrochloride exposure, replicate A, concentration 314

description: Library name: sertraline_A_314


title: in vitro pollen day 3 (not sorted)_rep3

description: read length 150

value: developing pollen

value: late unicellular microspores/bicellular pollen

value: pollen culture treated at 18C for 3 days


title: PHH-1

value: hepatocyte

value: WT


title: SPL-TLR stimulation N685

data_processing:
Cellranger (10x Genomics, v6.1.2) was used for demultiplexing and generation of barcodes and count matrices.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Mice were immunized intraperitoneally (i.p.) with or without 60 µg TLR stimulation in 100 µL PBS. Splenic cells were collected 18 hrs after  injection for cDCs (live MHCII+ CD11c+) FACS-sorting for scRNA-seq library preparation.
The scRNA-seq libraries were constructed using the Chromium Single Cell 3ʹ Library, Gel Bead & Multiplex Kit (10x Genomics, V3.1) following the manufacturer’s instructions.

value: Spleen

value: immune cells

value: wt

value: TLR stimulation


title: Sertraline hydrochloride exposure, replicate E, concentration 125

description: Library name: sertraline_E_125

value: whole cell

value: Carolina Biological


title: Spl-PBS N686

value: PBS


title: HS + 0.5 µM TSA (sorted with FACS)_rep1

description: read length 150

value: microspore culture

value: embryogenic cells

value: pLEC1:LEC1-GFP reporter in DH12075 background

value: late unicellular microspores

value: heat shock (HS) + 0.5 uM TSA, then sorted LEC1-GFP-expressing cells with FACS


title: Sertraline hydrochloride exposure, replicate D, concentration 125

description: Library name: sertraline_D_125

value: Sertraline (DTXSID6023577)

value: µg/L

value: 24 hour

value: Exponential Growth Stage


title: splenic cDCs CKO_D169 RNA-Seq

data_processing:
The raw FASTQ data were first processed through fastp v 0.23.2 and all the downstream analyses were based on high-quality clean data. An index of the reference genome was built and paired-end clean reads were aligned to the reference genome (mm10) using HISAT2 v2.2.1.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
RNA extraction with Rneasy Plus Micro kit(50). SMART-Seq v4 Ultra Low Input RNA Kit(TaKaRa,#634895) for Sequencing Componentsused to generate high-quality cDNA from  total RNA.
For RNA-seq library preparation, the assay was performed following the manufacturer’s instructions (Vazyme, #TD501).

value: DCs

value: CKO


title: IP AVJ16 rep1

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: IDR_IP3-4_treated01v02.IDR.out.0102merged.bed

data_processing:
eCLIP data was analyzed using CLIPper with default settings. Full pipeline available at: https://github.com/yeolab/eclip/
Replicates were merged using IDR with default settings. Full pipeline available at: https://github.com/yeolab/merge_peaks
Assembly: (hg38)
Supplementary files format and content: IDR  peaks output by CLIPer

source_name: Lung

growth_protocol: H1299 cells were maintained in RPMI medium,  (Biological Industries - Israel). media contained 10% FCS (Biological Industries) and 10 μg/mL ciprofloxacin (Bayer).

extract_protocol:
eCLIP experiments were performed as previously described using a IGf2BP1(MBL, #RN007P). see Eric L Van Nostrand,2016 DOI https://doi.org/10.1038/nmeth.3810
eCLIP experiments were performed as previously described using a IGf2BP1(MBL, #RN007P). see Eric L Van Nostrand,2016 DOI https://doi.org/10.1038/nmeth.3810

treatment_protocol: cells were  grown in 15-cm plate for (2 plates per condition). 1.5uM AVJ16 or 0.01% DMSO was then added for 24 h. Following this incubation period, cells were spin down at 300 x g for 3 min and resuspend pellet in 3ml of cold DPBS to a concentration of ~6 million cells/ml cells were UV crosslinked on ice at 400 mJoules/cm2 with 254 nm radiation. Cells were then colected on ice and pelleted at 4°C, and the supernatant was discarded before the samples were snap-frozen and stored at -80°C. To minimize variability, all samples were prepared in two batches from the same thaw of cells.

value: Lung

value: epithelial-like cell

value: WT


title: IP AVJ16 rep2


title: in vitro pollen day 3 (not sorted)_rep1

description: read length 150

value: developing pollen

value: late unicellular microspores/bicellular pollen

value: pollen culture treated at 18C for 3 days


title: in vitro pollen day 3 (not sorted)_rep2

description: read length 150

value: microspore culture


title: IP DMSO rep 2

description: IDR_IP1-2_nontreated01v02.IDR.out.0102merged.bed

value: DMSO


title: Sertraline hydrochloride exposure, replicate B, concentration 125

description: Library name: sertraline_B_125

value: whole cell

value: Carolina Biological


title: IP DMSO rep1


title: IN AVJ16 rep2


title: splenic cDCs WT_D164 RNA-Seq

value: Spleen

value: TLR stimulation


title: IN AVJ16 rep1


title: Sertraline hydrochloride exposure, replicate E, concentration 50

description: Library name: sertraline_E_50

value: Sertraline (DTXSID6023577)

value: µg/L


title: Sertraline hydrochloride exposure, replicate A, concentration 125

description: Library name: sertraline_A_125

value: 24 hour

value: Exponential Growth Stage


title: splenic cDCs WT_D154 RNA-Seq

value: DCs


title: Stressed sterile immature male, fish 6_5

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Labeled cRNA was hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Testis

label_protocol: RNA was amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon post smolts were kept in tanks within a flow-through system.

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Fertile fish were compared with salmon sterilized by temporal silencing of dnd gene in embryos. Part of fish were exposed to handling stress and sampled after 24 h.

value: Testis


title: splenic cDCs CKO_D163 RNA-Seq

value: CKO


title: splenic cDCs CKO_D149 RNA-Seq


title: Sertraline hydrochloride exposure, replicate C, concentration 50

description: Library name: sertraline_C_50


title: IN DMSO rep 2

value: Lung

value: epithelial-like cell

value: WT


title: splenic cDCs WT_D150 RNA-Seq


title: IN DMSO rep1


title: Stressed sterile immature male, fish 6_4


title: Sertraline hydrochloride exposure, replicate C, concentration 125

description: Library name: sertraline_C_125


title: Sertraline hydrochloride exposure, replicate B, concentration 50

description: Library name: sertraline_B_50


title: splenic cDCs WT_D142 RNA-Seq


title: N6-shA1-4-input

city: wuhan

first: Joshua

last: Guo

address: shuiguohulu

institute: wuhan university

library_source: genomic

data_processing:
ChIP–seq reads were quality controlled with fastqc (v0.11.5) and mapped to the human genome reference (GRCh38/hg38) using bowtie2 (v2.2.9) with default parameters or bowtie (v1.2.2) with parameters -v2 -k1–best. Bam files were generated with samtools 1.3.1, which was followed by making bigwig files with deeptools (v/3.0.2) (binsize 10). Reads were normalized to Reads Per Genome Coverage (RPGC) with deeptools (v/3.0.2) bamCoverage function. To analyse the intersections between different ChIP–seq and MeDIP-seq samples, peak calling of EZH2 and H3K27me3 was performed with SICER with ChIP–seq Input samples as control and using the default significance cutoff of False Discovery Rate (FDR) < 0.05. The bedtools ‘‘intersect’’ function was used to calculate overlaps with 6-mA peaks. For co-occupany analysis, peak calling was performed with MACS2 with Input ChIP–seq sample as control (-p 0.05–broad,–broad-cutoff 0.05, Fold Change > 3).
Reads from input and IP sequencing libraries were quality controlled with fastqc (v0.11.5) and mapped to the human genome reference (GRCh38/hg38) using bowtie2 (v2.2.9) with default parameters or bowtie (v1.2.2) with parameters -v2 -k1–best. Bam files were generated with samtools 1.3.1, which was followed by making bigwig files with deeptools (v/3.0.2) (binsize 10). Reads were normalized to Reads Per Genome Coverage (RPGC) with deeptools (v/3.0.2) bamCoverage function. To analyse the intersections between different ChIP–seq and MeDIP-seq samples, peak calling was performed with SICER with Input samples as control and using the default significance cutoff of False Discovery Rate (FDR) < 0.05. MACS2 was also used for peak calling, which generated similar results as SICER. For visualizing 6mA peaks, .bigwig files were loaded in IGV (v2.4) and adjusted to the same scale.
Assembly: hg38
Supplementary files format and content: bam

molecule: genomic DNA

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells for ChIP were cultured in 15 cm plates. Cells were first washed with cold PBS, crosslinked at room temperature with 1% formaldehyde (ThermoFisher Scientific) for 10 min.  Genomic DNA was purified with DNeasy kit (QIAGEN).
For ChIP–seq, NEBNext Ultra Directional RNA Library Prep Kit (NEB, #E7760) was used for library preparation. For MeDIP–seq, IP DNA and input DNA were PCR amplified with Illumina indexing primers.

value: HNSCC

tag: chip antibody

tag: transfection


title: Stressed sterile immature male, fish 5_5


title: Tx-HepArid1aKO-D1-3

source_name: Transplanted hepatocytes derived from Arid1a∆li donor harvested from FR mice at day 1 after transplantation

value: Liver

value: hepatocyte


title: splenic cDCs CKO_D146 RNA-Seq


title: Stressed sterile immature male, fish 1_6


title: N6-shA1-4-6mA


title: Sertraline hydrochloride exposure, replicate D, concentration 50

description: Library name: sertraline_D_50

value: whole cell


title: Sertraline hydrochloride exposure, replicate E, concentration 0

description: Library name: sertraline_E_0

value: Carolina Biological


title: Sertraline hydrochloride exposure, replicate D, concentration 0

description: Library name: sertraline_D_0


title: Stressed sterile immature male, fish 1_4


title: N6-mock-input

value: mock


title: Tx-HepArid1aKO-D1-1


title: Stressed sterile maturing male, fish 5_3


title: Stressed sterile maturing male, fish 5_1


title: Sertraline hydrochloride exposure, replicate C, concentration 0

description: Library name: sertraline_C_0


title: N6-shA1-3-input


title: N6-shA1-3-6mA


title: Tx-HepArid1aWT-D1-3

source_name: Transplanted hepatocytes derived from Arid1af/f donor harvested from FR mice at day 1 after transplantation


title: Sertraline hydrochloride exposure, replicate A, concentration 50

description: Library name: sertraline_A_50


title: Stressed sterile maturing male, fish 1_3


title: Tx-HepArid1aWT-D1-2


title: Stressed sterile maturing male, fish 5_8


title: Sertraline hydrochloride exposure, replicate B, concentration 0

description: Library name: sertraline_B_0


title: Sertraline hydrochloride exposure, replicate A, concentration 0

description: Library name: sertraline_A_0


title: Tx-HepArid1aWT-D1-1


title: N6-mock-input-3


title: Stressed sterile female, fish 5_4

source_name: Ovary

value: Ovary


title: Stressed sterile female, fish 5_2


title: Control_WT3

city: York

first: Fabiano

middle: Sviatopolk-Mirsky

last: Pais

state: Yorkshire

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

description: Library name: Control_WT3

data_processing:
Reads were processed and aligned to the reference genome as described in the bioinformatics pipeline from NF-core/rnaseq available at [https://github.com/nf-core/rnaseq/tree/3.14.0].
Assembly: MHOM/BR/75/M2903
Supplementary files format and content: Raw read counts were generated from the mapped BAM files with HTSeq. Then, raw counts were normalized as Transcripts per Million (TPM)

organism: Leishmania braziliensis

growth_protocol: Promastigotes of L. braziliensis M2903 (MHOM/BR/75/M2903) cell line expressing Cas9 and T7 RNA polymerase were cultured at 26°C in M199 medium. The selection drug Puromycin was added at 20 µg/ml  for the maintenance of the HA tagged cell lines.

extract_protocol:
Total RNA was extracted from L. braziliensis cultures using the Directzol kit Quick-RNA Miniprep (Zymo Research) according to the manufacturer’s instruction. After extraction, RNA samples were treated with TURBO™ DNAse to remove any DNA remains.
The libraries were prepared (Illumina Ribo-Zero plus rRNA Depletion & TruSeq Stranded Total RNA Library Prep Gold Kit) and then proceeded to sequencing (Illumina platform), generating approximately 40 million short (101bp), paired and strand-specific reads per library.

treatment_protocol: Log-phase promastigotes were harvested, washed twice with PBS and resuspended in 1mL of IP-Lysis Buffer. This material was immediately frozen in liquid nitrogen, defrosted and sonicated for 2 minutes twice (or until most of the parasites were lysed) and centrifuged 10,000 × g for 4 min at 4 °C. Supernatant was then incubated with 1mg of Pierce™ Anti-HA Magnetic Beads (Thermo Scientific™) for 2 hours at 4 °C under rotation. For the negative control (untagged parental cell line), magnetic beads were blocked with 100 μg of HA peptide for 30 minutes at 4 °C under rotation in IP-Lysis Buffer.

value: Procyclic promastigote

value: HA tagged cell line, UV crosslinked, lysated and submitted to Immunoprecipitation by using HA magnetic beads


title: N6-mock-6mA-3


title: Tx-HepArid1aKO-D1-2


title: Tx-HepHIR-D1-5

source_name: Transplanted hepatocytes harvested from c57 mice preconditioned with HIR at day 1 after transplantation


title: Tx-HepHIR-D1-4


title: Control_WT2

description: Library name: Control_WT2


title: Tx-HepHIR-D1-3


title: Control_WT1

description: Library name: Control_WT1


title: ChIP-2-shA1-4-H3


title: Stressed sterile female, fish 1_8


title: Stressed sterile female, fish 1_1


title: ChIP-2-mock-input


title: Stressed fertile immature male, fish 4_3


title: Tx-HepHIR-D1-1


title: Input_WT2

description: Library name: Input_WT2


title: Tx-HepWT-D1-2

source_name: Transplanted hepatocytes harvested from c57 mice at day 1 after transplantation


title: Stressed sterile female, fish 1_2


title: ChIP-2-mock-H3


title: ChIP-2-mock-EZH2


title: ChIP-2-shA1-4-input


title: Lb5-3

description: Library name: Lb5-3


title: Tx-Hep-D7-2

source_name: Transplanted hepatocytes harvested from FR mice at day 7 after transplantation


title: ChIP-1-shA1-3-input


title: Lb5-2

description: Library name: Lb5-2


title: ChIP-2-shA1-4-EZH2


title: Tx-HepWT-D1-1


title: Stressed fertile immature male, fish 2_5


title: Tx-HepHIR-D1-2


title: Lb5-1

description: Library name: Lb5-1


title: ChIP-1-shA1-3-EZH2


title: Tx-Hep-D7-1


title: Input_WT3

description: Library name: Input_WT3


title: Lb4-3

description: Library name: Lb4-3


title: Stressed fertile immature male, fish 2_2


title: Stressed fertile immature male, fish 4_5


title: Input_WT1

description: Library name: Input_WT1


title: Stressed fertile immature male, fish 3_1


title: Stressed fertile maturing male, fish 3_4


title: ChIP-1-mock-EZH2


title: Tx-Hep-D3-1

source_name: Transplanted hepatocytes harvested from FR mice at day 3 after transplantation


title: Lb4-2

description: Library name: Lb4-2


title: N6-SCC9-input-6.4


title: Tx-Hep-D1-4

source_name: Transplanted hepatocytes harvested from FR mice at day 1 after transplantation


title: Stressed fertile maturing male, fish 3_3


title: Lb3-3

description: Library name: Lb3-3


title: Stressed fertile maturing male, fish 4_8


title: N6-SCC9-input-5.27


title: Tx-Hep-D1-3


title: Tx-Hep-D1-2


title: Stressed fertile female, fish 3_2


title: N6-SCC9-6mA-5.27


title: N6-SCC9-6mA-6.4


title: Lb3-1

description: Library name: Lb3-1


title: Lb3-2

description: Library name: Lb3-2


title: Tx-Hep-D1-1


title: Tx-Hep-D3-2


title: N6-SCC25-input-5.27


title: Lb2-3

description: Library name: Lb2-3


title: Stressed fertile female, fish 2_6


title: Lb2-2

description: Library name: Lb2-2


title: Stressed fertile female, fish 2_1


title: LPLC-2

source_name: DDC diet for 2 weeks

value: Sox9creER; RS26-mTmG


title: Stressed fertile female, fish 2_3


title: LPLC-3


title: Stressed fertile female, fish 2_4


title: N6-SCC25-6mA-5.27


title: Lb4-1

description: Library name: Lb4-1


title: ChIP-1-mock-input


title: LPLC-1


title: N6-SCC25-6mA-5.20


title: Stressed fertile maturing male, fish 2_7


title: Sterile immature male, TP3, fish 6_4


title: Chol-3

source_name: CK19 labelling cholangiocytes

value: cholangiocytes

value: CK19creER; RS26-mTmG


title: Lb1-3

description: Library name: Lb1-3


title: ChIP-SCC9-input-5.25


title: Lb2-1

description: Library name: Lb2-1


title: Lb1-2

description: Library name: Lb1-2


title: ChIP-SCC9-H3K27me3-6.4


title: Sterile immature male, TP3, fish 5_8

value: Testis


title: Lb1-1

description: Library name: Lb1-1


title: Chol-1


title: Sterile immature male, TP3, fish 1_6


title: Sterile immature male, TP3, fish 1_4


title: N6-SCC25-input-5.20


title: P6_tumor_rep1

city: Chengdu

first: Xiaoping

last: Li

state: Sichuan

address: 32 West 2nd Section, First Ring Road, Qingyang District, Chengdu, Sichuan Province, China

institute: Sichuan Provincial People's Hospital

description: Library name: P6T

data_processing:
FASTQ files were processed with 10x Genomics Cell Ranger v7.1 using default settings against the GRCh38 reference (refdata-gex-GRCh38-2020-A) to perform alignment, barcode and UMI extraction, cell calling, and UMI deduplication, producing filtered single-cell expression matrices (matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz).
Assembly: GRCh38
Supplementary files format and content: Filtered single-cell UMI count matrix in Matrix Market format (matrix.mtx.gz), with accompanying cell barcode list (barcodes.tsv.gz) and feature (gene) list (features.tsv.gz) for use in downstream analysis.

source_name: cardiac myxoma

extract_protocol:
Fresh cardiac myxoma and matched normal heart tissues were collected and immediately immersed in single‐cell preservation solution, then stored on ice and shipped on dry ice to the sequencing facility.
Single‐cell suspensions were processed using the 10x Genomics Chromium Single Cell 3′ v3 kit according to the manufacturer’s instructions: cells were encapsulated with barcoded gel beads, reverse transcription and cDNA amplification performed on‐chip, followed by library construction via fragmentation, end repair, A‐tailing, adaptor ligation, and sample indexing. Final libraries were QC’d by Bioanalyzer and quantified prior to sequencing.

value: cardiac myxoma


title: ChIP-SCC9-H3K27me3-5.25


title: P5_tumor_rep1

description: Library name: P5T


title: ChIP-SCC9-EZH2-5.25


title: Hep-2

source_name: normal hepatocytes


title: P5_Heart_rep1

description: Library name: P5N

source_name: Heart tissue

value: Heart tissue


title: Hep-1


title: 3T3-L1, siYwhaz, +48 hr MDI, rep4

city: Montreal

first: Gareth

last: Lim

state: Quebec

address: R08.482- 900 rue St Denis

country: Canada

institute: CRCHUM

data_processing:
Trimming of adaptors from the ATAC-seq reads with Trim Galore (https://github.com/FelixKrueger/TrimGalore)
Reads alignment to mm10 with Bowtie2 (Langmead et Salzberg, Nat. Methods, 2012)
Alignment of 3T3-L1 adipocytes ChiP-seq reads with Bowtie2; GSM535755 (H3K4me3) GSM535758 (H3K27ac) and GSM535740 (input) downloaded from series GSE21365  (Mikkelsen et al, Cell, 2010)
Peak calling performed with MACS2 (Gaspar, bioRxiv, 2018), and ATAC-seq peaks quantification with featureCounts (Liao et al, Bioinformatics, 2014)
NovaSeq6000; single line in  S4 flow cell; v1.5, PE100 read per sample
Assembly: Mus_musculus:GRCm38
Supplementary files format and content: Peak counts, .csv and .xlsx

growth_protocol: Murine 3T3-L1 pre-adipocytes were maintained in 25 mM glucose DMEM supplemented with 1% pen/strep and 10% NBCS

extract_protocol:
Cells were lysed and nuclei were collected and stored in cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2,0.1% IGEPAL CA-630).
Nuclei were exposed to TDE1 Tagment DNA enzyme (Illumina), followed by transposition, DNA extraction, and amplification of DNA with Illumina Nextera ATAC Series (i5 and i7) primers

treatment_protocol:
48 hrs prior to differentiation, cells were transfected with a scrambled control siRNA (siCon) or siRNA against Ywhaz (siYwhaz) at a final concentration of 25 uM.
Cells were differentiated with MDI (25 mM glucose DMEM supplemented with 10% FBS, 1% P/S, 500 µM IBMX, 500 nM dexamethasone, and 172 nM insulin) for 0, 24 or 48 hours

value: murine pre-adipocyte

value: siYwhaz + MDI for 48 hours


title: P4_tumor_rep1

description: Library name: P4T


title: ChIP-SCC25-input-5.20

value: HNSCC


title: ChIP-SCC25-input-5.25


title: ChIP-SCC25-H3K27me3-5.25


title: P4_Heart_rep1

description: Library name: P4N


title: 3T3-L1, siYwhaz, +48 hr MDI, rep3


title: P3_tumor_rep1

description: Library name: P3T


title: Hep-3

value: Liver


title: ChIP-SCC9-EZH2-6.4


title: Chol-2


title: 3T3-L1, siYwhaz, +48 hr MDI, rep2


title: ChIP-SCC25-H3K27me3-5.20


title: 3T3-L1, siYwhaz, +48 hr MDI, rep1


title: Sterile maturing male, TP3, fish 5_4


title: ChIP-SCC25-EZH2-5.25


title: P3_Heart_rep1

description: Library name: P3N


title: 3T3-L1, siCon, +48 hr MDI, rep4

value: siCon + MDI for 48 hours


title: ChIP-SCC25-EZH2-5.20


title: P2_tumor_rep1

description: Library name: P2T1


title: 3T3-L1, siCon, +48 hr MDI, rep3


title: HeLa, sgG2E3, Input, rep3

first: Yuanyong

last: Huang

state: Shanghai

address: 500 Dongchuan Road, Shanghai,China

department: School of Life Science

institute: East China Normal University

data_processing:
raw reads were mapped by bowtie2 -p 15 -q --end-to-end --very-sensitive --maxins 2000 --no-mixed --no-discordant
peaks were called by macs2 callpeak --SPMR --nomodel --fix-bimodal -f BAMPE -g hs -B; H3K14Ub and H3K9me3 were broad peak; H3K4me3 were narrow peak
bigwig file were converted from bedGraph by bedGraphToBigWig
Assembly: GRCh38
Supplementary files format and content: bigwig files display the ChIP-seq signals; narrowPeak/broadPeak files contain ChIP-seq peaks (except for Input sample )

source_name: HeLa

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature following a final concentration of 125 mM and incubated for 5 min to stop crosslinking. After cell lysis, chromatin was sonicated.Subsequent ChIP assays for H3K4me3, H3K9me3 and H3K14Ub were performed essentially as described (Li et al., 2020). .
DNA degradation and contamination was monitored on 1% agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). A total amount of 50ｎg DNA per sample was used as input material for the Chip sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The control sgG2E3 HeLa cells line and G2E3 KO HeLa cells line were obtained by the CRISPR-Cas9 system essentially as described (Ran et al., 2013) with the  guide RNA: AACCAAGCGTTCTTACAACA.

value: HeLa

value: epithelial cell

value: sgG2E3 control


title: P1_tumor_rep2

description: Library name: P1T2


title: 3T3-L1, siCon, +48 hr MDI, rep2


title: HeLa, sgG2E3, Input, rep2


title: Sterile immature male, TP3, fish 1_8


title: Sterile maturing male, TP3, fish 1_3


title: 3T3-L1, siCon, +48 hr MDI, rep1


title: P2_tumor_rep2

description: Library name: P2T2


title: HeLa, sgG2E3, Input, rep1


title: Sterile maturing male, TP3, fish 1_2


title: P1_tumor_rep1

description: Library name: P1T1


title: Sterile immature male, TP3, fish 1_10


title: 3T3-L1, siYwhaz, +24 hr MDI, rep4

value: siYwhaz + MDI for 24 hours


title: Sterile maturing male, TP3, fish 1_5


title: Sterile maturing male, TP3, fish 5_1


title: Sterile female, TP3, fish 6_2

value: Ovary


title: Sterile female, TP3, fish 6_5


title: Sterile female, TP3, fish 6_8


title: P1_Heart_rep1

description: Library name: P1N1


title: HeLa, sgG2E3, H3K14Ub, rep3

value: H3K14Ub (This paper #K58P-2)


title: P1_Heart_rep2

description: Library name: P1N2


title: Sterile maturing male, TP3, fish 1_1


title: HeLa, sgG2E3, H3K14Ub, rep2


title: Sterile female, TP3, fish 5_7


title: Breast 9

city: HOUSTON

first: HONG

last: ZHAO

state: Texas

address: 6670 Bertner Ave

institute: HOUSTON METHODIST HOSPITAL

description: Library name: Breast 9

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: breast tumor

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

treatment_protocol: surgically resceted tissue

value: breast tumor

value: breast tumor tissue

value: female

value: surgical resection


title: HeLa, sgG2E3, H3K14Ub, rep1


title: 3T3-L1, siYwhaz, +24 hr MDI, rep1


title: Sterile female, TP3, fish 5_6


title: Breast 7

description: Library name: Breast 7


title: 3T3-L1, siCon, +24 hr MDI, rep4

value: siCon + MDI for 24 hours


title: HeLa, sgG2E3, H3K9me3, rep2


title: 3T3-L1, siYwhaz, +24 hr MDI, rep3


title: 3T3-L1, siCon, +24 hr MDI, rep3


title: 3T3-L1, siCon, +24 hr MDI, rep2


title: Breast 4

description: Library name: Breast 4


title: Breast 5

description: Library name: Breast 5


title: 3T3-L1, siCon, +24 hr MDI, rep1


title: HeLa, sgG2E3, H3K9me3, rep1


title: HeLa, sgG2E3, H3K4me3, rep3

value: H3K4me3 (Millipore #07-473)


title: Fertile immature male, TP3, fish 4_4

value: Testis


title: Breast 3

description: Library name: Breast 3


title: Fertile immature male, TP3, fish 4_8


title: 3T3-L1, siYwhaz, -MDI, rep4

value: murine pre-adipocyte

value: siYwhaz - MDI


title: Breast 8

description: Library name: Breast 8


title: Fertile maturing male, TP3, fish 3_5


title: HeLa, sgG2E3, H3K9me3, rep3


title: 3T3-L1, siYwhaz, +24 hr MDI, rep2


title: Fertile immature male, TP3, fish 4_2


title: Fertile immature male, TP3, fish 2_5


title: HeLa, sgG2E3, H3K4me3, rep1


title: Fertile maturing male, TP3, fish 3_4


title: Breast 2

description: Library name: Breast 2


title: Fertile immature male, TP3, fish 3_2


title: 3T3-L1, siYwhaz, -MDI, rep3


title: HeLa, G2E3_KO_10, Input, rep3

value: G2E3 KO


title: Breast 1

description: Library name: Breast 1


title: 3T3-L1, siYwhaz, -MDI, rep2


title: Brain 9

description: Library name: Brain 9

source_name: brain metastasis

value: brain metastasis

value: brain tissue


title: 3T3-L1, siYwhaz, -MDI, rep1


title: HeLa, G2E3_KO_10, Input, rep2

value: HeLa

value: epithelial cell


title: Fertile immature male, TP3, fish 4_3

source_name: Testis


title: HeLa, G2E3_KO_10, Input, rep1


title: Sterile female, TP3, fish 5_5


title: 3T3-L1, siCon, -MDI, rep4

value: siCon -MDI


title: HeLa, G2E3_KO_10, H3K14Ub, rep3


title: Fertile maturing male, TP3, fish 2_8


title: Brain 7

description: Library name: Brain 7


title: HeLa, sgG2E3, H3K4me3, rep2

value: sgG2E3 control


title: HeLa, G2E3_KO_10, H3K14Ub, rep2

value: H3K14Ub (This paper #K58P-2)


title: Fertile maturing male, TP3, fish 2_3


title: Brain 6

description: Library name: Brain 6


title: 3T3-L1, siCon, -MDI, rep3


title: 3T3-L1, siCon, -MDI, rep2


title: HeLa, G2E3_KO_10, H3K14Ub, rep1


title: Fertile maturing male, TP3, fish 2_7


title: Brain 5

description: Library name: Brain 5


title: 3T3-L1, siCon, -MDI, rep1


title: Brain 4

description: Library name: Brain 4


title: 20462X25_Liver_Keto_ALF_replicate5

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 108
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.9a in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: liver

treatment_protocol: 15 week old c57bl6j male mice were placed on one of 3 diets for 9 months, a 10% fat control diet, a 60% fat high fat diet, and an 89.9% fat ketogenic diet.

value: liver

value: WT


title: Fertile maturing male, TP3, fish 2_2


title: Fertile female, TP3, fish 4_7

value: Ovary


title: Fertile female, TP3, fish 4_6


title: HeLa, G2E3_KO_10, H3K9me3, rep3


title: Brain 8

description: Library name: Brain 8

value: female

value: surgical resection


title: 20462X24_Liver_Keto_ALF_replicate4


title: HeLa, G2E3_KO_10, H3K9me3, rep1


title: Brain 2

description: Library name: Brain 2


title: 20462X23_Liver_Keto_ALF_replicate3


title: Brain 3

description: Library name: Brain 3


title: Fertile female, TP3, fish 3_6


title: Brain 1

description: Library name: Brain 1


title: HeLa, G2E3_KO_10, H3K9me3, rep2


title: HeLa, G2E3_KO_10, H3K4me3, rep3

value: H3K4me3 (Millipore #07-473)


title: Fertile female, TP3, fish 4_1


title: 20462X20_Liver_Control_ALF_replicate5


title: Fertile female, TP3, fish 3_3


title: HeLa, G2E3_KO_10, H3K4me3, rep2


title: GBM34 FIBULIN-3 KD independent replicate 2

city: Syracuse

first: Mariano

middle: S

last: Viapiano

state: NY

address: 505 Irving Ave Rm 4604

department: Neuroscience and Physiology

institute: SUNY Upstate Medical University

description:
Library name: GBM34-KD2
Column name in all the processed files: GBM34-KD2

data_processing:
Samples were barcoded and run in a HiSeq 2000 instrument, generating 2 FASTQ files per sample. FASTQ files were not merged until gene quantification step
Basecalls were performed using Illumina's Real-Time Analysis (RTA) in the HiSeq instrument
Sequenced reads (150 bases, paired-end) were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to the human hg38 genome (with Ensemble v110 for mRNA transcripts) using STAR (provided by the Illumina software Partek Flow) with default alignment options
Aligned reads were quantified to the annotation model (hg38 / Ensemble v110) using Partek E/M tool (Partek Flow, default options) to generate total gene raw counts and total transcript raw counts
Raw counts were filtered to remove genes or transcripts with less than 15 counts in at least 50% of the samples. Filtered counts were normalized by TMM method (trimmed mean of M-values)
Filtered and normalized gene and transcript counts were batch adjusted (using general linear model, Partek Flow) to remove batch effects from cell line and cell*treatment interaction. This was done to identify changes caused by fibulin-3 knockdown that were common to both cell lines
Final batch adjusted counts were compared by ANOVA with multiple-comparison corrections (Q value <= 0.05)
Genes differentially expressed between control and KD conditions (Q<=0.05 and change <=-1.5 fold or >=1.5 fold) were uploaded to GO Consortium to identify geneset enrichment
Genes differentially expressed between control and KD conditions (Q<=0.05 and change <=-1.5 fold or >=1.5 fold) were uploaded to KEGG database to identify pathway enrichment
Assembly: Human hg38
Supplementary files format and content: Tab-delimited files with "unprocessed" counts represent total gene counts or total transcript counts after mapping to hg38 and before any processing
Supplementary files format and content: Tab-delimited files with "batch adjusted" counts represent total gene counts or total transcript counts after filtering out low-expressed genes, TMM normalization, and batch adjustment to remove cell line effects

source_name: Primary glioblastoma tumor

growth_protocol: Cells were seeded in triplicate in T25 flasks at a density of 1x10E5 cells/ml (5 ml total volume) and were cultured in suspension conditions until forming tumor spheroids at high density. Culture medium was DMEM/F12 supplemented with 20 ng/mL EGF, 20 ng/mL bFGF, 1X B27 supplement, 1X glutamax supplement and standard antibiotics. When confluent, cells were dissociated to achieve single-cell suspensions and were re-plated at 1x10E6 total cells in 35mm dishes (3 mL volume) for each transfection.

extract_protocol:
Total RNA isolated from frozen cell pellets was extracted using Invitrogen PureLink RNA Mini Kit Spin Column. RNA was quantified and assesed for integrity using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).
RNA was submitted to CRO Azenta. Vendor performed poly-A mRNA isolation, fragmentation, and library preparation using TruSeq kit for HiSeq RNA sequencing. Vendor's details for library construction were proprietary

treatment_protocol: Each cell plate was independently transfected with a mixture of two fibulin-3 siRNAs or a non-targeting control siRNA (Qiagen AllStars negative control), using Lipofectamine RNAiMax. Culture medium was changed to Opti-MEM 24h after transfection and the cells were collected after 24h in Opti-MEM (i.e., 48h after transfection).

value: Primary glioblastoma tumor

value: Mesenchymal tumor stem cells

value: Fibulin-3 KD

value: fibulin-3 siRNA transfection

value: batch 2023-Sep-06


title: Breast 6

description: Library name: Breast 6

value: breast tumor

value: breast tumor tissue


title: 20462X19_Liver_Control_ALF_replicate4


title: HeLa, G2E3_KO_10, H3K4me3, rep1

value: HeLa

value: epithelial cell

value: G2E3 KO


title: Fertile female, TP3, fish 2_4

source_name: Ovary


title: GBM34 FIBULIN-3 KD independent replicate 1

description:
Library name: GBM34-KD1
Column name in all the processed files: GBM34-KD1


title: Sterile male, TP1, fish 6_7

value: Testis


title: Sterile male, TP1, fish 6_5


title: 7d post infection, dsEcR, biol rep 4

city: Boston

first: Lisa

last: Verzier

state: MA

address: 677 Huntington Avenue

department: Department of Immunology and Infectious Diseases

institute: Harvard University

description:
Library name: SN0268067_S16
10X Genomics

data_processing:
The demultiplexing, barcode pre-processing, gene counting and aggregation was performed using 10X Cell Ranger software v7.0.1.
Assembly: Anopheles gambiae PEST, version 58 (Vectorbase.org); Plasmodium falciparum 3D7, version 58 (PlasmoDB.org)
Supplementary files format and content: gzip compressed archive of tab separated values and matrix files

organism:
Plasmodium falciparum
Anopheles gambiae

source_name: midgut

extract_protocol:
Freshly dissected midguts were kept on ice in PBS and blood bolus was removed when relevant. Sinlge cell isolation was performed by enzymatic digestion (1 mg/mL elastase and collagenase IV) for 30min at 30ºC shaking as well as mechanical disruption by pipetting. Cells were filtered sequentially in 70, 40 and 20 µm cell strainer (latest filtration was not performed for 7d samples), pelleted and resuspended in PBS.
Followed manufacturer's instruction (Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index) User Guide RevC)

value: midgut

tag: timepoint

value: 7 days post infectious blood meal

value: dsEcR-injected

value: biol rep 4


title: 20462X15_Liver_HFD_ALF_replicate5

tag: tissue

value: liver

value: WT


title: 20462X14_Liver_HFD_ALF_replicate4


title: GBM34 CONTROL independent replicate 3

description:
Library name: GBM34-CT3
Column name in all the processed files: GBM34-CT3

value: Primary glioblastoma tumor

tag: cell type

value: control

value: control siRNA transfection


title: 7d post infection, dsGFP, biol rep 4

description:
Library name: SN0268067_S15
10X Genomics

tag: treatment

value: dsGFP-injected


title: GBM34 CONTROL independent replicate 2

description:
Library name: GBM34-CT2
Column name in all the processed files: GBM34-CT2

value: Mesenchymal tumor stem cells

tag: genotype

value: batch 2023-Sep-06


title: 20462X13_Liver_HFD_ALF_replicate3


title: GBM34 CONTROL independent replicate 1

description:
Library name: GBM34-CT1
Column name in all the processed files: GBM34-CT1


title: 4d post infection, dsEcR, biol rep 4

description:
Library name: SN0268067_S14
10X Genomics

value: 4 days post infectious blood meal


title: 20462X9_Liver_Keto_ALF_replicate2


title: Sterile male, TP1, fish 5_6


title: 2d post infection, dsEcR, biol rep 4

description:
Library name: SN0268067_S12
10X Genomics

value: 2 days post infectious blood meal


title: 20462X8_Liver_Keto_ALF_replicate1


title: GBM09 FIBULIN-3 KD independent replicate 3

description:
Library name: GBM09-KD3
Column name in all the processed files: GBM09-KD3

value: Fibulin-3 KD

value: fibulin-3 siRNA transfection


title: 4d post infection, dsGFP, biol rep 4

description:
Library name: SN0268067_S13
10X Genomics


title: GBM09 FIBULIN-3 KD independent replicate 2

description:
Library name: GBM09-KD2
Column name in all the processed files: GBM09-KD2


title: 20462X18_Liver_Control_ALF_replicate3


title: GBM34 FIBULIN-3 KD independent replicate 3

description:
Library name: GBM34-KD3
Column name in all the processed files: GBM34-KD3


title: Sterile male, TP1, fish 1_7

value: Testis


title: 36h post infection, dsEcR, biol rep 4

description:
Library name: SN0268067_S10
10X Genomics

value: midgut

value: 36 hours post infectious blood meal


title: 2d post infection, dsGFP, biol rep 4

description:
Library name: SN0268067_S11
10X Genomics


title: Sterile female, TP1, fish 6_9

value: Ovary


title: Sterile female, TP1, fish 5_8


title: GBM09 FIBULIN-3 KD independent replicate 1

description:
Library name: GBM09-KD1
Column name in all the processed files: GBM09-KD1


title: Sterile female, TP1, fish 5_3


title: 20462X3_Liver_HFD_ALF_replicate1


title: Sterile female, TP1, fish 6_6


title: 36h post infection, dsGFP, biol rep 4

description:
Library name: SN0268067_S9
10X Genomics

value: biol rep 4


title: 20462X2_Liver_Control_ALF_replicate2

value: liver


title: GBM09 CONTROL independent replicate 3

description:
Library name: GBM09-CT3
Column name in all the processed files: GBM09-CT3


title: 7d post infection, dsEcR, biol rep 3

description:
Library name: SN0268067_S8
10X Genomics

value: 7 days post infectious blood meal

value: dsEcR-injected

value: biol rep 3


title: GBM09 CONTROL independent replicate 2

description:
Library name: GBM09-CT2
Column name in all the processed files: GBM09-CT2

value: Primary glioblastoma tumor

value: control

value: control siRNA transfection


title: 20462X4_Liver_HFD_ALF_replicate2

value: WT


title: GBM09 CONTROL independent replicate 1

description:
Library name: GBM09-CT1
Column name in all the processed files: GBM09-CT1

value: Mesenchymal tumor stem cells

value: batch 2023-Sep-06


title: 4d post infection, dsEcR, biol rep 3

description:
Library name: SN0268067_S6
10X Genomics

value: 4 days post infectious blood meal


title: downstream migrant lamprey multiome 2 (GEX)

city: Saint Louis

first: Joseph

middle: C.

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

description:
Library name: dm2_GEX
10x Genomics

data_processing:
The sequence data were processed by the Cell Ranger ARC version 2.0.0 pipeline (10x Genomics) for read filtering, alignment against the genome, and barcode counting.
Assembly: kPetMar1
Supplementary files format and content: Tab separated matrix files

molecule: nuclear RNA

organism: Petromyzon marinus

source_name: retina

extract_protocol:
The retinas of downstream-migrant lamprey were dissected and snap-frozen. The frozen nuclei were extracted using the Chromium Nuclei Isolation Kit (10x Genomics) in accordance with the manufacturer's instructions.
From a single nuclei suspension, two replicates of the multiome library were constructed using the Chromium Next GEM Single Cell Multiome Reagent Kit version 1 (10x Genomics), following the manufacturer’s instructions.

value: retina

tag: developmental stage

value: downstream migrant


title: 4d post infection, dsGFP, biol rep 3

description:
Library name: SN0268067_S5
10X Genomics

value: midgut

value: dsGFP-injected


title: downstream migrant lamprey multiome 1 (GEX)

description:
Library name: dm1_GEX
10x Genomics