title: liver902_ControlBPA

city: Ann Arbor

first: Kelly

last: Bakulski

state: MI

address: 1415 Washington Heights

department: Department of Epidemiology

institute: University of Michigan

description: Library name: S902

data_processing:
FastQC (v0.11.8) was used to assess quality of reads (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Trimming was done with TrimGalore (v0.4.5) (https://github.com/FelixKrueger/TrimGalore) with the parameters: –adapter AGATCGGAAGAGC -e 0.1 –stringency 6 –length 20 –nextseq 20. Reads were aligned to the ARS-UI-Ramb-v2.0 sheep genome build using Bowtie2 (v2.3.4) [46]. DNA methylation was called using MethylDackel (v0.4.0) (parameters -d 5 -D 2000 –mergeContext) (https://github.com/dpryan79/MethylDackel).
Assembly: ARS-UI-Ramb-v2.0
Supplementary files format and content: .bedGraph files with columns corresponding to chromosome name, start coordinate, end coordinate, methylation percentage, number of alignments reported methylated based, number of alignments reporting unmethylated bases

organism: Ovis aries

source_name: liver

growth_protocol: Suffolk sheep were maintained at the University of Michigan Sheep Research Facility (Ann Arbor, MI) where studies were conducted following the Institutional Animal Care and Use Committee of the University of Michigan approved protocol in accordance with the National Research Council’s Guide for the Care and Use of Laboratory Animals and the Animal Welfare Act. This study involved two cohorts of sheep: Cohort 1: control and prenatal testosterone (T) treated and Cohort 2: control and prenatal bisphenol A (BPA) treated. Animals from both cohorts were kept together under the same conditions and given a similar maintenance diet to prevent obesity.

extract_protocol:
At the conclusion of the second breeding season (~21 months of age), female offspring in the T cohort were subjected to ovariectomy to eliminate any confounding influences from varying steroid levels. Liver tissue samples were obtained during the artificially induced follicular phase, following established protocols. Early follicular phase estradiol levels were maintained using a subcutaneous estradiol implant, 1 cm in length. To synchronize estrous cycle, two controlled internal drug-release implants containing progesterone (CIDR-G; InterAg, Hamilton, New Zealand) were placed subcutaneously to mimic luteal phase levels of progesterone. The progesterone implants were removed after 14 days, and four 30-mm estradiol implants were inserted to produce late follicular phase levels of estradiol. Animals were euthanized 18 hours later during the late artificial follicular phase by a barbiturate overdose (Fatal Plus; Vortech Pharmaceuticals, Dearborn, MI). In the prenatal BPA-treated cohort, female offspring liver tissue samples were collected during the natural follicular phase after synchronization with two injections of Prostaglandin F2alpha, 11 days apart. Samples were taken 27 hours after the second Prostaglandin F2alpha injection. From all animals, liver tissue was collected from the tip of the left lobe, flash-frozen and stored at -80°C.
DNA was extracted from 30 micrograms of frozen liver tissue using AllPrep DNA/RNA kit (Qiagen, Germantown, MD) using manufacturer protocol. A total of 200ng of DNA was used for each whole genome bisulphite sequencing (WGBS).  Library preparation and WGBS were carried out at the University of Michigan, Epigenomics Core. Each sample was spiked-in with 0.5% (w/w) of unmethylated Lambda DNA prior to library preparation, according to the ENCODE consortium’s guidelines. DNA was fragmented to a 350bp peak on a Covaris S220 focused-ultrasonicator system. The samples were next processed for end-repair and A-tailing, before proceeding to the ligation of a truncated methylated adaptor at 16°C overnight. The ligation products were cleaned with two rounds of Omega Bio-tek Mag-Bind TotalPure NGS beads. The ligated products were submitted to bisulfite treatment using Zymo’s EZ DNA Methylation kit, with the following protocol: 55 cycles of 95 degrees C for 30sec, 55 degrees C for 15 minutes. Samples were kept at 4 degrees C until cleanup. Final library amplification was done using the KAPA HiFi Uracil+ polymerase and NEB’s dual indexing primers. A total of 10 cycles of amplification were used. The PCR products were then cleaned with Omega Bio-tek Mag-Bind TotalPure NGS beads, and the final libraries were quantitated using the Qubit High Sensitivity dsDNA kit. Libraries were quantified using the KAPA Library quantitation kit and pooled for sequencing with a S4 flowcell for 200 cycles (paired end, 100 base pairs in length) on a NovaSeq6000.

treatment_protocol: In Cohort 1, pregnant sheep were randomly assigned to control and prenatal T treatment groups. The prenatal T treated group received biweekly intramuscular injections of T propionate (~1.2mg/kg; Millipore Sigma, St. Louis, MO) suspended in corn oil, from gestational day 30 to day 90.  In Cohort 2, pregnant sheep were randomly assigned to control and prenatal BPA treatment groups. Control and treatment groups were administered daily, subcutaneous injections of vehicle (corn oil) and 0.5mg/kg/day BPA (purity ≥ 99%, catalog number 239658; Aldrich Chemical Co, Milwaukee, Wisconsin) solubilized in corn oil, respectively.

value: liver

tag: Sex

value: F

tag: cohort

value: BPA

tag: treatment

value: control


title: hESC(H1) FXR1-OE input rep1, Day4

status: Public on Aug 22 2025

type: SRA

city: Beijing

first: Zhongyang

last: Chen

address: No.5, Dongdan Santiao, Dongcheng District

country: China

institute: School of Basic Medicine, Peking Union Medical College (PUMC)

description:
sample31
Poly(A)+ RNA-seq after FXR1 overexpression in H1 cell line

library_source: transcriptomic

data_processing:
(Sample 13-32) For RNA-seq data of hESC differentiation into mesoderm, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5".
Uniquely mapped reads were retained for calculating gene counts by FeatureCounts.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.83
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Human ESC line H1 was maintained in mTeSR1 on matrigel-coated plates.

extract_protocol:
The collected cells and components were subjected to RNA extraction using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: H1 hESCs were transfected in mTesR1 medium with the addition of 4 µg/ml (working concentration) polybrene and concentrated viral particles (NC, FXR1 OE).  After 48-72 hours, hESCs were induced to differentiate into the mesoderm using differentiation medium containing BMP4 and bFGF for 0, 2, and 4 days.  The cytoplasmic and nuclear cell fractions of hESCs were separated using NE-PER nuclear and cytoplasmic extraction reagents (Thermo Fisher).

tag: cell line

tag: cell type

value: human embryonic stem cells

tag: genotype

value: FXR1 overexpression

value: hESC differentiation into mesoderm

tag: time

value: Day 4

tag: fraction

value: input


title: Cas13d_4h_alone_non_targeting_R1

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

country: USA

institute: Stowers Institute for Medical Research

description: Library name: Cas13d_4h_alone_non_targeting_R1

data_processing:
Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and bcl-convert-3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: Danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA then was extracted using Direct-zol RNA Miniprep Kit (#R2050, Zymo Research) following manufacturer’s instructions.
Libraries were made according to the manufacturer’s directions for the TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat. No. 20020594),

tag: tissue

value: whole embryo

tag: age

value: 4 hpf

value: Cas13d Control


title: HP1601201T2D_B20

city: Huddinge

first: Ping

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome hg38 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 40% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; and 4) >= 1000 genes with RPKM >= 1. In addition, doublets detected by Scrublet were further removed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell …

molecule: total RNA

source_name: Human pancreatic islet single cells

extract_protocol: The reverse-transcribed cDNA from single cells was amplified followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).

value: Pancreatic islets

tag: disease state


title: liver928_ControlBPA

description: Library name: S928

library_source: genomic

molecule: genomic DNA


title: Cas13d_4h_alone_non_targeting_R2

description: Library name: Cas13d_4h_alone_non_targeting_R2


title: hESC(H1) WT input rep2, Day4

description:
sample30
control Poly(A)+ RNA-seq in H1 cell line

value: WT


title: HP1605601T2D_L4


title: liver918_BPA

description: Library name: S918


title: Screening_Calm2a_R1

data_processing:
Illumina Primary Analysis version NextSeq RTA 2.4.11 and Secondary Analysis version bcl2fastq2 v2.20 were run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

extract_protocol:
Total RNA then was extracted using Direct-zol RNA Miniprep Kit (#R2050, Zymo Research) following manufacturer’s instructions.
Libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096)

value: Knockdown


title: HP1711701T2D_A23


title: HP1525401_N7

value: Healthy


title: liver908_ControlBPA

description: Library name: S908


title: hESC(H1) FXR1-OE Nuc. rep2, Day2

description:
sample28
Nuclear RNA-seq after FXR1 overexpression in H1 cell line

molecule: nuclear RNA

value: Day 2

value: Nuc


title: Screening_Cab39l_R2


title: hESC(H1) WT input rep1, Day4

description:
sample29
control Poly(A)+ RNA-seq in H1 cell line


title: hESC(H1) input rep2

description:
sample34
eCLIP-seq input in H1 cell line
input.r2.norm.neg.bw
input.r2.norm.pos.bw
FXR1-all.peak.bed

data_processing:
(Sample 33-36) For eCLIP-seq: Raw reads with distinct inline barcodes were demultiplexed and the 10-mer random sequence was appended to the reads name in bam file.
Cutadapt was used to trimming low quality reads and adapter sequence.
Reads were aligned with the sequence of human repetitive elements in the RepBase database by STAR to remove the repetitive reads and obtain the cleaned reads.
Cleaned reads were then mapped to human genome using STAR. Removing PCR duplicate reads based on sharing identical random sequence. Two biological replicates were merged by SAMtools.
Peaks calling and downstream data analysis were performed by clipper. Peaks normalization by “Peak_input_normalization_wrapper.pl” tools. The eCLIP-seq peaks were filtered by P-value < 10e-3 and fold change > 2.
Assembly: GRCh38.83
Supplementary files format and content: bw file, peak text file

extract_protocol:
The RNA bonded by FXR1 was purified by RNA Clean & Concentrator-5 kit (ZYMO).
Libraries were prepared for high-throughput sequencing using standard Illumina protocols.
eCLIP-Seq

treatment_protocol: About 10^8 hESCs were  UV crosslinked. RNA-FXR1 complexes were captured with RNase A digestion and anti-FXR1 antibody immunoprecipitation.

tag: rip antibody


title: HP1711001_A3


title: Screening_Cab39l_R1


title: hESC(H1) FXR1-OE Nuc. rep1, Day2

description:
sample27
Nuclear RNA-seq after FXR1 overexpression in H1 cell line


title: liver977_BPA

description: Library name: S977

value: liver

value: F


title: HP1601201T2D_G17


title: hESC(H1) FXR1-OE Cyto. rep2, Day2

description:
sample26
Cytoplasmic RNA-seq after FXR1 overexpression in H1 cell line

molecule: cytoplasmic RNA

value: Cyto


title: liver924_ControlBPA

description: Library name: S924

value: BPA

value: control


title: HP1605601T2D_J11


title: Screening_Cas13d_R3


title: liver910_BPA

description: Library name: S910


title: Screening_Vrk3_R2


title: HP1711001_N9


title: liver98_ControlT

description: Library name: S98

value: T


title: Screening_Vrk3_R1


title: Screening_Calm2a_R2


title: liver201_ControlT

description: Library name: S201


title: HP1714601_N15


title: H1hESC(H1) WT Nuc. rep1, Day2

description:
sample23
control Nuclear RNA-seq in H1 cell line

value: human embryonic stem cells

value: hESC differentiation into mesoderm


title: H1hESC(H1) WT Nuc. rep2, Day2

description:
sample24
control Nuclear RNA-seq in H1 cell line


title: Screening_Stk3_R2

value: whole embryo


title: liver131_ControlT

description: Library name: S131


title: Screening_Stk3_R1

value: 4 hpf


title: H1hESC(H1) WT Cyto. rep1, Day2

description:
sample21
control Cytoplasmic RNA-seq in H1 cell line


title: HP1602301T2D_F4


title: HP1711001_E1


title: Screening_Pdik1l_R2


title: liver984_BPA

description: Library name: S984


title: H1hESC(H1) WT Cyto. rep2, Day2

description:
sample22
control Cytoplasmic RNA-seq in H1 cell line


title: liver255_PreT

description: Library name: S255


title: HP1525901_F13


title: hESC(H1) FXR1-OE Nuc. rep2, Day0

description:
sample20
Nuclear RNA-seq after FXR1 overexpression in H1 cell line

value: FXR1 overexpression

value: Day 0


title: Screening_Pdik1l_R1


title: hESC(H1) FXR1-OE Cyto. rep1, Day2

description:
sample25
Cytoplasmic RNA-seq after FXR1 overexpression in H1 cell line


title: HP1711001_H6

value: Pancreatic islets


title: liver48_PreT

description: Library name: S48


title: hESC(H1) FXR1-OE Nuc. rep1, Day0

description:
sample19
Nuclear RNA-seq after FXR1 overexpression in H1 cell line


title: Screening_Mknk2a_R2

value: Knockdown


title: liver63_PreT

description: Library name: S63


title: liver132_ControlT

description: Library name: S132


title: HP1525901_L3

value: Healthy


title: liver233_PreT

description: Library name: S233


title: Screening_Mknk2a_R1


title: HP1605601T2D_D13


title: hESC(H1) FXR1-OE Cyto. rep1, Day0

description:
sample17
Cytoplasmic RNA-seq after FXR1 overexpression in H1 cell line


title: HP1711001_E3


title: Screening_Mknk1_R2


title: liver179_ControlT

description: Library name: S179


title: hESC(H1) WT Nuc. rep2, Day0

description:
sample16
control Nuclear RNA-seq in H1 cell line

value: WT


title: Screening_Mknk1_R1


title: liver185_PreT

description: Library name: S185


title: hESC(H1) WT Nuc. rep1, Day0

description:
sample15
control Nuclear RNA-seq in H1 cell line

value: Nuc


title: HP1525901_K20


title: E16.5_mouse_spinal_cord__zic14ko__replicate1

type: RNA

city: Bethesda

first: Brian

middle: R

last: Roome

state: MD

address: 35 Convent Drive

department: NINDS

institute: National Institutes of Health

description:
Sections were taken from three Zic1- and Zic4-null mouse embryos through the brachial, thoracic and upper lumbar spinal cord segments
XED3D3_mEmbryonic_spinal_cord_100g_gene_list.csv.gz

hyb_protocol: All tissues used for spatial transcriptomics were immersion fixed overnight during (20-24 h). As mutant tissue used in this study was was fixed-frozen, and as Xenium v1 did not yet have a supported fixed frozen tissue protocol, we followed the guide for fresh-frozen tissues with modifications detailed below. Cryosectioning was done as described in CG000579 revision C (10X Genomics) and fixation and permeabilization was done as described in CG000581 revision C (10X Genomics), except that the 30-minute incubation in fixation solution was omitted. Tissue chemistry was done as described in CG000582 revision F (10X Genomics). Probe-sets used were the v1 mouse brain panel (248 genes) plus 100 custom probes.

scan_protocol: Operation of the Xenium Analyzer instrument was done as described in CG000584 revision E (10X Genomics). Sections were grouped by animal or genotype during Xenium analyzer setup. Areas which contained overlapping sections were omitted from this step and were not further analyzed.

data_processing: Spatial transcriptomics - data processing: Raw 10X Xenium datasets obtained from the Xenium analyzer computer were imported into Seurat, cells with 0 transcripts were removed, all cells in a group were clustered using 60 PCs at 0.5 resolution, and Seurat objects were written as .RDS files. Subsequently, coordinates were assigned bounding each section, clusters and gene markers were displayed on a UMAP reduction, and non-neuronal and sensory neuron clusters were excluded from further processing. From filtered spinal neurons, annotations were predicted using Robust Cell-Type Decomposition (RCTD) from the R package spacexr and our single-cell RNA-sequencing annotations as reference. Based on predicted cell-types, broader metadata classes were assigned to each cell. Further, a section identifier, and an estimated spinal segment were added as metadata. When possible, cell-types which were more easily resolved using Xenium than single-cell RNA-sequencing (i.e. motor neuron subtypes) were included as a separate metadata class (xeniumtypes) but were not otherwise analyzed. Additional exclusion of non-neuronal clusters was done here, particularly for clusters which had widely indistinct or sparse annotation transfer; on inspection, these were often clusters with most cells bearing both neuronal and non-neuronal markers resulting from poor cell segmentation or minor cell overlay. Spinal cords were classified into six segmental zones (C1-C4 – Cervical, C5-C8 – Brachial, Thoracic, L1-L3 – Upper lumbar, L4-L6 – Lower lumbar or Sacral) for purposes of estimating cell-type proportions per zone. Finally, cell coordinates and appropriate metadata were exported as .csv files for localization analysis. Subsequently, anatomical landmarks to be used as anchors for coordinate normalization were identified for each individual section retained as this. Coordinates from all sections of a given genotype and/or spinal segment were combined and overlaid on each other to best visualize neuron-type location across sections when exported as scatter plots. Data are made available as raw Xenium outputs, Seurat objects containing all section ROIs filtered to remove non-neurons, normalized collated cell coordinates from all sections within the indicated segmental zone, and (for selected analyses) mirrored normalized collated cell coordinates from both wild-type (x<0) and null (x>0) embryos with wild-type cells downsampled to approximately match the number of null cells (each cell-type was downsampled based on the ratio of total null to total wild-type neurons).

label: Xenium_mBrain_v1.1 + 100 custom probes

organism: Mus musculus

source_name: Spinal cord

label_protocol: Xenium protocol

growth_protocol: A breeding pair of mice was set to mate for one overnight period, and were separated the following morning. Embryos were extracted from pregnant female mice 16 days post-mating.

extract_protocol: On the indicated embryonic day, female mice were administered CO2 euthanasia, and embryos were promptly dissected and washed in ice-cold 1X PBS (except in cold HBSS for preparation for single-cell suspensions in the 10X Chromium assay). The spinal column was severed at the spinal cord-hindbrain junction, and the column was further dissected from the torso. For experiments prepared at the National Institutes of Health (all control experiments and Zic1/4 KO), the vertebral body was further dissected to expose the ventral surface of the spinal cord to fixative; for experiments performed elsewhere, dissection only involved isolation of the column with contained spinal cord. Spinal columns were immersion-fixed in ice-cold 4% paraformaldehyde overnight (20-24 hours). After fixation, tissue samples were briefly rinsed in 1X PBS (<10 minutes) and then equilibrated to a solution of 30% sucrose plus 1X PBS overnight or until tissue sunk to the bottom of the vessel containing the tissue. Tissues were agitated on an orbital or nutating shaker (depending on the vessel type) during the fixation and cryoprotection intervals in order to facilitate equilibration of tissues to the PFA or sucrose solutions

treatment_protocol: Treatment did not differ between groups; only genotype, in which case embryos null for Gsx1/2, Ptf1a, Zic3 or Zic1/4 were obtained by mating appropriate heterozygous parents.

value: Embryonic day 16.5


title: Screening_Gbp_R2


title: hESC(H1) WT Cyto. rep2, Day0

description:
sample14
control Cytoplasmic RNA-seq in H1 cell line


title: Screening_Gbp_R1


title: HP1525901_M3


title: E16.5_mouse_spinal_cord__zic3ko__replicate1

description:
Sections were taken from three Zic3-katun (null) mouse embryos through the brachial and thoracic spinal cord segments
XED3D3_mEmbryonic_spinal_cord_100g_gene_list.csv.gz


title: hESC(H1) WT Cyto. rep1, Day0

description:
sample13
control Cytoplasmic RNA-seq in H1 cell line


title: E16.5_mouse_spinal_cord__ptf1ako__replicate1

description:
Sections were taken from one Ptf1a-null mouse embryo through the brachial spinal cord
XED3D3_mEmbryonic_spinal_cord_100g_gene_list.csv.gz


title: Screening_Calm1a_R2


title: Screening_Calm1a_R1


title: E16.5_mouse_spinal_cord__gsx12ko__replicate1

description:
Sections were taken from three Gsx1- and Gsx2-null mouse embryos through the upper thoracic spinal cord
XED3D3_mEmbryonic_spinal_cord_100g_gene_list.csv.gz


title: HP1525401_N4


title: HP1525401_I7


title: hESC(H1) FXR1-OE Cyto. rep2, Day0

description:
sample18
Cytoplasmic RNA-seq after FXR1 overexpression in H1 cell line


title: hESC(H1) FXR1-KD Nuc. rep1

description:
sample11
Nuclear RNA-seq after FXR1 knockdown in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.93
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

treatment_protocol: H1 hESCs were maintained in mTesR1 with the addition of 4 µg/ml (working concentration) polybrene and concentrated viral particles (shNC, shFXR1) for 24 hours. The lentivirus infection medium was replaced with fresh mTesR1. After 48-72 hours of transfection, hESCs were subjected to separate cytoplasmic and nuclear cell fractions by NE-PER nuclear and cytoplasmic extraction reagents (Thermo Fisher).

value: FXR1 knockdown


title: HP1525901_A10


title: E16.5_mouse_spinal_cord__control__replicate4

description:
Sections were taken from one wild-type mouse embryo from cervical and brachial segments
xenium_165_control_coordinates_brac.csv.gz
xenium_165_control_coordinates_thor.csv.gz
XED3D3_mEmbryonic_spinal_cord_100g_gene_list.csv.gz


title: hESC(H1) FXR1-KD Cyto. rep2

description:
sample10
Cytoplasmic RNA-seq after FXR1 knockdown in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.92
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: Cyto


title: E16.5_mouse_spinal_cord__control__replicate3

description:
Sections were taken from one wild-type mouse embryo from thoracic and lumbosacral segments
xenium_165_control_coordinates_brac.csv.gz
xenium_165_control_coordinates_thor.csv.gz
XED3D3_mEmbryonic_spinal_cord_100g_gene_list.csv.gz


title: Screening_TLk2_R1


title: Screening_Tlk2_R2


title: HP1711001_A6


title: Screening_Stk26_R2


title: HP1605601T2D_M8


title: HP1525401_H17


title: hESC(H1) FXR1-KD Cyto. rep1

description:
sample9
Cytoplasmic RNA-seq after FXR1 knockdown in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.91
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: E16.5_mouse_spinal_cord__control__replicate2

description:
Sections were taken from one wild-type mouse embryo throughout the length of the spinal cord
xenium_165_control_coordinates_brac.csv.gz
xenium_165_control_coordinates_thor.csv.gz
XED3D3_mEmbryonic_spinal_cord_100g_gene_list.csv.gz


title: hESC(H1) FXR1-KD input rep2

description:
sample8
Poly(A)+ RNA-seq after FXR1 knockdown in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.90
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: input


title: Screening_Stk26_R1


title: HP1602301T2D_C18


title: Screening_Hexim1_R2


title: E16.5_mouse_spinal_cord__control__replicate1


title: hESC(H1) FXR1-KD input rep1

description:
sample7
Poly(A)+ RNA-seq after FXR1 knockdown in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.89
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: d15_WT3

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

hyb_protocol: Manufacturer's instructions were followed throughout the experiment.

scan_protocol: H&E staining was performed on the Xenium slide following the experiment.

data_processing: The raw data was resegmented using xeniumranger 1.7, using --expansion-distance 10 and otherwise default parameters. The individual sections were merged, processed and annotated using the R VoltRon package (doi: 10.1101/2023.12.15.571667). The annotated data is in supplementary all_d0_mols_reg_ann_2.rds for the non-peptide immunized mice and in file all_d15_mols_reg_ann_lesions_v4.rds for the samples 15 days  after immunization.

label: Xenium Human Probe Set

source_name: spinal cord

label_protocol: The Xenium experiment was done using the Xenium mouse brain panel and a custom 50 gene panel.

growth_protocol: OTUD7Bfl/fl mice with C57BL/6 background were generated with C57BL/6N-Otud7btm1b(EUCOMM)Wtsi/Wtsi embryonic stem cells purchased from the European Mouse Mutant Archive. First, Otud7b mutant mice were crossed with B6.129S4-Gt(ROSA)26Sortm1(FLP1)Dym/RainJ (Stock No: 009086 , The Jackson Laboratory, Bar Habor, ME, USA) to delete the frt-flanked sequences. Thereafter, otud7b mutants were crossed with C57BL/6 GFAP-cre mice34 to obtain GFAP-cre Otud7bfl/fl mice.

extract_protocol: At d15 p.i., mice were perfused with 0.1M PBS followed by 4% PFA in PBS. Spinal cord tissue was removed, embedded in paraffin and 5um thick sections were cut for spatial transcriptomic analysis.

treatment_protocol: For active EAE induction, 8-12 weeks old Otud7bfl/fl and GFAP-Cre Otud7b mice were immunized with MOG peptide containing complete Freund's adjuvant containing killed Mycobacterium tuberclosis.

tag: mogpeptideimmunization

value: 15 days

tag: otudbgenotype

value: wt


title: HP1602301T2D_E22


title: hESC(H1) FXR1-KD Nuc. rep2

description:
sample12
Nuclear RNA-seq after FXR1 knockdown in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.94
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: human embryonic stem cells


title: Screening_Hexim1_R1


title: HP1525401_C20


title: Screening_Bckdk_R2


title: hESC(H1) PLKO Nuc. rep1

description:
sample5
control Nuclear RNA-seq in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.87
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: PLKO


title: d15_WT1


title: HP1605601T2D_N20


title: hESC(H1) PLKO Cyto. rep2

description:
sample4
control Cytoplasmic RNA-seq in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.86
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: d15_KO3_slice2

value: GFAP-Cre


title: Screening_Bckdk_R1

value: whole embryo

value: 4 hpf


title: hESC(H1) PLKO Cyto. rep1

description:
sample3
control Cytoplasmic RNA-seq in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.85
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: HP1605601T2D_K15


title: Screening_Cas13d_R2

value: Cas13d Control


title: hESC(H1) PLKO input rep2

description:
sample2
control Poly(A)+ RNA-seq in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.84
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: d15_KO2


title: HP1525401_N14

value: Pancreatic islets


title: d15_KO1


title: Screening_Cas13d_R1


title: hESC(H1) PLKO input rep1

description:
sample1
control Poly(A)+ RNA-seq in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.83
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: d0_WT3


title: Bckdk_KD_6h_R2

data_processing:
Illumina Primary Analysis version NextSeq RTA 2.11.3.0 and bcl-convert-3.10.5 were run to demultiplex reads for all libraries and generate FASTQ files.
Assembly: danrer11
Supplementary files format and content: tab-delimited txt file includes raw counts for each Sample

value: 6 hpf

value: Knockdown


title: HP1601201T2D_P5

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome hg38 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 40% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; and 4) >= 1000 genes with RPKM >= 1. In addition, doublets detected by Scrublet were further removed.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell …


title: HP1605601T2D_H15


title: SK-N-BE(2)-C-TSA-3

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Reads were mapped to the human GRCh38 transcriptome (Ensembl cDNA release 97) and quantified using Salmon v0.8.2
Assembly: GRCh38
Supplementary files format and content: Salmon quant.sf file: read counts and TPM per transcript

growth_protocol: Cells were maintained in cell culture flasks supplemented with 10% FBS and penicllin/streptomycin in DMEM. The cells were maintained at a log phase in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
Nucleospin 96 RNA
Illumina TruSeq stranded mRNA; ssRNA-Seq

treatment_protocol: Approximately 0.1 million cells were seeded in each well of 24-well cell culture plates, with 1 mL media. 24 h after seeding they were exposed to 0.8% DMSO, 1 μM TSA, or 25 μM E6R for 16 h in a humified 5% incubator at 37°C before harvesting.

value: neuroblastoma

value: 1 μM TSA (0.8% DMSO)


title: d0_WT2


title: Bckdk_KD_6h_R1


title: SK-N-BE(2)-C-TSA-2


title: HP1606401T2D_Tn5_M20


title: hESC(H1) PLKO Nuc. rep2

description:
sample6
control Nuclear RNA-seq in H1 cell line

data_processing:
(Sample 1-12) For nucleo-cytoplasmic fractionation RNA-seq data, all reads were aligned to human genome using STAR with the parameter "--outFilterMultimapNmax 1 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outBAMsortingThreadN 5 --quantMode TranscriptomeSAM GeneCounts".
Uniquely mapped reads were retained for calculating gene counts by RSEM.
The nucleo-cytoplasmic ratio of gene was conducted using DESeq2 and differential gene N/C ratio analysis was conducted using DESeq2 with the P-value < 0.05 and |log2 (Fold change)| > log2 (1.2).
Assembly: GRCh38.88
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

value: Nuc


title: d15_WT2


title: Cas13d_6h_R2


title: HP1601201T2D_J14


title: d0_WT1


title: d0_KO3


title: SK-N-BE(2)-C-TSA-1


title: Cas13d_6h_R1


title: HP1714601_E12

value: Healthy


title: d0_KO2_slice2


title: HP1525901_G20


title: SK-N-BE(2)-C-E6R-3


title: Alana_elevated-CO2+elevated-temp+drought_biol_rep3

city: Brno

first: Zbynek

last: Milec

address: Belidla 986

country: Czech Republic

institute: Global Change Research Institute

description:
Library name: Sample24
CTD_R3_FL

data_processing:
Raw sequencing reads were processed using Trim Galore v.0.4.1 to remove adaptor sequences and low-quality bases. Cleaned reads were subsequently aligned to the wheat reference genome (RefSeq v2.0, EnsemblPlants) using HISAT2.
Differential gene expression analyses were performed with Cuffdiff and DEseq2, considering genes with an FDR-adjusted p-value < 0.05 to be significantly differentially expressed.
Expression levels were given as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: Triticum aestivum, RefSeq v2.0, EnsemblPlants
Supplementary files format and content: Excel table with FPKM values for three biological replicates for each growth regime.

organism: Triticum aestivum

source_name: leaf

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen), including an on-column DNase I treatment
Libraries were prepared (NEBNext Ultra RNA Library Prep Kit for Illumina, poly-A enrichment) and sequenced on an Illumina NovaSeq 6000 (150 bp paired-end, Novogene Ltd, UK

value: leaf

value: Alana

value: elevated CO2 (700 ppm) + elevated temperature (up to 31°C) + drought (soil water content 25 ± 5%)


title: SK-N-BE(2)-C-E6R-2


title: Alana_elevated-CO2+elevated-temp+drought_biol_rep2

description:
Library name: Sample23
CTD_R2_FL


title: d0_KO1_slice1


title: HP1602301T2D_L2


title: HP1606401T2D_Tn5_K11


title: SK-N-BE(2)-C-DMSO-3

value: 0.8% DMSO


title: S18_primary white preadipocytes (iWAT), FGF9, repl. 3

city: Freising

first: Katharina

last: Küllmer

state: Bavaria

address: Gregor-Mendel Straße 2

institute: Technical University of Munich

description: Library name: Sample 18

data_processing:
Alignmet was done using the Galaxy Europe Server. Before, reads got trimmed using TrimGalore. Mapping was done using HISAT2.
Assembly: mm39
Supplementary files format and content: countmatrix as txt file

source_name: iWAT

growth_protocol: Primary white preadipocytes (iWAT) were maintained in high-glucose DMEM medium supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere at 5% CO2 and 37°C.

extract_protocol:
RNA was extracted using the Promega Kit (SV Total RNA Isolation System )
Library preparation was performed using the Illumina Kit following the instructions.

treatment_protocol: Cells were treated upon 70-80% confluency with 5.5 nM FGF1, 2, 4, 8, or 9 or left untreated.

value: iWAT

value: primary cells (stromal vascular fraction)

value: white preadipocytes


title: HP1601201T2D_N18


title: HP1525401_P22


title: Alana_elevated-CO2+elevated-temp_biol_rep2

description:
Library name: Sample20
CT_R2_FL

value: elevated CO2 (700 ppm) + elevated temperature (up to 31°C)


title: S17_primary white preadipocytes (iWAT), FGF8, repl. 3

description: Library name: Sample 17


title: S16_primary white preadipocytes (iWAT), FGF4, repl. 3

description: Library name: Sample 16


title: SK-N-BE(2)-C-DMSO-2


title: SK-N-BE(2)-C-DMSO-1


title: HP1601201T2D_J9


title: S15_primary white preadipocytes (iWAT), FGF2, repl. 3

description: Library name: Sample 15


title: Alana_elevated-CO2+elevated-temp_biol_rep1

description:
Library name: Sample19
CT_R1_FL


title: Alana_elevated-CO2+drought_biol_rep2

description:
Library name: Sample17
CD2_FL

value: elevated CO2 (700 ppm) + drought (soil water content 25 ± 5%)


title: HP1602301T2D_P2


title: Alana_elevated-CO2+drought_biol_rep3

description:
Library name: Sample18
CD3_FL


title: S14_primary white preadipocytes (iWAT), FGF1, repl. 3

description: Library name: Sample 14


title: HP1525901_O11


title: Alana_elevated-CO2+drought_biol_rep1

description:
Library name: Sample16
CD1_FL


title: Alana_elevated-CO2+elevated-temp+drought_biol_rep1

description:
Library name: Sample22
CTD_R1_FL


title: S13_primary white preadipocytes (iWAT), untreated, repl. 3

description: Library name: Sample 13

value: untreated


title: S12_primary white preadipocytes (iWAT), FGF9, repl. 2

description: Library name: Sample 12


title: CLDX TTFM 03

city: Bangkok

first: Ariya

last: Kkamwut

country: Thailand

institute: Chulalongkorn University

description: Tumor tissues were isolated for total RNA extraction and subsequent analysis of 750 tumor-related genes.

hyb_protocol: Gene expression profiling was performed with the nCounter® Mouse PanCancer Pathways Panel (nanoString Technologies, Inc.), assessing 750 cancer-related genes. RNAs (100 ng) was hybridized and processed per the manufacturer’s protocols.

scan_protocol: The hybridized target-probe complexes were immobilized and aligned on a cartridge, followed by imaging and counting of the barcodes using an nCounter® system.

data_processing: Data were generated using nSolver software.

label: No

source_name: Breast cancer

label_protocol: No-label protocol

growth_protocol: Mice were injected with 3 × 10⁵ 4T1 cells into the left mammary fat pad via subcutaneous injection under aseptic conditions.

extract_protocol: Total RNA was isolated from tumor tissue using the Qiagen RNeasy Kit (Qiagen GmbH).

treatment_protocol: Mice were treated with or without TTFM.

tag: tag

value: Female

value: Tumor tissue


title: HP1525401_K8

value: Pancreatic islets


title: SK-N-BE(2)-C-E6R-1

value: neuroblastoma


title: CLDX TTFM 02


title: HP1714601_A10


title: Alana_elevated-CO2+elevated-temp_biol_rep3

description:
Library name: Sample21
CT_R3_FL


title: CLDX Saline 03


title: CLDX TTFM 01


title: S11_primary white preadipocytes (iWAT), FGF8, repl. 2

description: Library name: Sample 11


title: HP1601201T2D_L13


title: S10_primary white preadipocytes (iWAT), FGF4, repl. 2

description: Library name: Sample 10


title: Alana_elevated-temp+drought_biol_rep2

description:
Library name: Sample14
TD2_FL

value: elevated temperature (up to 31°C) + drought soil water content 25 ± 5%)


title: HP1714601_D15


title: Alana_elevated-temp+drought_biol_rep1

description:
Library name: Sample13
TD1_FL


title: CLDX Saline 02


title: S9_primary white preadipocytes (iWAT), FGF2, repl. 2

description: Library name: Sample 9


title: CLDX Saline 01


title: HP1711701T2D_J12


title: Alana_elevated-CO2_biol_rep2

description:
Library name: Sample11
eC_R2_FL

value: elevated CO2 (700 ppm)


title: S8_primary white preadipocytes (iWAT), FGF1, repl. 2

description: Library name: Sample 8


title: iPSC-derived cerebral organoid, rep 1

city: Chicago

first: Federico

last: Salas-Lucia

state: IL

address: 5841 S Maryland Ave

department: Medicine

institute: The University of Chicago

description:
In the same slide, we have FOV regions that are either WT (Control) and MCT8KO (MCT8 deficient)
CosMx Human 6K Discovery Panel

hyb_protocol: The slide was then permeabilized at 40ºC for 30 minutes. Fiducials were applied following alternating vortex and sonication, then slides were post-fixed in 10% NBF. Slides were incubated in NHS-acetate for 15 minutes at room temperature, and then in-situ hybridization of RNA probes was performed overnight at 37ºC according to the Manual Slide Preparation Guide for RNA Assays (Nanostring-Bruker). Incubation ended at 17 hours and stringent washes were performed twice for 20 minutes each in equal parts 4X SSC and 100% formamide at 37ºC. Slide was then washed again in 2X SSC and then nuclear and cell segmentation markers were applied at room temperature protected from light. Several washes were performed in 1X PBS before slide was placed on CosMx apparatus for run.

scan_protocol: Settings for imaging pre-bleaching profile configuration B, and cell segmentation profile for configuration B. This decision was made based on the CosMX SMI Instrument User Manual 10161-03-02, the latest version at the time of processing. Segmentation and Reagent configurations were kept as default settings for the a la carte markers included in the Human Universal 1,000-plex RNA Assay kit. Bulk reagents were added to the instrument along with the imaging tray, and flow cells were scanned according to the automated imaging process on the Nanostring-Bruker CosMx instrument. Tissue scan area was selected following the overview scan based on presence or absence of tissue, and FOVs were selected based on the presence of cell and nuclear segmentation marker presence.

data_processing:
Data processed through the AtoMx Spatial Informatics platform cloud-based system from Nanostring-Bruker. All images were run through the same foundational QC pipeline from AtoMx (v1.3.2) using default settings for cell segmentation, exported following foundational pipeline from AtoMx (v1.3.2), and rendered from coordinates data into LumeVR for visualization and further transcript analysis/NN.
SCT normalized counts of mRNA molecules per cell
seurat_object.RDS: RDS file with Seurat object for the CosMx dataset, includes cell coordinates and SCT transformation
metadata.csv: CSV file with metadata per cell, fov column can be use to split between Control (fovs 41 and 43) and MCT8Deficient (fovs 29 and 30)
sct_normalized.csv: CSV file with SCT normalized counts per cell

label: RNA probes

source_name: 5 microns slide of a brain organoid derived from CS01ictr cell line

label_protocol: Following NBF fixation, target retrieval was performed using the FFPE protocol for neural tissue due to materials availability. Target retrieval was performed using the pressure cooker method of incubation in a proprietary target retrieval solution at 100ºC for 15 minutes, washed in MilliQ water briefly, and then 100% ethanol for 3 minutes.

growth_protocol: Cerebral organoids were generated and growth till day 20 following the StemCell echnologies kit (SCT 08570). From that point on, organoids were culture in BrainPhys and the supplements SM1, N2A, NEAA (Gibco), Glutamax (Gibco), insulin (MilliporeSigma), BME (MilliporeSigma), and 2 ng/mL brain-derived neurotrophic growth factor (Tocris). Every 3 days, half of the medium was replaced with a fresh one)

extract_protocol: Organoids were fixed in 4% PFA and then cryosectioned and individually placed onto a Leica BOND Plus slide and allowed to adhere at room temperature. A map of the slide was drawn for clarity on localization data. The slide was prepped according to the fresh frozen Manual Slide Preparation for RNA Assays protocol from Nanostring-Bruker from January 2024, utilizing 10% normal buffered formalin fixation and incubation in hybridization oven at 60ºC for 30 minutes.

treatment_protocol: No treatment

value: Human induced pluripotent stem cells

value: WT and MCT8 deficient


title: Alana_elevated-CO2_biol_rep3

description:
Library name: Sample12
eC_R3_FL

value: leaf

value: Alana


title: human_skin_tissue_microarray

city: San Diego

first: Kellen

last: Cavagnero

state: California

address: 9500 Gilman Dr

institute: Univeristy of California, San Diego

description: 9 human FFPE skin sections (5µm) were combined onto a single slide. Spatial transcriptomic was performed by Nanostring as part of the Technology Access Program using the DASH system. See supplemental file 'Skin_fov_sample_metadata.csv' for sample deconvolution.

hyb_protocol: Hybridization was performed as in He, S., Bhatt, R., Brown, C. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol 40, 1794–1806 (2022) (https://doi.org/10.1038/s41587-022-01483-z)

scan_protocol: Scanning was performed as in He, S., Bhatt, R., Brown, C. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol 40, 1794–1806 (2022) (https://doi.org/10.1038/s41587-022-01483-z)

data_processing: DAPI staining and immunofluorescent staining of PanCK, CD298/B2M, CD45, and SMA facilitated cell segmentation with machine learning algorithm Cellpose. Counts were assigned to individual cells based on cell segmentation borders.

label: SMI imaging barcodes

source_name: Skin

label_protocol: Labeleing was performed as in He, S., Bhatt, R., Brown, C. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol 40, 1794–1806 (2022) (https://doi.org/10.1038/s41587-022-01483-z)

extract_protocol: Extraction was performed as in He, S., Bhatt, R., Brown, C. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat Biotechnol 40, 1794–1806 (2022) (https://doi.org/10.1038/s41587-022-01483-z)

value: Human skin tissue microarray. See supplemental file 'Skin_fov_sample_metadata.csv' for individual sample metadata.


title: Sample11_scRNAseq_White_leghorn_contour_repeat

city: Los Angeles

last: Wu

address: 2011 Zonal Ave HMR313A

institute: University of Southern California

description: Library name: Sample11

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: GRCg6a, Ensembl
Supplementary files format and content: Matrix files

organism: Gallus gallus

source_name: feather follicle

extract_protocol:
Regenerating feather follicles were surgically dissected and only 0.5 cm feather follicles with DP and DS were used for scRNA-seq (Fig. 4A). Feather follicles were cut to small pieces and incubated in 5 ml RPMI solution containing 232U DNAse I (Sigma-Aldrich), 1.25mg Liberase (Sigma-Aldrich), 5mg dispase:collagenase (Sigma-Aldrich) for 2 hours at 37°C and quenched with chelated FBS. Cells were passed through a 70-µm filter and centrifuged at 500g for 5 min, and the pellet was resuspended in PBS free of Ca2+ and Mg2+and 1% BSA. Dead cells were removed by using Dead Cell Removal Kit (Miltenyi Biotec). Live cells were resuspended in 0.04% UltraPure BSA (Sigma-Aldrich) and counted using the automated cell counter Countess (Thermo Fisher Scientific).
Cells were captured using Chromium (10X Genomics). GEM (Gel Bead-In EMulsions) generation, barcoding, post–GEM-RT (reverse transcription) cleanup, complementary DNA (cDNA) amplification, and cDNA library construction were performed using Single-Cell 3′ v2 chemistry (10X Genomics).

value: feather follicle

value: Whole follilcle

value: White leghorn chicken

tag: batch


title: Alana_elevated-temp+drought_biol_rep3

description:
Library name: Sample15
TD3_FL


title: Bckdk_IgG

description: Library name: Bckdk_IgG

data_processing:
CUT&RUN reads were aligned to the GRCz11 (danRer11) zebrafish genome assembly using Bowtie
C&R peaks were called using MACS2
Assembly: danrer11
Supplementary files format and content: narrowPeak files with peaks called with macs2 and bigwig files.
Library strategy: CUT&Run

extract_protocol:
DNA was purified using the Epichypher CUTANA ChIC/CUT&RUN Kit
Library were prepared following Epichypher CUTANA ChIC/CUT&RUN Kit protocol

value: whole embryo

value: 4 hpf

value: Knockdown


title: Alana_elevated-CO2_biol_rep1

description:
Library name: Sample10
eC_R1_FL


title: Alana_elevated-temp_biol_rep3

description:
Library name: Sample09
eT_R3_FL

value: elevated temperature (up to 31°C)


title: S6_primary white preadipocytes (iWAT), FGF9, repl. 1

description: Library name: Sample 6

value: iWAT

value: primary cells (stromal vascular fraction)

value: white preadipocytes


title: RNA-Seq, GaHV-3-SB-1-infected ESCDL-1 cell line

city: Namur

first: Camille

last: Ponsard

state: Namur

address: Rue de Bruxelles, 61

department: Veterinary Medecine

country: Belgium

institute: Unamur

description: Library name: Sample 2

data_processing:
Viral reads recovery (alignment using BWA mem -a -T15) (BWA v0.7.11)
Adapter trimming (Trimmomatic v0.39. Included the trimming of the adapters, quality trimming (Sliding Window 4:15), and a minimal length filter of 70 nucleotides
PCR duplicates removal (dedupe.sh (BBMap v1.0))
part of vCircTrappist v1.0 pipeline for spliced transcripts reads identification (including Samtools v1.10 and BWA v0.7.11)
Assembly: DQ530348 without bases 103681-103781, NC_002577 without bases 99640-99740,NC_002641 without bases 93872-93972
Supplementary files format and content: bigwig file with coverage data at each position of a reference genome

extract_protocol:
RNA was extracted using TRI-reagent (Thermofisher) and 5ug were sent to sequencing (Novogene).
5µg of total RNA was sent to Novogene for the library preparation and sequencing. Library preparation include : ribosomal depletion, linear RNA degradation, RNA fragmentation, reverse transcription, second strand synthesis (using dUTPs), end-repair, A-tailing, adapter ligation, enzyme digestion to remove dUTPs-containing second strand cDNAs, size selection, PCR amplification

value: WT


title: Bckdk_H3K27ac_R2

description: Library name: Bckdk_H3K27ac_R2


title: Alana_elevated-temp_biol_rep2

description:
Library name: Sample08
eT_R2_FL


title: RNA-Seq, GaHV-2-CVI-988-infected ESCDL-1 cell line

description: Library name: Sample 1


title: S4_primary white preadipocytes (iWAT), FGF4, repl. 1

description: Library name: Sample 4


title: Bckdk_H3K27ac_R1

description: Library name: Bckdk_H3K27ac_R1


title: MeHV-1-FC-126-infected ESCDL-1 cell line

description: Library name: Sample 3

data_processing:
Viral reads recovery (alignment using BWA mem -a -T15) (BWA v0.7.11)
Adapter trimming (Trimmomatic v0.39. Included the trimming of the adapters, quality trimming (Sliding Window 4:15), and a minimal length filter of 70 nucleotides
PCR duplicates removal (dedupe.sh (BBMap v1.0))
vCircTrappist v1.0 pipeline for circRNA-originating reads identification (including Samtools v1.10 and BWA v0.7.11)
Assembly: DQ530348, NC_002577, NC_002641
Supplementary files format and content: csv file including raw circRNA-derived reads count, circularization sites sequences, splicing pattern, strandness of the reads, 5' and 3' positions of the circularization sites, max size of the circRNAs, colocalized genes, common k-mers between circularization sites, viral segment, read identifiers


title: S3_primary white preadipocytes (iWAT), FGF2, repl. 1

description: Library name: Sample 3


title: Cas13d_H3K27ac_R2

description: Library name: Cas13d_H3K27ac_R2

value: Control


title: S2_primary white preadipocytes (iWAT), FGF1, repl. 1

description: Library name: Sample 2


title: GaHV-3-SB-1-infected ESCDL-1 cell line

description: Library name: Sample 2


title: Alana_drought_biol_rep2

description:
Library name: Sample05
D_R2_FL

value: drought (soil water content 25 ± 5%)


title: Cas13d_H3K27ac_R1

description: Library name: Cas13d_H3K27ac_R1


title: Alana_drought_biol_rep1

description:
Library name: Sample04
D_R1_FL


title: S1_primary white preadipocytes (iWAT), untreated, repl. 1

description: Library name: Sample 1

value: untreated


title: GaHV-2-CVI-988-infected ESCDL-1 cell line

description: Library name: Sample 1


title: B816 Kidney Organoids

city: Ames

first: Christopher

last: Zdyrski

state: Iowa

address: 1800 Christensen Dr, Bms 1072 Vet Med, Bms 1072 Vet Med

institute: Iowa State University

description: Library name: Sample 4

data_processing:
Read quality was assessed using FastQC (Andrews, 2010) and high-quality reads were mapped to the canine reference genome (ROS_Cfam_1.0, GCF_014441545.1). CellRanger was used to conduct read alignment and gene expression counts for single-cell RNA sequencing (Zheng et al., 2017). Single-cell RNA sequencing data was normalized and log transformed using R package Seurat (Butler et al., 2018; Hao et al., 2021, 2024; Satija et al., 2015; Stuart et al., 2019). R and corresponding R scripts were then used for data preparation procedures, analysis procedures, and visualization (R Core Team, 2021). Data was stored on GitHub, and Zenodo was used to create Digital Object Identifiers (DOIs) for publication citations.
Assembly: ROS_Cfam_1.0, GCF_014441545.1
Supplementary files format and content: FINAL_B816-organoids.RData

organism: Canis lupus familiaris

source_name: kidney organoid

extract_protocol:
Samples were expanded after thawing in CMGF + R/G and directly harvest as opposed to removing the R/G. Media was removed from wells and 500 µL of Cell Recovery Solution was added to each well, vigorously pipette mixed, and transferred to a 15 mL tube on ice for 20 minutes. The tube was then spun at 100 x g for 5 min at 4 °C and the supernatant was removed down to 500 µL. Then 1 mL of TrypLE Express was added to the sample, mixed, and the tube incubated in a 37°C heat bath for 8 minutes and shaken halfway through to mix the sample. After the incubation, the sample was pipette mixed to assist in dissociation of the organoids. Next, 7 mL of cold DMEM was used to stop dissociation. The sample was then strained through a pre-wet 40 µm filter and spun again. The sample was resuspended in 1 mL of DMEM and counted on an Invitrogen Countess 3 Automated Cell Counter. The sample was again spun, supernatant was removed, the pellet was resuspended in Cryostor CS10 and placed in a cryovial. The vial was immediately placed in a Mr. Frosty, incubated in a 4 °C fridge for 10 minutes, and transferred to a -80 °C for at least 24 hours. The samples were then either placed in liquid nitrogen for storage or shipped on dry ice.
Single-cell RNA libraries were generated using the Chromium Single Cell 3’ kit (10X Genomics, CA, USA). Loading onto the Chromium Controller was performed to target capture of ~6,000 GEMs per sample for downstream analysis and processed through the Chromium Controller following the standard manufacturer’s specifications. The sequencing libraries were evaluated for quality on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Libraries were quantified using qPCR (Applied Biosystems, Carlsbad, CA, USA) prior to loading onto an Illumina NovaSeq XPlus instrument. The samples were sequenced at a configuration compatible with the recommended guidelines as outlined by 10X Genomics. Raw sequence data (.bcl files) were converted into fastq files and de-multiplexed using the 10X Genomics’ cellranger mkfastq command.

value: kidney organoid


title: B816 Bladder Organoids

description: Library name: Sample 3

source_name: bladder organoid

value: bladder organoid


title: S7_primary white preadipocytes (iWAT), untreated, repl. 2

description: Library name: Sample 7


title: S5_primary white preadipocytes (iWAT), FGF8, repl. 1

description: Library name: Sample 5


title: Sample10_scRNAseq_Phoenix_main_sickle2

description:
Library name: Sample10
Sample10_scRNAseq_Phoenix_main_sickle2

value: Phoenix chicken

value: No treatment


title: Alana_control_biol_rep3

description:
Library name: Sample03
CTR_R3_FL

value: leaf

value: Alana

value: control


title: Sample9_scRNAseq_Phoenix_main_sickle1

description:
Library name: Sample9
Sample9_scRNAseq_Phoenix_main_sickle1

value: feather follicle

value: Whole follilcle


title: RNA-Seq, MeHV-1-FC-126-infected ESCDL-1 cell line

description: Library name: Sample 3


title: Cas13d_IgG

description: Library name: Cas13d_IgG

value: whole embryo

value: 4 hpf


title: B816 Pancreas Organoids

description: Library name: Sample 2

source_name: pancreas organoid

value: pancreas organoid


description:
Library name: Sample8
Sample8_scRNAseq_White_leghorn_lesser_sickle

value: White leghorn chicken


title: iBAT_primaryPreatipocytes

description:
Library name: Sample 2
samples are tagged per treatment (5=untreated, 6=FGF1, 7=FGF2, 8=FGF8)

data_processing:
Demultiplexing and alignment was done using the SevenBridges platform (https://www.sevenbridges.com/). All subsequent analyses were performed using the R package Seurat (v.5.0.0).
Assembly: Mouse mm39
Supplementary files format and content: tap separated features and barcodes files and matrix files

source_name: interscapular brown adipose tissue

growth_protocol: SVFs were cultured in DMEM high-glucose until (80%) confluency

extract_protocol:
Stromal vascular fractions (SVF) were isolated from pooled inguinal white and interscapular brown adipose tissues of 8–12-week-old mice. Tissues were minced and digested with collagenase at 37°C for 45–60 min with intermittent vortexing. Digests were filtered, and SVF cells were collected by centrifugation. After washing, cells were seeded in culture medium and maintained at 37°C with 5% CO₂.
Single-cell whole transcriptome libraries were prepared using the BD Rhapsody™ system with a 40,000-cell cartridge, following the manufacturer's protocol (BD Biosciences). Four samples were multiplexed using BD Sample Tags, and 10,000 cells per sample were loaded. Library preparation was performed according to the BD WTA protocol.

treatment_protocol: treatement with 5.5 nM FGF for 48 hours

value: interscapular brown adipose tissue

tag: strain

value: stromal vascular fraction

value: wild-type

value: FGF


title: Alana_control_biol_rep2

description:
Library name: Sample02
CTR_R2_FL


title: Alana_elevated-temp_biol_rep1

description:
Library name: Sample07
eT_R1_FL

value: elevated temperature (up to 31°C)


title: B816 Lung Organoids

description: Library name: Sample 1

source_name: lung organoid

value: lung organoid


title: Sample7_scRNAseq_White_leghorn_contour

description:
Library name: Sample7
Sample7_scRNAseq_White_leghorn_contour


title: Alana_drought_biol_rep3

description:
Library name: Sample06
D_R3_FL

value: drought (soil water content 25 ± 5%)


title: PBMCs, RRMS, S14

status: Public on Aug 21 2025

city: Campinas

first: Natalia

last: Munhoz Alves

state: SP

address: Rua Engenheiro Humberto Soares Camargo, 08

country: Brazil

institute: University of Campinas (UNICAMP)

description:
Library name: Ale_H7_S14
10X Genomics

data_processing:
Demultiplexing and processing were performed with Cell Ranger v7.0.0. When applicable, basecalls were converted to FASTQ with cellranger mkfastq (or facility-provided FASTQs were used). Per-library alignments, UMI counting, cell calling, and gene quantification were run with cellranger count against the human_hg38_gencode_v32_cellranger_v6 reference.
Assembly: Human GRCh38/hg38 (10x Genomics reference: human_hg38_gencode_v32_cellranger_v6)
Supplementary files format and content: RDS (R object, Seurat) file containing gene-by-cell UMI count matrix (Seurat RNA assay, counts slot) and per-cell metadata (e.g., sample/library ID, donor group).

source_name: Peripheral blood

extract_protocol:
PBMCs were isolated from whole blood by Ficoll density-gradient centrifugation, washed in PBS + 0.04% BSA, and kept on ice. Nuclei were prepared according to the 10x Genomics demonstrated protocol CG000365 (Nuclei Isolation for Single Cell RNA Sequencing): brief lysis on ice, quenching, gentle trituration, filtration through a 40-µm strainer, and washes in 10x Nuclei Buffer. Intact nuclei were counted and resuspended in 10x Nuclei Buffer at the target concentration for Chromium loading.
Single-nucleus 3′ gene expression libraries were generated on the Chromium Next GEM platform using the Single Cell 3′ Reagent Kit v3.1 (Dual Index) following the manufacturer’s instructions. Nuclei were encapsulated in GEMs with gel beads, reverse transcription was performed within GEMs to barcode cDNA with a cell barcode and UMI, GEMs were broken, cDNA was purified and amplified, and sequencing libraries were constructed by fragmentation, end-repair, A-tailing, adaptor ligation, and sample index PCR. Libraries were quantified and sequenced on an Illumina platform (paired-end).

value: Peripheral blood

value: Peripheral blood mononuclear cells (PBMCs)

tag: condition

value: Multiple sclerosis (RRMS)

tag: age (years)

tag: Sex

value: female


title: PBMCs, RRMS, S9

description:
Library name: Ale_G7_S9
10X Genomics

value: male


title: PBMCs, CTRL, S8

description:
Library name: Ale_F7_S8
10X Genomics

value: Heathy (CTRL)


title: PBMCs, RRMS, S7

description:
Library name: Ale_E7_S7
10X Genomics


title: PBMCs, CTRL, S4

description:
Library name: Ale_D7_S4
10X Genomics


title: PBMCs, RRMS, S2

description:
Library name: Ale_B7_S2
10X Genomics


title: PBMCs, CTRL, S3

description:
Library name: Ale_C7_S3
10X Genomics


title: PBMCs, RRMS, S1

description:
Library name: Ale_A7_S1
10X Genomics


title: AMIGO2-over expressing cell

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: colon cancer cell line SW480

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM; 05919, Nissui Pharmaceuticals, Tokyo, Japan) supplemented with 10% fetal bovine serum (FBS; 1370978, Gibco, Gaithersburg, MD, USA) and 30 mg/mL L-glutamine (Nacalai Tesque, Kyoto, Japan). The cells were cultured at 37 °C in an atmosphere containing 95% air and 5% CO2.

extract_protocol: Total RNA was extracted from the cells using TRIzol reagent (15596026, Thermo Fisher Scientific).

treatment_protocol: No treatment was performed.

value: large intestin, cancer

tag: histology

value: adenocarcinoma


title: iWAT_primaryPreadipocytes

description:
Library name: Sample 1
samples are tagged per treatment (1=untreated, 2=FGF1, 3=FGF2, 4=FGF8)

source_name: inguinal white adipose tissue

value: inguinal white adipose tissue

tag: cell type

tag: treatment


title: Detroit562 control replicate 2

city: SEOUL

first: Minji

last: An

address: 52, Ewhayeodae-gil, Seodaemun-gu

country: South Korea

institute: Ewha Womans University

description:
Library name: Detroit562_si-con_2_S20_L001
Detroit562 treated with sicon, replicate 2

data_processing:
Raw sequencing reads in FASTQ format were quality trimmed and filtered using fastp (v0.23.4).
Filtered reads were aligned to the human reference genome (GRCh38_v34) using STAR (v2.7.9a).
Gene-level quantification was performed using RSEM (v1.3.1) to obtained raw read counts.
Assembly: GRCh38, version 34 reference genome and corresponding GTF annotation.
Supplementary files format and content: csv files include raw count values from RSEM and ensembl gene identifiers for all samples
Supplementary files format and content: RData files include normalized expression values from RSEM (TPM) for all samples

source_name: oral cavity

growth_protocol: Cal27 cells were cultured in DMEM supplemented with 10% FBS and 1% penicilin-streptomycin (PS). Detroit562 cells were cultured in EMEM supplemented with 10% FBS and 1% PS.

extract_protocol:
Total RNA was extracted from each sample according to the manufacturer’s recommended protocol for the Illumina TruSeq Stranded mRNA library preparation workflow.
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s protocol.

treatment_protocol: For siRNA transfection, siRNAs(si-con or si-THBS1) were diluted in Opti-MEM to a final concentration of 10 nM, mixed with Lipofectamine RANiMax at a 1:1 ratio and after 15 min incubation, the mixture was addded to the cells.

value: oral cavity

tag: cell line

value: squamous carcinoma cell

tag: genotype

value: WT


title: Detroit562 control replicate 3

description:
Library name: Detroit562_si-con_3_S21_L001
Detroit562 treated with sicon, replicate 3

tag: tissue


title: Detroit562 siTHBS1 replicate 3

description:
Library name: Detroit562_si-THBS1_3_S24_L001
Detroit562 treated with siTHBS1, replicate 3

value: THBS1 Knockdown


title: Detroit562 control replicate 1

description:
Library name: Detroit562_si-con_1_S19_L001
Detroit562 treated with sicon, replicate 1


title: Detroit562 siTHBS1 replicate 2

description:
Library name: Detroit562_si-THBS1_2_S23_L001
Detroit562 treated with siTHBS1, replicate 2


title: Detroit562 siTHBS1 replicate 1

description:
Library name: Detroit562_si-THBS1_1_S22_L001
Detroit562 treated with siTHBS1, replicate 1


title: Cal27 siTHBS1 replicate 2

description:
Library name: Cal-27_si-THBS1_2_S0_L009
Cal-27 treated with siTHBS1, replicate 2


title: Cal27 siTHBS1 replicate 1

description:
Library name: Cal-27_si-THBS1_1_S16_L001
Cal-27 treated with siTHBS1, replicate 1


title: Cal27 control replicate 3

description:
Library name: Cal-27_si-con_3_S15_L001
Cal-27 treated with sicon, replicate 3


title: Alana_control_biol_rep1

description:
Library name: Sample01
CTR_R1_FL

value: leaf

value: Alana

value: control


title: Cal27 control replicate 1

description:
Library name: Cal-27_si-con_1_S13_L001
Cal-27 treated with sicon, replicate 1


title: Cal27 control replicate 2

description:
Library name: Cal-27_si-con_2_S14_L001
Cal-27 treated with sicon, replicate 2


title: LNCaP_16D_2

city: Seattle

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

description: Library name: LNCaP_16D_2

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Gene level abundance was quantitated using the GenomicAlignments summarizeOverlaps function using mode=IntersectionStrict, restricting to primary aligned reads, and counting reads mapping to the exonic regions of genes.
Assembly: hg38
Supplementary files format and content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

extract_protocol:
Total RNA was prepared with the Qiagen AllPrep Kit (Valencia, CA).
RNA-seq libraries were constructed from total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.

value: prostate tumor cell line

tag: passage

tag: growth serum

value: RPMI 1640 / 10% FBS / Pen-Strep


title: LNCaP_42F_1

description: Library name: LNCaP_42F_1

value: RPMI 1640 / 10% FBS / Pen-Strep / 10uM Enza


title: LNCaP_42F_2

description: Library name: LNCaP_42F_2


title: LNCaP_42D_2

description: Library name: LNCaP_42D_2


title: LNCaP_16D_1

description: Library name: LNCaP_16D_1


title: LNCaP_C4_p18_2

description: Library name: LNCaP_C4_p18_2


title: LNCaP_abl_p3_2

description: Library name: LNCaP_abl_p3_2

source_name: LNCaP-abl

value: LNCaP-abl

value: RPMI 1640 / 10% CSS / Pen-Strep


title: LNCaP_C42_p9_2

description: Library name: LNCaP_C42_p9_2

value: male


title: LNCaP_abl_p3_1

description: Library name: LNCaP_abl_p3_1


title: Cal27 siTHBS1 replicate 3

description:
Library name: Cal-27_si-THBS1_3_S18_L001
Cal-27 treated with siTHBS1, replicate 3


title: SET1B-Dam_hyp_rep2

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description: Library name: SET1B_Hyp_2

data_processing:
Files generated with DamMapper (https://github.com/niekwit/damid-seq)
Assembly: Ensembl hg38 build 110
Supplementary files format and content: BigWig files of RPKM normalised aligned reads
Library strategy: DamID-seq

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM (Sigma Aldrich) and supplemented with 10% FCS. Hypoxic cell culture was in a Whitley H35 Hypoxystation (Don Whitley Scientific) at 37 °C, 5% CO2, 1% O2 and 94% N2

extract_protocol:
Marshall et al. Nat Protoc, 2016
NEBNext Ultra II DNA Library Prep kit

treatment_protocol: 1% Oxygen 24 hours

value: HeLa

value: Hypoxia


title: HIF1A-Dam_hyp_rep2

description: Library name: HIF1A_Hyp_2


title: SET1B-Dam_hyp_rep1

description: Library name: SET1B_Hyp_1


title: HIF1A-Dam_hyp_rep1

description: Library name: HIF1A_Hyp_1


title: Patient 71, unstim

city: Nedlands

first: Jonatan

last: Leffler

address: 15 Hospital Ave

country: Australia

institute: Telethon Kids Institute

description: Library name: 71-unstim

data_processing:
The sequencing resulted in varying read lengths (15-65 million reads), thus samples were merged and adaptors trimmed using BBDuk [27] from left-hand side 5 bp to remove short random unique molecular identifiers (UMIs), and simultaneously trimmed from right-hand side to 100 bp, resulting in library sizes ranging between 15-45 million reads. Six samples (R1 and R2) where subsampled using seqtk [28] to 45M reads. The paired-end reads were aligned to the human reference genome Gencode v35 (hg38) using STAR aligner [29] and quantified at the gene level using featureCount() [30]. Raw sequencing quality control was carried out with FASTQC [31] and summarised with MultiQC [32].
Assembly: The sequencing data were analysed in the R (4.3.3) statistical computing environment. The data were filtered to retain genes with a HGNC gene symbol and at least 10 counts per million in at least 5 samples.
Supplementary files format and content: The EDASeq [33] was used for exploratory analysis using standard plots: density distribution, boxplots, relative log expression (RLE), principal component analysis (PCA) and inter-sample correlation heatmap and multi-dimensional scaling plots. Seven samples were removed due to insufficient sequencing depth (<10,000 reads), retaining 62 samples with library sizes ranging from 5 to 20 million reads for downstream analysis. These are the samples included with raw data in the "count matrix.csv"
Supplementary files format and content: In preparation for network analysis, samples were log transformed and normalised utilising Surrogate Variable Analysis in Omics playground (BigOmics Analytics). This is the data included in the "processed.csv" data

source_name: Blood

growth_protocol: PBMC grown in RPMI + 10% Hi-FCS for 18 h with or without R848 and/ Rb anti-IgE

extract_protocol:
For each sample, an average of 240 pDC (range 8 - 500) were sorted directly into a 96-well plate containing 10x SMART-Seq Lysis Buffer with RNase inhibitors (Takara Bio) and stored at -80°C. Samples were block-randomised prior to sorting, so that two participants with and without asthma were not sorted on the same day. From 24 individuals exposed to 3 culture conditions, 6 samples were sorted onto a 96-well plate across 12 sorting days/plate.
cDNA was prepared by Genomics WA using SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) and libraries using SureSelect XT HS2 DNA Library Preparation Kit (Agilent) for ILM (Pre PCR), SureSelect XT HS2 Index Primer Pairs 1-96 for ILM (Pre PCR, Agilent) and sequenced on a NovaSeq 6000 across two lanes and three flow cells.

treatment_protocol: Following stimulation, pDC were isolated using FACS directly into SMART-Seq lysis buffer

value: Blood

value: pDC

value: no Asthma

value: no stim


title: Patient 71, R848

description: Library name: 71-R848


title: Patient 69, anti-IgE

description: Library name: 69-Anti-IgE

value: R848 + anti-IgE


title: Patient 60, unstim

description: Library name: 60-unstim

value: unknown


title: Patient 69, unstim

description: Library name: 69-untsim


title: Dam_only_hyp_rep2

description: Library name: Dam_Hyp_2

value: WT


title: Patient 71, anti-IgE

description: Library name: 71-Anti-IgE


title: Dam_only_hyp_rep1

description: Library name: Dam_Hyp_1


title: Patient 69, R848

description: Library name: 69-R848


title: Patient 58, unstim

description: Library name: 58-untsim


title: Patient 60, R848

description: Library name: 60-R848


title: Patient 60, anti-IgE

description: Library name: 60-Anti-IgE


title: LNCaP_42D_1

description: Library name: LNCaP_42D_1


title: Patient 54, R848

description: Library name: 54-R848

value: Asthma


title: LNCaP_C42_p9_1

description: Library name: LNCaP_C42_p9_1


title: Patient 58, anti-IgE

description: Library name: 58-Anti-IgE


title: Patient 54, unstim

description: Library name: 54-unstim


title: Patient 58, R848

description: Library name: 58-R848


title: Patient 53, anti-IgE

description: Library name: 53-Anti-IgE


title: Patient 42, unstim

description: Library name: 42-unstim


title: Patient 53, unstim

description: Library name: 53-untsim


title: Patient 53, R848

description: Library name: 53-R848


title: Patient 42, R848

description: Library name: 42-R848


title: Patient 42, anti-IgE

description: Library name: 42-Anti-IgE


title: LNCaP_C4_p18_1

description: Library name: LNCaP_C4_p18_1


title: Patient 36, unstim

description: Library name: 36-unstim


title: Patient 41, R848

description: Library name: 41-R848


title: Patient 36, anti-IgE

description: Library name: 36-Anti-IgE


title: Patient 34, unstim

description: Library name: 34-unstim


title: Patient 41, anti-IgE

description: Library name: 41-Anti-IgE


title: Patient 36, R848

description: Library name: 36-R848


title: Patient 34, R848

description: Library name: 34-R848


title: Patient 30, anti-IgE

description: Library name: 30-Anti-IgE


title: Patient 28, anti-IgE

description: Library name: 28-Anti-IgE


title: Patient 34, anti-IgE

description: Library name: 34-Anti-IgE


title: Patient 28, unstim

description: Library name: 28-unstim


title: Patient 28, R848

description: Library name: 28-R848


title: Patient 24, unstim

description: Library name: 24-unstim


title: Patient 24, anti-IgE

description: Library name: 24-Anti-IgE


title: Patient 24, R848

description: Library name: 24-R848


title: Patient 23, anti-IgE

description: Library name: 23-Anti-IgE


title: Patient 23, unstim

description: Library name: 23-unstim


title: Patient 20, unstim

description: Library name: 20-unstim


title: Control cell

value: large intestin, cancer

value: adenocarcinoma


title: Patient 20, R848

description: Library name: 20-R848


title: Patient 20, anti-IgE

description: Library name: 20-Anti-IgE


title: Patient 41, unstim

description: Library name: 41-untsim


title: Patient 12, unstim

description: Library name: 12-unstim


title: Patient 12, R848

description: Library name: 12-R848


title: Patient 19, R848

description: Library name: 19-R848


title: Patient 19, anti-IgE

description: Library name: 19-Anti-IgE


title: Patient 12, anti-IgE

description: Library name: 12-Anti-IgE


title: Patient 10, anti-IgE

description: Library name: 10-Anti-IgE


title: Patient 10, unstim

description: Library name: 10-untsim


title: Patient 6, unstim

description: Library name: 6-unstim


title: Patient 6, R848

description: Library name: 6-R848


title: Patient 30, R848

description: Library name: 30-R848


title: Patient 5, anti-IgE

description: Library name: 5-Anti-IgE


title: Patient 6, anti-IgE

description: Library name: 6-Anti-IgE


title: Patient 5, R848

description: Library name: 5-R848


title: Patient 2, R848

description: Library name: 2-R848


title: Patient 23, R848

description: Library name: 23-R848


title: Patient 1, anti-IgE

description: Library name: 1-Anti-IgE


title: Patient 2, anti-IgE

description: Library name: 2-Anti-IgE


title: Patient 1, R848

description: Library name: 1-R848


title: LNCaP.PN.FBS_INPUT_rep1

description: Library name: LNCaP.PN.FBS_INPUT_rep1

data_processing:
Fastq files were aligned to hg38 using the Burrows-Wheeler Aligner[1] version 0.7.17-r1188 using the BWA-mem function.
Samtools[2] was used to filter for alignments with a MAPQ score of at least 30.
PCR duplicates were marked using Picard MarkDuplicates v2.24.1[3] and then removed using Samtools.
BigWig files were prepared using deepTools v3.5.4[6]) bamCoverage using RPGC normalization, bin size of 10, and effective genome size 2913022398.
Peaks were called using MACS3 v3.0.0[4] against Input controls
Peaks of all lines except those with R1881 were concatenated together and merged with bedtools merge to produce LNCaP_AR_ChIP_CatPeaks.bed
Assembly: hg38
Supplementary files format and content: bigWig files of coverage
Supplementary files format and content: Merged peaks

growth_protocol: All cells were grew under their standard growth medium with either 10%FBS or 10%CSS.

extract_protocol:
Chromatin isolation, immunoprecipitation and sequencing. Cells were seeded in 15 cm² dishes in their respective growth medium and cultured for 3 days before performing ChIP experiments. Cells were fixed with 1% formaldehyde at room temperature for 10 minutes, and then quenched with 125 mM glycine. Cell nuclei were sequentially isolated using LB1 buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) followed by LB2 buffer (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA). The nu-clei were then lysed with ChIP lysis buffer (1% SDS, 5 mM EDTA, and 50 mM Tris-HCl, pH 8.1). Chromatin was sheared into ~300 bp fragments using the Bioruptor Plus Sonicator (Diagenode). Immunoprecipitation was performed using an anti-AR antibody (ab108341). The precipitated protein-DNA complexes were reverse cross-linked overnight at 65°C. The following day, both input and ChIP DNA were purified using the QIAquick PCR Purification Kit (Qiagen, 28104).
ChIP-seq libraries were prepared using the ThruPLEX DNA-Seq Prep Kit (Takara Bio, R400675). Next-generation sequencing (100 bp, paired-end) was conducted on an Illumina NovaSeq 6000 at the Fred Hutch Genomics Core.

treatment_protocol: LNCaP_42D and LNCaP_42F were seed with 10µM of enzalutamide during all seeding period. Samples labled with "R1881" were treated with 10 nM of R1881 for 4 hours prior to ChIP experiment.

value: prostate tumor cell line


title: LNCaP.PN.FBS_AR-N_rep1

description: Library name: LNCaP.PN.FBS_AR-N_rep1


title: LNCaP.PN.FBS_AR-N_rep2

description: Library name: LNCaP.PN.FBS_AR-N_rep2


title: LNCaP.PN.FBS_AR-N_rep3

description: Library name: LNCaP.PN.FBS_AR-N_rep3


title: Patient 19, unstim

description: Library name: 19-untsim


title: LNCaP.PN.FBS.10nMR1881_AR-N_rep1

description: Library name: LNCaP.PN.FBS.10nMR1881_AR-N_rep1

value: 10 nM of R1881 for 4 hours


title: LNCaP.AR909.PN.FBS_AR-N_rep3

description: Library name: LNCaP.AR909.PN.FBS_AR-N_rep3


title: LNCaP.AR909.PN.FBS_AR-N_rep1

description: Library name: LNCaP.AR909.PN.FBS_AR-N_rep1


title: LNCaP.AR907.PN_INPUT_rep1

description: Library name: LNCaP.AR907.PN_INPUT_rep1


title: Patient 10, R848

description: Library name: 10-R848


title: LNCaP.AR909.PN.FBS.10nMR1881_AR-N_rep1

description: Library name: LNCaP.AR909.PN.FBS.10nMR1881_AR-N_rep1


title: LNCaP.AR907.PN.FBS_AR-N_rep3

description: Library name: LNCaP.AR907.PN.FBS_AR-N_rep3


title: Patient 2, unstim

description: Library name: 2-unstim


title: LNCaP.AR907.PN.FBS_AR-N_rep1

description: Library name: LNCaP.AR907.PN.FBS_AR-N_rep1


title: LNCaP.AR907.PN.FBS_AR-N_rep2

description: Library name: LNCaP.AR907.PN.FBS_AR-N_rep2


title: LNCaP.AR907.PN.FBS.10nMR1881_AR-N_rep1

description: Library name: LNCaP.AR907.PN.FBS.10nMR1881_AR-N_rep1


title: LNCaP95.PN.CSS_AR-N_rep3

description: Library name: LNCaP95.PN.CSS_AR-N_rep3


title: LNCaP95.PN.CSS_INPUT_rep1

description: Library name: LNCaP95.PN.CSS_INPUT_rep1


title: LNCaP95.PN.CSS_AR-N_rep2

description: Library name: LNCaP95.PN.CSS_AR-N_rep2


title: LNCaP.42F.PN.FBS.10uMENZA_AR-N_rep3

description: Library name: LNCaP.42F.PN.FBS.10uMENZA_AR-N_rep3

value: 10 µM of enzalutamide during all seeding period


title: LNCaP.42F.PN_INPUT_rep1

description: Library name: LNCaP.42F.PN_INPUT_rep1


title: LNCaP95.PN.CSS_AR-N_rep1

description: Library name: LNCaP95.PN.CSS_AR-N_rep1


title: LNCaP.42F.PN.FBS.10uMENZA_AR-N_rep2

description: Library name: LNCaP.42F.PN.FBS.10uMENZA_AR-N_rep2


title: LNCaP.42D.PN.FBS.10uMENZA_AR-N_rep3

description: Library name: LNCaP.42D.PN.FBS.10uMENZA_AR-N_rep3


title: LNCaP.42F.PN.FBS.10uMENZA_AR-N_rep1

description: Library name: LNCaP.42F.PN.FBS.10uMENZA_AR-N_rep1


title: LNCaP.42D.PN.FBS.10uMENZA_AR-N_rep2

description: Library name: LNCaP.42D.PN.FBS.10uMENZA_AR-N_rep2


title: LNCaP.42D.PN_INPUT_rep1

description: Library name: LNCaP.42D.PN_INPUT_rep1


title: LNCaP.16D.PN_INPUT_rep1

description: Library name: LNCaP.16D.PN_INPUT_rep1


title: LNCaP.42D.PN.FBS.10uMENZA_AR-N_rep1

description: Library name: LNCaP.42D.PN.FBS.10uMENZA_AR-N_rep1


title: LNCaP.AR909.PN_INPUT_rep1

description: Library name: LNCaP.AR909.PN_INPUT_rep1


title: LNCaP.16D.PN.FBS_AR-N_rep2

description: Library name: LNCaP.16D.PN.FBS_AR-N_rep2


title: Input_abl-R-rep2

description: Library name: Input_abl-R-rep2


title: LNCaP.16D.PN.FBS_AR-N_rep3

description: Library name: LNCaP.16D.PN.FBS_AR-N_rep3


title: C4.PN_INPUT_rep1

description: Library name: C4.PN_INPUT_rep1


title: LNCaP.16D.PN.FBS_AR-N_rep1

description: Library name: LNCaP.16D.PN.FBS_AR-N_rep1


title: C4.PN.FBS_AR-N_rep3

description: Library name: C4.PN.FBS_AR-N_rep3


title: LNCaP.AR909.PN.FBS_AR-N_rep2

description: Library name: LNCaP.AR909.PN.FBS_AR-N_rep2


title: C4.PN.FBS_AR-N_rep2

description: Library name: C4.PN.FBS_AR-N_rep2


title: C4.PN.FBS_AR-N_rep1

description: Library name: C4.PN.FBS_AR-N_rep1


title: C42.PN.FBS_AR-N_rep3

description: Library name: C42.PN.FBS_AR-N_rep3


title: C42.PN.FBS_AR-N_rep2

description: Library name: C42.PN.FBS_AR-N_rep2


title: C42B.PN.FBS_INPUT_rep1

description: Library name: C42B.PN.FBS_INPUT_rep1


title: C42.PN_INPUT_rep1

description: Library name: C42.PN_INPUT_rep1


title: C42.PN.FBS_AR-N_rep1

description: Library name: C42.PN.FBS_AR-N_rep1


title: C42B.PN.FBS_AR-N_rep2

description: Library name: C42B.PN.FBS_AR-N_rep2


title: AR-abl-R-4

description: Library name: AR-abl-R-4


title: C42B.PN.FBS_AR-N_rep1

description: Library name: C42B.PN.FBS_AR-N_rep1


title: AR-abl-R-2

description: Library name: AR-abl-R-2


title: AR-abl-R-3

description: Library name: AR-abl-R-3


title: AR-abl-R-1

description: Library name: AR-abl-R-1


title: 42D.PN.FBS_INPUT_rep1

description: Library name: 42D.PN.FBS_INPUT_rep1


title: 16D.PN.FBS_INPUT_rep1

description: Library name: 16D.PN.FBS_INPUT_rep1


title: LNCaP_AR_909_2

description: Library name: LNCaP_AR_909_2

value: RPMI 1640 HEPES Glutamine / 10% FBS /Sodium Pyruvate / Pen-Strep


title: LNCaP_AR_909_1

description: Library name: LNCaP_AR_909_1

value: male


title: 42F.PN.FBS_INPUT_rep1

description: Library name: 42F.PN.FBS_INPUT_rep1


title: Input_abl-R-rep1

description: Library name: Input_abl-R-rep1


title: LNCaP_AR_907_1

description: Library name: LNCaP_AR_907_1


title: LNCaP_42F_ENZR_p20_2

description: Library name: LNCaP_42F_ENZR_p20_2

value: RPMI 1640 / 10% FBS / Pen-Strep / 10uM Enza


title: LNCaP_42F_ENZR_p20_1

description: Library name: LNCaP_42F_ENZR_p20_1


title: LNCaP_42D_ENZR_p14_2

description: Library name: LNCaP_42D_ENZR_p14_2


title: LNCaP_16D_p30_2

description: Library name: LNCaP_16D_p30_2

value: RPMI 1640 / 10% FBS / Pen-Strep


title: LNCaP_42D_ENZR_p14_1

description: Library name: LNCaP_42D_ENZR_p14_1


title: LNCaP_16D_p30_1

description: Library name: LNCaP_16D_p30_1


title: LNCaP_APIPC_p28_2

description: Library name: LNCaP_APIPC_p28_2

source_name: LNCaP-APIPC

value: LNCaP-APIPC

value: RPMI 1640 / 5% CSS / Pen-Strep / 2.5 μg/mL blasticidin + 1 μg/ml puromycin + 25 μg/ml Zeocin + 1 μg/mL doxycycline


title: LNCaP_APIPC_p28_1

description: Library name: LNCaP_APIPC_p28_1


title: LNCaP_shAR_pATK_p43_2

description: Library name: LNCaP_shAR_pATK_p43_2

value: RPMI 1640 / 5% CSS / Pen-Strep / 2.5 μg/mL blasticidin + 1 μg/ml puromycin + 25 μg/ml Zeocin


title: LNCaP_shAR_pATK_p43_1

description: Library name: LNCaP_shAR_pATK_p43_1


title: LNCaP_C42B_p6_2

description: Library name: LNCaP_C42B_p6_2


title: C42B.PN.FBS_AR-N_rep3

description: Library name: C42B.PN.FBS_AR-N_rep3


title: LNCaP_C42B_p6_1

description: Library name: LNCaP_C42B_p6_1


title: LNCaP_95_p25_2

description: Library name: LNCaP_95_p25_2

value: RPMI 1640 / 10% CSS / Pen-Strep


title: LNCaP_abl_p13_2

description: Library name: LNCaP_abl_p13_2

value: LNCaP-abl


title: LNCaP_FGC_p29_1

description: Library name: LNCaP_FGC_p29_1

source_name: LNCaP-FGC

value: LNCaP-FGC


title: LNCaP_95_p25_1

description: Library name: LNCaP_95_p25_1


title: LNCaP_FGC_p29_2

description: Library name: LNCaP_FGC_p29_2


title: U87 biol rep 3

city: Brussels

first: Sandra

last: Tuyaerts

address: Laarbeeklaan 103

department: Translational Oncology Research Centre

institute: Vrije Universiteit Brussel

description: Library name: Sample 32

data_processing:
we used STAR to align the reads to the hg19 reference genome and htseq-count to quantify the counts per transcript.
Assembly: hg19
Supplementary files format and content: tab-delimited text files contain raw counts

growth_protocol: 624-mel/938-mel/BXPC3/ASPC1: RPMI1640 + 10% FBS + pen/strep + L-Glu; LN229/PaTu8988t: DMEM + 10% FBS + pen/strep + L-Glu; Capan-1/SW1990: IMDM + 20% FBS + pen/strep + L-Glu; U87: MEM + 10% FBS + pen/strep + L-Glu; MiaPaca-2: DMEM + 10% FBS + 2,5% HI horse serum + pen/strep + L-Glu; SUIT2: DMEM + 5% FBS + 5% HI horse serum + pen/strep + L-Glu

extract_protocol:
RNA was extracted using the NucleoSpin® RNA Plus kit.
150 ng of RNA was processed through the Watchmaker RNA Library Prep Kit with Polaris™ Depletion, version v1.1.1122. The following modifications were made : (1) library prep reagents were reduced to 50%, (2) fragmentation was performed for intact/high quality RNA (fragmentation for 5 minutes at 85°C), (3) the optional 2nd post-ligation cleanup was performed and (4) libraries were amplified using 14 PCR cycles.

value: glioblastoma cell line

value: WT


title: U87 biol rep 2

description: Library name: Sample 31


title: LNCaP_AR_907_2

description: Library name: LNCaP_AR_907_2


title: SW1990 biol rep 2

description: Library name: Sample 28

value: pancreatic adenocarcinoma cell line


title: SUIT2 biol rep 3

description: Library name: Sample 26


title: SUIT2 biol rep 1

description: Library name: Sample 24


title: U87 biol rep 1

description: Library name: Sample 30


title: SW1990 biol rep 1

description: Library name: Sample 27


title: SUIT2 biol rep 2

description: Library name: Sample 25


title: PaTu8988t biol rep 3

description: Library name: Sample 23


title: MiaPaca-2 biol rep 3

description: Library name: Sample 20


title: PaTu8988t biol rep 1

description: Library name: Sample 21


title: MiaPaca-2 biol rep 2

description: Library name: Sample 19


title: LN229 biol rep 2

description: Library name: Sample 17


title: PaTu8988t biol rep 2

description: Library name: Sample 22


title: Capan-1 biol rep 3

description: Library name: Sample 15


title: Capan-1 biol rep 2

description: Library name: Sample 14


title: SW1990 biol rep 3

description: Library name: Sample 29


title: LN229 biol rep 1

description: Library name: Sample 16


title: MiaPaca-2 biol rep 1

description: Library name: Sample 18


title: Capan-1 biol rep 1

description: Library name: Sample 13


title: LNCaP_abl_p13_1

description: Library name: LNCaP_abl_p13_1


title: BXPC3 biol rep 3

description: Library name: Sample 12


title: BXPC3 biol rep 2

description: Library name: Sample 11


title: BXPC3 biol rep 1

description: Library name: Sample 10


title: ASPC1 biol rep 3

description: Library name: Sample 9


title: 938-mel biol rep 3

description: Library name: Sample 6

value: melanoma cell line


title: 938-mel biol rep 2

description: Library name: Sample 5


title: ASPC1 biol rep 1

description: Library name: Sample 7


title: 938-mel biol rep 1

description: Library name: Sample 4


title: 624-mel biol rep 2

description: Library name: Sample 2


title: 624-mel biol rep 1

description: Library name: Sample 1


title: hESC,ZM11,Het4

city: Cincinnati

first: Jason

last: Tchieu

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw FASTQ files were quality checked using FastQC. Adapter sequences were trimmed using fastp with parameters "-q 20 -n7". Trimmed reads were then aligned to hg38 using HISAT2 with default parameters. The raw count files was generated using featureCounts in Subread with default parameters.
Genes with no raw counts in >= 75% samples were filtered out. Differential gene expression analysis was performed using "DESeq2" with p.adjust < 0.05 and fold change > 1.5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: Human embryonic stem cells (hESCs) were maintained in Essential 8 medium in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen).
mRNA-Seq libraries (poly A enrichment) for hESCs were prepared using TruSeq Stranded mRNA library kit and sequenced at Roy J. Carver Biotechnology Center (CBC) at the University of Illinois at Urbana-Champaign (UIUC) for 150bp paired-end (PE) sequencing on an Illumina NovaSeq platform. mRNA-Seq libraries (poly A enrichment) for NSCs were prepared by Novogene for 150bp paired-end (PE) sequencing on an Illumina NovaSeq platform.

treatment_protocol: Cortical neural stem cells (NSCs) were directly differentiated from hESCs using dual-SMAD strategies for the first 8 days, and subsequently treated with FGF8 to pattern prefrontal cortical lineage until day 18. For overexpression studies, doxycycline treatment starts at d15 till d18.

value: embryonic stem cells

value: ZMYND11 +/-


title: hESC,ZM11,Homo,2

value: ZMYND11 -/-


title: hESC,ZM11,Homo,1


title: hESC,ZM11,Het2


title: hESC,ZM11,WT,2


title: hESC,ZM11,WT,1


title: ZIKV only 3

city: Columbia

first: Pallav

last: Singh

address: CE720 Clinical Support and Education

department: Institute for Data Science and Informatics

institute: University of Missouri

data_processing:
cutadapt version 4.6 was used for removing Illumina adapters, ambiguous nucleotides (N’s), any sequence reads with total read length < 20 bp and the quality Phred score < 20
Hisat2 version 2.2.1 was used for alinging the sequences with the assembely
Cufflinks version 2.2.1 was used for obtaining the FPKM values as well as cuffdiff method within the package was used for finding out the differentially expressed genes
Assembly: GRCh38.111
Supplementary files format and content: comma separated values with FPKM and annotation

source_name: Healthy subject TM cells from a caucasian female

growth_protocol: HTMC cells were grown in DMEM media with 10% FBS and 1X 1X penicillin-streptomycin solution.

extract_protocol:
Total RNA was extracted uisng Qiagne RNA mini kit.
NEBNext Ultra™ II RNA Library Prep kits

treatment_protocol: Cells were treted with HCQ or Rapa 1h before infection followed by viral adsorption. The drug were kept for the entire time during the incubation.

value: Trabecular meshwork

value: Primary

value: ZIKV only


title: ZIKV only 2


title: Rapamycin + ZIKV 3

value: Rapamycin + ZIKV


title: ZIKV only 1


title: Rapamycin + ZIKV 1


title: Hydroxychloroquine + ZIKV 2

value: Hydroxychloroquine + ZIKV


title: Hydroxychloroquine + ZIKV 1


title: Rapamycin + ZIKV 2


title: Mock 2

value: Mock


title: Hydroxychloroquine + ZIKV 3


title: Mock 1


title: Mock 3


title: 624-mel biol rep 3

description: Library name: Sample 3


title: ASPC1 biol rep 2

description: Library name: Sample 8