title: JQ_153

city: Ann Arbor

first: Pei-Suen

last: Tsou

address: 109 Zina Pitcher Pl. 4025 BSRB

institute: University of Michigan

data_processing:
We trimmed adapters using Cutadapt (v2.3). FastQC (v0.11.8) was used to ensure the quality of data. Reads were mapped to the reference genome hg38 (EMSEMBL), using STAR (v2.6.1b) and assigned
count estimates to genes with RSEM (v1.3.1). Alignment options followed ENCODE standards for RNA-seq. FastQC was used in an additional post-alignment step to ensure that only high-quality
Data were pre-filtered to remove genes with 0 counts in all samples. Differential gene expression analysis was performed using DESeq2, using a negative binomial generalized linear model
(thresholds: linear fold change >1.5 or <-1.5, Benjamini-Hochberg FDR (Padj) <0.05). Plots were generated using variations of DESeq2 plotting functions and other packages with R version 3.3.3. Genes
were annotated with NCBI Entrez GeneIDs and text descriptions.
Genome_build: hg38
Supplementary_files_format_and_content: text count file

source_name: Dermal fibroblasts

growth_protocol: Two 4 mm punch biopsies from the distal forearm of healthy volunteers and SSc patients were obtained for cell isolation. After skin digestion, cells were grown to 75% confluency on collagen-coated plates before purification. ECs were purified through positive selection using the CD31 MicroBead Kit (Miltenyi Biotech) while negatively selected cells eluted were fibroblasts. Fibroblasts were grown in RPMI media with 10%FBS, antibiotics, and L-glutamine. Passages between 3 and 6 were used.

extract_protocol:
Total RNA was extracted using Direct-zol™ RNA MiniPrep Kit (Zymo Research) before converted to cDNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fibroblasts were treated with JQ1 (1μM) for 48 hours before RNA was collected.

tag: tissue

value: Skin

tag: cell type

value: Fibroblasts

value: JQ1 1uM for 48 hours


title: NT_153

status: Public on Mar 01 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment


title: DSP-1001250007864-D-H09

city: Seattle

first: Stephanie

last: Zimmerman

state: WA

address: 530 Fairview Ave N

institute: NanoString Technologies

description: RNA ISH

data_processing:
Library strategy: GeoMx-Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Kidney_Sample_Annotations.txt: txt file containing sample annotations
Supplementary_files_format_and_content: Kidney_Raw_BioProbeCountMatrix.txt: txt file containing raw probe counts for each AOI
Supplementary_files_format_and_content: Kidney_Raw_TargetCountMatrix.txt: txt file containing collapsed target-level counts for each AOI
Supplementary_files_format_and_content: Kidney_Q3Norm_TargetCountMatrix.txt: txt file containing Q3 normalized target-level counts for each AOI

source_name: Human FFPE kidney

extract_protocol:
Samples were incubated with the human Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: slide name

tag: class

value: DKD

tag: region

value: tubule

tag: pathology

tag: nuclei


title: JQ1_131


title: DSP-1001250007864-D-H08

description: RNA ISH


title: UUO5d rep1

city: Jinhua

first: Weiqiang

last: Lin

state: Zhejiang

address: Shangcheng street N1

country: China

institute: The Fourth Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were build index by hisat2, and masked for low-complexity or low-quality sequence
Mapped to mm9 whole genome using hisat2 and  exported StringTie readable format files
Expression values for all genes in each sample (FPKM) were calculated by StringTie
Differentially expressed miRNAs between the paired groups were analyzed by using DEGseq
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: Kidney

extract_protocol:
Total RNA was extracted from each tissue sample using Trizol method
RNA libraries were prepared for sequencing using standard illumina protocls

value: Mouse kidneys

tag: group

value: unilateral ureteral obstruction (UUO)

tag: age

value: 8~10 weeks

tag: strain


title: Amazonia_FMTHVD-116,122

type: RNA

city: Ribeirao Preto

first: Victor

middle: Hugo

last: Aquino

state: Sao Paulo

address: Avenida do Cafe, s/n

department: Fculty of Pharmaceutical Sciences

country: Brazil

institute: University of Sao Paulo

hyb_protocol: PCR products were hybridized against the DNA microarray using the Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent, USA), following manufacturer’s recommendations.

scan_protocol: The slides were scanned with the Axon GenePix 4000B scanner (Molecular Devices, USA) at a 532 nm wavelength with a pixel size of 10-μm resolution.

data_processing: The median fluorescence intensity of each spot with local background subtraction was calculated from the scanned images using GenePix Pro 7 software (Molecular Devices, USA). The raw data of the sports were normalized against the negative control probes, which were randomly distributed on each sub-array. The normalized data were log2-transformed to reduce variability. The spots containing the probes for each virus species were grouped, and the mean signal intensity of all groups was calculated. The mean signal intensity of the group of probes corresponding to each virus species was compared to the mean signal intensity of the negative control probes, using the Welch’s t-test. A virus was considered present in an analyzed sample when the mean signal intensity of the group of probes was significantly (p<0.05) higher than the mean signal intensity of the negative control probes and showed a normalized mean intensity of at least 2, i.e., it was at least fourfold higher than the mean signal intensity of the negative control probes, thus reducing the chance of virus misidentification due to cross-hybridization.

source_name: Peripheral Blood

label_protocol: Individual or pool of equimolar amount of cDNAs were used for a random PCR amplification, which contained 1 nmol of the fluorescent labelling Cy3-dUTP (SIGMA ALDRICH, USA).

extract_protocol: Total RNA was purified from 200 µL of serum samples, using the PureLink Viral RNA/DNA Mini Kit (Invitrogen, USA), following manufacturer’s recommendations.

value: Whole blood

tag: subject 1

tag: subject 1 gender

value: Female

tag: subject 1 age

value: 56 years

tag: subject 2

tag: subject 2 gender

value: Male

tag: subject 2 age

value: 29 years


title: UUO5d rep2

tag: tissue


title: NT_131

tag: cell type


title: DSP-1002510007866-C-A02

description: RNA ISH

value: normal

value: glomerulus


title: Ac5d rep2

value: acute-chronic (AC)


title: JQ1_159

tag: treatment


title: Ac5d rep1


title: Amazonia_FMTHVD-115,121

value: 63 years

value: 38 years


title: Amazonia_FMTHVD-117,123

value: 61 years

value: 51 years


title: WT rep3

value: control


title: DSP-1001250007864-D-H05

description: RNA ISH

tag: slide name

value: DKD

value: tubule


title: DSP-1001250007864-D-H04

description: RNA ISH

tag: class


title: JQ_158

value: Skin

value: Fibroblasts

value: JQ1 1uM for 48 hours


title: Amazonia_FMTHVD-113,119

value: Whole blood

value: 35 years

value: Female

value: 41 years


title: Amazonia_FMTHVD-114,120

value: Male

value: 56 years

value: 34 years


title: Amazonia_FMTHVD-104,112

value: 39 years

value: 60 years


title: Amazonia_FMTHVD-103,111

value: 33 years

value: 37 years


title: WT rep1

value: Mouse kidneys

value: control

value: 8~10 weeks


title: DSP-1001250007864-D-H02

description: RNA ISH

value: DKD

tag: region

value: tubule


title: Lymph node, EAE d16 Clec1a–/–

city: Noda

first: Yulia

last: Makusheva

state: Chiba

address: Yamazaki 2669

department: Research Institute for Biomedical Sciences

country: Japan

institute: Tokyo University of Science

data_processing:
Illumina Novaseq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 (mm10) whole genome.
BAM files resulting from the alignments were summarized to genes using the Stringtie algorithm.
Transcript per million (TPM) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes FPKM and TPM values for each sample.

source_name: lymph node

extract_protocol:
Lymph nodes were removed, flash frozen on liquid nitrogene, and RNA was harvested using Mammalian Total RNA Miniprep kit (MilliporeSigma, USA).
RNA libraries were prepared for sequencing using NEBNext® Ultra RNA Library Prep Kit for Illumina® (E7530).

value: lymph node

tag: genotype

value: EAE d16


title: Amazonia_FMTHVD-102,110

value: Whole blood

value: 43 years

value: 54 years


title: WT rep2


title: DSP-1001250007864-D-H03

description: RNA ISH

tag: pathology

tag: nuclei


title: NT_159

value: Skin

value: Fibroblasts


title: Lymph node, EAE d16 WT

value: wild type


title: JQ1_133.2

value: JQ1 1uM for 48 hours


title: NT_130


title: Amazonia_FMTHVD-101,109

value: Male

value: 48 years

value: 34 years


title: NT_133.2


title: Amazonia_FMTHVD-100,108

value: 55 years

value: Female

value: 41 years


title: DSP-1001250007864-D-H06

description: RNA ISH

value: DKD


title: Lymph node, EAE d10 WT

value: EAE d10


title: DSP-1001250007864-D-H01

description: RNA ISH

value: tubule


title: DSP-1001250007864-D-H07

description: RNA ISH


title: NT_158


title: DSP-1001250007864-D-G12

description: RNA ISH

value: normal

value: glomerulus

value: abnormal


title: Amazonia_FMTHVD-98,106

value: Whole blood

value: 49 years

value: 31 years


title: Amazonia_FMTHVD-99,107

value: 27 years

value: 30 years


title: DSP-1001250007864-D-G11

description: RNA ISH


title: DSP-1001250007864-D-G10

description: RNA ISH


title: Amazonia_FMTHVD-88,96

value: 64 years


title: DSP-1001250007864-D-G09

description: RNA ISH


title: Lymph node, no EAE Clec1a–/–

value: lymph node

value: no EAE


title: Amazonia_FMTHVD-97,105

value: Male

value: 61 years

value: 42 years


title: KO iPSC-derived neurons E4 differentiation3 rep2

first: Jessica

last: Young

state: Washington

address: 850 Republican St

department: Pathology

institute: University of Washington

data_processing:
Base calls generated in real-time on the NovaSeq6000 instrument (RTA 3.1.5).
Demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4).
Sequence read and base quality are checked using the FASTX-toolkit (v0.0.13).
Sequences are aligned to GRCh38 with reference transcriptome GENCODE release 29 using STAR (v2.6.1d).
Gene level expression quantification is generated with RNA-SeQC (v2.3.3) and RSEM (v1.3.1). RPKM and TPM for transcript isoforms are quantitated on the merged lane-level data with RSEM (v1.3.1).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files contain read-counts for every gene.
Supplementary_files_format_and_content: Matrix table with read-counts for every gene and every sample

source_name: iPSC-derived neurons

growth_protocol: hiPSCs were differentiated to neurons using dual-SMAD inhibition(Chambers et al., 2009; Shi et al., 2012). Briefly, hiPSCs were plated on Matrigel coated 6-well plates at a density of 3.5 million cells per well and fed with Basal Neural Maintenance Media (1:1 DMEM/F12 + glutamine media/neurobasal media, 0.5% N2 supplement, 1% B27 supplement, 0.5% GlutaMax, 0.5% insulin-transferrin-selenium, 0.5% NEAA, 0.2% b-mercaptoethanol; Gibco, Waltham, MA) + 10mM SB-431542 + 0.5mM LDN-193189 (Biogems, Westlake Village, CA). Cells were fed daily for seven days. On day eight, cells were incubated with Versene, gently dissociated using cell scrapers, and passaged at a ratio of 1:3. On day nine, media was switched to Basal Neural Maintenance Media with 20 ng/mL FGF (R&D Systems, Minneapolis, MN) and fed daily. On day sixteen, cells were passaged again at a ratio of 1:3. Cells were fed until approximately day twenty-three. At this time, cells were FACS sorted to obtain the CD184/CD24 positive, CD44/CD271 negative neural precursor cell (NPC) population. Following sorting, NPCs were expanded for neural differentiation. For cortical neuronal differentiation, NPCs were plated out in 10cm cell culture dishes at a density of 6 million cells/10cm plate. After 24 hours, cells were switched to Neural Differentiation media (DMEM-F12 + glutamine, 0.5% N2 supplement, 1% B27 supplement, 0.5% GlutaMax) + 0.02ug/mL brain-derived neurotrophic factor (PeproTech, Rocky Hill, NJ) + 0.02ug/mL glial-cell-derived neurotrophic factor (PeproTech) + 0.5mM dbcAMP (Sigma Aldrich, St Louis, MO). Media was refreshed twice a week for three weeks. After three weeks, neurons were selected for CD184/CD44 negative population by MACS sorting and plated for experiments.

extract_protocol:
RNA was collected from 2 million purified neurons for each sample. Purification of total RNA was completed using the PureLink RNA Mini Kit (Thermo Fisher 12183018A). Assessment of purified RNA was completed using a NanoDrop. Final RNA quantification was completed using the Quant-iT RNA assay (Invitrogen) and RNA integrity analysis was completed using a fragment analyzer (Advanced Analytical).
Library preparation was completed using the TruSeq Stranded mRNA kit (Illumina RS-122-2103) per manufacturer instructions.

value: iPSC-derived neurons

value: SORL1 KO

tag: clone

tag: differentiation batch


title: Lymph node, no EAE WT

tag: strain

value: wild type


title: JQ1_130

value: Skin

value: Fibroblasts

value: JQ1 1uM for 48 hours


title: KO iPSC-derived neurons E4 differentiation3 rep3


title: Lymph node, EAE d10 Clec1a–/–

value: EAE d10


title: KO iPSC-derived neurons E4 differentiation3 rep1


title: Amazonia_FMTHVD-86,94

value: Whole blood

tag: subject 1

tag: subject 1 gender

value: 52 years

value: 37 years


title: AKB6 PDAC Tumor

city: Buffalo

first: Prasenjit

last: Dey

state: NY

address: Elm & Carlton Sts. CGP/BLSC-L5 307

department: Immunology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
cellranger was used to generate the fastq files using mkfastq
cellranger was used to generate the barcode and gene expression count matrix using mouse mm10 reference genome
Seurat R package was used for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: gene expression count matrix

source_name: PDAC Tumor

growth_protocol: not applicable

extract_protocol:
tissue dissociation to prepare single cell suspension
Single cell libraries are generated using the 10X Genomics Chromium Single Cell 3’ Reagent V3 Kit according to manufacturer’s protocol.  Cell suspensions are first assessed with Trypan Blue using a Countess FL automated cell counter (ThermoFisher), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells are loaded into the Chromium Controller (10X Genomics) where they are partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription is performed and the resulting cDNA is amplified.  The full-length amplified cDNA is used to generate gene expression libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  The resulting libraries are evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies), and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina. They are then pooled, denatured, and diluted to 300pM with 1% PhiX control library added.  The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).
10X Genomics Chromium Single Cell 3’ Reagent V3 Kit

treatment_protocol: not applicable

value: CD45 positive immune cells


title: Amazonia_FMTHVD-87,95

value: Female

tag: subject 1 age

value: 41 years

tag: subject 2

value: 54 years


title: WT iPSC-derived neurons A6 differentiation3 rep3


title: WT iPSC-derived neurons A6 differentiation3 rep2


title: KPC PDAC tumor 2


title: DSP-1001250007864-D-G07

description: RNA ISH

value: normal

value: glomerulus


title: KPC PDAC tumor 1


title: Amazonia_FMTHVD-85,93

value: Male

value: 57 years

value: Sample 93

tag: subject 2 gender

tag: subject 2 age

value: 55 years


title: DSP-1001250007864-D-G06

description: RNA ISH


title: KO iPSC-derived neurons E1 differentiation2 rep2

tag: cell type

value: iPSC-derived neurons

value: SORL1 KO


title: WT iPSC-derived neurons A6 differentiation3 rep1

value: wild type


title: DSP-1001250007864-D-G05

description: RNA ISH


title: DSP-1001250007864-D-G04

description: RNA ISH


title: DSP-1001250007864-D-G08

description: RNA ISH

value: abnormal


title: adipose + daily prednisone 3

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Reads were trimmed using Trimmomatic and aligned to mm10 using HiSat2
Isoform counts were obtained through Kallisto as CPM
Genome_build: mm10
Supplementary_files_format_and_content: Table reporting CPM values for each RNA isoform for each sample

source_name: white adipose tissue

extract_protocol:
Total RNA was isolated through Trizol and purified through Qiagen Rneasy columns
True-Seq stranded mRNA library (Illumina)

treatment_protocol: Prednisone (Sigma #P6254) was injected  as once-weekly versus once-daily IP solution of 1mg/kg in 100ul PBS from a 5mg/kg stock solution in DMSO in male WT mice of approximately 20 weeks of age, after 12 weeks on high-fat diet. High-fat diet was maintained during drug treatments for additional 12 weeks. 24 hours after last injection muscle and white adipose tissues were obtained from each mouse and RNA isolated and purified.

tag: drug treatment

value: 12-week-long daily prednisone

tag: sample type

value: RNA-seq

tag: model specs

value: ~20wo DBA/2J WT male mouse


title: Amazonia_FMTHVD-84,92

tag: tissue

value: Whole blood

value: 52 years

value: 45 years


title: DSP-1001250007864-D-G03

description: RNA ISH

tag: slide name

tag: class

tag: region


title: KO iPSC-derived neurons E1 differentiation2 rep1

tag: genotype

tag: clone


title: WT iPSC-derived neurons A7 differentiation2 rep2

tag: differentiation batch


title: Amazonia_FMTHVD-83,91

tag: subject 1

value: 24 years


title: DSP-1001250007864-D-G02

description: RNA ISH

value: normal

tag: pathology

tag: nuclei


title: adipose + daily prednisone 2


title: adipose + weekly prednisone 3

value: 12-week-long weekly prednisone


title: adipose + daily prednisone 1


title: Amazonia_FMTHVD-82,90

tag: subject 1 gender

value: Female

tag: subject 1 age

value: 32 years

tag: subject 2


title: Amazonia_FMTHVD-81,89

value: Male

value: 50 years

tag: subject 2 gender

tag: subject 2 age

value: 66 years


title: DSP-1001250007864-D-G01

description: RNA ISH

value: tubule


title: WT iPSC-derived neurons A7 differentiation2 rep1

tag: cell type

value: iPSC-derived neurons

value: wild type


title: adipose + weekly prednisone 2

tag: drug treatment

tag: sample type

tag: model specs


title: DSP-1001250007864-D-F12

description: RNA ISH

tag: slide name

tag: class


title: Amazonia_FMTHVD-73

tag: tissue

value: 35 years


title: KO iPSC-derived neurons E4 differentiation1 rep1

tag: genotype

value: SORL1 KO

tag: clone


title: KO iPSC-derived neurons E4 differentiation1 rep2

tag: differentiation batch


title: adipose + weekly prednisone 1

value: RNA-seq

value: ~20wo DBA/2J WT male mouse


title: Amazonia_FMTHVD-72

value: Whole blood

tag: subject 1

value: 42 years

value: 56 years


title: adipose + vehicle 3

value: 12-week-long daily vehicle


title: DSP-1001250007864-D-F11

description: RNA ISH

value: normal

tag: region

tag: pathology

tag: nuclei


title: Amazonia_FMTHVD-71

tag: subject 1 gender

value: Female

tag: subject 1 age

value: 36 years

tag: subject 2


title: WT iPSC-derived neurons A6 differentiation1 rep2

tag: cell type


title: DSP-1001250007864-D-F10

description: RNA ISH


title: adipose + vehicle 2

tag: drug treatment


title: Amazonia_FMTHVD-70

tag: subject 2 gender

tag: subject 2 age

value: 33 years


title: DSP-1001250007864-D-F09

description: RNA ISH

tag: slide name


title: adipose + vehicle 1

tag: sample type

tag: model specs


title: WT iPSC-derived neurons A6 differentiation1 rep1

tag: genotype


title: Amazonia_FMTHVD-69

tag: tissue

value: 45 years

value: Male

value: 68 years


title: DSP-1001250007864-D-F08

description: RNA ISH

tag: class

value: tubule


title: muscle + daily prednisone 3

source_name: quadriceps muscle

value: 12-week-long daily prednisone


title: RPE-1 cells, siMondoA treated with DXR_rep2

city: Suita

first: Ryuya

last: Edahiro

institute: Osaka University

description:
gene_count.txt
gene_RPKM.txt
D5_siMondo-10

data_processing:
Illumina package bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using TopHat (v2.1.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene_count.txt, gene_RPKM.txt

source_name: siMondoA treated with DXR

growth_protocol: Cells were cultured in Dulbecco’s Modifed Eagle’s medium (D6046, Sigma) supplemented with 10% fetal bovine serum (10270106, Gibco) and penicillin-streptomycin (P4333, Sigma).

extract_protocol:
Isolation of total RNA was performed using RNeasy® Plus Mini Kit (74134, QIAGEN). TruSeq Stranded mRNA Library Prep Kit (Cat#RS-122-2103) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: siRNA of MondoA or Mlx were transfected for two days using Lipofectamine RNAiMax (13778150, Invitrogen) as manufacturer’s instructions and then cells were incubated with 150 ng/ml DXR (040-21521, Wako) for three days.

tag: cell line

value: hTERT-immortalized retinal pigment epithelial cell line (RPE-1 cells)

tag: transfection

value: siMondoA

tag: treatment

value: treated with DXR for three days


title: muscle + daily prednisone 2

value: RNA-seq

value: ~20wo DBA/2J WT male mouse


title: DSP-1001250007864-D-F07

description: RNA ISH

tag: region

tag: pathology

tag: nuclei


title: Amazonia_FMTHVD-67

value: Whole blood

tag: subject 1

value: Sample- 67

tag: subject 1 gender

tag: subject 1 age

value: 50 years

tag: subject 2

value: Sample- 74

value: 38 years


title: muscle + daily prednisone 1

tag: drug treatment


title: Amazonia_FMTHVD-66

tag: gender

value: Female

tag: age

value: 53 years


title: RPE-1 cells, siMondoA treated with DXR_rep1

description:
gene_count.txt
gene_RPKM.txt
D5_siMondo-09


title: Amazonia_FMTHVD-68

value: 61 years

tag: subject 2 gender

tag: subject 2 age

value: 42 years


title: RPE-1 cells, siMlx treated with DXR_rep2

description:
gene_count.txt
gene_RPKM.txt
D5_siMlx-10

source_name: siMlx treated with DXR

value: siMlx


title: DSP-1001250007864-D-F05

description: RNA ISH

tag: slide name

value: normal

value: tubule


title: DSP-1001250007864-D-F06

description: RNA ISH

tag: class


title: RPE-1 cells, siMlx treated with DXR_rep3

description:
gene_count.txt
gene_RPKM.txt
D5_siMlx-11

tag: cell line

value: hTERT-immortalized retinal pigment epithelial cell line (RPE-1 cells)


title: DSP-1001250007864-D-F04

description: RNA ISH


title: muscle + weekly prednisone 1

value: 12-week-long weekly prednisone

tag: sample type

tag: model specs


title: DSP-1001250007864-D-F03

description: RNA ISH

tag: region


title: muscle + weekly prednisone 2


title: Amazonia_FMTHVD-65

tag: tissue

value: Male


title: RPE-1 cells, siMlx treated with DXR_rep1

description:
gene_count.txt
gene_RPKM.txt
D5_siMlx-09

tag: transfection

tag: treatment

value: treated with DXR for three days


title: RPE-1 cells, siMondoA treated with DXR_rep3

description:
gene_count.txt
gene_RPKM.txt
D5_siMondo-11

value: siMondoA


title: RPE-1 cells, siControl treated with DXR_rep3

description:
gene_count.txt
gene_RPKM.txt
D5_siLuci-11

source_name: siControl treated with DXR

value: siControl


title: muscle + vehicle 3

value: 12-week-long daily vehicle

value: RNA-seq

value: ~20wo DBA/2J WT male mouse


title: Amazonia_FMTHVD-62

value: Whole blood


title: DSP-1001250007864-D-F01

description: RNA ISH

value: glomerulus

tag: pathology

tag: nuclei


title: muscle + vehicle 2


title: Amazonia_FMTHVD-61

value: 40 years


title: Amazonia_FMTHVD-63

value: 38 years


title: Amazonia_FMTHVD-64

value: Female

value: 25 years


title: muscle + weekly prednisone 3


title: Amazonia_FMTHVD-60

value: 32 years


title: muscle + vehicle 1


title: RPE-1 cells, siMondoA_rep3

description:
gene_count.txt
gene_RPKM.txt
D0_siMondo-11

source_name: siMondoA

value: untreated


title: RPE-1 cells, siControl treated with DXR_rep1

description:
gene_count.txt
gene_RPKM.txt
D5_siLuci-09

value: hTERT-immortalized retinal pigment epithelial cell line (RPE-1 cells)


title: DSP-1001250007864-D-E12

description: RNA ISH

value: normal


title: RPE-1 cells, siMondoA_rep2

description:
gene_count.txt
gene_RPKM.txt
D0_siMondo-10


title: DSP-1001250007864-D-E11

description: RNA ISH


title: DSP-1001250007864-D-E10

description: RNA ISH


title: DSP-1001250007864-D-E09

description: RNA ISH


title: DSP-1005210003239-F-A06

data_processing:
Library strategy: GeoMx Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: mouse_CPA_RawCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, probe information, and raw probe count matrix for each probe and sample
Supplementary_files_format_and_content: mouse_CPA_CollapsedTargetCounts: xlsx file outputted from the GeoMx DSPDA analysis software containing sample annotations, processing information, and target-level count matrix for each gene target and sample

molecule: other

source_name: FFPE mouse cell pellet array

extract_protocol:
Samples were incubated with the mouse Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: panel

value: (v1.2) TAP Mouse Whole Transcriptome Atlas

tag: roilabel

tag: area


title: DSP-1005210003239-F-A07


title: RPE-1 cells, siMondoA_rep1

description:
gene_count.txt
gene_RPKM.txt
D0_siMondo-09


title: Amazonia_FMTHVD-58

tag: gender

value: Male

tag: age

value: 56 years


title: DSP-1005210003239-F-A05


title: RPE-1 cells, siMlx_rep3

description:
gene_count.txt
gene_RPKM.txt
D0_siMlx-11

source_name: siMlx

value: siMlx


title: RPE-1 cells, siControl treated with DXR_rep2

description:
gene_count.txt
gene_RPKM.txt
D5_siLuci-10

value: siControl

value: treated with DXR for three days


title: DSP-1001250007864-D-E08

description: RNA ISH

value: abnormal


title: Amazonia_FMTHVD-57

value: Whole blood

value: 59 years


title: DSP-1001250007864-D-F02

description: RNA ISH

value: tubule


title: RPE-1 cells, siMlx_rep2

description:
gene_count.txt
gene_RPKM.txt
D0_siMlx-10


title: DSP-1001250007864-D-E07

description: RNA ISH

value: glomerulus


title: DSP-1005210003239-F-A04


title: RPE-1 cells, siMlx_rep1

description:
gene_count.txt
gene_RPKM.txt
D0_siMlx-09


title: DSP-1005210003239-F-A03


title: Amazonia_FMTHVD-59

value: 47 years


title: DSP-1005210003239-F-A02


title: Amazonia_FMTHVD-55

value: 48 years


title: Amazonia_FMTHVD-54


title: RPE-1 cells, siControl_rep3

description:
gene_count.txt
gene_RPKM.txt
D0_siLuci-11

source_name: siControl


title: DSP-1001250007864-D-E05

description: RNA ISH


title: DSP-1005210003239-F-A01

value: No Template Control


title: Amazonia_FMTHVD-56


title: RPE-1 cells, siControl_rep2

description:
gene_count.txt
gene_RPKM.txt
D0_siLuci-10

value: untreated


title: DSP-1001250007864-D-E06

description: RNA ISH


title: DSP-1005210003238-E-H12


title: RPE-1 cells, siControl_rep1

description:
gene_count.txt
gene_RPKM.txt
D0_siLuci-09

value: hTERT-immortalized retinal pigment epithelial cell line (RPE-1 cells)


title: Amazonia_FMTHVD-52

value: 42 years


title: Amazonia_FMTHVD-53

value: 44 years


title: DSP-1001250007864-D-E03

description: RNA ISH

value: normal


title: DSP-1005210003238-E-H10

value: (v1.2) TAP Mouse Whole Transcriptome Atlas


title: Amazonia_FMTHVD-51

value: Male

value: 20 years


title: DSP-1001250007864-D-E02

description: RNA ISH


title: Peripheral blood cells isolated from patients with arthritis-irAE 76B

city: Houston

first: Linghua

last: Wang

address: 1881 EAST ROAD

department: Genomic medicine

institute: MD Anderson Cancer Center

data_processing:
Reagents, consumables, reaction master mixes, reaction volumes, cycling numbers, cycling conditions, and clean-up steps were completed following 10X Genomics’ guidelines (found in 10X Genomics’ Chromium Single Cell V(D)J Reagent Kits User Guide-Revision L). Quality control steps after cDNA amplification and library preparation steps were carried out by running QubitTM 1X dsDNA HS Assay (Thermo Fisher Scientific) along with Bioanalyzer High-Sensitivity DNA Analysis (Agilent) for concentration and quality assessments. Library sample concentrations were verified with quantitative polymerase chain reaction using a KAPA Library Quantification Kit (Roche). Samples were normalized to 10 nM for pooling. The gene expression libraries and TCR libraries were pooled in a ratio of 5 volumes gene expression library to 1 volume TCR library. The pool was sequenced using a NovaSeq6000 S4-200 cycle flow cell (Illumina). The run parameters used were 26 cycles for read 1, 91 cycles for read 2, 8 cycles for index 1, and 0 cycles for index 2, as stipulated in the protocol mentioned above. Raw sequencing data (fastq file) was demultiplexed and analyzed with 10X Genomics Cell Ranger software using the standard default settings and the cell ranger count command to generate html quality control metrics and cloupe/vloupe files for each sample.
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v3.1.0), including demultiplexing the FASTQ reads.
Aligning fastq files to the human reference genome (GRCh38, v3.0.0, from 10X Genomics)
Counting the unique molecular identifier (UMI) (by using ‘‘cellranger count’’ function).
All patient samples from each dataset were then aggregated by using the ‘‘cellranger aggr’’ function without depth normalization. As a result, a digital cell by gene expression matrix was generated, containing the number of UMIs for each gene detected in each cell.
In addition, we carried out a number of steps to filter out poor quality data. First, we removed cells with high mitochondrial gene expression because damaged and dead cells often exhibit extensive mitochondrial contamination 60. Specifically, we calculate the proportion of UMIs from mitochondrial genes (all genes with names start with “MT-” or “mt-”) for each cell, then remove cells which contain more than 15% mitochondrial UMIs. Second, we removed cells for which less than 200 genes were detected. Third, doublets were identified using a multi-step approach: 1) library complexity: cells with high complexity libraries (in which detected transcripts are aligned to more than 6500 genes) were removed; 2) Cluster distribution: doublets or multiplets likely form distinct clusters with hybrid expression features and exhibit an aberrantly high gene count; 3) cluster marker gene expression: cells of a cluster express markers from distinct lineages (e.g., cells in the T-cell cluster showed expression of myeloid cell markers and vice versa); 4) doublet detection algorithm: scrublet(version 2020 update) , an algorithm to predict doublets in scRNA-seq data, was applied to further identify and clean doublets that could have been missed by steps 1-3.
We carefully reviewed canonical marker genes expression on UMAP plots and repeated the above steps multiple times to ensure elimination of most barcodes associated with cell doublets. Forth, we use “RunHarmony” function of “harmony” R package 62 to offset the batch effect. In the end, we retained a total of 116,797 cell datasets.
Supplementary_files_format_and_content: barcodes.tsv.gz: cell IDs, tab-seperated text file.  Features.tsv.gz: gene IDs, tab-separated text file. Matrix.mtx.gz: the 2D matrix in sparse format. Tab-separated. Value and x, y-D index.subT_data_metadata.tsv.gz, tab-separated, T cell annotation, such sub-T cell type, cluster information. whole_data_metadata.tsv.gz, whole cell annotation.

source_name: Peripheral blood

extract_protocol:
cDNA were generated for sequencing using standard 10X Genomic protocols
RNA libraries were prepared for sequencing using standard 10X Genomic protocols

tag: cell types

value: Peripheral blood mononuclear cells


title: Amazonia_FMTHVD-50

value: 45 years


title: Peripheral blood cells isolated from patients with arthritis-irAE 65B


title: DSP-1001250007864-D-E01

description: RNA ISH

tag: slide name


title: Amazonia_FMTHVD-48

value: Whole blood

value: Female

value: 32 years


title: DSP-1001250007864-D-D12

description: RNA ISH

tag: class

value: glomerulus


title: Amazonia_FMTHVD-49


title: Peripheral blood cells isolated from patients with arthritis-irAE 63B


title: DSP-1005210003238-E-H08


title: DSP-1005210003238-E-H07


title: Amazonia_FMTHVD-47

value: 55 years


title: Peripheral blood cells isolated from patients with arthritis-irAE 62B


title: DSP-1001250007864-D-E04

description: RNA ISH


title: Amazonia_FMTHVD-46


title: Peripheral blood cells isolated from patients with arthritis-irAE 56B


title: Peripheral blood cells isolated from patients with arthritis-irAE 45B


title: Amazonia_FMTHVD-45

value: 69 years


title: DSP-1001250007864-D-D09

description: RNA ISH


title: DSP-1005210003238-E-H05


title: DSP-1005210003238-E-H06


title: DSP-1005210003238-E-H11


title: Peripheral blood cells isolated from patients with arthritis-irAE 40B


title: Amazonia_FMTHVD-44


title: DSP-1005210003238-E-H04


title: DSP-1005210003238-E-H03


title: DSP-1001250007864-D-D07

description: RNA ISH


title: DSP-1005210003238-E-H09


title: Peripheral blood cells isolated from patients with arthritis-irAE 7B


title: Synovial fluid cells isolated from patients with arthritis-irAE 76

source_name: Synovial fluid

value: Synovial fluid cells


title: Synovial fluid cells isolated from patients with arthritis-irAE 65


title: DSP-1001250007864-D-D05

description: RNA ISH

source_name: Human FFPE kidney


title: Amazonia_FMTHVD-43

value: 50 years


title: DSP-1005210003238-E-H02


title: DSP-1005210003238-E-H01


title: Amazonia_FMTHVD-42

value: 61 years


title: DSP-1001250007864-D-D11

description: RNA ISH


title: Synovial fluid cells isolated from patients with arthritis-irAE 63


title: DSP-1001250007864-D-D10

description: RNA ISH


title: Synovial fluid cells isolated from patients with arthritis-irAE 62


title: DSP-1001250007864-D-D04

description: RNA ISH


title: DSP-1001250007864-D-D03

description: RNA ISH


title: DSP-1005210003238-E-G11


title: DSP-1001250007864-D-D08

description: RNA ISH


title: DSP-1001250007864-D-D02

description: RNA ISH


title: Amazonia_FMTHVD-41

value: 56 years


title: Amazonia_FMTHVD-39

value: 53 years


title: Synovial fluid cells isolated from patients with arthritis-irAE 56


title: Amazonia_FMTHVD-40

value: 41 years


title: DSP-1005210003238-E-G10

value: (v1.2) TAP Mouse Whole Transcriptome Atlas


title: Amazonia_FMTHVD-38

value: 52 years


title: DSP-1001250007864-D-D01

description: RNA ISH

value: normal


title: Amazonia_FMTHVD-37

value: Male

value: 43 years


title: DSP-1005210003238-E-G09


title: DSP-1001250007864-D-D06

description: RNA ISH


title: Synovial fluid cells isolated from patients with arthritis-irAE 45


title: DSP-1001250007864-D-C12

description: RNA ISH


title: Synovial fluid cells isolated from patients with arthritis-irAE 7


title: Amazonia_FMTHVD-36

value: Whole blood

value: 47 years


title: DSP-1005210003238-E-G07


title: DSP-1005210003238-E-G12


title: DSP-1001250007864-D-C10

description: RNA ISH


title: DSP-1005210003238-E-G06


title: PC9_GSK712_N2_D5

city: Collegeville

first: Satyajit

last: Rajapurkar

state: PA

address: 1250S. Collegeville Rd.

institute: GlaxoSmithKline LLC

description: For each pairwise comparison, a gene has been filtered out if it does not meet the minimum expression cutoff (FPKM < = 1)

data_processing:
QC of the Fastq files was performed using FastQC
Salmon v0.12.0 was used to quantify reads from Fastq files using  "-l A --gcBias --seqBias --validateMappings" flags
DESeq2 was used to compute pairwise differential expression results using custom scripts in R
Custom scripts were used to filter the output (FPKM >1, adj.pvalue <= 0.05) and generate relevant plots
Genome_build: GRCh38 (gencode v28)
Supplementary_files_format_and_content: Tab delimited text file containing a narrow table with the concatenated output of DESeq2 of all pairwise comparisons.

source_name: Non-small cell lung cancer cell line

extract_protocol:
Total RNA, including miRNA, was isolated from cell pellet using the Qiagen miRNeasy Mini Kit
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit (Illumina).Samples were sequenced at a depth of 100 million paired-end reasds per sample, 151base-pair read length

tag: cell line

tag: replicate


title: Amazonia_FMTHVD-33

source_name: Peripheral Blood

value: 60 years


title: Amazonia_FMTHVD-35

value: 29 years


title: DSP-1001250007864-D-C09

description: RNA ISH

value: glomerulus


title: PC9_GSK712_N1_D5


title: DSP-1005210003238-E-G05


title: PC9_DMSO_N2_D5

value: DMSO


title: DSP-1005210003238-E-G04


title: DSP-1001250007864-D-C08

description: RNA ISH


title: DSP-1005210003238-E-G03


title: DSP-1001250007864-D-C07

description: RNA ISH


title: PC9_DMSO_N1_D5


title: NCIH522_GSK712_N2_D5


title: DSP-1005210003238-E-G02


title: DSP-1001250007864-D-C06

description: RNA ISH


title: Synovial fluid cells isolated from patients with arthritis-irAE 40

value: Synovial fluid cells


title: DSP-1005210003238-E-G08


title: DSP-1001250007864-D-C11

description: RNA ISH


title: Amazonia_FMTHVD-31

value: 36 years


title: Amazonia_FMTHVD-29

value: Female

value: 46 years


title: Amazonia_FMTHVD-30

value: 57 years


title: DSP-1001250007864-D-C05

description: RNA ISH

value: abnormal


title: DSP-1005210003238-E-G01

value: (v1.2) TAP Mouse Whole Transcriptome Atlas


title: Amazonia_FMTHVD-28

value: 27 years


title: Amazonia_FMTHVD-34

value: 30 years


title: DSP-1005210003238-E-F12


title: NCIH522_DMSO_N2_D5


title: DSP-1001250007864-D-C04

description: RNA ISH

value: normal


title: DSP-1001250007864-D-C03

description: RNA ISH


title: NCIH522_DMSO_N1_D5


title: NCIH1975_GSK712_N2_D5


title: DSP-1005210003238-E-F11


title: DSP-1005210003238-E-F10


title: DSP-1001250007864-D-C02

description: RNA ISH


title: Amazonia_FMTHVD-27

value: Male

value: 19 years


title: Amazonia_FMTHVD-26

value: Whole blood

value: 48 years


title: DSP-1001250007864-D-C01

description: RNA ISH


title: NCIH1975_GSK712_N1_D5


title: Amazonia_FMTHVD-25

value: 33 years


title: DSP-1005210003238-E-F09

source_name: fixed frozen mouse cell pellet array


title: NCIH1975_DMSO_N2_D5


title: DSP-1005210003238-E-F08


title: DSP-1001250007864-D-B12

description: RNA ISH

value: glomerulus


title: NCIH1975_DMSO_N1_D5

value: DMSO


title: NCIH522_GSK712_N1_D5


title: NCIH1563_GSK712_N2_D5


title: DSP-1001250007864-D-B11

description: RNA ISH


title: Amazonia_FMTHVD-24


title: DSP-1001250007864-D-B10

description: RNA ISH


title: DSP-1005210003238-E-F06


title: Amazonia_FMTHVD-23

value: 52 years


title: Amazonia_FMTHVD-22

value: 41 years


title: NCIH1563_GSK712_N1_D5


title: DSP-1001250007864-D-B09

description: RNA ISH


title: DSP-1005210003238-E-F05


title: Amazonia_FMTHVD-20

value: Female

value: 58 years


title: NCIH1563_DMSO_N2_D5


title: NCIH1563_DMSO_N1_D5


title: DSP-1005210003238-E-F04


title: DSP-1001250007864-D-B07

description: RNA ISH


title: DSP-1001250007864-D-B08

description: RNA ISH


title: SW900_GSK712_N2_D5


title: DSP-1005210003238-E-F03


title: DSP-1001250007864-D-B06

description: RNA ISH


title: DSP-1005210003238-E-F02


title: DSP-1005210003238-E-F07


title: Amazonia_FMTHVD-19


title: SW900_GSK712_N1_D5


title: Amazonia_FMTHVD-32

value: 50 years


title: DSP-1005210003238-E-F01


title: DSP-1001250007864-D-B05

description: RNA ISH


title: Amazonia_FMTHVD-21

value: 64 years


title: Amazonia_FMTHVD-18

value: 42 years


title: DSP-1005210003238-E-E12

value: (v1.2) TAP Mouse Whole Transcriptome Atlas


title: SW900_DMSO_N1_D5


title: SW900_DMSO_N2_D5


title: DSP-1001250007864-D-B04

description: RNA ISH


title: DSP-1001250007864-D-B03

description: RNA ISH


title: Amazonia_FMTHVD-16

value: 68 years


title: Amazonia_FMTHVD-15

value: 60 years


title: Amazonia_FMTHVD-14

value: Male

value: 75 years


title: DSP-1005210003238-E-E11


title: DSP-1001250007864-D-B01

description: RNA ISH

value: normal

value: tubule


title: Amazonia_FMTHVD-17

value: Whole blood

value: 62 years


title: DSP-1001250007864-D-A12

description: RNA ISH


title: DSP-1001250007864-D-B02

description: RNA ISH

value: glomerulus


title: DSP-1005210003238-E-E10


title: SKMES1_GSK712_N1_D5


title: DSP-1005210003238-E-E07


title: SKMES1_DMSO_N1_D5

value: DMSO


title: DSP-1005210003238-E-E08


title: SKMES1_DMSO_N2_D5


title: DSP-1005210003238-E-E06


title: Amazonia_FMTHVD-11


title: DSP-1001250007864-D-A09

description: RNA ISH


title: DSP-1005210003238-E-E09


title: Amazonia_FMTHVD-7

value: 28 years


title: DSP-1001250007864-D-A10

description: RNA ISH


title: DSP-1001250007864-D-A08

description: RNA ISH


title: Amazonia_FMTHVD-8

value: 39 years


title: DSP-1005210003238-E-E04


title: Amazonia_FMTHVD-10

value: 30 years


title: Amazonia_FMTHVD-9

value: 36 years


title: NCIH520_DMSO_N2_D5


title: SKMES1_GSK712_N2_D5


title: NCIH520_GSK712_N1_D5


title: Amazonia_FMTHVD-13

value: 43 years


title: DSP-1001250007864-D-A11

description: RNA ISH


title: NCIH520_DMSO_N1_D5


title: Amazonia_FMTHVD-12

value: 44 years


title: DSP-1001250007864-D-A07

description: RNA ISH


title: DSP-1005210003238-E-E03

value: (v1.2) TAP Mouse Whole Transcriptome Atlas


title: NCIH520_GSK712_N2_D5


title: Amazonia_FMTHVD-5

value: Female

value: 47 years


title: DSP-1005210003238-E-E01


title: Amazonia_FMTHVD-4


title: NCIH226_GSK712_N1_D5


title: Amazonia_FMTHVD-6

value: Male

value: 37 years


title: DSP-1005210003238-E-E05


title: NCIH226_DMSO_N1_D5


title: DSP-1001250007864-D-A02

description: RNA ISH

value: normal


title: DSP-1005210003238-E-D09


title: DSP-1005210003238-E-D11


title: LK2_GSK712_N2_D5


title: DSP-1005210003238-E-D10


title: Amazonia_FMTHVD-3

value: 50  years


title: DSP-1001250007864-D-A01

description: RNA ISH

value: No Template Control


title: NCIH226_DMSO_N2_D5


title: DSP-1005210003238-E-D12


title: DSP-1001250007864-D-A05

description: RNA ISH

value: tubule


title: LK2_GSK712_N1_D5


title: Amazonia_FMTHVD-1

value: Whole blood

value: 35 years


title: DSP-1001250007851-H-F12

description: RNA ISH

value: DKD

value: glomerulus

value: abnormal


title: DSP-1001250007864-D-A03

description: RNA ISH


title: Ae. aegypti ovary 13 days post-blood-meal with eggs laid >1 week prior replicate 3

city: New York

first: Krithika

last: Venkataraman

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Sequence and transcript coordinates for the Aedes aegypti mosquito genome and gene models were obtained by merging the Aaeg_L5 RefSeq annotation from NCBI with a manual chemoreceptor annotation. Information related to generating this annotation is available at https://github.com/VosshallLab/Jove_Vosshall_2020/tree/master/RNAseq_merged_annotation from Jové et al., 2020a (PMID: 33049200)
Transcript expression was calculated using the Salmon quantification software (version 0.8.2) from Patro et al., 2017 (PMID: 28263959). Gene expression levels were obtained using Tximport (version 1.8.0) as transcripts per million (TPMs).
For sample variability assessment (and any differential expression analysis), raw read counts in genes were normalized and rlog transformed using DESeq2 (version 1.20.0) as per Love et al., 2014 (PMID: 25516281). Subsequently, principal component analysis was performed, and sample distance correlations were calculated to assess between sample variability with hierarchical clustering.
Genome_build: aal5_genome.fa
Supplementary_files_format_and_content: tab-delimited text file of abundance measurements in transcripts per million (TPM) for all samples

organism: Aedes aegypti

source_name: Ae. aegypti Ovary

extract_protocol:
RNA extraction was done using the PicoPure Kit (ThermoFisher, KIT0204), with one modification to homogenize tissue: instead of lysis buffer, 100 µL of TRIzol (ThermoFisher, 15596026) was added to the collection tube on ice. Manual tissue homogenization was done for 30 seconds using the Pellet Pestle Motor (Kimble, 749540) and RNase-Free pellet pestle (VWR, KT749510-0590) with 140 µL of TRIzol added to a total volume of 240 µL. After 5 minutes of room temperature incubation, 48 µL of chloroform:isoamyl alcohol 24:1 was added (Sigma, C0549), and tubes were shaken by hand for 30 seconds and left to stand for 2 minutes. The aqueous TRIzol layer was removed after centrifuging (12,000 RPM for 15 minutes at 4°C) and added to the PicoPure column, <130 µL at a time. All subsequent steps, including DNAse treatment, were performed following PicoPure manufacturer protocols.
RNA-seq libraries were prepared using Illumina TruSeq stranded mRNA LT kit (Illumina, 20020594) following manufacturer protocol using 100 ng of total RNA. Libraries prepared with unique dual indexes were pooled at equal molar ratios.

tag: strain

value: Liverpool

value: Ovary

tag: group

value: 19-to-20-day old adults

tag: genotype

value: Wild type

tag: Sex


title: LK2_DMSO_N2_D5

tag: treatment

value: DMSO


title: NCIH226_GSK712_N2_D5


title: DSP-1001250007864-D-A06

description: RNA ISH

tag: region

tag: pathology


title: Ae. aegypti ovary 13 days post-blood-meal with eggs laid >1 week prior replicate 2

tag: tissue

value: Female


title: DSP-1005210003238-E-E02

tag: panel

value: (v1.2) TAP Mouse Whole Transcriptome Atlas

tag: roilabel


title: Amazonia_FMTHVD-2

tag: gender

value: 57  years


title: Ae. aegypti ovary 13 days post-blood-meal with eggs laid >1 week prior replicate 1

tag: age


title: DSP-1005210003238-E-D08

tag: area


title: DSP-1001250007864-D-A04

description: RNA ISH

tag: slide name

value: normal

tag: nuclei


title: LK2_DMSO_N1_D5

tag: cell line


title: DSP-1001250007851-H-F11

description: RNA ISH

tag: class


title: Ae. aegypti ovary 6 days post-blood-meal with eggs laid <5 hours prior replicate 3

tag: strain


title: DSP-1005210003238-E-D07


title: EBC1_GSK712_N2_D5

tag: replicate


title: DSP-1005210003238-E-D06


title: DSP-1001250007851-H-F09

description: RNA ISH


title: Ae. aegypti ovary 6 days post-blood-meal with eggs laid <5 hours prior replicate 2

tag: group

tag: genotype


title: DSP-1001250007851-H-F10

description: RNA ISH


title: EBC1_DMSO_N2_D5

tag: treatment


title: Ae. aegypti ovary 6 days post-blood-meal with eggs laid <5 hours prior replicate 1

tag: Sex


title: EBC1_GSK712_N1_D5


title: DSP-1005210003238-E-D05


title: EBC1_DMSO_N1_D5


title: DSP-1005210003238-E-D04


title: Ae. aegypti ovary 6 days post-blood-meal with eggs retained replicate 3


title: DSP-1001250007851-H-F07

description: RNA ISH

tag: region

tag: pathology


title: DSP-1001250007851-H-F06

description: RNA ISH


title: DSP-1005210003238-E-D03

tag: panel


title: Ae. aegypti ovary 6 days post-blood-meal with eggs retained replicate 2

tag: tissue


title: Ae. aegypti ovary 6 days post-blood-meal with eggs retained replicate 1


title: DSP-1005210003238-E-D02

tag: roilabel


title: Ae. aegypti ovary 96 hours/4 days post-blood-meal with eggs retained replicate 3

tag: age


title: DSP-1001250007851-H-F05

description: RNA ISH


title: DSP-1005210003238-E-D01

tag: area


title: Samples-1-61-CCTATACC

city: Manhattan

first: Aliza

last: Rubenstein

address: 1 Gustave L. Levy Pl

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalling performed using Illumina RTA v3.
bcl2fastq used to convert BCL files to fastq files
Quality control using FastQC v0.11.07
Quality control using Picard 2.7.1 RNASeqMetrics STRAND_SPECIFICITY=FIRST_READ_TRANSCRIPTION_STRAND
Reads were aligned using STAR v2.5.2b
Gene counts were quantified using rsem v1.2.22 in paired-end mode
Genome_build: hg38
Supplementary_files_format_and_content: space-delimited matrix of counts per transcript per sample (rows represent transcripts, columns represent samples)

source_name: vastus lateralis muscle

extract_protocol:
Approximately 10 mg of skeletal muscle tissues were homogenized in a Bead Ruptor Elite bead mill homogenizer (Omni International, Kennesaw, GA) cooled by liquid nitrogen and homogenized for 2 x 20 seconds at 4.2 m/s. Muscle homogenates were processed using the Agencourt RNAdvance Tissue Kit (Beckman Coulter, Indianapolis, IN) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter, Indianapolis, IN) according to the manufacturer’s instructions. The purity and concentration of the RNA samples were evaluated on a NanoDrop One/One spectrophotometer (ThermoFisher Scientific) and quantified using Quant-iT RiboGreen RNA Assay Kit (ThermoFisher Scientific). The RNA integrity was assessed with an RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, United States). RNA integrity numbers (RINs) for all samples were above 8.0 with a median RIN of 8.9.
 mRNA libraries were prepared using the Universal Plus mRNA-Seq Library preparation kit (NuGEN). Briefly, mRNA was isolated from purified 400 ng total RNA using oligo-dT beads and used to synthesize cDNA following the NuGEN’s instructions. The transcripts for ribosomal RNA (rRNA) and globin were further depleted using the AnyDeplete kit (NuGEN) prior to the amplification of libraries except for a subset of 15 sedentary muscle samples. The purified libraries were quantified using the Qubit dsDNA HS Kit (ThermoFisher Scientific). Library size and distribution were determined by Bioanalyzer using the High Sensitivity DNA kit (Agilent) or by Fragment Analyzer using High Sensitivity NGS Analysis kit (Agilent).

tag: cohort

value: Active

value: Post

tag: gender

value: Male


title: Samples-1-61-AACGCCTT


title: Samples-1-61-CCTTAGGT

value: Pre


title: DSP-1001250007851-H-F04

description: RNA ISH

tag: slide name

tag: nuclei


title: DSP-1005210003238-E-C12


title: Ae. aegypti ovary 96 hours/4 days post-blood-meal with eggs retained replicate 2

tag: strain


title: DSP-1001250007851-H-F03

description: RNA ISH

tag: class


title: Samples-1-61-AACCGAAC


title: DSP-1001250007851-H-F08

description: RNA ISH


title: DSP-1005210003238-E-C11


title: Ae. aegypti ovary 96 hours/4 days post-blood-meal with eggs retained replicate 1

tag: group


title: Samples-1-61-CTAAGACC


title: DSP-1001250007851-H-F02

description: RNA ISH


title: DSP-1005210003238-E-C10


title: DSP-1001250007851-H-F01

description: RNA ISH


title: Samples-1-61-ACGGACTT


title: DSP-1001250007851-H-E12

description: RNA ISH

value: tubule


title: Samples-1-61-CTCGAACA


title: Ae. aegypti ovary 72 hours/3 days post-blood-meal with eggs retained replicate 3

tag: genotype


title: DSP-1005210003238-E-A01

source_name: No Template Control


title: Samples-1-61-TCTAGGAG


title: D7_MI_4

city: Oxford

first: Shoumo

last: Bhattacharya

address: Roosevelt Drive

department: RDM Cardiovascular Medicine

country: United Kingdom

institute: Wellcome Centre For Human Genetics, University of Oxford

data_processing:
fastq was generated using bcl2fastq2 (version 2.20.0, Illumina)
Reads were mapped to mouse reference genome using RSubread 2.49
Counts for individual Ensembl gene features were summarised using featureCounts (multi-mapping reads excluded)
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file of gene counts

source_name: Murine Heart

extract_protocol:
RNA from mouse hearts was extracted using RNeasy Mini Kit (Qiagen, Cat#74104) following the manufacturer’s instructions..
Purification of mRNA, generation of double stranded cDNA and library construction were performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) with minor modifications to manufacturer specifications
RNA Seq 150 bp paired end reads on Illumina NovaSeq 6000

treatment_protocol: Myocardial infraction (MI)mice had isoflurane anaesthesia, throracotomy, pericardium removed, and coronary artery ligation on day 0. underwent the same protocol except for the ligation of the coronary artery.

value: wild type

tag: treatment

value: myocardial infarction (MI)

tag: day

value: Murine Heart


title: Ae. aegypti ovary 72 hours/3 days post-blood-meal with eggs retained replicate 1

value: Liverpool

tag: Sex


title: Ae. aegypti ovary 72 hours/3 days post-blood-meal with eggs retained replicate 2

value: Ovary


title: DSP-1001250007851-H-E11

description: RNA ISH

value: DKD

tag: region

tag: pathology


title: Samples-1-61-CCAACACT


title: Ae. aegypti ovary 48 hours/2 days post-blood-meal replicate 3

tag: tissue

value: 48 hours/2 days post-blood-meal

value: 19-to-20-day old adults

value: Wild type


title: DSP-1001250007851-H-E10

description: RNA ISH


title: D7_MI_5


title: Ae. aegypti ovary 48 hours/2 days post-blood-meal replicate 2

value: Female


title: DSP-1001250007851-H-E09

description: RNA ISH


title: Samples-62-121-TCTTCGAC

value: Sedentary


title: D7_MI_2


title: D7_MI_3


title: DSP-1001250007851-H-E08

description: RNA ISH


title: Samples-62-121-GCACACAA


title: DSP-1001250007851-H-E07

description: RNA ISH


title: Ae. aegypti ovary 48 hours/2 days post-blood-meal replicate 1


title: D7_MI_1


title: Ae. aegypti ovary 24 hours/1 day post-blood-meal replicate 3

value: 24 hours/1 day post-blood-meal


title: D7_Sham_5

value: Sham


title: Ae. aegypti ovary 24 hours/1 day post-blood-meal replicate 2


title: D7_Sham_4


title: DSP-1001250007851-H-E06

description: RNA ISH


title: Samples-1-61-ATCGTCTC

value: Active


title: DSP-1001250007851-H-E05

description: RNA ISH


title: Samples-1-61-TACATCGG

value: Post


title: D7_Sham_3


title: D7_Sham_2


title: DSP-1001250007851-H-E04

description: RNA ISH


title: Ae. aegypti ovary 12 hours post-blood-meal replicate 3

value: 12 hours post-blood-meal


title: Samples-1-61-CGACCTAA

value: Pre


title: D7_Sham_1

value: wild type


title: DSP-1001250007851-H-E03

description: RNA ISH

value: tubule


title: Ae. aegypti ovary 12 hours post-blood-meal replicate 1


title: Samples-1-61-ACGAGAAC


title: Samples-62-121-ATGACAGG

value: Male


title: Ae. aegypti ovary 6 hours post-blood-meal replicate 3

value: Liverpool

value: 6 hours post-blood-meal


title: Samples-1-61-GTACACCT


title: DSP-1001250007851-H-E01

description: RNA ISH

value: DKD


title: D4_MI_3

value: myocardial infarction (MI)

value: Murine Heart


title: Ae. aegypti ovary 6 hours post-blood-meal replicate 2

value: Ovary

value: 19-to-20-day old adults

value: Wild type


title: D4_MI_4


title: Samples-1-61-AACTTGCC

value: Female


title: Ae. aegypti ovary 6 hours post-blood-meal replicate 1


title: DSP-1001250007851-H-D12

description: RNA ISH

value: glomerulus

value: abnormal


title: Samples-62-121-CTCCTAGT

value: Sedentary


title: Samples-1-61-CGTCCATT


title: DSP-1001250007851-H-E02

description: RNA ISH


title: DSP-1001250007851-H-D11

description: RNA ISH


title: D4_MI_2


title: Ae. aegypti ovary 24 hours/1 day post-blood-meal replicate 1

value: 24 hours/1 day post-blood-meal


title: Ae. aegypti ovary 3 hours post-blood-meal replicate 3

value: 3 hours post-blood-meal


title: DSP-1001250007851-H-D10

description: RNA ISH


title: Ae. aegypti ovary 3 hours post-blood-meal replicate 2


title: D4_MI_1

value: wild type


title: Ae. aegypti ovary 12 hours post-blood-meal replicate 2

value: 12 hours post-blood-meal


title: Samples-1-61-CTTCCTTC

value: Pre


title: Samples-1-61-ACCATCCT

value: Post


title: Samples-62-121-AACTCGGA

value: Male


title: Ae. aegypti ovary 3 hours post-blood-meal replicate 1

value: Liverpool


title: D4_MI_5

value: myocardial infarction (MI)


title: DSP-1001250007851-H-D08

description: RNA ISH

value: DKD


title: D4_Sham_4

value: Sham

value: Murine Heart


title: Ae. aegypti ovary non-blood-fed replicate 3

value: Ovary

value: non-blood-fed

value: 19-to-20-day old adults

value: Wild type


title: Samples-62-121-GTCGAGAA

value: Sedentary


title: DSP-1001250007851-H-D07

description: RNA ISH

value: glomerulus

value: abnormal


title: DSP-1001250007851-H-D06

description: RNA ISH


title: Ae. aegypti ovary non-blood-fed replicate 2

value: Female


title: Samples-62-121-ACAACAGC


title: Samples-1-61-ACTCCTAC


title: iPSC derived cerebral organoid - Neg 3

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
Reference Genome was generated by combining the raw sequences for hg19 and human herpesvirus strain 5 (Genbank ID : EF999921.1)
Trascript sequences were extracted from the combined gtf file
The index for reference transcript genome was created using "Salmon index"
Mapping -based mode using "Salmon quant" to quantify only transcript sequences against combined transcripts
Genome_build: HG19 + Human herpesvirus strain 5
Supplementary_files_format_and_content: ReadCounts_Day30.xlsx in spreadasheet format giving the details of estimated readcounts

molecule: polyA RNA

organism:
Homo sapiens
Human betaherpesvirus 5

source_name: Cerebral Organoid

growth_protocol: iPSCs were maintained as colonies prior to the start of differentiation, cerebral organoid differentiation was initiated by dissociation of colonies to single cells, plating of 9,000 cells in a round bottom 96 well where they spontaneously form embryoid bodies, from there they're patterned to a neuroepithelial fate through media changes and rocking on a rocker. At D30 the organoids are mature an infected with HCMV TB40eGFP @ MOI of 1 or left uninfected.

extract_protocol:
Infected organoids were sorted for GFP expression 14 days post infection, this resolved three populations GFP (+), GFP Inter, and GFP (-) plus the mock group, which was used to set gates. After sorting, the cells were spun down and RNA was isolated from each population. As mentioned above, three organoids were combined within infected groups from the same line and differentiation to ensure high enough cell numbers.
After RNA was isolated and quantified, the NEBNext Poly(A) mRNA Magnetic Isolation Module Kit was used to generate cDNA libraries which were then quantified using qPCR and the tapestation ultimately run on a Illumina HiSeq 2000

treatment_protocol: For infection at D30 of organoid differentiation, organoids were weighed and then the amount of virus was determined based on weight with MOI of 1 being used and viral strain TB40eGFP. Fresh media and virus were left on the organoids for 2 hours while rocking, after this 2 hour period the virus was removed and organoids washed with PBS. Fresh media was then added and the infection was monitered for 14 days prior to sorting.

tag: cell type

value: iPSC derived cerebral organoid

tag: line

value: HCMV TB40eGFP Infected


title: Samples-1-61-GACTACGA

value: Post


title: DSP-1001250007851-H-D05

description: RNA ISH


title: DSP-1001250007851-H-D04

description: RNA ISH


title: D2_MI_5

value: wild type


title: Ae. aegypti ovary non-blood-fed replicate 1

value: Liverpool

tag: age


title: D4_Sham_3


title: iPSC derived cerebral organoid - Neg 2


title: Samples-1-61-TCTTCGAC

tag: cohort

value: Pre


title: DSP-1001250007851-H-D03

description: RNA ISH

value: DKD


title: D2_MI_4

value: myocardial infarction (MI)


title: DSP-1001250007851-H-D09

description: RNA ISH


title: DSP-1001250007851-H-D02

description: RNA ISH


title: iPSC derived cerebral organoid - Neg 1


title: D4_Sham_5

value: Sham

value: Murine Heart


title: D2_MI_3


title: Samples-1-61-TAGGAGCT

value: Active

tag: gender

value: Male


title: DSP-1001250007851-H-D01

description: RNA ISH

tag: slide name


title: Samples-62-121-CGAACAAC


title: D2_MI_2


title: iPSC derived cerebral organoid - Inter 3


title: iPSC derived cerebral organoid - Inter 2


title: Samples-62-121-CATTCGTC


title: iPSC derived cerebral organoid - Inter 1


title: DSP-1001250007851-H-C12

description: RNA ISH

tag: nuclei


title: D4_Sham_2

tag: strain


title: D2_MI_1


title: D4_Sham_1


title: Samples-1-61-GCACACAA


title: D2_Sham_5


title: Samples-1-61-CTCCTAGT


title: DSP-1001250007851-H-C10

description: RNA ISH

tag: class


title: D2_Sham_4


title: iPSC derived cerebral organoid - Pos 1


title: DSP-1001250007851-H-C09

description: RNA ISH


title: Samples-1-61-AGAACCAG


title: Botrytis inoculated - 28 hpi - replicate 3

city: Leuven

first: Matthias

last: Naets

address: Willem de Croylaan 42

country: Belgium

institute: KU Leuven

description: Malus x domestica Borkh. & Botrytis cinerea B05.10

data_processing:
Remove adaptor, low Q
Remove polyA/T
Remove rRNA
Remove virus
Genome_build: MJAX00000000.1

organism:
Malus domestica
Botrytis cinerea

source_name: Peel and cortex tissue of fruit at its equator. Cylinder with diameter 13.75 mm and depth 15 mm.

extract_protocol:
Total RNA was extracted by adding 800 µL of CTAB extraction buffer (2 % CTAB, 2 % PVP40, 100 mM Tris-HCl (pH8), 25 mM EDTA, 2 M NaCl, 0.5 g L-1 spermidine, 1 % β-mercaptoethanol) to 150-200 mg finely crushed tissue sample. Subsequently, 80 µL N-laurylsarcosine sodium salt (20 %) and a glass bead were added, and the mixture was incubated for 10 min in a thermomixer set at 70 °C and 1400 rpm. Next, 900 µL chloroform:isoamylalcohol (24:1) was added and the samples were centrifuged at 21500 G and 22 °C for 10 min. The supernatant was transferred to the gDNA eliminator spin column of the RNeasy Plus Mini kit from Qiagen (Manchester, UK). From here on, the manufacturer’s guidelines for the kit were followed. Quality and concentration of the extracts were verified using a NanodropTM2000 (Leusden, Netherlands) and by gel electrophoresis. Equal amounts of RNA were pooled across experiments to obtain three unique replicates per treatment per time point. The pooled RNA was precipitated by adding 2 vol 100 % ethanol and 0.1 vol 3 M sodium acetate (pH5.2-5.5), incubating at -80 °C overnight, and centrifugating at 21500 G. The precipitate was washed twice with 70 % ethanol before being resuspended in nuclease free water. All A260/A280 and A260/A230 ratios were above 2.
A stranded library was constructed for each sample with fragment lengths of 75 bp, as described by Zhong and coworkers (Zhong et al., 2011). Sequencing was performed on an Illumina Nextseq500 platform (San Diego, USA). Generated reads were cleaned up and subsequently aligned to the ‘Golden Delicious’ apple genome (Daccord et al., 2017).

treatment_protocol: Three wounds were made on the shadow side of the fruit at its equator with a depth of 10.5 mm and a diameter of 1.8 mm. Each wound was inoculated with either 2 µL of the spore suspension containing 10^6 conidia mL-1 of B. cinerea in 12 g L-1 PDB, or 12 g L-1 PDB (mock inoculated). The control consisted of samples from non-treated fruit (not wounded, not inoculated). The middle one of the three inoculated spots was sampled at specific time points post inoculation using a cork borer of size 8 (13.75 mm diameter). Samples were cut off at a depth of 15 mm and were immediately quenched in liquid nitrogen.

tag: apple cultivar

value: Jonagold

tag: apple tissue

value: Peel and cortex

tag: botrytis cinerea strain


title: DSP-1001250007851-H-C08

description: RNA ISH

value: glomerulus


title: D2_Sham_2

tag: genotype

tag: treatment

tag: day


title: Botrytis inoculated - 28 hpi - replicate 2


title: Samples-1-61-GAATGGCA


title: D2_Sham_1


title: Botrytis inoculated - 28 hpi - replicate 1


title: Samples-1-61-AGGCAATG


title: Botrytis inoculated - 12 hpi - replicate 3


title: DSP-1001250007851-H-C06

description: RNA ISH

tag: region

tag: pathology

value: abnormal


title: empty LP

city: Shanghai

first: Sikai

last: Ling

address: Dongchuan Road 800

institute: Shanghai Jiao Tong University

description: Mice were treated with empty lentiviral particles by subretinal injection.

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 30%;    Cell Gene Number < 10000;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: RPE layer

extract_protocol:
The tissues were removed surgically and placed in MACS Tissue Storage Solution (Miltenyi Biotec, Cat# 130100008) until further processing. Briefly, the samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1 mm3) on ice, and digested with 200 U/mL collagenase I (Worthington, Cat# LS004197) and 200 U/mL DNase I (Worthington, Cat# LS002147) for 45 min at 37 °C, with agitation. Subsequently, the samples were sieved through a 70-µm cell strainer and harvested by centrifugation at 300 ×g for 5 min at room temperature. After washing with PBS containing 0.04% bovine serum albumin (BSA), the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35-μm cell strainer. The viability of the dissociated single cells was assessed using Calcein-AM (Thermo Fisher Scientific, Cat# c3099) and Draq7 (BD Biosciences, Cat# 564904).
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

tag: tissue

value: RPE

value: 8 week


title: D2_Sham_3


title: Samples-1-61-ACAACAGC

value: Sedentary


title: Botrytis inoculated - 12 hpi - replicate 2


title: Samples-1-61-GTCGAGAA

value: Post


title: DSP-1001250007851-H-C05

description: RNA ISH

data_processing:
Library strategy: GeoMx-Seq
GeoMx NGS Pipeline v2.3.3.10 with the following parameters: quality-trim-score = 20, 2color-trimming = True, adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT, adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3, barcode-max-mismatch = 1, stitching-max-mismatch = 2
Genome_build: NA
Supplementary_files_format_and_content: Digital Count Conversion (DCC) files: format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary_files_format_and_content: Kidney_Sample_Annotations.txt: txt file containing sample annotations
Supplementary_files_format_and_content: Kidney_Raw_BioProbeCountMatrix.txt: txt file containing raw probe counts for each AOI
Supplementary_files_format_and_content: Kidney_Raw_TargetCountMatrix.txt: txt file containing collapsed target-level counts for each AOI
Supplementary_files_format_and_content: Kidney_Q3Norm_TargetCountMatrix.txt: txt file containing Q3 normalized target-level counts for each AOI

extract_protocol:
Samples were incubated with the human Whole Transcriptome Atlas RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.


title: RLP

description: Mice were treated of lentivirus particles carrying CRISPR/Cas9 targeting Vegfa gene by subretinal injection.

value: wild type


title: DSP-1001250007851-H-C04

description: RNA ISH


title: DSP-1001250007851-H-C11

description: RNA ISH


title: PBS

description: Mice were treated with PBS by subretinal injection.


title: Botrytis inoculated - 1 hpi - replicate 3


title: Samples-1-61-ATGACAGG


title: Botrytis inoculated - 12 hpi - replicate 1


title: propranolol_r2

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Alignment was done with STAR v2.7.1a
Filtering:  samtools v.1.9. -q 30 -F 780, and only keep properly paired reads (samtools fixmate)
Reads counting by featureCounts v.1.6.4. Optional arguments: -t exon --primary -C )
Differential expression analysis: DESeq2 v.1.39.0
Genome_build: mm10
Supplementary_files_format_and_content: reads counting by featureCounts v.1.6.4. Optional arguments: -t exon --primary -C )

source_name: MCA205 fibrosarcoma propranolol

growth_protocol: Experimental mice were females between 8 and 16 weeks of age. The right flank of mice was subcutaneously (s.c.) injected with one million MCA205 cells. Propranolol hydrochloride (propranolol) (Sigma) was dissolved in room temperature drinking water at 0.5 g/L and offered to mice ad libitum, starting on the day of cancer cell inoculation. Water bottles for all mice were changed every 3-4 days.

extract_protocol:
RNA from sorted TAMs was extracted immediately after sorting, using RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Quality of RNA samples was determined by Bioanalyzer (Agilent). Only samples with RNA integrity number (RIN) of more than 7.5 were used for RNA sequencing.
400 ng RNA was prepared for sequencing using polydT enrichment according to the manufacturer’s instructions (Illumina). Library preparation was performed using the NEBNext RNA library prep kit for Illumina. The library quality was assessed using a Fragment Analyzer followed by library quantification using the Illumina library quantification kit.

treatment_protocol: Tumor-associated macrophages (TAMs) were isolated by single cell suspensions from MCA205 tumors from control and propranolol treated mice. Cells were labeled with CD45 microbeads (Miltenyi) and the CD45+ cells were purified using magnetic separation. The CD45+ cell fractions were stained with Zombie Aqua viability dye, anti-CD11b, and anti-F4/80 antibodies. CD11b+ F4/80+ live cells were sorted by FACS on the ARIA III (BD Biosciences).

value: tumor

tag: cell type

value: macrophages sorted from tumors

value: propranolol


title: iPSC derived cerebral organoid - Pos 2

value: iPSC derived cerebral organoid

tag: line

value: HCMV TB40eGFP Infected


title: DSP-1001250007851-H-C07

first: Stephanie

last: Zimmerman

institute: NanoString Technologies

description: RNA ISH

value: DKD


title: DSP-1001250007851-H-C02

description: RNA ISH


title: Botrytis inoculated - 1 hpi - replicate 2


title: propranolol_r1


title: vehicle_r2

source_name: MCA205 fibrosarcoma control

value: vehicle


title: DSP-1001250007851-H-C01

description: RNA ISH


title: Botrytis inoculated - 1 hpi - replicate 1


title: vehicle_r1


title: Samples-62-121-CGTCTAAC

tag: cohort

value: Pre

value: Male


title: DSP-1001250007851-H-B12

description: RNA ISH


title: Samples-1-61-CATACGGA

value: Active

tag: gender


title: TH-treated NASH

city: Singapore

first: Jin

last: Zhou

address: 8 College Road

department: CVMD

country: Singapore

institute: Duke-NUS Medical School

data_processing:
data assesment
mapping to referenced genome using TopHat2
FPKM value was used to determine the expression level, which was generated using HTSeq software
differential expression analysis with Log2 (fold change>1) and q-value<0.005
Go enrichemnt analysis
Supplementary_files_format_and_content: FPKM value for each sample

source_name: TH

extract_protocol:
The liver tissue was homogenized in Qiazol, followed by extraction using
After the QC procedures, mRNA from eukaryotic organisms is enriched using oligo(dT) beads. For prokaryotic samples, rRNA is removed using a specialized kit that leaves the mRNA. The mRNA from either eukaryotic or prokaryotic sources is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol: Tenweek old male C57BL/6J normal chow diet (NCD) or WDF for 16 weeks, at which point half of the WDF-fed mice began receiving T3 (35 ng/g mice) and T4 (7 ng/g mice) in 15% (w/v) fructose drinking water for the next 8 weeks

tag: diet

value: western diet with liquid fructose

value: treated with thyroid hormone for 8 weeks

value: liver

value: male


title: DSP-1001250007851-H-B11

city: Seattle

address: 530 Fairview Ave N

description: RNA ISH

tag: slide name

value: glomerulus

value: abnormal

tag: nuclei


title: Samples-1-61-TGCGTAAC

value: Post


title: Botrytis inoculated - 0 hpi - replicate 2

value: Jonagold

value: Peel and cortex


title: NASH

tag: strain

value: untreated


title: Botrytis inoculated - 0 hpi - replicate 1

tag: apple cultivar


title: DSP-1001250007851-H-B10

description: RNA ISH

tag: class


title: DSP-1001250007851-H-B09

description: RNA ISH


title: Samples-1-61-AACTCGGA

value: Sedentary


title: DSP-1001250007851-H-B08

description: RNA ISH


title: DSP-1001250007851-H-C03

description: RNA ISH


title: 5dpi_CDS_5

city: Zurich

first: Sina-Maria

last: Schalbetter

address: Winterthurerstrasse 260

country: Switzerland

institute: Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse

data_processing:
RNA Seq reads were mapped to mouse genome (GRCm38.p5) with STAR-version 2.7.3a (Dobin et al., 2013) using the default parameters.
Reads were assigned to genes with featureCounts (Liao et al., 2014) with folowing parameters: -t exon -g gene_id, gene annotation - Gencode GRCm38/vM12.
The differential expression analysis was carried out with DESeq2-version 1.22.1 (Love et al., 2014) using the deafult parameters. We kept genes that have at least 5 reads in at least 5 samples
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: XLSX file contains results of the differential expression analysis (Log2FC) and q-values

source_name: brain tissue

extract_protocol:
The medial prefrontal cortex was removed from frozen brain specimens. Total RNA was isolated using the SPLIT RNA Extraction Kit (Lexogen), according to the manufacturer's instructions.
The TruSeq Stranded Total RNA Library prep kit (Illumina) with Ribosomal depletion, and dual barcoding (2x10 base pairs) was used to produce library constructs with an input of 400 ng total RNA.

value: CDS

value: medial prefrontal cortex

tag: age

value: post natal day 47


title: Samples-1-61-TAGTGCCA


title: Samples-1-61-CAGGTTCA

value: Pre


title: Samples-1-61-TCGTGCAT

value: Male


title: Samples-62-121-CGCTACAT


title: 5dpi_CDS_4


title: DSP-1001250007851-H-B07

description: RNA ISH

value: DKD


title: Samples-1-61-CTACATCC

value: Active


title: Samples-62-121-AATCCAGC


title: flower, knox 1-1

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to the reference genome using HIST2
Reads counts for all genes
Genome_build: Cannabis sativa Assembly cs10 (GenBank Accession #: GCA_900626175.2)
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for each Sample

organism: Cannabis sativa

source_name: flower

growth_protocol: Plants were grown in 7-inch clay pots containing a standard greenhouse mix of 40% Canadian Peat, 40% Coarse Vermiculite, 15% Masonry Sand, and 5% screened topsoil. The Standard Greenhouse Mix was amended with 7.5 lbs Waukesha fine lime, 1 lbs Micromax, 1 lb AquaGro (wetting agent) and 1 lb GreenGuard (iron) per cubic yard. They were fertilized once per week using a 20-10-20 K-N-P mixture. In the growth chamber and greenhouses, the conditions were roughly similar: the temperatures were 81° F and 85° F during the day and 63° F and 67° F at night. The photoperiod was 16 hours for the first 10 weeks and after that was reduced to 11 hours to induce flowering. The relative humidity varied between 50% and 75%. Plants were watered as needed. Fertilizer of (20-10-10, K-N-P) was dissolved in water to 250 ppm and applied daily.

extract_protocol:
Used the RNeasy mini kit (Qiagen) by following the manufacturer’s instructions, including the on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: flower

tag: Sex

tag: location

value: Knox, NE


title: flower, madison 2-1

value: Madison, NE


title: 5dpi_CDS_3

tag: treatment


title: flower, merick 1-1

value: Merick, NE


title: DSP-1001250007851-H-B06

description: RNA ISH

tag: region

value: glomerulus

value: abnormal


title: Botrytis inoculated - 0 hpi - replicate 3

value: Jonagold

tag: apple tissue

tag: botrytis cinerea strain


title: Samples-62-121-AGCCAACT


title: DSP-1001250007851-H-B05

description: RNA ISH

tag: pathology


title: 5dpi_CDS_2

tag: tissue


title: 3OC8-HSL-treated Arabidopsis Cy5 vs. Control Arabidopsis Cy3

city: Shijiazhuang

first: Fang

last: Liu

state: HeBei

address: 46th, South Street of Friendship

department: Biology Institute

institute: Biology Institute, Hebei Academy of Sciences

description: 17-day-old  Arabidopsis seedling, treated with 1μM 3OC8-HSL, harvested after 24h treatment vs. 17-day-old  Arabidopsis seedling, untreated, harvested after 24h.

hyb_protocol: Oligoarray control targets and hybridization buffer (3×SSC, 0.2%SDS, 5×Denhart’s, 25%Formamid) were added, and samples were applied to microarrays overnight in 42℃. After hybridization, slides were washed sequential

scan_protocol: Scanned on  the LuxScan 10KA two-channel laser scanner (CapitalBio, Beijing, China).Images were quantified using the LuxScan 3.0 (CapitalBio, Beijing, China) software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.

organism: Arabidopsis thaliana

source_name: 3OC8-HSL-treated Arabidopsis wlid-type Col-0 seedling

label_protocol: The probes were prepared using the CapitalBio® cRNA amplified labeling kit (Capitalbio, Beijing, China) and fluorescently labeled with Cy5-dCTP and Cy3-dCTP (GE Healthcare).

growth_protocol: Seedlings germinated on MS agar plates for 10 days were transplanted into a sterile hydroponic system containing sterile Hoagland medium. After 7 days, seedlings were used for N-acyl-homoserine lactones (AHLs) treatments.

extract_protocol: Total RNA was extracted from treated and control plants using the RNAiso Plus reagent (TaKaRa, Dalian, China) and purified using the NucleoSpin® RNA clean-up kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions.

treatment_protocol: 17-day-old seedling roots were soaked in Hoagland medium with1µM 3OC6-HSL. After 24h seedlings were harvested for RNA extraction.

source_name: Arabidopsis wild-type Col-0 seedling


title: flower, merick 2-4

value: Female


title: 5dpi_CDS_1


title: Samples-62-121-GCCTTAAC

tag: cohort

value: Post


title: DSP-1001250007851-H-B04

description: RNA ISH

source_name: Human FFPE kidney


title: flower, madison 1-1


title: Samples-62-121-ATTCCGCT

tag: gender


title: control

source_name: NCD

tag: diet

value: normal chow

value: untreated

value: liver

value: male


title: 5dpi_PBS_5

value: PBS

value: medial prefrontal cortex

value: post natal day 47


title: DSP-1001250007851-H-B03

description: RNA ISH

tag: slide name

value: DKD


title: flower, knox 2-3

value: flower


title: 5dpi_PBS_4


title: DSP-1001250007851-H-B02

description: RNA ISH

tag: nuclei


title: Samples-62-121-CTTCCTTC

value: Sedentary

value: Male


title: DSP-1001250007851-H-B01

description: RNA ISH


title: Samples-62-121-ACCATCCT


title: 5dpi_PBS_3

tag: strain


title: Samples-62-121-CGTCCATT

value: Pre


title: 3C-seq of cells carrying SpSmc-ScpAB and chimeric BsSpParB BSG3887_rep

city: Lausanne

first: Anna

last: Anchimiuk

state: Vaud

address: UNIL-Sorge District

department: Department of Fundamental Microbiology

institute: University of Lausanne

description: 3C-seq of cells carrying SpSmc-ScpAB and chimeric BsSpParB in exponential phase in SMG at 37°C

library_source: genomic

data_processing:
Sequencing data from 3C-seq experiments was demultiplexed, adapters trimmed, and PCR duplicates removed using custom scripts. Next, data was processed as described at https://github.com/axelcournac/3C_tutorial.
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
Iterative alignment: Min-leght=20, step=5, bowtie2 --very-sensitive-local followe by filtering, mapping quality=30, no ambiguous reads
Assignment to restriction fragments
Removal of uninformative events (uncuts, loops etc) as described in Cournac et al. BMC 2012. Binning at 10kb.
Genome_build: NC_000964
Supplementary_files_format_and_content: 422x422 raw and normalized contact matrices in txt format

molecule: genomic DNA

organism: Bacillus subtilis

growth_protocol: strains were grown overnight in SMG, diluted to OD600 0.004 in fresh SMG and grown at 37°C until reached an OD600 between 0.022-0.026

extract_protocol:
3C libraries were prepared as previously described (Marbouty et al., 2015). Minimal media (SMG) was used instead of LB. Briefly, cells were grown in 400 ml of SMG medium to exponential phase (OD = 0.022-0.030) and fixed with fresh formaldehyde (3% final concentration) for 30 minutes at RT, followed by 30 minutes at 4°C and quenched for 30 minutes with 0.25 M glycine at 4°C. Fixed cells were harvested by filtering, washed in fresh SMG, frozen in liquid nitrogen and stored at -80°C until further use.  Frozen pellets were resuspended in 600 µl 1x TE and incubated at RT for 20 minutes with 4 µl of Ready-lyze lysozyme (35U/ul, Tebu Bio). Next, SDS was added to a final concentration of 0.5% and incubated at RT for 10 minutes.  50 µl of lysed cells were aliquoted to 8 tubes containing 450 µl of digestion mix (1x NEB 1 buffer, 1% triton X-100, and 100 U HpaII enzyme (NEB)) and incubated at 37°C for 3 hours with constant shaking. Digested DNA was collected by centrifugation, diluted into 4 tubes containing 8 ml of ligation mix (1x ligation buffer: 50 mM Tris-HCl, 10 mM MgCl2, 10 mM DTT), 1 mM ATP, 0.1 mg/ml BSA, 125 U T4 DNA ligase 5 U/ml) and incubated at 16°C for 4 hours. Ligation reaction was followed by O/N decrosslinking at 65°C in the presence of 250 µg/ml proteinase K (Eurobio) and 5 mM EDTA.  DNA was precipitated with 1 volume of isopropanol and 0.1 Volume of 3 M sodium acetate (pH 5.2, Sigma) at -80°C for 1 hour. After centrifugation, the DNA pellet was resuspended in 1x TE at 30°C for 20 minutes. Next, DNA was extracted once with 400 µl phenol-chloroform-isoamyl alcohol solution and precipitated with 1.5 volume cold 100% ethanol in the presence of 0.1 volume 3 M sodium acetate at -80°C for 30 minutes. The pellet was collected and resuspended in 30 µl TE with RNaseA at 37°C for 30 minutes. All tubes were pooled and the resulting 3C library was quantified on gel using ImageJ.
1 ug of 3C library was suspended in water (final volume 130 µl) and sonicated using Covaris S220 (following manufacturers recommendations to obtain 500 bp target size). Next, DNA was purified with Qiagen PCR purification kit, eluted in 40 µl EB and quantified using NanoDrop. 1 ug of DNA was processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters for 4 hours at RT, followed by inactivation step at 65°C for 20 minutes. DNA was purified with 0.75x AMPure beads and 3 µl were used for 50 µl PCR reaction (12 cycles). Amplified libraries were purified on Qiagen columns and pair end sequenced on an Illumina platform (HiSeq4000 or NextSeq).

tag: genotype

value: 1A700, SpnSmc ftsY::erm, specR::SpnScpAB, parB(SpnParB(1-83), BsParB(102-282))::kanR, trpC2


title: 3C-seq of del parA cells carrying SpSmc-ScpAB and chimeric BsSpParB with a single parS (parS359, -9kb) BSG3937

description: 3C-seq of del parA cells carrying SpSmc-ScpAB and chimeric BsSpParB with a single parS (parS359, -9kb) in exponential phase in SMG at 37°C

value: 1A700, delta-7-parS(parS359+),SpnSmc::ermB, SpScpAB::specR, delta-parA:parB(SpnParB(1-83), BsParB(102-282))::kanR


title: 5dpi_PBS_2


title: Samples-62-121-GACTACGA


title: DSP-1001250007851-H-A12

description: RNA ISH

tag: class

value: glomerulus

value: abnormal


title: Samples-62-121-ACTCCTAC


title: DSP-1001250007851-H-A10

description: RNA ISH


title: 3C-seq of cells carrying SpSmc-ScpAB and chimeric BsSpParB BSG3887


title: 3C-seq of del parA cells carrying SpSmc-ScpAB and chimeric BsSpParB BSG2984_rep

description: 3C-seq of del parA cells carrying SpSmc-ScpAB and chimeric BsSpParB in exponential phase in SMG at 37°C

value: 1A700, SpnSmc ftsY::erm, specR::SpnScpAB, delta-parA:parB(SpnParB(1-83), BsParB(102-282))::kanR, trpC2


title: eIF2α flox/+ rep4

city: Beijing

first: Yilie

last: Liao

address: Zhongguancun Street

institute: Tsinghua University

data_processing:
fastx_toolkit (Version 0.0.14), Sickle, SeqPrep and fastp (Version 0.19.5) for quality control.
Bowtie2 (Version 2.2.9) for sequence alignment.
GATK (Version 3.8) and samtools (Version 1.9) for SNP/Indel analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read counts values for each sample.

source_name: Liver

growth_protocol: lean, wild-type mice, 12/12h light on/off, ad libum fed

extract_protocol:
Livers were removed, snap-frozen in liquid nitrogen, and RNA was extracted using Trizol reagent. RNA was treated with DNaseI and cleaned with Ribo-zero magnetic core kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were sacrifice at 6:30am, fed state

tag: age

tag: genotype/variation

value: Eif2a flox/+


title: Huh7 cells, Neil3 KD

city: Tainan

first: Wenya

last: Huang

address: No.1, University Road

country: Taiwan

institute: NCKU

data_processing:
Illumina official tool, BCL2FASTQ conversion Software v2.20 was used to convert BCL files from the Illumina sequencing platform.
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases.
Trimmed reads were aligned to the reference genome sequence using HISAT2 v2.1.0 aligner to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Differential expression analysis was performed using CUFFDIFF of CUFFLINKS package v2.2.1 to produce gene/transcript read count and FPKM profiles for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: Excel file include gene ID, gene type, gene name, EntrezGene ID, locus and FPKM values for each sample

source_name: Huh7 liver cancer cell line

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm
All RNA sample preparation procedures were carried out according to the Illumina's official protocol. Agilent's SureSelect Strand-Specific RNA Library Preparation Kit was used for library construction followed by AMPure XP beads (Beckman Coulter, USA) size selection. using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technology, USA).

tag: cell line

value: Huh7 liver cancer cell line

tag: passages

value: Neil3 KD


title: 3C-seq of del parA cells carrying SpSmc-ScpAB and chimeric BsSpParB BSG2984


title: eIF2α flox/+ rep3

value: liver


title: 3C-seq of cells carrying SpSmc-ScpAB BSG2828_rep

description: 3C-seq of cells carrying SpSmc-ScpAB in exponential phase in SMG at 37°C

value: 1A700, S.p. smc ftsY::erm, specR::S.p. scpAB, trpC2


title: Huh7 cells, shGFP

value: control


title: DSP-1001250007851-H-A08

description: RNA ISH

tag: region


title: 3C-seq of cells carrying SpSmc-ScpAB BSG2828


title: eIF2α flox/+ rep2


title: TPb3

city: Halle

first: Robert

last: Eckenstaler

address: Kurt-Mothes-Str. 3

department: Institute of Pharmazie

country: Germany

institute: Martin-Luther-University

description: TPb overexpression replicate 3

data_processing:
Sequencing and data procession were performed by Novogene.
Alignment: to human genome (GRCh38) with HiSat2 (v2.0.5)
Annotations: Ensembl (GRCh38.p13)
Abundance measurements: HTSeq (v0.6.1)
Differential gene expression: DESeq2 software package (v1.20.0)
Genome_build: human genome (GRCh38)
Supplementary_files_format_and_content: tab-delimited text files including FPKM for abundance measurements

source_name: cultured endothelial cells

growth_protocol: HUVECs were cultured in ready-to-use basal endothelial cell medium (EBM-2, Promocell) supplemented with 2% fetal calf serum (FCS), basic fibroblast growth factor (bFGF), VEGF, insulin-like growth factor-1 (IGF-1), epidermal growth factor (EGF), hydrocortisone, ascorbic acid, gentamycin sulfate and amphotericin-B at 37°C in humidified air with 5% CO2.

extract_protocol:
RNA was extracted using TRIZOLTM reagent (Thermo Fisher Scientific) according to manifacturer's instructions.
NEBNext® UltraTM RNA Library Prep Kit for Illumina®.

treatment_protocol: HUVECs were infected with VSV-G-pseudotyped lentiviral particles derived from pHIV-SFiG-1335 (EGFP) transfer plasmids with a multiplicity of infection (MOI) of 100. For control cells (Ctr.), empty pHIV-SFiG-1335 was infected. For thromboxan A2 receptor overexpressing cells, transfer plasmids expressing either tromboxan A2 receptor alpha (TPa) or tromboxan A2 receptor beta (TPb) were used. After infection, cell were cultured for 48h before RNA isolation.

tag: cell type

value: human umbilical vein endothelial cells (HUVECs)

tag: passage

value: 2 to 7

tag: excpression level

value: overexpression of TPb


title: DSP-1001250007851-H-A07

description: RNA ISH

value: DKD

tag: pathology


title: eIF2α flox/+ rep1

tag: tissue


title: TPb2

description: TPb overexpression replicate 2


title: 3C-seq of del parB cells BSG1050

description: 3C-seq of del parB cells in exponential phase in SMG at 37°C

value: 1A700, delta-parB::kanR, trpC2


title: DSP-1001250007851-H-A06

description: RNA ISH


title: TPb1

description: TPb overexpression replicate 1


title: DSP-1001250007851-H-A05

description: RNA ISH


title: WT rep3

description: control

value: wild type


title: 5dpi_PBS_1

tag: treatment

value: PBS

value: medial prefrontal cortex

value: post natal day 47


title: DSP-1001250007851-H-A11

description: RNA ISH

value: glomerulus

value: abnormal


title: DSP-1001250007851-H-A04

description: RNA ISH


title: WT rep2

description: control


title: TPa3

description: TPa overexpression replicate 3

value: overexpression of TPa


title: TPa2

description: TPa overexpression replicate 2


title: WT rep1

description: control