title: WT_Hi-C_MseI-merged

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

description: genomic DNA (Hi-C ligation products)

data_processing:
All in situ Hi-C contact maps and other analyses presented in this manuscript were generated using the program suite HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/index.html) (Ramírez et al. 2018), using version 3.5 for all analyses, except the program hicFindEnrichedContacts (version 2.2.3) for observed vs. expected matrix generation. Briefly, raw fastq files were mapped to the Neurospora genome (either version 12 or version 14 [this work]) using bowtie2 (version 2.3), with the --local and --reorder flags, and the Hi-C contact matrix was built with hicBuildMatrix using the default settings; resulting images of the contact matrix images were made with hicPlotMatrix. Contact maps are either presented as raw or Knight-Ruiz corrected (Knight and Ruiz 2012) images to account for differences in restriction enzyme site distribution or sequencing bias of underlying DNA.
Since Hi-C replicate datasets showed local reproducibility (Figure S4), fastq files of DpnII or MseI replicates were merged, resulting in a merged DpnII dataset with 269.9M reads (89.0M valid reads) and a merged MseI dataset with 93.8M reads (20.4M valid reads). To generate a comprehensive dataset representative of the chromatin composition of the WT Neurospora genome from individual DpnII (euchromatic-specific; GATC recognition sequence) and MseI (heterochromatic-specific; TTAA recognition sequence) datasets, we calculated the percent of the Neurospora genome covered by H3K9me3 demarcating constitutive heterochromatin, which have an increased number of MseI sites due to the AT-rich nature of the underlying DNA. To this end, we generated bed files of a previously published H3K9me3 merged dataset (Jamieson et al. 2016; Klocko et al. 2019), subtracted the end point from the starting point to calculate the number of basepairs covered by H3K9me3 at each region, summed the total number of bases, and divided the H3K9me3-covered bases by the genome size to get the percentage (15.76%) of the Neurospora genome covered by H3K9me3. The comprehensive in situ Hi-C dataset was built by combining Hi-C matrices created from appropriate numbers of valid MseI or DpnII PE100 reads that, when combined, would provide 15.76% MseI-derived contacts and 84.24% DpnII-derived contacts. In this case, 21.4M reads (3.8M valid reads) were removed from MseI replicate #4, and the resulting MseI matrix using 72.4M reads (16.7M valid reads) was combined to the complete DpnII matrix (270M reads, 89.2M valid reads). The total dataset, comprising 342.2M reads (105.9M valid reads) was subject for all further analysis.
For mining specific loci for interacting partners within Hi-C ligation products, promoter regions (+/-1000 bp) of specific genes were extracted from the mapped R1_bam files using samtools, unique identifiers for each read (column 1 of bam files) were extracted using the awk command, and this list was used to extract the reads from that unique ligation product from the mapped R2_bam files using samgrep, a tool within the JVarkit (Lindenbaum 2015). Resultant sam files were converted to bam files, sorted, indexed, and converted to TDF files for display on Integrative Genomics Viewer (Robinson et al. 2011); IGV images were used for figure generation.
Genome_build: GSE71024_neurospora_crassa_or74a_12_genome_FIXED.fasta (version 12; Galazka et al., 2016, Genome Research) or nc14_genome-seq-name.fasta (version 14; this work)
Supplementary_files_format_and_content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins, and the interactions between the bins is reported - either raw contact counts or Knight-Ruiz corrected percentages.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: To grow WT Neurospora culture, 25 mL cultures containing 1x Vogel’s medium + 1.5% sucrose were inoculated with 1.25x10^8 conidia, (harvested from ~six baby slants by vortexing with water; conidia were washed twice prior to use) and grown at 32 °C with shaking at 200 revolutions per minute (RPM) for ~four hours until ~90% of conidia had germinated, and growth tubes were ~4x the length of the initial conidia.

extract_protocol:
First, the concentration of genomic DNA per spheroplast aliquot was determined by resuspending one aliquot per culture replicate in 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM sodium ethylenediaminetetraacetic acid [Na EDTA], 0.5% [w/v] sodium dodecyl sulfate [SDS]) plus 100 mg proteinase K (Invitrogen) and incubated at 65°C for 16 hours. The volume was then increased to a total of 500 μL using TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA), and 40 mg RNase A (Invitrogen) was added. Aliquots were incubated at 37 °C for 30 min, and genomic DNA was extracted with twice 25:24:1 phenol:chloroform:isoamyl alcohol (25:24:1; ThermoFisher cat# AC327115000), once with chloroform, and precipitated with 0.1 volume sodium acetate (pH 5.2) and 1 volume isopropanol, centrifuged (10 minutes, 13k rpm), and the resulting DNA pellet was washed once with 70% (v/v) ethanol, dried for 10 min in a Savant SpeedVac (ThermoFisher, Model # DNA120-115), and resuspended in 50 μL TE. The total DNA concentration per pellet was determined by quantifying 2 μL of the total resuspension of genomic DNA (50 μL) using a Qubit 3.0 HS DNA quantification kit (ThermoFisher cat# Q33217). Spheroplasts containing 3.5 μg of genomic DNA were resuspended in 270 μL of 1x restriction enzyme buffer (either DpnII or MseI, above) and 50 μL hydrated glass beads were added (Sigma-Aldrich #G1145, Acid washed, 150-212 μm). Spheroplasts were lysed by vortexing tubes for 30 seconds followed by 30 seconds on ice; five total cycles were performed. Following the settling of the beads, 270 μL of supernatant (and cell debris, if possible) were moved to a new tube. SDS was added to 0.625% final concentration (30 μL of 6.25% stock), tubes incubated at 62 °C for 7 minutes, and immediately placed on ice. Triton X-100 was added to a final concentration of 1% [33 μL of 10% (v/v)] and 10x DpnII or MseI buffer was added to account for added volumes of SDS, Triton and enzymes. Genomic DNA in chromatin was then digested with 200 U DpnII or MseI for 16 hours at 37°C while nutating. Samples were then centrifuged for 3000 rpm for 10 minutes, the supernatant was removed, and the pellets, which contained permeabilized nuclei and chromatin, were resuspended in 83 μL of 1x DpnII or MseI buffer. Sticky ends were blunted in a 100 μL reaction with 30 μM each of dCTP, dGTP, dTTP, Biotin-14-dATP (Invitrogen cat# 19524-016), and 25 U of Klenow (large fragment). Reactions were mixed by pipetting and incubated at 37°C for 60 minutes with nutating. An additional 110 μL of 1x DpnII or MseI buffer was added to the samples (210 μL total chromatin volume), and ligation reactions with 1x T4 Ligation buffer, 1% Triton X-100, 100 μg/mL BSA, and 1675 U of T4 DNA ligase were immediately prepared and incubated at 16 °C for 4 hours. Proteinase K (250 μg total; Gold Biotechnology cat# 97062-238) was added and reactions were decrosslinked at 65°C once overnight (~16 hours) and following the addition of another 250 μg of proteinase K, reactions were decrosslinked a second time for 2 hours. Cooled samples were extracted twice with phenol:chloroform:isoamyl alcohol, the aqueous fraction was transferred to a 2.0 mL microcentrifuge tube, and the volume increased to 500 μL with additional TE buffer. Ligated DNA circles were precipitated by addition of 0.1x volume 3M sodium acetate pH 6.0, 2.5x volumes 100% ethanol, 40 μg glycogen (ThermoFisher cat# R0561), incubation at -80 °C for 30 minutes followed by centrifugation at 13,000 rpm for 15 minutes. Pellets were washed once with 70% ethanol, dried at RT for 10 minutes in a speedvac, and resuspended in 50 μL TE. RNaseA (20 μg; SigmaAldrich cat# R4875) was added and samples were incubated at 37 °C for 30 minutes. An additional 450 μL TE was added, and ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform. The aqueous fraction was transferred to a new 2.0 mL microcentrifuge tube, and ligation products were precipitated (0.1x 3M sodium acetate pH 6.0 and 2.5x 100% ethanol were added, and tubes were incubated at -80 °C for 20 minutes and centrifuged at 13,000 rpm for 10 minutes), washed, dried, resuspended in 25 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA) and stored at -20 °C. To remove biotin-dATP from unligated DNA ends, 50 μL reactions consisting of 1x NEB buffer 2.1, 100 μM each of dATP and dGTP, and 5 U of T4 DNA polymerase were incubated at 12 °C for 2 hours and quenched with EDTA (final concentration 10 mM), and the reaction volume was increased to 500 μL with TE/10. DNA ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform, transferred to a 2.0 mL microcentrifuge tube, and ethanol precipitated (0.1x volume 3M sodium acetate, pH 6.0 and 2.5x volume 100% ethanol were added, tubes were incubated at -80 °C for 20 minutes, centrifuged at 13,000 rpm for 10 minutes, washed, dried, and DNA pellets were resuspended in 500 μL TE/10). Ligation products were sheared by sonication (Qsonica, Model Q55; amplitude = 30%, 30 seconds sonication, 30 second incubation on ice between pulses). Sheared, biotinylated ligation products were captured on streptavidin magnetic beads (Dynabeads M280, Invitrogen cat# 11205D) equilibrated with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) at RT for 30 minutes, with pipetting every 10 minutes. Beads were washed on a magnetic rack three times with 1x BW buffer, twice with TE/10, and resuspended in 25 uL TE/10 buffer.
Hi-C libraries for Illumina sequencing were prepared using a NEBNext Ultra II kit (New England Biolabs cat# E7645) with corresponding Multiplex Barcode sets (NEB cat# E7335 and E7500) according to the manufacturer’s protocol, with the following exceptions, as all steps were performed using the Hi-C library attached to the magnetic streptavidin beads: following the adapter ligation and USER enzyme digestion, magnetic beads were washed five times with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) and once with TE/10, and resuspended in 15 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA); PCR enrichment of the barcoded Hi-C library off streptavidin beads used either eight or 15 cycles (or an initial fifteen PCR cycles, whereupon the beads were washed three times with TE/10, and were re-amplified by an additional 8 cycles, for a total of 23 cycles) and following the separation of the aqueous PCR product from the magnetic beads, the PCR product was cleaned with a 1:1 ratio of Ampure XP beads (Agencourt, Beckman-Coulter) per the manufacturer’s protocol, resuspended in 25 μL TE/10, and quantified by a Qubit HS reaction. Prior to sequencing, all libraries were assessed for quality via Fragment Analyzer and qPCR (Genomics and Cell Characterization Core Facility [GC3F], University of Oregon). Indexed in situ Hi-C libraries were pooled and sequenced on an Illumina HiSeq 4000 at the Genomics and Cell Characterization Core Facility [GC3F] at the University of Oregon as 100 nucleotide (nt) paired-end (PE100) sequencing runs. Hi-C dataset fastq files are provided in table S1.

treatment_protocol: Methanol-free formaldehyde was added to a final concentration of 1% and cultures were incubated 10 minutes at room temperature (RT; ~25°C) with shaking at 100 RPM for crosslinking; 1 M Tris-HCl [pH 8 at 25°C] (Hoffman et al. 2015) was added to a final concentration of 125 mM and cultures were incubated at RT for 10 minutes, shaking at 100 RPM, to quench the reaction. Conidia were harvested by centrifugation (4000 RPM, 3 min) and resuspended gently in 20 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4 [pH 7.5]) with b-mercaptoethanol added to 30mM. Conidia were pelleted again and resuspended in 20 mL spheroplasting buffer with b-mercaptoethanol added to 1mM. VinoTaste (Novozymes; powder dissolved in water to a stock solution of 50 mg/mL) was added to 50mg and strains were digested at 30°C, shaking at 100 RPM, for 60 min. Spheroplasts were harvested by centrifugation (3500 RPM, 2 min) and pellets were washed twice with 20 mL Spheroplasting buffer, followed by three washes of the buffer of the 1x restriction enzyme to be used for digestion, either MseI buffer (50 mM NaCl, 10 mM Tris-HCl [pH 7.9 at 25°C], 10 mM MgCl2, 100 μg/mL bovine serum albumin [BSA]) or DpnII buffer (100 mM NaCl, 50 mM Tris-HCl [pH 7.9 at 25°C], 10 mM MgCl2, 100 μg/mL BSA). Washed pellets were resuspended in 3.5 mL of the same restriction enzyme buffer, split into four – 1 mL aliquots in 1.7 mL Eppendorf tubes, pelleted (10,000 rpm, 5 min), whereupon the supernatant was removed, and spheroplast pellets were stored at -80°C.

tag: developmental stage

value: asexual, unsynchronized cells


title: DSP-1001250007851-H-A03

status: Public on Mar 01 2022

type: SRA

city: Seattle

first: Stephanie

last: Zimmerman

state: WA

address: 530 Fairview Ave N

country: USA

institute: NanoString Technologies

description: RNA ISH

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

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: glomerulus

tag: pathology

value: abnormal

tag: nuclei


title: TPa1

city: Halle

first: Robert

last: Eckenstaler

address: Kurt-Mothes-Str. 3

department: Institute of Pharmazie

country: Germany

institute: Martin-Luther-University

description: TPa overexpression replicate 1

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 TPa


title: DSP-1001250007851-H-A09

description: RNA ISH


title: WT_Hi-C_DpnII-merged

description: genomic DNA (Hi-C ligation products)

library_source: genomic

molecule: genomic DNA


title: WT_N3752_Hi-C_MseI_8PCR

description: genomic DNA (Hi-C ligation products)


title: shEif4ebp3 rep4

city: Beijing

first: Yilie

last: Liao

address: Zhongguancun Street

country: China

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.

organism: Mus musculus

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: 0.1OD of adenovirus injection, 1 week afterwards, fast overnight and then sacrifice

tag: strain

tag: tissue

value: liver

tag: age

tag: treatment

value: Eif4ebp3 knockdown


title: Ctr3

description: control replicate 3

value: wildtype levels of TP


title: DSP-1001250007851-H-A01

description: RNA ISH

value: No Template Control


title: Ctr2

description: control replicate 2


title: WT_N3752_Hi-C_DpnII_8PCR

description: genomic DNA (Hi-C ligation products)


title: shEif4ebp3 rep2


title: WT_N150_Hi-C_MseI_8PCR

description: genomic DNA (Hi-C ligation products)


title: WT_N150_Hi-C_DpnII_23PCR

description: genomic DNA (Hi-C ligation products)


title: WT rep4

description: control

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

tag: genotype/variation

value: wild type


title: Ctr1

description: control replicate 1


title: CFBE SUB rep2 (ATAC-seq)

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
Paired-end reads were aligned to the human hg19 database (GRCh37.p13) using BWA.
The mitochondrial reads and reads with mapQuality <30 were removed. Duplicate reads were cleaned by MarkDuplicates tool. The narrowpeaks were called using MACS2 from the converted BED files. Normalized bigwig files were generated by Wig/BedGraph-to-BigWig tool on Galaxy platform
Peak annotations and feature distributions were performed by ChipSeeker (Bioconductor) and KEGG pathways were analyzed by PathfindR in R studio.
Genome_build: hg19
Supplementary_files_format_and_content: callpeak normalized reads

source_name: Epithelial cells

growth_protocol: Human bronchial epithelial CFBE41o- cells stably expressing F508del-CFTR (CFBE) or wild-type CFTR (WTBE) were cultured in MEM medium, supplemented with 10% fetal bovine serum (Hyclone), 0.5% Penicillin/Streptomycin and 2mM L-glutamine. 0.5µg/mL puromycin (InvivoGen) were added for WTBE while 25µg/mL puromycin for CFBE cells to select stably transfected cells. Cells were maintained in a humidified chamber with 5% CO2 at 37C.

extract_protocol:
60,000 cells (>95% viability) were trypsinized and lysed in 50L cold lysis buffer (10mm Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% NP40, 10% Tween-20, and 0.01% Digitonin) and incubated on ice for 5min. Then 1mL wash buffer (10mm Tris-HCl, 10mM NaCl, 3mM MgCl2 and 10% Tween-20) was added and tube were inverted 3 times gently.
Nuclei were pelleted at 500g for 5min at 4°C and resuspended in 50 µL of transposition mixture (TDE1 tagment DNA enzyme and TD buffer, illumina) and incubated for 30 min at 37 °C. Isolated DNA samples were purified using DNA Clean and Concentrator-5 (Zymo Research), which can be stored in -20°C. Purified DNA products were pre-amplified for 5 cycles with NEBNext High-Fidelity 2x PCR MasterMix (NEB). Additional cycles were added based on qPCR results of partially-amplified library. PCR reactions were purified and qualified using an Agilent High Sensitivity DNA Bioanalyzer Kit (Agilent).  The libraries were quantified using a sensitive fluorescence dye-based Qubit dsDNA HS Assay Kit (ThermoFisher). Libraries were pooled at a final concentration of 650pM

treatment_protocol: For transwell-cultured (ALI) condition, cells were seeded on Millicell cell culture insert (Millipore) placed in 24-well plates. Media on the apical surface was removed daily until complete confluency (dry membrane) and basolateral media were replaced every other two days. Confluent cells were cultured for at least another 10days for polarization. For submerged cells, cells were also cultured in 24well plates and cultured till fully confluent.

tag: culture condition

value: Submerge

tag: cell line

value: CFBE (CFBE41o- cells stably expressing F508del mutant CFTR)

value: Cystic fibrosis (CF) bronchial epithelial cells


title: shEif4ebp3 rep1


title: shEif4ebp3 rep3


title: shLacZ rep4

description:
control group
CTL_D10

value: LacZ knockdown


title: CFBE SUB rep1 (ATAC-seq)


title: WT-_N150_Hi-C_double-digest_DpnII+MseI

description: genomic DNA (Hi-C ligation products)


title: WT_N150_Hi-C_DpnII_15PCR

description: genomic DNA (Hi-C ligation products)


title: WTBE SUB rep3 (ATAC-seq)

value: WTBE (CFBE41o- cells stably expressing wild-type CFTR)


title: WTBE SUB rep2 (ATAC-seq)


title: HCT116_Pellet

city: Hangzhou

first: Kai

last: Ma

state: Zhejiang

address: No.18 Shilongshan Road，Cloud Town, Xihu District

institute: Westlake University

description: The pellet fraction of the mitotic HCT116 cells

data_processing:
Sequencing adaptors and low quality (base quality score<20) reads were trimmed by trim galore (v0.6.6). Reads shorter than 20nt were discarded.
The trimmed reads were aligned to the 45S rDNA locus sequences by STAR (v2.7.8a). The 45S rDNA annotation file was transformed to GTF format used gffread(v0.12.1).
The expression level of 18S, 5.8S, 28S rRNA, ITS1, ITS2, 5’ETS, 3’ETS were quantified by FeatureCounts (v2.0.1). The normalized count (counts per million---CPM) in 18S rRNA, 28S rRNA, ITS1, ITS2, 5’ETS, 3’ETS regions were quantified in each 100bp bin, and the normalized count in 5.8S rRNA region were quantified in each 10bp bin.
Genome_build: U13369.1 downloaded from GenBank
Supplementary_files_format_and_content: rDNA_Count_Binned.txt (tab-delimited text file includes raw counts values of the binned regions for each Sample)

growth_protocol: HCT116 cells were cultured in DMEM containing 10 % fetal bovine serum and supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin at 37 °C with 5 % CO2 (v/v).

extract_protocol:
The mitotic HCT116 cells were lysed by NETN100, and then the RNAs were extracted from the soluble and pellet fraction.
Library preparation and sequencing were finished by BGI company (Shenzhen, China). The protocol is as follows: 1) RNA fragment and reverse transcription; 2) End repair, add A and adaptor ligation; 3) PCR; 4)Single strand separation and cyclization; 5) DNA nanoball synthesis; 7) Sequencing on DNBseq platform.

treatment_protocol: The HCT116 cells were treated with Colcemid for overnight to be arrested at prometaphase.

value: Treated with Colcemid overnight

tag: cell state

value: mitotic

tag: fraction

value: Pellet


title: shLacZ rep2

description:
control group
CTL_C4


title: MDA-MB-231_shA_1

city: DA LIAN

first: Liu

last: Quentin

address: Lvshunkou District, Dalian, Liaoning

institute: DA LIAN MEDIACAL UNIVERSITY

data_processing:
Illumina bcl2fastq version 2.19 were used to the basecalling.
Reads was aligned to hg38 by star 2.5.3a with default parameters
Read count was summarized with HTSeq 0.8.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: MDA-MB-231 cells were cultured in Leibovitz's L-15 Medium supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA samples were extracted according to RNeasy plus kit (#74104, Qiagen).
Libraries were prepared according to the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations.

tag: genotype

value: AURKA KD


title: MDA-MB-231_shC_2

value: control


title: WTBE SUB rep1 (ATAC-seq)


title: DSP-1001250007851-H-A02

description: RNA ISH

tag: slide name

tag: class

value: DKD

value: glomerulus

value: abnormal


title: MDA-MB-231_shA_2


title: shLacZ rep1

description:
control group
CTL_C2

value: liver


title: WT_N150_Hi-C_DpnII_8PCR

description: genomic DNA (Hi-C ligation products)

tag: developmental stage

value: asexual, unsynchronized cells


title: Larvae E4

status: Public on Feb 28 2022

city: Saint Martin d'Hères

first: Stéphane

last: REYNAUD

address: 2233 rue de la piscine

country: France

institute: Grenoble-Alpes University

data_processing:
After unplexing and quality check using FastQC, reads were then filtered based on their length, pairing and quality using Trimmomatic (v0.32.1)
Cleaned reads were mapped to the AgamP4 assembly annotated with the AgamP4.12 gene set using HISAT2 (Kim et al., 2015).
The Cufflinks (v0.0.7) tool was applied to aligned reads to enumerate for each library the number of short reads overlapping annotated genes.
Cuffmerge (v0.0.6) was used to merge multiple transcriptome assemblies from each sample. Gene transcription levels were computed from aligned reads and compared statistically using the Cuffdiff (v0.0.7) tool (Trapnell et al., 2012) implemented in a Galaxy pipeline (http://galaxyproject.org).
Gene transcription levels were computed from aligned reads and compared statistically using the Cuffdiff (v0.0.7) tool (Trapnell et al., 2012) implemented in a Galaxy pipeline (http://galaxyproject.org).
Genome_build: AgamP4
Supplementary_files_format_and_content: Cufflink files

organism: Anopheles gambiae

source_name: Whole body

extract_protocol:
Total RNA was extracted from four pools of 20 individuals sampled for each life stage (larvae or adult females)  and condition (treated with pesticide mixture or not). RNA extractions were performed using Trizol (Life Technologies) according to manufacturer's instructions.
RNAseq libraries were prepared from 150 ng total RNA using the NEBNext® Ultra ™ II Directional mRNA Library Preparation Kit for Illumina (New England Biolabs) following manufacturer's instructions. Libraries were quantified using the Qubit DNA BR assay (Thermofisher Scientific) and quality checked using Bioanalyzer DNA 1000 assay (Agilent). Libraries were sequenced in multiplex as single 75 bp reads on a NextSeq 500 sequencer (Illumina) by Helixio (Clermont-Ferrand, France). After unplexing and quality check using FastQC, reads

tag: common name

value: African malaria mosquito

tag: exposure condition

value: Exposed Larave

tag: devlopmental stage

value: 4th stage Larvae

value: Whole body


title: Larvae E3


title: Larvae E2


title: CFBE SUB rep3 (ATAC-seq)

value: Submerge

value: CFBE (CFBE41o- cells stably expressing F508del mutant CFTR)

tag: cell type

value: Cystic fibrosis (CF) bronchial epithelial cells


title: Larvae T3

value: Control Larvae


title: Larvae E1


title: Larvae T2


title: Larvae T4


title: Adult E4

value: Adults from exposed Larvae

value: 4-day old non-blood fed adult females


title: Larvae T1


title: Adult E3


title: Adult E2


title: Adult E1


title: Adult T4

value: Control Adult


title: Adult T2


title: Adult T3


title: shLacZ rep3

description:
control group
CTL_C5

tag: strain

value: LacZ knockdown


title: rainbow trout gill cell line RTgill-W1 (ATCC®CRL-2523™) 100 mg/L LPS-treated Replicate1

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

data_processing:
Raw fastq files from all lanes (L001-L004) were concatenated. Reads were trimmed using Trimmomatic v0.38 (Phred score > 20; minimum length of 35 bp).
Trimmed fastq files were pseudoaligned to the reference Rainbow Trout (Oncorhynchus mykiss) transcriptome (NCBI Accession GCF_013265735.2; OmykA_1.1).
Only features with at least 5 counts per million in at least 3 samples were kept for differential expression analyses. Significance of differentially expressed genes was assessed using EdgeR in omicsBox in R, with a cut-off FDR (Benjamini-Hochberg) < 0.05 and an effect size threshold |FC| ≥ 1.5.
Genome_build: Rainbow Trout (Oncorhynchus mykiss) NCBI Accession GCF_013265735.2 OmykA_1.1.
Supplementary_files_format_and_content: csv and tabular - raw (estimated) counts using Kallisto.
Supplementary_files_format_and_content: rbt-UF_DEG_results.xlsx - differential expression results using edgeR.

organism: Oncorhynchus mykiss

source_name: RTgill-W1 cells

growth_protocol: Cells were cultured in 75 cm2 tissue culture flasks at 20°C. Leibowitz’s L-15 medium was used as the culture medium and supplemented with 10% fetal bovine serum (FBS), 100 units mL-1 penicillin, and 100 μg mL-1 streptomycin (all obtained from Thermo Fisher Scientific, Waltham, USA). The cells were harvested at approx. 95% confluency for subsequent bioassays.

extract_protocol:
Cells were washed with PBS and the plates stored at -80°C upon completion of treatment protocol. Upon thawing, total RNA was extracted from each replicate well using RNeasy Plus Mini kits (QIAGEN), following the manufacturer’s protocol. Only samples with an RNA Integrity Number (RIN) > 8 were used for dsDNA library preparation. Libraries were prepared using the TruSeq® Stranded mRNA Library Prep kit (Illumina Inc, San Diego CA, USA) and were subsequently run for paired-end sequencing (75 bp x 2, 150 cycles) using the NextSeq 500/550 High Output Kit v2.5 (Illumina Inc) on an Illumina NextSeq 500 System (Illumina Inc). Sequencing was conducted on four control replicates and three 100 mg L-1 LPS treatment group replicates.
Only samples with an RNA Integrity Number (RIN) > 8 were used for dsDNA library preparation. Libraries were prepared using the TruSeq® Stranded mRNA Library Prep kit (Illumina Inc, San Diego CA, USA). The quality of dsDNA libraries were assessed using Agilent high sensitivity DNA analysis kit in a 2100 Bioanalyzer instrument (Agilent Technologies, Waldbronn, Germany). Libraries were quantified in a Qubit 4 fluorometer (Thermo Fisher Scientific).

treatment_protocol: Cells were seeded into 24-well microplates (1 mL well-1, 500,000 cells mL-1) and allowed to adhere for 24 h. Subsequently, cells were exposed in quadruplicate to either L-15/ex media alone as the control treatment, or 100 mg LPS L-1 in L-15/ex media (both at pH 7.4) and incubated for 4 h.

tag: exposure compound

value: 100 mg/L bacterial lipopolysaccharide (LPS)

tag: time point

value: 4hr exposure after 24 hours adherence


title: rainbow trout gill cell line RTgill-W1 (ATCC®CRL-2523™) 100 mg/L LPS-treated Replicate2


title: rainbow trout gill cell line RTgill-W1 (ATCC®CRL-2523™) 100 mg/L LPS-treated Replicate3


title: rainbow trout gill cell line RTgill-W1 (ATCC®CRL-2523™) untreated/control Replicate2

value: L-15/ex media at pH 7.4


title: HCT116_Soluble

description: The soluble fraction of the mitotic HCT116 cells

tag: treatment

value: Treated with Colcemid overnight

value: mitotic

value: Soluble


title: MDA-MB-231_shC_1

value: control


title: Sham_uterus_5

type: RNA

city: Kyoto

first: Shiho

last: Iwasaki

state: Kyoto

address: 14, Nishinosho-monguchi-cho, Kisshoin, Minami-ku

country: Japan

institute: Nippon Shinyaku Co., Ltd.

description: Gene expression data from uterus of sham mouse

hyb_protocol: Following fragmentation, 2.3 μg of cDNA was hybridized for 16 hr at 45°C on a Clariom S Mouse Array (Thermo Fisher Scientific, Inc.) according to the manufacturer’s instructions. GeneChips were washed and stained using a GeneChip Fluidics Station 450 according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G  (Thermo Fisher Scientific, Inc.).

data_processing: CEL files were processed using Affymetrix Expression Console software (Thermo Fisher Scientific, Inc.) and subjected to normalization using the Signal Space Transformation-Robust Multiarray Analysis (SST-RMA) method. We conducted two patterns of data processing. One is the data processed from 10 CEL files of model ectopic cyst and model uterus. The other is the data processed from 10 CEL files of model uterus and sham uterus.

label: biotin

source_name: uterus of sham mouse

label_protocol: Fragmented and labeled cDNA was prepared by using the GeneChip WT Plus Reagent Kit (Thermo Fisher Scientific, Inc.) from 250 ng total RNA according to the manufacturer’s instructions.

growth_protocol: Twenty-eight days after construction of the model, the ectopic cystic tissue and the eutopic endometrium from the model mice or the endometrium from the sham mice were removed for RNA extraction.

extract_protocol: Total RNA was isolated from the mouse ectopic cystic tissue using an RNeasy Lipid Tissue Mini Kit (Qiagen Inc., Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: To construct the syngeneic mouse endometriosis model, uterine tissues in the medium from the donor mice were transferred into the peritoneal cavities of the recipient mice. For the sham group, the same volume of medium was injected into the peritoneal cavities of the mice.

value: BALB/cCrSlc

tag: tissue

value: uterus


title: rainbow trout gill cell line RTgill-W1 (ATCC®CRL-2523™) untreated/control Replicate3


title: Sham_uterus_2


title: rainbow trout gill cell line RTgill-W1 (ATCC®CRL-2523™) untreated/control Replicate4


title: Sham_uterus_1


title: rainbow trout gill cell line RTgill-W1 (ATCC®CRL-2523™) untreated/control Replicate1


title: Model_uterus_5

description: Gene expression data from eutopic uterus of mouse endometriosis model

source_name: uterus of model mouse


title: Model_uterus_4


title: Sham_uterus_3


title: Model_uterus_2


title: Model_ectopic_cyst_5

description: Gene expression data from ectopic cystic tissue of mouse endometriosis model

source_name: cystic tissue of model mouse

value: cystic tissue


title: Model_uterus_3


title: Model_ectopic_cyst_4


title: Model_ectopic_cyst_3


title: Model_ectopic_cyst_2


title: Model_ectopic_cyst_1


title: UPF3-KO_rep1

city: Gothenburg

first: Per

last: Sunnerhagen

address: Box 462

department: Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

data_processing:
library strategy: SH-Linked Alkylation for the Metabolic Sequencing of RNA (SLAM-Seq)
SLAM DUNK through the nf core SLAM Seq processing and analysis pipeline V1 (Ewels 2020 The nf-core framework for community-curated bioinformatics pipelines) using the default setting with the exception of designating the read length manually.
Genome_build: S. cerevisiae S288C (assembly R64)
Supplementary_files_format_and_content: Comma separated file containing the RNA conversion rate for each transcript

organism: Saccharomyces cerevisiae

source_name: BY4741 upf3Δ

extract_protocol:
Quick-RNA Fungal/Bacterial Kit (Zymo Research) as per manufacturer instructions with the modification of adding Reducing agent (RA) from the SLAM-Seq Kinetics Kit – Catabolic Kinetics Module (Lexogen) to the isolation, wash, and elution buffers of the RNA extraction kit at a ratio of 1:1000, 1:1000 and 1:100, respectively
200 ng of alkylated total RNA was used as input for generating 3’-end mRNA sequencing libraries using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) and the and PCR Add-on Kit for Illumina (Lexogen) according to the QuantSeq 3‘ mRNA-Seq Library Prep Kit User Guide (Lexogen)

tag: strain background

tag: sample type

value: Yeast cell culture


title: WT-rep3

value: wild type


title: UPF3-KO_rep2


title: Adult T1

value: African malaria mosquito

value: Whole body


title: UPF3-KO_rep3


title: WT-rep2


title: WT-rep1


title: Sham_uterus_4


title: HTS donor 20

city: Melbourne

first: Jacky

middle: Yisheng

last: Li

state: Victoria

address: 50 Flemington Rd

department: Cellular Biology

country: Australia

institute: MCRI

data_processing:
For bulk sequencing data sequenced reads were mapped to GrCh38 whole human genome with the Spliced Transcript Alignment to a Reference (STAR) software using default parameters. Nonuniquely mapping reads and read pairs with unpaired alignments were excluded.
For single cell data, sequenced reads were mapped to the GrCh38 whole human genome with cell ranger software using the default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: count matrix for bulk sequencing data, features and barcodes and count matrix for single cell data

source_name: Cultured human thymic stromal cells

growth_protocol: Neonatal human thymic stromal cells were grown on Geltrex-coated cell cutlure plate and cultured with a chemically defined serum- and ablbumin-free medium.

extract_protocol:
RNA was isolated using the ISOLATEII RNA micro-Kit (Bioline, BIO-52075) as described by the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 5 ng/ml KGF

value: Thymus

tag: isolated population

value: Live cell above 90%


title: s1.contact

city: Montreal

first: Olivier

last: Tastet

address: 900 Saint-Denis

institute: crCHUM

description: brain-resection path (normal tissue) from neurosurgery for epilepsy for oligodendrocytes, memory CD4 T cells isolated from peripheral blood mononuclear cells and activated for 6 days in the presence of IL-23 for Th17 cells

data_processing:
cell ranger analysis pipeline
reads aligned to reference genome GRCh38
Seurat preliminary processing of cellranger output files
Platform Illumina NovaSeq 6000 (Homo sapiens)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample, basic annotation of cells

source_name: Co-culture of adult human oligodendrocytes in primary culture and IL-23 polarized human CD4 T cells (Th17 cells)

growth_protocol: For oligodendrocytes see Cui et al. Ann Neurol 2017. For Th17 cells see Larochelle et al. Brain 2012. Oligodendrocytes: brain tissue was obtained from adults undergoing surgical resections as a treatment for non–tumor-related intractable epilepsy in accordance with the guidelines set by the Biomedical Ethics Unit of McGill University. Tissue specimens were enzymatically digested and placed on a linear 30% Percoll density gradient. Microglia were separated and removed by an initial adhesion step in which the total cell fraction was cultured for 24 hours in non-coated flasks. The floating cell fraction was subjected to immunomagnetic bead selection with the A2B5 antibody (IgM), which recognizes gangliosides to remove a progenitor cell pool that comprises 3 to 5% of white matter cells. OLs (A2B5-depleted pool) were plated on poly-lysine–coated 24 wells, and cultured in defined medium (DFM) consisting of Dulbecco modified essential medium DMEM-F12 supplemented with N1, 0.01% bovine serum albumin, 1% penicillin-streptomycin and B27 supplement, platelet-derived growth factor (PDGF)-AA (10ng/ml), basic fibroblast factor (bFGF, 10ng/ml), and triiodo-thyronine (T3, 2nM) for 4 days. Media was changed every 48 hours. Th17 cells: human CD4CD45RO cells were isolated magnetically (negative selection) and activated with plate-bound anti-CD3 (2.5ug/ml) and soluble anti-CD28 (2ug/ml) in X-vivo medium in the presence of IL-23 (25ng/ml).

extract_protocol:
cells were harvested, filtered and processed for single cell capture (1 sample per chip)
cDNA libraries were created using the Chromium Single Cell 3' technology

treatment_protocol: co-culture of oligodendrocytes and Th17 cells in direct contact or separated by an insert

value: Day 10 in vitro human oligodendrocytes in primary culture, day 6 in vitro activated CD4 Th17 cells

tag: condition

value: Direct contact between oligodendrocytes and Th17 cells, co-culture for 12h


title: s2.no.contact

value: brain-resection path (normal tissue) from neurosurgery for epilepsy

value: No direct contact, oligodendrocytes and Th17 cells separated by an insert with a porous membrane, co-culture for 12h


title: D_Bait_RAG1K-O_T0_Rep2

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

data_processing:
Library strategy: LAM-HTGTS
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the hg19 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) to map translocations
Reads were aligned to the bait and the prey region using Bowtie2 and filtered to identify the DSBs (prey).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); and the entire stitched paired end read sequence (Seq)

source_name: Human embryonic kidney cells

growth_protocol: HEK293T cells were cultured at 37 °C and 5% CO2 in DMEM supplemented with 10% (vol/vol) FCS, 50 U/mL penicillin/streptomycin (ThermoFisher), 2 mM L-glutamine (ThermoFisher), 1× MEM-NEAA (ThermoFisher), 1 mM sodium pyruvate (ThermoFisher), 50 μM 2-mercap- toethanol (Sigma), and 20 mM Hepes (pH 7.4)

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
Libraries were generated as described in Hu et al., 2016 Nature Protocols (PMC4895203), with the enzyme blocking step being omitted, using primers associated with the target locus and Illumina NovaSeq sequencing

treatment_protocol: Polyethyleneimine-mediated transfection of px330 plasmids bearing various sgRNAs were applied when the HEK293T cells grow at 70% confluence, growth media changed 6 hours post-transfection and cultured for another three days.

tag: cell line

tag: transfection

tag: bait

tag: target locus

tag: number of raw reads used for normalization

tag: pipeline used for the analysis

value: HTGTS-Rep-Rejoin

tag: figure displaying results for this library


title: HTS donor 21


title: D_Bait_RAG1K-O_T0_Rep1


title: D_Bait_RAG1K-O_T2_Rep1


title: HTS donor 19


title: D_Bait_RAG1K-O_T2_Rep2


title: HTS donor 18


title: D_Bait_RAG1K-O_T1_Rep2


title: L_Bait_RAG1B,C,D_T1_Rep2


title: D_Bait_Ctr_Rep2


title: L_Bait_RAG1B,C,D_T1_Rep1


title: L_Bait_RAG1B,C,D_T2_Rep1


title: HCCLM3-shSPC25-REP03

city: Zhengzhou

first: Wen-Kai

last: Shi

state: Henan

address: Jianshedong Road No.1

department: Department of hepatopancreatobiliary surgery

institute: The first affiliated hospital of Zhengzhou university

description: HCCLM3-KD gene expression after transfected with lentiviral

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-072363 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

treatment_protocol: HCCLM3 cells were transfected with lentiviral, then cultured in DMEM medium supplemented with 10% fetal bovine serum. The cultures were incubated 37 ºC in a humidified incubator with 5% CO2.

tag: genotype/variation

value: SPC25 KD


title: HCCLM3-shNC-REP01


title: D_Bait_Ctr_Rep1


title: HCCLM3-shSPC25-REP02


title: HCCLM3-shNC-REP03


title: L_Bait_RAG1B,C,D_T2_Rep2


title: Model_uterus_1

tag: strain


title: HCCLM3-shSPC25-REP01


title: L_Bait_RAG1B,C,D_T0_Rep2


title: HCCLM3-shNC-REP02


title: A_Bait_RAG1B,C,D_T2_Rep2


title: L_Bait_Ctr_Rep1


title: A_Bait_RAG1B,C,D_T1_Rep2


title: D_Bait_RAG1K-O_T1_Rep1


title: A_Bait_RAG1B,C,D_T0_Rep2


title: A_Bait_RAG1B,C,D_T1_Rep1


title: L_Bait_Ctr_Rep2


title: A_Bait_Ctr_Rep1


title: E9.5_embryo_puck_201112_04

city: Cambridge

first: Luyi

last: Tian

state: MA

address: 415 main st Cambridge

institute: Broad institute

description: wild type embryos from in vitro fertilized zygotes - saggital section

data_processing:
Library strategy: Spatial Transcriptomics
Base-calling from images was performed by a custom MATLAB package ArrayCaller (https://github.com/MacoskoLab/ArrayCaller/).
The sequenced reads were processed by Slide-seq tools pipeline (https://github.com/MacoskoLab/slideseq-tools) to generate the gene count matrix and match bead barcode between array and sequenced reads.
Genome_build: mouse GRCm38.81
Supplementary_files_format_and_content: XXX.digital_expression.txt.gz is the gene count matrix where the rows are genes and columns are beads. XXX_matched_bead_location.txt is the bead spatial location file where the rows are in the order as XXX.digital_expression.txt.gz.   Read1 contains the transcript sequence and Read2 contains bead barcode (14bp) followed by  bead UMI sequence (8bp). puck_rawimage_XXX.tar contains the raw image from puck sequencing, which is used to obtain the spatial location of the bead barcodes.

source_name: E9.5 embryo

growth_protocol: Pre-implantation embryos were cultured in standard embryo media. In brief, 25uL of KSOM media drops were added to the petridish and covered with mineral oil. The culture dish with KSOm was pre-gassed prior to transfer of embryos. Embryos were re-transferred bilaterally to uetrine horn of pseudopregnant 2.5dpc surrogate CD1 female mice

extract_protocol: Slide-seq v2

treatment_protocol: Zygotes electroporated with Cas9-RNP with guides targeting GFP (mock)/Tbx6 (Tbx6 KO)

value: E9.5 embryo

tag: genotype

value: WT

tag: section

value: saggital

tag: cross

value: B6D2F1 (F1 oocyte) x CAST sperm

value: mock electroporated


title: L_Bait_RAG1B,C,D_T0_Rep1


title: E9.5_embryo_puck_201112_05

tag: tissue

tag: treatment


title: E9.5_embryo_puck_201104_33


title: E9.5_embryo_puck_201104_36


title: E9.5_embryo_puck_201104_32


title: E8.5_embryo_puck_201104_29

source_name: E8.5 embryo

value: E8.5 embryo


title: E8.5_embryo_puck_201104_28


title: Sample 1

first: Takuro

last: Okamura

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

institute: Kyoto Prefectural University of Medicine

data_processing: The FASTQ files obtained from the sequences were processed using the BD Rhapsody Targeted Analysis Pipeline with V(D)J processing incorporated (BD Biosciences) in the Seven Bridges Platform (https://www.sevenbridges.com/ ). First, low-quality read pairs were removed based on read length, average base quality score, and highest single-base frequency. High-quality R1 reads were analyzed to identify cell labels and unique molecular identifier (UMI) sequences. The high-quality R2 reads were aligned with the reference panel sequences (Human T cell Expression panel) and TCR gene segments from the international ImMunoGeneTics information system® (IMGT.org) using the program Bowtie2. IGBlast was utilized for CDR3 determination. Reads with identical cell labels, identical UMI sequences, and identical genes were folded into a single molecule. The obtained counts were subjected to error correction algorithms (recursive substitution error correction (RSEC) and distribution-based error correction (DBEC)) developed by BD Biosciences. The DBEC-adjusted number of molecule data obtained from the Rhapsody pipeline was imported into SeqGeq version 1.6.0, and quality control was then performed to gate out cells that were significantly smaller and with low numbers of expressed genes (dead cells).

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation, counted, and resuspended in 650 μL of cold sample buffer for loading on a BD Rhapsody cartridge.
Targeted scRNA-seq with TCR analysis was performed using the BD Rhapsody Express system (BD Biosciences, NJ, USA). Cell capture and library preparation were performed using the BD Rhapsody Targeted mRNA and AbSeq Reagent Kit (BD Biosciences) . Briefly, cells from each sample were captured in a microwell plate with beads. This was followed by cell lysis, bead retrieval, cDNA synthesis, template switching, Klenow extension, and library preparation (targeted gene library using human T-cell expression panel and TCR gene library) following the BD Rhapsody VDJ CDR3 protocol. The final pooled libraries were spiked with 20% PhiX control DNA to increase the sequence complexity and subsequently sequenced (75 bp × 225 bp paired-end) on a HiSeq X Ten sequencer (Illumina, San Diego, CA).

tag: disease

value: Type 1 Diabetes Mellitus

tag: gender

value: Male

tag: age


title: Sample 4

value: SPIDDM


title: Sample 3


title: Sample 2

value: Female


title: E8.5_embryo_puck_201104_18


title: E8.5_embryo_puck_201104_26


title: E8.5_embryo_puck_201104_19


title: E8.5_embryo_puck_201104_24


title: E8.5_embryo_puck_201104_22


title: E8.5_embryo_puck_201104_17


title: E8.5_embryo_puck_201104_23


title: A_Bait_RAG1B,C,D_T2_Rep1

tag: cell line


title: Control_palatal tissue at E13.5

city: Los Angeles

first: Tingwei

last: Guo

state: CA

address: 2250 Alcazar St

department: CCMB

institute: usc

data_processing:
ATAC-seq reads were aligned to the UCSC mm10 reference genome using BWA-MEM (Li, 2013). ATAC-seq peaks were called by MACS2 (Zhang et al., 2008). Peaks were annotated and known transcription factor binding motifs were analyzed in the ATAC-seq peaks by HOMER (Heinz et al., 2010)).
Genome_build: mm10
Supplementary_files_format_and_content: peaks

source_name: Palate

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Single cells suspension were prepared from E13.5-E14.0 using trypLE digestion at 37 degree.
ATAC-seq libraries were prepared according to a published protocol (Buenrostro et al., 2015). Sequencing was performed on the NextSeq 500 platform (Illumina, San Diego, CA).

treatment_protocol: Not applicable

value: wild type

value: Palate


title: A_Bait_RAG1B,C,D_T0_Rep1

tag: transfection


title: E8.5_embryo_puck_201104_16


title: E8.5_embryo_puck_201104_13


title: E8.5_embryo_puck_201104_14


title: E9.5_embryo_puck_201112_03


title: A_Bait_Ctr_Rep2

tag: bait


title: E8.5_embryo_puck_201104_08


title: E8.5_embryo_puck_201104_07


title: E8.5_embryo_puck_201104_12


title: input_control

city: New York

first: Abderhman

last: Abuhashem

state: NY

address: Rockefeller Research Labs, 430 E 67th St

department: Developmental Biology Program

institute: Sloan-Kettering Institute for Cancer Research

data_processing:
Reads are aligned to mm10 using Bowtie2.
Alignments were filtrered for MAPQ >30 and mm10 blacklisted regions excluded
BigWig files generated using bamCoverage in R (DeepTools)
Peaks were called using MACS2.0 using default parameters in relation to a sample input. Specific parameters avaialble in peaks excel files
Visualized using WashU genome browser
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files, and MACS2.0 files

source_name: 20 x 10^6 cells

growth_protocol: Culture in serum/LIF at 37C and 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
nonstranded, generated using KAPA HTP Library Prep Kit

treatment_protocol: DMSO or dTAG-13 mixed with the culture medium

value: Control

tag: antibody

value: Nelfb deg


title: SPT5_dTAG_1

value: 30 mins of 500nM dTAG-13

value: Anti-DSIF BD (BD611106)


title: input_dTAG


title: SPT5_dTAG_2


title: NELFE_dTAG_2

value: Anti-NELFe abcam (ab170104)


title: E8.5_embryo_puck_201104_27


title: NELFB:HA_dTAG_2

value: HA-Tag CST (C29F4)


title: SPT5_2


title: NELFE_dTAG_1


title: NELFB:HA_dTAG_1


title: NELFE_1


title: NELFE_2


title: NELFB:HA_1


title: NELFB:HA_2


title: ScRNA-seq of Aortic VSMCs

city: Shijiazhuang

first: Yakun

last: Gao

state: China

address: Department of Biochemistry and Molecular Biology College of Basic Medicine Hebei Medical UniversityNo. 361, Zhongshan Road, Shijiazhuang, Hebei, China

institute: Hebei Medical University

description:
scRNA-seq
mRNA

data_processing:
The Cell Ranger software was obtained from 10x Genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest). Alignment, filtering, barcode counting, and UMI counting were performed with cellranger count module to generate feature-barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle components were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
The other clustering method is Seurat 3.0 (R package). Cells whose gene number was less than 200, or gene number ranked in the top 1%, or mitochondrial gene ratio was more than 25% were regarded as abnormal and filtered out. Dimensionality reduction was performed using PCA, and visualization was realized by TSNE and UMAP.
GO enrichment, KEGG enrichment, Reactome enrichment and Disease enrichment (human only) of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment, using top 20 markers gene of cluster. The results were visualized using R package.
Single-cell trajectories were built with Monocle (R package) that introduced pseudotime. Genes were filtered by the following criteria: Expressed in more than 10 cells; The average expression value was greater than 0.1; Qval was less than 0.01 in different analysis.
Cell type was annotated by singleR (https://bioconductor.org/packages/devel/bioc/html/SingleR.html). Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files; barcodes.tsv, features.tsv, matrix.mtx.

source_name: aorta

extract_protocol:
The aorta was dissected from the root (distal to the aortic valve) to the femoral artery bifurcation. Enzymatic dissociation protocol was used to separate the medial cell layer and prepare single cells.
Using Single Cell 3' Library and Gel Bead Kit V3 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs.
The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: Aorta

tag: cell type

value: Medial vascular smooth muscle cells

value: Wild type

tag: diagnosis

value: Healthy


title: E8.5_embryo_puck_201104_09

value: E8.5 embryo

value: WT

value: saggital

value: B6D2F1 (F1 oocyte) x CAST sperm

value: mock electroporated


title: C1 MLN, HTO2

first: Peter

last: Smibert

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
10x pool lane 2 HTO
HTO_list.csv

data_processing:
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)
cDNA data were processed using cellranger v5
ADT counts matrices were generated using kallisto | bustools (kallisto v0.46.0, bustools v0.39.3)
HTO counts matrices were generated using kallisto | bustools (kallisto v0.46.0, bustools v0.39.3)
Genome_build: mm10
Supplementary_files_format_and_content: counts matrices (barcode, feature name, matrix)
Supplementary_files_format_and_content: ADT*antibody_names.txt (raw counts matrix antibody name)
Supplementary_files_format_and_content: ADT*barcodes.txt (raw counts matrix cell barcodes)
Supplementary_files_format_and_content: ADT*matrix.mtx (raw counts matrix)
Supplementary_files_format_and_content: cDNA*barcodes.tsv.gz (raw counts matrix cell barcodes)
Supplementary_files_format_and_content: cDNA*features.tsv.gz (raw counts matrix gene names)
Supplementary_files_format_and_content: cDNA*matrix.mtx.gz (raw counts matrix)
Supplementary_files_format_and_content: HTO*antibody_names.txt (raw counts matrix hashtag name)
Supplementary_files_format_and_content: HTO*barcodes.txt (raw counts matrix cell barcodes)
Supplementary_files_format_and_content: HTO*matrix.mtx (raw counts matrix)
Supplementary_files_format_and_content: ADT_barcode_list.csv (kallisto barcode list)
Supplementary_files_format_and_content: HTO_list.csv (kallisto barcode list)

molecule: protein

source_name: mouse cells

extract_protocol: Stained, sorted, and washed cells were processed through the 10x Genomics Single Cell 3' V3 protocol

treatment_protocol: Cells were stained as described for CITE-seq (Stoeckius et al, 2017)

value: C1 MLN

tag: tag length

value: 15 base tag

tag: molecule

value: antibody oligo

tag: library type

value: HTO

tag: library protocol

value: 10x Genomics Single Cell 3' V3

tag: 10x lane

value: lane 2

tag: infection

value: Heliobacter

tag: mouse type


title: C1 MLN, HTO1

description:
10x pool lane 1 HTO
HTO_list.csv

value: lane 1


title: C1 MLN, ADT1

description:
10x pool lane 1 ADT
ADT_barcode_list.csv

value: 12 or 15 base tag

value: ADT


title: C1 MLN, ADT2

description:
10x pool lane 2 ADT
ADT_barcode_list.csv


title: C1 MLN, cDNA2

description: 10x pool lane 2 cDNA

molecule: polyA RNA

value: polyA mRNA

value: mRNA


title: C1 MLN, cDNA1

description: 10x pool lane 1 cDNA


title: PD1-Tim3-

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

data_processing:
Basecalling was performed using Illumina RealTimeAnalysis software
FASTQ sequences adapter trimmed (trimglore) and mapped to the hg19 by BSMAP2.7.4
CpGs were extracted by the methratio.py in the BSMAP package
Genome_build: hg19 (human WGBS)
Supplementary_files_format_and_content: methylation ratio are in bed formats that contains methylation ratio for each CpG

source_name: Germ Cell Tumor

extract_protocol:
gDNA was extracted using a Macherey-Nagel kit. Less than 500 ng of gDNA was bisulfite (BS) treated using the EZ DNA Methylation-Gold (Zymo Research).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA Methylation Kit (Part# EGMK81312). Briefly, Bisulfite converted DNA was annealed with random hexamer with tagging sequence. DNA copy was synthesized using TruSeq DNA Methyl Polymerase. Then Exonuclease I was used to digest excess random primer.  The 3’ ends of the strands are then selectively tagged with a second specific sequence tag to generate di-tagged DNA using DNA polymerase. The di-tagged DNA with known sequence tags at both ends was cleaned up by the AMPureXP Beads. The dsDNA library was generated by PCR amplification with Illumina primers for 10 cycles and library fragments of ~350 bp (insert plus adaptor and PCR primer sequences). The library was purified by the AMPureXP Beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Novaseq 6000 following the manufacturer's protocols.

tag: tissue

value: Germ Cell Tumor

tag: processing

value: ex vivo

tag: developmental stage


title: PD1+Tim3-


title: PD1+Tim3+


title: Young (4 weeks old)

data_processing:
Fastq files for each library were processed using CellRanger v3.0.2 with a custom mm10 reference that included the mCherry sequence. Note: these outputs were not utilized for analysis of the corresponding manuscript.
Outputs for each library were aggregated using CellRanger v3.0.2 with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tsv for barcodes and gene,mtx for gene-barcode matrix

source_name: Tumor

extract_protocol: 10x Genomics 3' kit, V2

value: mCherry+


title: Adult (24 weeks old)


title: dPTO_033

city: Groningen

first: Rob

last: Coppes

address: Ant. Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

description: Matrigel-cultured differentiated organoid derived from hyperplastic parathyroid gland tissue

data_processing:
Base-calling: bcl2fastq software (Illumina Inc.) version 2.20.0.422.
QuantSeq 3′ mRNA-Seq analysis: Bluebee (Lexogen) version 015UG108V0311
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hyperplastic parathyroid gland tissue

growth_protocol: PTOs were cultured in Matrigel, complete growth medium (parathyroid medium) consisting of 50% conditioned Wnt3a medium, 10% conditioned R-Spondin medium and 40% DMEM:F12 containing B27 (Gibco, 0.5x), HEPES (Gibo, 10 mM), ROCK inhibitor Y-27632 (10 μM, Abcam, Cambridge, UK), Nicotinamide (100 uM, Sigma), FGF-10 (50 ng/mL, peprotech), Noggin (25 ng/mL, Peprotech, NJ, USA), EGF (20 ng/mL, Sigma), TGF-β inhibitor A 83-01 (5 uM, Tocris bioscience), VEGF-121 (10 ng/mL, Immunotools) and Angiotensin (0.1 nmol/mL, Sigma) was added and replaced on a weekly basis.

extract_protocol:
RNA was isolated with the RNeasy Mini Kit (Qiagen, 74104) according to manufacturer’s instructions including DNase I treatment
QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen)

treatment_protocol: dPTOs were treated with Activin A and SHH for 2 weeks.

tag: sample

value: differentiated organoid

tag: culture condition

value: Matrigel

tag: tissue source

value: Hyperplastic parathyroid gland


title: PTO_033

description: Matrigel-cultured organoid derived from hyperplastic parathyroid gland tissue

value: organoid


title: Tissue_031

description: fresh human hyperplastic parathyroid gland tissue

value: tissue


title: Tissue_033


title: dPTO_031


title: PTO_030


title: PTO_031


title: dPTO_030


title: SPT5_1

tag: cell line

tag: treatment

value: Control

value: Anti-DSIF BD (BD611106)

tag: genotype

value: Nelfb deg


title: pHLIP-PNA33

city: New Haven

first: Xinbo

last: Zhang

state: Connecticut

address: Rm320, 10 Amistad St

department: Comparative Medicine

institute: Yale University

data_processing:
Reads were aligned against mouse genome mm9 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R (version 3.0) using Seurat v3. Cells were filtered for more than 500 genes detected in each cell, 20,000 or less total number of molecules detected within a cell and 5% or less mitochondrial gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test, and clusters were calculated with 30 PCs
Differential expression analysis was done using wilcox
Genome_build: mmp9
Supplementary_files_format_and_content: Cell-gene-barcode matrices

source_name: Whole cell

growth_protocol: Age-matched (8-week-old) Ldlr-/- mice were fed a western diet for 3 months to induce atherosclerosis and then transferred to chow diet (CD) for 1 month.

extract_protocol:
Atherosclerotic aorta was digested with 1 mg/ml Collagenase  A for 7 min (Roche, Cat 11088785103) at 37 °C to remove the adventitia under microscope. Aortic tissue  was cut into small pieces and subjected to enzymatic digestion with 1.5 mg/ml Collagenase A and 0.5  mg/ml Elastase (Worthington, Cat LS006365) for 40 min at 37 °C while shaking. Viable  cells were sorted by FACS Aria III (BD Biosciences) with gating on live, single cells using ive/dead viability dye eFluor 450  (Thermo Fisher Scientific).
Cells were captured on a 10x Chromium instrument (10x Genomics, Pleasanton, CA) using the V3 chemistry for 3' whole transcriptome analysis. Manufacturer's instructions for GEM (Gelbead EMulsion) generation, downstream reverse transcription, cDNA isolation, PCR amplification and library preparation were followed without any significant alterations

treatment_protocol: anti-miR-33pHLIP and ScrpHLIP constructs were administered by intravenous injection at a dose of 1 mg/kg body weight in PBS with 5% DMSO. Injections were performed once every week (totally 5 times) during CD feeding before harvest.

tag: strain

value: Ldlr-/-

value: Aorta

value: Western diet for 3 months, transferred to chow diet for 1 month


title: Tissue_030


title: pHLIP-SCR

value: ScrpHLIP


title: Chrna5_KO_treatment_with_imiquimod

city: Jinan

first: Dianhao

address: 6699 Qingdao Road

department: Institute of Basic Medicine

institute: shandong first medical university

description: 7 days' mouse after imiquimod treatment

data_processing:
The samples of KO and WT mice after IMQ treatment were processed in terms of alignment, barcode assignment, and UMI counting with Cell Ranger, version 3.0.2 (https://github.com/10XGenomics/cellranger) count pipeline.
The cell clustering in primary tissues was performed by the R package Seurat (version 3.0, https://satijalab.org/seurat/) involving normalization.
On acquiring the dataset, each sample contained at least 3 cells, cells which have more than 7,500 or less than 500 unique genes were excluded from the analysis. Only genes which were expressed in 10 or more cells were used for further analysis. Cells with a percentage of mitochondrial genes more than 7%, ribosomal RNA genes more than 40%, and log10GenesPerUMI (the gene numbers of per UMI) less than 0.8 were removed from the dataset.
Anchor strategy was used to integrate these datasets, which were produced across multiple technologies. Finding an accurate set of anchors is the basis for subsequent integration analyses. Thus, these datasets were integrated with 2000 anchors, resulting in a batch corrected expression matrix for all cells.
The new integrated matrix was used for scaling and the principal component analysis (PCA). Non-linear dimensional reduction was performed using the Uniform Manifold Approximation and Projection (UMAP) method, with resolution at 0.6.
The cluster biomarkers were also obtained by FindMarkers. Identification of cell clusters was performed using R package Single R.
The keratinocytes were divided into 5 subclusters. Functional Enrichment Analysis of Cell Clusters-Gene Ontology (GO) enrichment analysis of cell clusters was used to identify the biological significance of keratinocytes subcluster3 in the DAVID portal (https://david.ncifcrf.gov/). To identify sample-specific genes, we calculated the expression difference of each gene between the KO and WT samples using “FindMarkers” function of Seurat. The candidate genes with log2FC >=1 and q-value < 0.05 were used for DAVID analyses.
Genome_build: mm10
Supplementary_files_format_and_content: mtx,barcodes, features

source_name: Skin

growth_protocol: In our laboratory, KO mice have been backcrossed with C57BL/6N mice for more than 10 generations, and they have been crossed with heterozygous knockout mice to breed and maintain this pattern; each mouse has been genotyped . Female C57BL/6N mice (6-8 weeks old) were used for imiquimod (IMQ) modeling and follow-up research.

extract_protocol:
C57BL/6J mice back skin after imiquimod treatment were removed, fat scrapped off, and then skin was minced I nto pieces less than 1 mm in diameter. The minced samples were placed in 15-mL conical tubes and digested with 10 mL of collagenase mix [0.25% collagenase (Sigma; C9891), 0.01M HEPES(Fisher; BP310), 0.001M sodium pyruvate (Fisher; BP356), and 0.1 mg/mL DNase (Sigma; DN25)]. Samples were incubated at 37℃for 2 hours with rotation, and thenfiltered through 70-μm and 40-μm filters, spun down, and resuspended in 2% FBS. Cells were stained with SytoxBlue (Thermo Fisher; S34857) as per manufacturer’s instructions and live cells (SytoxBlue-negative) were sorted using BD FACSAria Fusion Sorter.
RNA libraries were prepared for sequencing using standard llumina protocols

treatment_protocol: IMQ cream (5%; 3M Health Care Limited, England) was used externally in the experimental group. The control group received an external application of the cream base（vaseline）. The experimental groups (n=5) were received 62.5 mg IMQ cream on the backs of the shaved mice for 6 consecutive days, and they were euthanized on the 7th day.

value: dorsal skin

value: imiquimod treatment


title: WT_treatment_with_imiquimod

description: 7 days' mouse after imiquimod treatment


title: MS4_CD14

type: genomic

city: Moscow

first: Ivan

middle: S

last: Kiselev

address: Ostrovitianov st. 1

country: Russia

institute: Pirogov Russian National Research Medical Universitty

description: CD14 MicroBeads, human (Miltenyi Biotec)

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: Probes containing single nucleotide polymorphisms within 10 bp of the CpG-site and probes overlapping with repeat DNA elements within 15 bp of the CpG-site were excluded from the analysis. Probes with a detection p-value greater than 0.05 in more than 5% of samples and probes located on the X and Y chromosomes were also excluded.

source_name: CD14+ monocytes

label_protocol: Standard Illumina protocol

extract_protocol: Cells were extracted using CD14 microbeads (Miltenyi Biotec). DNA was prepared using QIAamp DNA Mini Kit (Qiagen)

tag: group

value: relapsing-remitting MS, remission

tag: Sex

value: male


title: MS6_CD14


title: MS1_CD14

value: female


title: RasVal cells_IPTG (+) ZnCl2 (+)

status: Public on Feb 27 2022

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

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

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

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

organism: Rattus norvegicus

source_name: RasVal cells_IPTG (+) ZnCl2 (+)

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

growth_protocol: Rat-1·RasValA1 cells were routinely cultured in DMEM supplemented with 10% FBS, G418, and hygromycin B. Twenty-four hours before RNA collection, the medium was replaced with DMEM supplemented with 0.1% bovine serum albumin, from which FBS, G418, and hygromycin B were omitted.

extract_protocol: Total RNA was extracted with TRIzol.

treatment_protocol: Rat-1·RasValA1 cells were treated with or without 5 mM IPTG in serum-free DMEM supplemented with or without 3 microM ZnCl2 for 24 h.

tag: stable cell line

value: Rat-1·RasValA1, where HrasG12V expression is governed by an IPTG-inducible promoter

tag: iptg-induced expression of hrasg12v

value: plus

tag: zncl2 addition to serum-free dmem


title: MS5_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)

source_name: CD4+ T lymphocytes

extract_protocol: Cells were extracted using CD4 microbeads (Miltenyi Biotec). DNA was prepared using QIAamp DNA Mini Kit (Qiagen)


title: MS3_CD14


title: MS3_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: HC1_CD14

value: Healthy control


title: RasVal cells_IPTG (-) ZnCl2 (+)

source_name: RasVal cells_IPTG (-) ZnCl2 (+)

value: minus


title: HC4_CD14


title: MS5_CD14


title: HC2_CD14


title: HC6_CD14


title: HC7_CD14


title: HC8_CD14


title: MS2_CD14


title: HC3_CD14


title: HC6_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: RasVal cells_IPTG (+) ZnCl2 (-)

source_name: RasVal cells_IPTG (+) ZnCl2 (-)


title: HC2_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: RasVal cells_IPTG (-) ZnCl2 (-)

source_name: RasVal cells_IPTG (-) ZnCl2 (-)


title: MS1_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: MS4_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: MS2_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: HC5_CD14


title: Normal culture condition zur KO rep 1

status: Public on Feb 26 2022

city: Tuebingen

first: Mehmet

middle: Direnc

last: Mungan

address: Auf der Morgenstelle, 28

institute: University of Tuebingen

description:
16c02
24_wt_vs_zurko_features.txt

data_processing:
Real-Time Analysis (RTA v2) software is used for basecalling.
Corresponding fastq files trimmed and filtered by fastp, mapped by Hisat2 with default parameters with –no-spliced-alignment option set and the BAM files were generated via samtools. Read count per gene is summarized by featureCounts and differentially expressed genes were generated by DESeq2 package.
Genome_build: GCF_000732925.1_ASM73292v1
Supplementary_files_format_and_content: Matrix of raw read counts for each gene (Geneid Chr Start End Strand Length protein_id product SAMPLES) for each sample in two different experiments (6 samples in each experiment). Each experiment has two different conditions and each condition has 3 replicates.

organism: Amycolatopsis japonica

source_name: Amycolatopsis Japonica

growth_protocol: Amycolatopsis japonicum wildtype and A. japonicum Δzur were cultured in baffled, EDTA-treated flasks according to Zwicker et al. (1997) for the whole experiment. For the seed-culture the strains were grown in 100 ml of complex culture medium consisting of 20 g/L glycerol and 20 g/L soy flour at pH 7.5. After 48 h of growth, 5 ml of the seed-culture were used to inoculate 100 ml of the production medium containing 25 g/L glycerol, 1.2 g/L MgSO4 x 7 H2O, 60 mg/L ferric(III)citrate, 8 g/L KH2PO4, 12 g/L Na2HPO4 x 2 H2O and 11.3 g sodium glutamate monohydrate. For RNA analyses the strains were grown for 24 h, in production medium containg zinc or no zinc . All liquid cultures of A. japonicum were grown on a rotary shaker (120 rpm) at 27 °C. RNA experiments were performed in triplicates.

extract_protocol:
RNA was isolated as described in Frasch et al. (2015)
RNA libraries were prepared for sequencing using standard Illumina protocols according to NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: For cultivation in the presence of zinc, zinc sulfate to a final concentration of 6 µM was added to the production medium

tag: hour

value: Cell line at 24 hours

tag: condition

value: Normal culture condition

value: zur-KO


title: Normal culture condition zur KO rep 3

description:
16c04
24_wt_vs_zurko_features.txt


title: ZINC treated culture condition zur KO rep 3

description:
16d05
zn24_wt_vs_zurko_features.txt

value: ZINC treated culture condition


title: HC5_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: HC8_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: ZINC treated culture condition zur KO rep 2

description:
16d02
zn24_wt_vs_zurko_features.txt


title: HC4_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: HC7_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: HC3_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: Normal culture condition WT rep 3

description:
16a03
24_wt_vs_zurko_features.txt

value: WT


title: HC1_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)


title: ZINC treated culture condition zur KO rep 1

description:
16d01
zn24_wt_vs_zurko_features.txt


title: er_erl2_MOCK_rep2

status: Public on Feb 25 2022

city: Knoxville

first: Elena

middle: D

last: Shpak

state: Tennessee

address: 1311 Cumberland Ave

department: BCMB

institute: University of Tennessee

data_processing:
Base calling was performed with RTA3 and bcl2fastq
Reads were aligned using STAR 2.7.6a intron size was set to 15000nt
Reads were counted using featureCounts 2.0.0 at the meta feature (gene) level, chimeric reads and multimapping reads were filtered out
Genome_build: TAIR10.1 (Genome) Araport 11 (Reference)
Supplementary_files_format_and_content: Processed data file is a matrix containing the raw gene level counts for each sample. Each row is a gene (AGI) and each column is a sample.

organism: Arabidopsis thaliana

source_name: er erl2

growth_protocol: Three-day-old post germination WT (Col-0) or mutant (er-105 erl2-1) seedlings grown on MS solid medium were acclimated to MS liquid media for 30 min before treatment.

extract_protocol:
Total RNA for library construction was extracted using a Spectrum Plant Total RNA Kit (Sigma). RNA quality was assessed using an Agilent 4200 TapeStation.
Total RNA was poly-A selected and stranded libraries were constructed using a NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Plants were treated for 30 minutes with either mock (0.02% DMSO) or 1uM IAA (0.02% DMSO). Refer to individual samples.

tag: age

value: 3 DAG

tag: tissue

value: whole seedling

value: er erl2

tag: ecotype

value: Mock (0.02percent DMSO)


title: Normal culture condition WT rep 1

description:
16a01
24_wt_vs_zurko_features.txt


title: er_erl2_IAA_rep3

value: 1uM IAA (0.02percent DMSO).


title: er_erl2_IAA_rep2


title: Normal culture condition WT rep 2

description:
16a02
24_wt_vs_zurko_features.txt


title: er_erl2_MOCK_rep1


title: MS6_CD4

description: CD4 MicroBeads, human (Miltenyi Biotec)

value: relapsing-remitting MS, remission


title: WT_IAA_rep3

value: wildtype


title: Normal culture condition zur KO rep 2

description:
16c03
24_wt_vs_zurko_features.txt


title: WT_IAA_rep2


title: er_erl2_IAA_rep1


title: Yaa TCRseq- sorted CD4 and CD8 TCR sequences

status: Public on Feb 24 2022

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

description: CD4+ and CD8+ T cell_Kidney_Rep2

data_processing:
The 10x raw data from each sample were demultiplexed and FASTQ files were generated using the “mkfastq” Cell Ranger pipeline (v5.0.0, 10X Genomics).
Cell Ranger “count” was used to align reads to the mm10 reference genome, and mRNA transcript, and HTO unique molecular identifier (UMI) quantification tables were generated.
The raw barcode matrix files generated from the Cell Ranger pipeline were further utilized for downstream analysis using the Seurat package (v4.0.0) in R (v3.4.3).
Genome_build: Mus musculus reference genome (mm10).
Supplementary_files_format_and_content: Raw count output file from Cellranger.

source_name: Kidney

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
10X Genomics Chromium system (5' V1)
RNA libraries were prepared for sequencing using standard Illumina protocols, using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takata Cat# 634894).

treatment_protocol: Cells were isolated from tissue (spleen or kidney), surfaced stained using antibodies for flow cytometry, and sorted on BD FacsAria for CD90+ CD4+ or CD90+ CD8+ cells

value: Kidney

tag: cell type

value: CD4+ and CD8+ T cell


title: ZINC treated culture condition WT rep 2

description:
16b02
zn24_wt_vs_zurko_features.txt


title: MRL-TCRseq- sorted CD4 and CD8 TCR sequences

description: CD4+ and CD8+ T cell_Kidney_Rep1

value: MRL/lpr (MRL.Faslpr)


title: WT_MOCK_rep3


title: WT_IAA_rep1


title: WT_MOCK_rep2


title: WT_MOCK_rep1


title: ZINC treated culture condition WT rep 1

description:
16b01
zn24_wt_vs_zurko_features.txt


title: B_ACY_3

status: Public on Feb 23 2022

city: Tampa

first: Dennis

last: Adeegbe

state: FL

address: 13131 USF Magnolia Drive

department: Immunology

institute: Moffitt Cancer Center

data_processing:
Raw data (reads) of FASTQ format were first processed to obtain clean reads by removing adapters, poly-N sequences and reads with low quality. The STAR aligner (v2.6.1) was then utilized to align the data to the mouse reference genome mm10, (Ensemble gene annotations).
FeatureCounts (v1.5.0) was used to count the read numbers mapped of each gene and Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene (21).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts matrix with gene names
Supplementary_files_format_and_content: FPKM gene expression matrix with gene names

source_name: ACY241-treated tumor TAMS

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
The library preparations were sequenced on an Illumina NextSeq 2000 platform and paired-end reads were generated.

treatment_protocol: KP mice were treated i.p. with ACY241 (25 mg/kg body weight) 3x/week for three weeks. Control mice received vehicle (5% DMSO in 10% 2-hydroxylpropyl β-cyclodextrin)

tag: disease state

value: mouse model of non-small cell lung cancer

value: Kras+/LSL-G12D; Trp53L/L

value: Lung adenocarcinoma

value: TAMS


title: B_ACY_1


title: Main seq- sorted CD4 and CD8 T cells

description: CD4+ and CD8+ T cell_Kidney, Spleen_Rep1

source_name: Kidney , Spleen

value: MRL/lpr (MRL.Faslpr) and C57/Bl6

value: Kidney, Spleen


title: ZINC treated culture condition WT rep 3

description:
16b03
zn24_wt_vs_zurko_features.txt

value: Cell line at 24 hours

value: ZINC treated culture condition

value: WT


title: Yaa-TCRseq- sorted CD4 and CD8 T cells GEX

description: CD4+ and CD8+ T cell_Kidney_Rep3


title: B_Vehi_3

source_name: Vehicle-treated tumor TAMS

value: Vehicle


title: B_ACY_2


title: B_Vehi_2


title: er_erl2_MOCK_rep3

value: 3 DAG

value: whole seedling

value: er erl2

value: Mock (0.02percent DMSO)


title: A_Vehi_2

source_name: Vehicle-treated tumor T cells

value: T cells


title: A_ACY_1

source_name: ACY241-treated tumor T cells


title: B_Vehi_1


title: A_ACY_3


title: A_Vehi_1


title: DSK30_13monthJ147

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Reads were mapped to mm10 reference genome by STAR v2.5.3a with default parameters. Only uniquely mapped reads were considered for downstream analysis.
RNA-Seq gene expression was quantified by HOMER analyzeRepeats command, summing reads mapped across all gene exons of RefSeq genes. Mitochondria encoded genes were quantified by HOMER using Ensembl reference.
RNA-Seq differential expression was carried out using DESeq2 v1.18.1 on the raw counts of replicates. FDR < 0.05 and  absolutelogFC > 0.5 was used as cutoff to identify the DE genes.
Genome_build: mm10
Supplementary_files_format_and_content: SAMP8_liver147_Total_exons_MT.raw.xlsx; raw count gene expression table

source_name: SAMP8 mice liver tissue

growth_protocol: All experiments with the SAMP8 animals were performed in accordance with the US Public Health Service Guide for Care and Use of Laboratory Animals and protocols approved by the IACUC at the Salk Institute.

extract_protocol:
RNA from mouse liver was isolated using the RNeasy Plus Universal mini kit (Qiagen).
RNA-seq libraries were performed using stranded mRNA kit from Illumina and sequenced in an Illumina HiSeq 2500 device.

treatment_protocol: Mice were fed control diet or diet containing J147 for 4 months.

value: liver

value: 13 month


title: BC308_PBMC

city: Duarte

middle: P

last: Lee

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

institute: Beckman Research Institute at City of Hope

description: BD Precise Platform

data_processing:
The raw counts were imputed by scImpute R package (v0.0.7) with kcluster = 5.
The imputed counts were analyzed by Seurat R package (v3.1.4). Briefly, nonviable cells (defined as the cells in which more than 20% expressing genes are mitochondrial genes) were removed. In addition, the potential empty well or duplets (defined as cells in which less than 200 genes are expressed or more than 2500 genes are expressed, respectively) were also discarded for further analysis
The normalization was implemented by Seurat with default settings.
The top 1,000 most variable protein-encoding genes were selected for principle component analysis. Based on the two heuristic methods in Seurat (modified Jack Straw procedure and ranking variance method), the top 12 principal components were used for the further non-linearly dimensional reduction (i.e., tSNE) and clustering analysis.
Genome_build: hg18
Supplementary_files_format_and_content: Both raw counts and imputed counts were provided here with the meta-data table for each cell

source_name: CD8+ T cells from PBMC

extract_protocol:
CD8+ T cells were stained with monoclonal antibodies for CD8, PD-1, CD39, CD103, CD69, CD137, and CCR7 as described above and then single-cell index sorted using a BD ARIA III FACS system into BD Genomics Precise WTA 96 well plates for whole transcriptome analysis.
Single-cell libraries were prepared as recommended.

value: PBMC

tag: patient


title: DSK29_13monthJ147


title: BC308_Tumor

description: BD Precise Platform

source_name: CD8+ T cells from tumor

value: Tumor


title: DSK28_13monthJ147


title: DSK27_13monthJ147


title: DSK9_13month

value: control


title: DSK11_13month


title: DSK6_9month

value: 9 month


title: DSK4_9month


title: DSK5_9month


title: DSK8_13month


title: DSK2_9month


title: DSK26_13monthJ147


title: MRL-TCRseq- sorted CD4 and CD8 T cells GEX

description: CD4+ and CD8+ T cell_Kidney_Rep2

value: MRL/lpr (MRL.Faslpr)

value: Kidney

value: CD4+ and CD8+ T cell


title: DSK25_13monthJ147


title: MAC-T cells, S3.Input

city: Wuhan

first: Changmin

last: Hu

state: Hubei

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

description: CircRNA Expression Profiling.xlsx

data_processing:
After paired-end sequencing, raw circRNA data were obtained. According to Q30 for quality control, cutadapt software (v1.9.3) was used to obtain high-quality reads.
STAR software (v2.5.1b) was used to compare high-quality reads to the reference genome/transcriptome (bosTau9)
DCC software (v0.4.4) was used for circRNA detection and identification.
The circBase database and Circ2Traits were used to annotate the identified circRNA.
edgeR software (v3.16.5) was used for data standardization and differential expression circRNA screening (fold change>=1.5, P value <= 0.05).
Genome_build: bosTau9
Supplementary_files_format_and_content: Excel format (Number of raw junction reads)

organism: Bos taurus

source_name: MAC-T cells

growth_protocol: MAC-T were cultured in DME/F12 medium (Hyclone, China) with 10% fetal bovine serum (Gibco, United States), which incubated at 37℃ in 5% CO2. The cells were digested and passed by 0.25% trypsin - 0.02% EDTA solution.

extract_protocol:
Total RNA of the above 9 samples was extracted according to the instructions of the commercial reagent manufacturer and the RNA isolation steps. A NanoDrop ND-1000 instrument (Agilent Inc. USA) was used to measure RNA concentration and purity, and the quality control index of RNA purity was based on the OD260/OD280 value between 1.8-2.0. Denaturing agarose gel electrophoresis was used to measure RNA integrity and gDNA contamination. The sample was stored at -80 °C for later use.
Nine samples under different treatments were sent to Cloud-Seq Biotech (Shanghai, China) for MeRIP-CircRNA sequencing. The operation was briefly described as follows: 1) To enrich circRNA, a circRNA Enrichment Kit (Cloud-seq, USA) was used according to the supplier's instructions. 2) An NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) was used to pretreat RNA, and a sequencing library was constructed by immunoprecipitation. 3) Quality control and quantification of the library were performed with the BioAnalyzer 2100 system (Agilent Technologies, USA), and the Illumina HiSeq instrument was used to perform 150 bp paired-end sequencing.

treatment_protocol: MAC-T cells were seeded in 6-well plates (Corning, US) at a density of 2×10^5 cells/well. After 12 h of culture, inactivated bacteria were added at an MOI of 10:1. Inactivated bacteria and cells were cocultured for 24 hours.

value: bovine mammary epithelial cells (MAC-T cells)

value: S. aureus

tag: ip fraction

value: Input

tag: rna fraction

value: total RNA


title: DSK3_9month

tag: treatment


title: MAC-T cells, S2.IP

value: Me-RIP

value: m6A RNA


title: MAC-T cells, S2.Input

description: CircRNA Expression Profiling.xlsx


title: A_ACY_2

value: mouse model of non-small cell lung cancer

tag: genotype

value: Kras+/LSL-G12D; Trp53L/L

value: Lung adenocarcinoma


title: MAC-T cells, S3.IP


title: DSK10_13month

value: liver

tag: strain

value: 13 month


title: MAC-T cells, S1.IP


title: MAC-T cells, E3.Input

description: CircRNA Expression Profiling.xlsx

value: E. coli


title: DSK1_9month

value: control


title: A_Vehi_3

value: T cells

value: Vehicle


title: MAC-T cells, E1.IP


title: MAC-T cells, E2.IP


title: MAC-T cells, E2.Input

description: CircRNA Expression Profiling.xlsx


title: DSK12_13month


title: MAC-T cells, C3.Input

description: CircRNA Expression Profiling.xlsx

value: untreated


title: MAC-T cells, C1.IP


title: MAC-T cells, C2.IP


title: MAC-T cells, C3.IP


title: MAC-T cells, C2.Input

description: CircRNA Expression Profiling.xlsx


title: SKBR3_pROR2_3

status: Public on Feb 21 2022

city: Göttingen

first: Darius

last: Wlochowitz

address: Goldschmidtstr. 1

department: Bioinformatics

institute: Institute of Bioinformatics

description: RNA_Seq_featureCount_counts_BT474_SKBR3.csv

data_processing:
Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1.8.2.  RNA sequencing data were first quality checked via FastQC (Babraham Bioinformatics). For MCF-7 the reads were then mapped against the reference genome GRCh38 with the STAR RNA-Seq alignment tool and gene-level abundances were estimated using the RSEM algorithm. For SK-BR-3 and BT-474 cells sequence reads were aligned with the reference genome GRCh38 using the HISAT2 (v2.1.0) alignment tool, while incorporating database information from Ensembl (v38.87) during the reference indexing step.   Gene-level abundances were estimated using featureCounts (v1.6.3).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with gene-level counts for every sample

source_name: SK-BR-3 cells

growth_protocol: MCF-7 and SK-BR-3 cells were cultured in RPMI-1640, BT-474 cells in DMEM/F12, all supplemented with 10% heat-inactivated (56°C, 30 min) fetal calf serum (FCS).

extract_protocol:
Total RNA was isolated with the Trizol reagent for MCF-7 cells and with the High Pure RNA isolation kit (Roche) for BT-474 and SK-BR-3 cells. RNA concentration was measured at the Nanodrop ND-1000 and RNA integrity was checked with the Bioanalyzer 2100 (Agilent).
For MCF-7 cells, library preparation for RNA-Seq was performed using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) starting from 1,000 ng of total RNA. For SK-BR-3 and BT-474 cells libraries for RNA-Seq were prepared with the NEBNext Ultra RNA II directional kit including NEBNext mRNA enrichment. RNA and library quality control was checked by TapeStation (Agilent).

treatment_protocol: To achieve gene overexpression, cells were transfected with Fugene HD transfection reagent (Promega) and stable clones generated by geneticin or zeocin selection (750 µg/ml or 100 µg/ml, respectively).  For siRNA-mediated gene knockdown, cells were transfected with 10 nM siRNA (santa cruz) using the RNAimax transfection reagent (Invitrogen). Cells were used 72h post transfection for expression analysis.

value: SK-BR-3 (DSMZ, ACC 736)

value: mammary gland, breast adenocarcinoma; derived from a pleural effusion

value: epithelial

value: SK-BR-3 human breast cancer cells were transfected with a hROR2 overexpression plasmid (pROR2).


title: SKBR3_pROR2_1


title: MAC-T cells, S1.Input

description: CircRNA Expression Profiling.xlsx

value: bovine mammary epithelial cells (MAC-T cells)

value: S. aureus

value: Input

value: total RNA


title: BT474_pROR2_1

source_name: BT-474 cells

value: mammary gland, ductal carcinoma

value: BT-474 human breast cancer cells were transfected with a hROR2 overexpression plasmid (pROR2).


title: BT474_pcDNA_1

value: BT-474 human breast cancer cells were transfected with an empty vector (pcDNA).


title: SKBR3_pcDNA_1

value: SK-BR-3 human breast cancer cells were transfected with an empty vector (pcDNA).


title: BT474_pcDNA_2


title: BT474_pcDNA_3


title: SKBR3_pcDNA_3


title: SKBR3_pcDNA_2