title: Nebulized_FLAMOD_24h_N_biol_rep4

city: LILLE

first: Florence

last: MAURIER

address: 1 rue du Professeur Calmette BP 245

department: Plateformes Lilloises en Biologie & Santé

institute: Institut Pasteur de Lille

description: Library name: Library-334

data_processing:
Genome index was generated using genome Sus_scrofa.Sscrofa11.1 and annotation file Sus_scrofa.Sscrofa11.1.113.gtf through STAR-2.7.10a (sjdbOverhang 149)
Sequence reads were mapped to generated genome using STAR-2.7.10a (-quantMode using bidirectional input (R1/R2))
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: ReadsPerGene.out.tab file with four columns (gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA)  was generated by STAR for each sample
Supplementary files format and content: TAB files include read counts for each sample (only first two columns were used :Gene ID and read counts for unstranded RNA-seq)

organism: Sus scrofa

source_name: Nasal

growth_protocol: Twelve male six-week-old pigs (Sus scrofa domestica, line LRxLW TOPIGS 20, Lelystad) were randomized in an unbiased manner by the animal caretakers. Four animals were allocated to each of the three experimental groups, i.e. group 1 exposed to buffer solution and followed for 24 h, group 2 exposed to FLAMOD for 4 h and group 3 exposed to FLAMOD for 24 h.

extract_protocol:
Nasal, tracheal, bronchial, lung tissues and blood samples were collected for RNA extraction and sequencing. Tissues were preserved in NucleoProtect® RNA (Macherey-Nagel, Duren, Germany) at -80°C until ready for processing. Tissue was dried on paper towels and any visible cartilage was removed. The remaining tissue was weighed and depending on size of tissue was added to 1-3 ml RA1 lysis buffer (Macherey-Nagel) supplemented with 2% TCEP (Sigma) and disintegrated with an UltraTurrax homogenizer (IKA-Werke, Staufen, Germany). For nasal, bronchial and tracheal samples, a pretreatment with proteinase K was performed to remove collagen. Briefly, 350 l of lysate was added to 595 l water substituted with 10 l proteinase K (20 mg/ml) and incubated at room temperature for 10 min, followed by 10 min incubation at 55 °C and centrifugation at 10,000 rpm for 3 min. The supernatant was then mixed with 490 l of 100% ethanol and the mixture was loaded onto the NucleoSpin® RNA Plus extraction kit columns, and RNA was extracted as per manufacturer’s instructions (Macherey-Nagel) and eluted in 30 l RNAse-free water. Lung samples were eluted in 60 l RNAse-free water.
RNA libraries for RNA-seq were prepared using QIAseq stranded mRNA library kit (Qiagen) as well as QIAseq FastSelect-Globin Kit for blood samples (Qiagen). 200 ng of total RNA.

treatment_protocol: Aerosol administration (at day 0 in the morning): pigs were transferred to a separate room, anaesthetized by intramuscular injection with a mixture of Tiletamine-Zolazepam (Zoletil®250, 50 mg/ml, Virbac) and Xylazinehydrochloride (Sedaxylan® 20mg/ml, Dechra, NL) at 0.1 ml/kg and then laid into a half pipe in sternal position. Aerosol was administered using the Aerogen® Solo nebulizer in combination with the Aerogen® ProX controller system coupled to a mask specially adapted to pig snout. Briefly, a standard animal mask with rubber face seal was modified to incorporate 1-way valves to ensure unidirectional inhalation and exhalation through the mask. Filters were placed at entry and exit ports in order to eliminate the risk of environmental exposure from aerosolized FLAMOD. The Aerogen® Solo nebuliser was combined with the Aerogen 22 mm T-piece and included in the mask. On inhalation, the aerosol was entrained in the inspiratory flow and delivered to the respiratory tract. On exhalation, the exhaled volume passed out the dedicated exhalation 1-way valve only. Aerosol was continuously generated throughout the treatment, but as exhalation was via a single port, remote from the nebuliser, a bolus of aerosol was generated and available for inhalation immediately on the next breath. Previous studies in pigs using this mask indicate that approximately 30% of the nominal dose placed in the nebuliser is delivered to the lung [25]. The aerosol was produced from 1 ml of the FLAMOD-containing solution at a concentration of 1.5 mg/ml, while the control animals received 1 ml of the diluent buffer; the aerosol exposure time per animal was 5 minutes.

tag: tissue

value: Nasal

value: LRxLW TOPIGS 20

value: Flagellin

tag: animal id

tag: time


title: TV, agit, no antiox, rep2

status: Public on Feb 19 2025

type: SRA

city: Golden

first: Davinia

last: Salvachua

state: CO

address: 15013 Denver West Parkway

country: USA

institute: National Renewable Energy Laboratory

library_source: transcriptomic

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read-trimming was conducted using bbduk (http://jgi.doe.gov/data-and-tools/bb-tools/) with parameters trimq=10, qtrim="rl", maq=10.
Reads were aligned to the Trametes versicolor and Gelatoporia subvermispora genomes using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). using parameters -local, --sensitive-local
Aligned reads were mapped to genes using htseq-count (https://pubmed.ncbi.nlm.nih.gov/25260700/) with parameters -a=1, --mode="union".
Assembly: Trametes versicolor genome https://www.ncbi.nlm.nih.gov/assembly/GCF_000271585.1/
Assembly: Gelatoporia subvermispora genome https://www.ncbi.nlm.nih.gov/assembly/GCA_000320605.2/
Supplementary files format and content: read counts per gene

molecule: total RNA

organism: Trametes versicolor

growth_protocol: For fungal strain maintenance, we developed a minimal and defined medium which is an adapted version of Czapek-Dox medium (CDM). CDM consists of 2 g ammonium tartrate (Sigma-Aldrich, St. Louis, MO), 0.5 g MgSO4 x 7H2O (Fisher Scientific, NJ, USA), 1 g KH2PO4 (Sigma-Aldrich, St. Louis, MO), 0.5 g KCl (Sigma-Aldrich, St. Louis, MO), 1 mL sterile vitamins supplement (ATCC® MD-VS™), and 1 mL trace elements solution per liter in H2O. The trace elements solution contains 0.1 g Na2B4O7 x 10H2O (Sigma-Aldrich, St. Louis, MO), 0.07 g ZnSO4 x 7H2O (Sigma-Aldrich, St. Louis, MO), 0.01 g CuSO4 x 5H2O (Sigma-Aldrich, St. Louis, MO), 0.01 g MnSO4  x 4H2O (Sigma-Aldrich, St. Louis, MO), 0.05 g FeSO4 x 7H2O (Fisher Scientific, NJ, USA), and 0.01 (NH4)6MoO2 x 4H2O (Fluka, NC, USA) per liter in H2O. Trace element solution was filter sterilized through 0.2 µM PES filters (Millipore, MA, USA) and added after autoclaving (30 min at 121°C) of the rest of the CDM components. For seed culture preparation, an agar plug with fungal mycelia was taken from agar plates maintained at 4°C, deposited in the center of an YMPG agar plate, and incubated for 7 days at 28°C. Then, 4-5 agar plugs with mycelia were inoculated in 50 mL of liquid YMPG and incubated at 220 rpm and 28°C for 7 days (pre-seed). Fungal pellets were then homogenized (10 s, speed 6) in sterile conditions using an Omni Mixer 115V with a 50 mL SS Chamber PTFE (Omni International, GA, USA). The fungal suspension (2 mL) was re-inoculated in YMPG under the same conditions than the pre-seed culture and incubated for 5 days. A ratio of 2:25 (v:v) of further homogenized fungal suspension per media volume was used to inoculate the cultivations.

extract_protocol:
Frozen fungal cultures (100-200 mg) were transferred to a pre-chilled mortar and ground to a fine powder in liquid nitrogen.  The liquid nitrogen was allowed to evaporate and the sample was transferred to a pre-chilled 15 mL centrifuge tube. All steps were performed on dry ice to ensure samples remained frozen. RLT buffer (700 µL)(Qiagen) containing 10% β-mercaptoethanol was added to the frozen samples and the samples were allowed to thaw with periodic vortexing at high speed. Samples were vortexed at high speed continuously for 1 min or until the sample was completely homogenous. Samples were transferred to a QIAshredder column (Qiagen) and processed using the RNeasy mini kit and subjected to DNase gDNA digestion according to the manufacturers protocol (Qiagen). The RNA samples are assessed using the Agilent 2100 Bioanalyzer, RNA with RIN >7 proceed with cDNA library.
TruSeq Stranded Total RNA (cat#20020596) is used to generate cDNA library for illumina NextSeq550 platform according to the manufacture protocol.

treatment_protocol: T. versicolor and G. subvermispora cultivations were conducted in 250 mL flasks containing 25 mL of Czapek-Dox medium (CDM) with cellobiose (15 mM). Cultivations were incubated at 28°C in either agitation (220 rpm) or static conditions using a humidity-controlled incubator (˃50 % humidity). After 6 and 10 days of incubation with T. versicolor and G. subvermispora, respectively, we induced all the cultivations with 4-HBA (~2 mM) from a 4-HBA stock solution of xxx. Antioxidants (5 mM ascorbic acid and 1 mM α-tocopherol), and prepared as previously described,6 were also added in the media 30 min before the induction in half of the cultivations incubated in either static or agitation conditions. Cultivations were harvested 24 h after the induction, corresponding to 7 days and 11 days for T. versicolor and G. subvermispora, respectively.

tag: strain

tag: growth medium

value: Czapek-Dox medium w/15mM cellobiose

tag: treatment

value: agitation 220 rpm

tag: culture temperature

value: 28 deg C

tag: incubation time

value: 6 days

value: 2 mM HBA

tag: additional incubation

value: 24 hours


title: retinal organoid, knockout, vehicle treated, rep4

city: London

first: Michael

last: Cheetham

address: 11-43 Bath St

department: Institute of Ophthalmology

country: United Kingdom

institute: University College London

data_processing:
FastQC 0.12.1 to check for sequence quality and adaptor contamination
BBDuk (from BBMap 39.01) to trim Illumina TruSeq adaptors from samples with adaptor contamination (options ‘ktrim=r, k=23, mink=12, hdist=1, tpe, tbo’)
Decoy-aware Gencode v44 hg38 index generated with Salmon 1.10.2, using the entire genome as decoy sequence
Trimmed sequences underwent transcript quantification with Salmon 1.10.2 in mapping-based mode (options ‘--validateMappings --gcBias --numBootstraps 30')
Salmon quantification results imported directly into DESeq2 1.40.2 with tximeta 1.18.3
Assembly: Hg38
Supplementary files format and content: Each sample has a tab-delimited quant.sf file containing information on transcript length, TPM, and number of reads for each transcript

molecule: polyA RNA

organism: Homo sapiens

source_name: retinal organoids

growth_protocol: iPSCs were grown in 6-well plates coated in Geltrex and in (Essential 8™ Flex Medium) and when they reached about 90-95% confluency, Essential 6 medium was added for two days (Day 0 and Day 1 of differentiation). At Day 2, cells were maintained in Neural induction medium (NIM) (Advanced DMEM/F-12 (1:1) supplemented with 1% N2 supplement (100X), 100  mM Glutamine and 100 U/m penicillin/streptomycin. On Day 6, 1.5 nM bone morphogenetic protein 4 (BMP4 R&D Systems) was added to fresh NIM and half media changes were performed every other day until Day 16. Neuroretinal vesicles (NRVs) started to form between (2-4 weeks) and when they were fully defined, they manually dissected and /or checkerboarded, transferred to 96 ultra - low attachment plates and cultured in retinal differentiation medium (RDM) (DMEM/F12 nutrient mix (3:1 ratio), 10% fetal bovine serum (FBS), 2% B27 supplement (without vitamin A), 2 mM GlutaMAX and 100U/ml penicillin/streptomycin) for 6 days. At D30 medium was changed to Retinal maturation media 1 (RMM1) (DMEM/F12 nutrient mix (3:1 ratio), 10% fetal bovine serum (FBS), 2% B27 supplement (without vitamin A), 100uM taurine (Tocris Bioscience), 2 mM GlutaMAX and 100U/ml penicillin/streptomycin). From Day 50-70, medium was supplemented with 1  μM Retinoic Acid (RA) which was added fresh in every media change and from Day 70 RA was reduced to 0.5  μM and 1% N2 supplement was added to the media (RMM2). From Day 100, RA and B27 were removed from media (RMM3) and retinal organoids were transferred in 25 cm dishes until collection.

extract_protocol:
Control and LCA5 KO retinal organoids were processed for RNA extraction using an RNeasy MicroKit (QIAGEN)
cDNA synthesis was performed using a Tetro cDNA synthesis kit (Bioline)

treatment_protocol: Retinal organoids were treated from D190-D220 with either vehicle (DMSO), eupatilin (Adipogen) (10  μM), fasudil hydrochloride (Cell Guidance Systems (SM-49) (5  μM) or a combination of eupatilin (10  μM) and fasudil (5  μM) (FAS/EUP). Drug treatments were carried out at routine media changes with RMM3, three times per week.

tag: cell line

value: retinal organoids

tag: genotype

value: homozygous LCA5 KO

value: Vehicle (DMSO) treated

tag: age

value: 220 days old


title: Nebulized_FLAMOD_24h_N_biol_rep2

country: France

description: Library name: Library-332


title: HIC_R377C_ID_rep1

city: new york

first: Jane

middle: A

last: Skok

state: NEW YORK

address: Smilow Research Center, Third floor, Room 307, 522 First Avenue

department: Pathology

institute: NYU

description:
HIC_R377C_ID_rep1
HIC_R377C_ID_rep1_rep2_10kb.matrix
HIC_R377C_ID_rep1_rep2_10kb_abs.bed

library_source: genomic

data_processing:
HiC-Pro (and bowtie2) was used to align and filter the Hi-C data.
Alignemnet was performed using local mode for the second step of HiC-Pro alignment (--very-sensitive -L 20 --score-min G,20,8 --local) to ignore the molecular barcode UMI sequences and dark bases introduced by Arima library prep kit at the 5’ end of the read. Singleton, ambiguous and duplicated reads were filtered out.
Ligation sites for Arima HiC kit were set up using GATCGATC,GANTGATC,GANTANTC,GATCANTC. Low mapping quality (MAPQ<30), self circle, dangling ends and re-ligation reads were filtered out through the HiC-pro pipeline.
Samples were downscaled to the same number of good quality uniquely aligned reads using HiCExplorer. Of note, we did not use the number of valid pairs to downscale the samples to not overcorrect some conditions such as IAA and mutant H455R which were expected to show a dramatic biological decrease in valid interactions.
After downscaling, replicates were merged and interaction matrices were generated using Hic-pro.
Assembly: mm10
Supplementary files format and content: Hic-pro matrices and bin files (bed)  generated at 10 kb resolution for each condition

molecule: genomic DNA

organism: Mus musculus

source_name: mESC

growth_protocol: Mouse embryonic stem cells E14Tg2a and all clones derived from these were cultured under feeder-free conditions in 0.1% gelatin coated dishes at 37°C and 5% CO2 in a humidified incubator. The cells were grown in DMEM supplemented with 15% fetal bovine serum , 100 U/ml penicillin - 100 μg/ml streptomycin, 1 X GlutaMax supplement, 1 mM sodium pyruvate, 1 X MEM non-essential amino-acids, 50 μM b-mercaptoethanol, 104 U/ml leukemia inhibitory factor, 3 μM CHIR99021 and 1 μM MEK inhibitor PD0325901. The cells were passaged every alternate day by dissociation with TrypLE.

extract_protocol:
Hi-C was performed using around 1 million cells each. mESCs were dissociated using TrypLE. Cells were  double cross linked using 25mM EGS (ethylene glycol bis(succinimidyl succinate)) followed by 1% formaldehyde.
Samples were subsequently processed using the Arima Hi-C kit as per the manufacturer's protocol and sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 600 million 150bp paired-end reads per sample.

treatment_protocol: For degradation of endogenous CTCF, the auxin-inducible degron was induced by adding 500 μM indole-3-acetic acid (IAA, chemical analog of auxin) to the media. Expression of transgenes was achieved by the addition of doxycycline (Dox, 1 μg/ml) to the media. The cells were treated with IAA and/or Dox for 2 days.

value: mESC

value: IAA+Doxyxycline

tag: replicate

value: replicate 1


title: retinal organoid, knockout, fasudil treated, rep4

value: Fasudil treated


title: retinal organoid, knockout, eupatilin treated, rep2

value: Eupatilin treated


title: retinal organoid, knockout, vehicle treated, rep3


title: Nebulized_FLAMOD_24h_N_biol_rep1

description: Library name: Library-331

value: Nasal

value: LRxLW TOPIGS 20


title: HIC_R342C_ID_rep2

description:
HIC_R342C_ID_rep2
HIC_R342C_ID_rep1_rep2_10kb.matrix
HIC_R342C_ID_rep1_rep2_10kb_abs.bed

value: replicate 2


title: retinal organoid, knockout, vehicle treated, rep1


title: retinal organoid, knockout, vehicle treated, rep2


title: Nebulized_FLAMOD_4h_N_biol_rep4

description: Library name: Library-330

value: Flagellin


title: HIC_R377H_ID_rep1

description:
HIC_R377H_ID_rep1
HIC_R377H_ID_rep1_rep2_10kb.matrix
HIC_R377H_ID_rep1_rep2_10kb_abs.bed


title: HIC_R342C_ID_rep1

description:
HIC_R342C_ID_rep1
HIC_R342C_ID_rep1_rep2_10kb.matrix
HIC_R342C_ID_rep1_rep2_10kb_abs.bed


title: HIC_R339Q_ID_rep1

description:
HIC_R339Q_ID_rep1
HIC_R339Q_ID_rep1_rep2_10kb.matrix
HIC_R339Q_ID_rep1_rep2_10kb_abs.bed


title: Nebulized_FLAMOD_4h_N_biol_rep3

description: Library name: Library-329


title: retinal organoid, knockout, untreated, rep4

value: no treatment


title: Nebulized_FLAMOD_4h_N_biol_rep2

description: Library name: Library-328


title: Nebulized_FLAMOD_4h_N_biol_rep1

description: Library name: Library-327


title: HIC_Q418R_ID_rep1

description:
HIC_Q418R_ID_rep1
HIC_Q418R_ID_rep1_rep2_10kb.matrix
HIC_Q418R_ID_rep1_rep2_10kb_abs.bed


title: retinal organoid, knockout, untreated, rep3


title: TV, agit, no antiox, rep1

value: Czapek-Dox medium w/15mM cellobiose

value: agitation 220 rpm

value: 28 deg C

value: 6 days


title: retinal organoid, knockout, untreated, rep2

value: retinal organoids

value: homozygous LCA5 KO


title: Nebulized_buffer_24h_N_biol_rep4

description: Library name: Library-326

value: Buffer


title: retinal organoid, knockout, untreated, rep1

value: 220 days old


title: retinal organoid, WT, untreated, rep5

value: isogenic control

value: 200 days old


title: HIC_R339Q_ID_rep2

description:
HIC_R339Q_ID_rep2
HIC_R339Q_ID_rep1_rep2_10kb.matrix
HIC_R339Q_ID_rep1_rep2_10kb_abs.bed

value: mESC

value: IAA+Doxyxycline


title: HIC_K365T_ID_rep2

description:
HIC_K365T_ID_rep2
HIC_K365T_ID_rep1_rep2_10kb.matrix
HIC_K365T_ID_rep1_rep2_10kb_abs.bed


title: HIC_K365T_ID_rep1

description:
HIC_K365T_ID_rep1
HIC_K365T_ID_rep1_rep2_10kb.matrix
HIC_K365T_ID_rep1_rep2_10kb_abs.bed

value: replicate 1


title: Nebulized_buffer_24h_N_biol_rep2

description: Library name: Library-324

value: Nasal

value: LRxLW TOPIGS 20


title: Nebulized_buffer_24h_N_biol_rep3

description: Library name: Library-325


title: Nebulized_buffer_24h_N_biol_rep1

description: Library name: Library-323


title: retinal organoid, WT, untreated, rep4


title: TV, static, no antiox, rep1

value: static

value: 2 mM HBA

value: 24 hours


title: Nebulized_FLAMOD_24h_T_biol_rep4

description: Library name: Library-322

source_name: Trachea

value: Trachea

value: Flagellin


title: HIC_H455R_ID_rep1

description:
HIC_H455R_ID_rep1
HIC_H455R_ID_rep1_rep2_10kb.matrix
HIC_H455R_ID_rep1_rep2_10kb_abs.bed


title: retinal organoid, WT, untreated, rep2

value: no treatment


title: Nebulized_FLAMOD_24h_T_biol_rep3

description: Library name: Library-321


title: retinal organoid, WT, untreated, rep1

value: retinal organoids


title: OmniATAC_WT_ID_rep2

description:
OmniATAC_WT_ID_rep2
OmniATAC_WT_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_WT_ID_rep1_rep2.peaks.bed

data_processing:
Data were processed using Seq-N-Slide pipeline.
Nextera adaptor were trimmed using TrimGalore.
Reads were aligned against the mouse reference genome (mm10) using the Bowtie2 aligner.
PCR duplicates were removed using Sambamba.
Replicates were merged and peaks were called using MACS2. Peaks overlapping ENCODE blacklisted regions were filtered out. Bigwig files were generated using deeptools (bamCoverage) with RPKM normalization (1bp bin).
Assembly: mm10
Supplementary files format and content: Bigwig with RPKM normalization merged per condition
Supplementary files format and content: MACS2 peaks (q<0.05)

extract_protocol:
We used an improved ATAC-seq protocol (Omni-ATAC) adopted from Corces et al., (Corces, Trevino et al. 2017). Briefly, cells in culture were treated with 200 U/ml DNase and were then harvested via trypsinization and resuspended in regular medium.  Cells were resuspended in 500μl of cold ATAC-seq resuspension buffer 1 (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40 and 0.1% Tween-20 in water). 50ul (50.000 cells) were transferred to a new 1.5ml Eppendorf tube and 0.5ul 1% Digitonin (Promega #G9441) was added. The cell lysis reaction was incubated on ice for 3 min. After lysis,nuclei were resuspended in 45μl of transposition mix (25μl 2X TD buffer (Illumina #20034198), 16.5μl 1X PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween-20 and 2.5μl water).
5ul of transposase enzyme  was added to the nuclei. Transposed DNA fragments were then amplified as described previously in Buenrostro et al., (Buenrostro, Wu et al. 2015). Final libraries were purified with with Zymo DNA Clean and Concentrator-5 kit. Libraries were then sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 50 million 150bp paired-end reads per sample.

value: WT

value: replicate 2


title: Nebulized_FLAMOD_24h_T_biol_rep2

description: Library name: Library-320


title: WSR006 [O-T2DM15]

city: beijing

first: Guangjian

last: Jiang

address: Beijing University of Traditional Chinese Medicine, No. 11 North Third Ring East Road, Beijing City

country: China

institute: Beijing University of Chinese Medicine, Beijing

data_processing:
Screen cDNA fragments of approximately 370~420 bp using AMPure XP beads, amplify by PCR, and purify the PCR product again using AMPure XP beads to obtain the final library. Determine the quality of the library using the Agilent 2100 System (NanoDrop ND-1000) analyzer and accurately quantify it (library effective concentration higher than 2nM) through quantitative real-time polymerase chain reaction before data analysis.
Assembly: Remove ribosome RNA (rRNA) using the Epicentre Ribozero™ rRNA removal kit (Epicentre, USA) before data analysis. Remove linear RNA using RNase R (Epicentre, USA). Finally, merge libraries according to the requirements of effective concentration and data volume, and sequence them using the Illumina NovaSeq 6000.
Supplementary files format and content: The values in the expression matrix are FPKM and TPM values for gene expression in subjects

source_name: blood

extract_protocol:
The total RNA was extracted from venous blood collected from people with T2DM using Trizol (Invitrogen, USA).  To further control quality, agarose gel electrophoresis was used to test samples' integrity and NanoDrop-1000 was used to quantify them.
To construct each library, 1-2 g of total RNA were selected. Total RNA was first subjected to mRNA enrichment with NEB Next@ Poly A (or rRNA removal using RiboZero Magnetic Gold Kit). In this study, stranded RNA-seq libraries were prepared with KAPA Stranded RNA-Seq Library Prep kit. The KAPA kit uses a dUTP-based method for the construction of chain-specific libraries, which included the following steps: 1) Fragmentation of mRNA enrichment products, 2) reverse transcription of the first strand of cRNA, 3) dUTP synthesis of double-stranded cDNA, 4) Rt-PCR amplification was used to repair double-stranded cDNA ends to create RNA sequencing libraries. For circRNA, find_circ and CIRI, two of the most used circRNA identification software, are used to identify circRNA to improve the accuracy of circRNA identification. Use find_circ to align reads to reference sequences, and identify circRNAs that qualify and have a read count greater than or equal to 2. They were then identified with CIRI.

value: blood

tag: disease

value: obese diabetic patients


title: OmniATAC_WT_ID_rep1

description:
OmniATAC_WT_ID_rep1
OmniATAC_WT_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_WT_ID_rep1_rep2.peaks.bed


title: OmniATAC_S354F_ID_rep2

description:
OmniATAC_S354F_ID_rep2
OmniATAC_S354F_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_S354F_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_24h_T_biol_rep1

description: Library name: Library-319


title: IDC  Fixed Fresh

city: Madrid

first: Silvia

last: Gonzalez-Martinez

address: M-607, Km. 9, 100, Fuencarral-El Pardo

department: Pathological Anatomy

country: Spain

institute: Ramon y Cajal University Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Barcoded processing, gene counting and aggregation were madre using Cell Ranger software v7.1.0 (10x Genomics)
Assembly: Hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Invasive ductal breast carcinoma

extract_protocol:
CG000477 from 10X Genomics and CG000632 from 10X Genomics
CG000477 from 10X Genomics

tag: cell type

value: Breast cancer

value: Invasive ductal breast carcinoma


title: OmniATAC_S354F_ID_rep1

description:
OmniATAC_S354F_ID_rep1
OmniATAC_S354F_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_S354F_ID_rep1_rep2.peaks.bed

value: mESC

value: IAA+Doxyxycline


title: HIC_H455R_ID_rep2

description:
HIC_H455R_ID_rep2
HIC_H455R_ID_rep1_rep2_10kb.matrix
HIC_H455R_ID_rep1_rep2_10kb_abs.bed


title: ILC  FFPE

description: 10x Genomics

source_name: Invasive lobular breast carcinoma

value: Invasive lobular breast carcinoma


title: Nebulized_FLAMOD_4h_T_biol_rep3

description: Library name: Library-317

value: LRxLW TOPIGS 20


title: WSR005 [O-T2DM14]


title: Nebulized_FLAMOD_4h_T_biol_rep2

description: Library name: Library-316


title: OmniATAC_R448Q_ID_rep1

description:
OmniATAC_R448Q_ID_rep1
OmniATAC_R448Q_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R448Q_ID_rep1_rep2.peaks.bed

value: replicate 1


title: OmniATAC_R448Q_ID_rep2

description:
OmniATAC_R448Q_ID_rep2
OmniATAC_R448Q_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R448Q_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_4h_T_biol_rep1

description: Library name: Library-315


title: Nebulized_FLAMOD_4h_T_biol_rep4

description: Library name: Library-318


title: ILC  Fixed Fresh

description: 10x Genomics


title: retinal organoid, WT untreated, rep3

value: isogenic control

value: 200 days old


title: IDC FFPE

description: 10x Genomics


title: Nebulized_buffer_24h_T_biol_rep4

description: Library name: Library-314

value: Trachea

value: Buffer


title: OmniATAC_R377H_ID_rep1

description:
OmniATAC_R377H_ID_rep1
OmniATAC_R377H_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R377H_ID_rep1_rep2.peaks.bed


title: WSR004 [O-T2DM13]


title: WSR003 [O-T2DM12]


title: OmniATAC_R377C_ID_rep2

description:
OmniATAC_R377C_ID_rep2
OmniATAC_R377C_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R377C_ID_rep1_rep2.peaks.bed


title: HIC_Q418R_ID_rep2

description:
HIC_Q418R_ID_rep2
HIC_Q418R_ID_rep1_rep2_10kb.matrix
HIC_Q418R_ID_rep1_rep2_10kb_abs.bed


title: Nebulized_buffer_24h_T_biol_rep3

description: Library name: Library-313


title: Nebulized_FLAMOD_24h_N_biol_rep3

description: Library name: Library-333

value: Nasal

value: Flagellin


title: Nebulized_buffer_24h_T_biol_rep2

description: Library name: Library-312


title: WSR002 [O-T2DM11]


title: OmniATAC_R377C_ID_rep1

description:
OmniATAC_R377C_ID_rep1
OmniATAC_R377C_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R377C_ID_rep1_rep2.peaks.bed


title: SRKPD011 [O-T2DM8]


title: SRKPD015 [O-T2DM10]


title: SRKPD010 [O-T2DM7]


title: SRKPD014 [O-T2DM9]


title: SRKPD009 [O-T2DM6]


title: OmniATAC_R339Q_ID_rep2

description:
OmniATAC_R339Q_ID_rep2
OmniATAC_R339Q_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R339Q_ID_rep1_rep2.peaks.bed


title: OmniATAC_R342C_ID_rep2

description:
OmniATAC_R342C_ID_rep2
OmniATAC_R342C_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R342C_ID_rep1_rep2.peaks.bed


title: HOM_M_11_OD3

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V4.2.1, RStudio 2022.07.1+554 "Spotted Wakerobin" Release (7872775ebddc40635780ca1ed238934c3345c5de, 2022-07-22) for Windows, and biomaRt V2.52.0
DESeq2  V1.36.0 differential gene expression
JMP Genomics V10.0 quality control, principal components, ANOVA, hierarchical clustering
Assembly: Mus musculus/GRCm38
Supplementary files format and content: tab-delimited text containing raw counts

source_name: Lung

growth_protocol: Diabetic Leprdb mice and lean heterozygote mice were intranasally inoculated with 20,000 PFU of mouse-adapted SARS-CoV-2 MA10 strain and lungs (~20mg) were collected and processed for analysis at 2 and 4 days post-infection. Total RNA was isolated from homogenized lung and subjected to RNAseq

extract_protocol:
RNA was extracted from ~20mg of lung (previously frozen at -80C) using the Qiagen RNeasy plus mini kit. RNA concentrations were measured using Nanodrop and samples were diluted to 35 ng/ul in RNase free water.
Lexogen Quant-Seq

value: Lung

value: BKS.Cg-Dock7m +/+ Leprdb/J

value: 10-week old

tag: virus strain

tag: phenotype

value: diabetic

value: Homozygote for Leprdb

tag: infection

value: 4 dpi


title: OmniATAC_R339Q_ID_rep1

description:
OmniATAC_R339Q_ID_rep1
OmniATAC_R339Q_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R339Q_ID_rep1_rep2.peaks.bed

value: mESC


title: Nebulized_buffer_24h_T_biol_rep1

description: Library name: Library-311

tag: tissue

tag: animal id


title: Nebulized_FLAMOD_24h_L2_biol_rep2

description: Library name: Library-308

source_name: Lung 2

value: Lung 2

tag: time


title: OmniATAC_Q418R_ID_rep2

description:
OmniATAC_Q418R_ID_rep2
OmniATAC_Q418R_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_Q418R_ID_rep1_rep2.peaks.bed

tag: strain

value: IAA+Doxyxycline

value: replicate 2


title: Nebulized_FLAMOD_24h_L2_biol_rep3

description: Library name: Library-309

value: LRxLW TOPIGS 20

tag: treatment


title: OmniATAC_R342C_ID_rep1

description:
OmniATAC_R342C_ID_rep1
OmniATAC_R342C_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R342C_ID_rep1_rep2.peaks.bed

value: replicate 1


title: HOM_M_09_OD3


title: OmniATAC_Q418R_ID_rep1

description:
OmniATAC_Q418R_ID_rep1
OmniATAC_Q418R_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_Q418R_ID_rep1_rep2.peaks.bed


title: SRKPD008 [O-T2DM5]

value: blood

value: obese diabetic patients


title: OmniATAC_R377H_ID_rep2

description:
OmniATAC_R377H_ID_rep2
OmniATAC_R377H_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_R377H_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_4h_L2_biol_rep4

description: Library name: Library-306


title: HOM_M_12_OD3

value: Mock


title: OmniATAC_K365T_ID_rep2

description:
OmniATAC_K365T_ID_rep2
OmniATAC_K365T_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_K365T_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_4h_L2_biol_rep3

description: Library name: Library-305


title: Nebulized_FLAMOD_24h_L2_biol_rep4

description: Library name: Library-310


title: HOM_M_08_OD3


title: Nebulized_FLAMOD_24h_L2_biol_rep1

description: Library name: Library-307


title: SRKPD007 [O-T2DM4]


title: OmniATAC_K365T_ID_rep1

description:
OmniATAC_K365T_ID_rep1
OmniATAC_K365T_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_K365T_ID_rep1_rep2.peaks.bed


title: HOM_M_07_OD3


title: Nebulized_buffer_24h_L2_biol_rep4

description: Library name: Library-302

value: Buffer


title: SMC3_IgG_rep2

description:
SMC3_IgG_rep2
SMC3_IgG_rep1_rep2.bin1.rpkm.bw

data_processing:
Data were processed using Seq-N-Slide pipeline.
Nextera adaptor were trimmed using TrimGalore.
Reads were aligned against the mouse reference genome (mm10) using the Bowtie2 aligner.
PCR duplicates were removed using Sambamba.
After scaling down each samples to 100M reads, replicates were merged per condition. Narrow peaks were called using MACS2 in pair-end mode with IgG as control for Smc3 ChIP-seq or WT untreated condition (in which FLAG CTCF is not expressed) for CTCF FLAG ChIP-seq to control for unspecific binding. Peaks overlapping ENCODE blacklisted regions were filtered out. Bigwig files were generated using deeptools (bamCoverage) with RPKM normalization (1bp bin).
Assembly: mm10
Supplementary files format and content: Bigwig with RPKM normalization, merged per condition after scaling down to 100M reads
Supplementary files format and content: narrow peaks (except for IgG and WT untreated, q<0.05) using merged replicates

extract_protocol:
mESCs were dissociated using TrypLE and and double cross linked using 25mM EGS (ethylene glycol bis(succinimidyl succinate)) and 1% formaldehyde. Fixed cells (10 million) were resuspended in 350 μl ice cold lysis buffer (10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.1% sodium deoxycholate, 0.5% N-lauroysarcosine and 1X protease inhibitors) and lysed for 10 min by rotating at 4° C. Chromatin was sheared using a bioruptor (Diagenode) for 15 minutes ( 30 sec on, 30 sec off, high output level). FLAG M2 Magnetic Beads were used for FLAG immunoprecipitation. In other cases ( Cohesin, IgG) antibodies were bound to protein A magnetic beads by incubation on a rotator for one hour at room temperature.
Samples were washed and tagmentation were performed as per the original ChIPmentation protocol (Schmidl et al., 2015) using 1 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina #20034198 ). Chromatin was then eluted and de-crosslinked and DNA was purified using MinElute Reaction Cleanup Kit. Purified DNA was amplified as per the ChIPmentation protocol (Schmidl, Rendeiro et al. 2015) using indexed and non-indexed primers and NEBNext High-Fidelity 2X PCR Master Mix. Library quality and quantity were estimatred using Tapestation and were then sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 200 million 150bp paired-end total per sample.

value: IgG

value: Untreated

tag: antibody


title: SMC3_WT_ID_rep2

description:
SMC3_WT_ID_rep2
SMC3_WT_ID_rep1_rep2.bin1.rpkm.bw
SMC3_WT_ID_rep1_rep2.peaks.bed

value: WT


title: Nebulized_FLAMOD_4h_L2_biol_rep2

description: Library name: Library-304

value: Flagellin


title: HET_M_01_OD3

value: Lung

value: BKS.Cg-Dock7m +/+ Leprdb/J

value: 10-week old

value: lean

value: Heterozygote for Leprdb


title: Nebulized_buffer_24h_L2_biol_rep3

description: Library name: Library-301

value: Lung 2


title: SRKPD003 [O-T2DM2]


title: HET_M_03_OD3

value: 4 dpi


title: HET_M_05_OD3


title: Nebulized_buffer_24h_L2_biol_rep2

description: Library name: Library-300

value: LRxLW TOPIGS 20


title: SMC3_IgG_rep1

description:
SMC3_IgG_rep1
SMC3_IgG_rep1_rep2.bin1.rpkm.bw

value: mESC

value: replicate 1


title: OmniATAC_H455R_ID_rep2

description:
OmniATAC_H455R_ID_rep2
OmniATAC_H455R_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_H455R_ID_rep1_rep2.peaks.bed

value: IAA+Doxyxycline

value: replicate 2


title: Nebulized_FLAMOD_4h_L2_biol_rep1

description: Library name: Library-303


title: ZC056 [Control15]

value: blood

value: obese diabetic patients

value: Control


title: SRKPD006 [O-T2DM3]


title: Nebulized_buffer_24h_L2_biol_rep1

description: Library name: Library-299

value: Buffer


title: Nebulized_FLAMOD_24h_L1_biol_rep4

description: Library name: Library-298

source_name: Lung 1

value: Lung 1

value: Flagellin


title: ZC052 [Control12]


title: SMC3_WT_ID_rep1

description:
SMC3_WT_ID_rep1
SMC3_WT_ID_rep1_rep2.bin1.rpkm.bw
SMC3_WT_ID_rep1_rep2.peaks.bed

value: WT


title: HET_M_04_OD3

value: Lung

value: BKS.Cg-Dock7m +/+ Leprdb/J

value: 10-week old


title: Nebulized_FLAMOD_24h_L1_biol_rep3

description: Library name: Library-297


title: HOM_M_27_OD2

value: diabetic

value: Homozygote for Leprdb

value: Mock


title: ZC055 [Control14]


title: HOM_M_26_OD2


title: SRKPD001 [O-T2DM1]


title: HOM_M_25_OD2


title: OmniATAC_H455R_ID_rep1

description:
OmniATAC_H455R_ID_rep1
OmniATAC_H455R_ID_rep1_rep2.bin1.rpkm.bw
OmniATAC_H455R_ID_rep1_rep2.peaks.bed

value: mESC


title: ZC053 [Control13]


title: SMC3_S354F_ID_rep2

description:
SMC3_S354F_ID_rep2
SMC3_S354F_ID_rep1_rep2.bin1.rpkm.bw
SMC3_S354F_ID_rep1_rep2.peaks.bed


title: ZC047 [Control8]


title: ZC049 [Control9]


title: SMC3_R448Q_ID_rep2

description:
SMC3_R448Q_ID_rep2
SMC3_R448Q_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R448Q_ID_rep1_rep2.peaks.bed


title: HOM_M_18_OD2

value: 2 dpi


title: ZC044 [Control7]


title: SMC3_R448Q_ID_rep1

description:
SMC3_R448Q_ID_rep1
SMC3_R448Q_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R448Q_ID_rep1_rep2.peaks.bed

value: IAA+Doxyxycline

value: replicate 1


title: HOM_M_19_OD2


title: HOM_M_17_OD2


title: SMC3_R377H_ID_rep2

description:
SMC3_R377H_ID_rep2
SMC3_R377H_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R377H_ID_rep1_rep2.peaks.bed

value: replicate 2


title: Nebulized_FLAMOD_24h_L1_biol_rep2

description: Library name: Library-296

value: LRxLW TOPIGS 20


title: Nebulized_FLAMOD_4h_L1_biol_rep2

description: Library name: Library-292


title: Nebulized_FLAMOD_24h_L1_biol_rep1

description: Library name: Library-295


title: HOM_M_20_OD2


title: ZC050 [Control10]

value: blood

value: obese diabetic patients

value: Control


title: SMC3_R377H_ID_rep1

description:
SMC3_R377H_ID_rep1
SMC3_R377H_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R377H_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_4h_L1_biol_rep1

description: Library name: Library-291

value: Lung 1

value: Flagellin


title: Nebulized_FLAMOD_4h_L1_biol_rep4

description: Library name: Library-294


title: Nebulized_FLAMOD_4h_L1_biol_rep3

description: Library name: Library-293


title: ZC015 [Control5]


title: HET_M_16_OD2

value: Lung

value: lean

value: Heterozygote for Leprdb


title: ZC051 [Control11]


title: SMC3_R377C_ID_rep2

description:
SMC3_R377C_ID_rep2
SMC3_R377C_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R377C_ID_rep1_rep2.peaks.bed


title: HET_M_15_OD2

value: BKS.Cg-Dock7m +/+ Leprdb/J

value: 10-week old


title: SMC3_R377C_ID_rep1

description:
SMC3_R377C_ID_rep1
SMC3_R377C_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R377C_ID_rep1_rep2.peaks.bed


title: ZC012 [Control4]


title: Nebulized_buffer_24h_L1_biol_rep3

description: Library name: Library-289

value: Buffer


title: HET_M_14_OD2

value: Mock


title: SMC3_S354F_ID_rep1

description:
SMC3_S354F_ID_rep1
SMC3_S354F_ID_rep1_rep2.bin1.rpkm.bw
SMC3_S354F_ID_rep1_rep2.peaks.bed

value: mESC


title: ZC042 [Control6]


title: Nebulized_buffer_24h_L1_biol_rep4

description: Library name: Library-290


title: HET_M_13_OD2


title: SMC3_R342C_ID_rep2

description:
SMC3_R342C_ID_rep2
SMC3_R342C_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R342C_ID_rep1_rep2.peaks.bed

value: IAA+Doxyxycline


title: ZC001 [Control1]


title: ZC011 [Control3]


title: ZC002 [Control2]


title: SMC3_R339Q_ID_rep2

description:
SMC3_R339Q_ID_rep2
SMC3_R339Q_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R339Q_ID_rep1_rep2.peaks.bed


title: Nebulized_buffer_24h_L1_biol_rep2

description: Library name: Library-288


title: HET_M_02_OD2

value: 2 dpi


title: SMC3_R339Q_ID_rep1

description:
SMC3_R339Q_ID_rep1
SMC3_R339Q_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R339Q_ID_rep1_rep2.peaks.bed

value: replicate 1


title: SMC3_R342C_ID_rep1

description:
SMC3_R342C_ID_rep1
SMC3_R342C_ID_rep1_rep2.bin1.rpkm.bw
SMC3_R342C_ID_rep1_rep2.peaks.bed


title: HET_M_04_OD2


title: Nebulized_FLAMOD_24h_BLD_biol_rep3

description: Library name: Library-227

source_name: Blood

value: Blood

value: LRxLW TOPIGS 20


title: HET_M_03_OD2


title: MiaPaCa2_Apilimod_2uM_17d

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

data_processing:
Basecalling was performed using bcl2fastq 2 (Illumina).
Reads were trimmed to the bare sgRNA sequence using cutadapt 4.1. Paired-end mates were trimmed separately using a sequence 5’-adjacent to the sgRNA position within the vector (TATATCTTGTGGAAAGGACGAAACACCG), requiring a minimum match of 18 bases to the sequence amd followed by truncation to 20 bases (relevant cutadapt command parameters: -m 18 -O 18 -l 20 --discard-untrimmed).
Trimmed reads were then combined and aligned using bowtie2 2.4.5 to a reference built from each sgRNA in the library flanked by vector sequences (5’ GTTATCAACTTGAAAAAGTGGCACCG and 3’ CTAGATCTTGAGACAAATGGC). The bowtie2 parameter --norc was used to prevent reverse compliment alignment.
Guide RNA counting was performed for sample alignments using MAGeCK 0.5.9.5
Assembly: hg38
Supplementary files format and content: Sample count files are tab-delimited text files with header and contain sgRNA ID ("sgRNA"), target gene name ("Gene"), and read count (sample name).
Library strategy: CRISPR screen

source_name: MIA PaCa-2

growth_protocol: 75 million MIA PaCa-2 cells were seeded at a density of 5 x 105 cells/mL in 6-well plates containing 2 mL of DMEM, 8mg/mL polybrene and the CRISPR screen library virus.

extract_protocol:
Genomic DNA was isolated using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol.
For each condition, sgRNA was amplified from 50mg gDNA using Herculase II Fusion DNA Polymerase (Agilent Technologies), column purified using Select-a-Size DNA Clean & Concentrator kit (Zymo Research), and then gel-purified using 6% Novex TBE gel (Thermo), followed by isolation from the gels with Gel Breaker Tubes and Gel Filters (BioChain). The resulting PCR products then underwent end-repair and A-tail addition followed by New England Biolabs (NEB) adapter ligation. The final library was prepared by enriching adapter-ligated DNA fragments using 2x KAPA HiFi HotStart mix and NEB dual code barcode following the manufacter’s protocol. The libraries were then sequenced on an Illumina NovaSeq 6000 (paired-end, 300 cycles).

treatment_protocol: Spin infection was caried out by centrifugation at 1,200 x g for 45 minutes at 37C. After 24-hour incubation, the media was replaced with fresh DMEM. After a subsequent 24-hour incubation, cells were transferred to T-150 flasks (at a density of 3 wells into 1 T150 flask) containing 20 mL of DMEM containing puromycin at 2mg/mL. After 3 days of selection, cells were seeded into sixteen total T-150 flasks at a density of 5 x 106 cells/flask in 20 mL of DMEM containing either DMSO or 200nM of apilimod. Cells were passaged every 3-4 days and re-seeded back to the original cell density. After 14 days, a pool of 15 million cells from each condition were harvested for genomic DNA.

value: MIA PaCa-2

value: pancreatic ductal adenoarcinoma cells

value: apilimod 2uM

value: 17 days


title: SMC3_Q418R_ID_rep1

description:
SMC3_Q418R_ID_rep1
SMC3_Q418R_ID_rep1_rep2.bin1.rpkm.bw
SMC3_Q418R_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_24h_BLD_biol_rep4

description: Library name: Library-228

value: Flagellin


title: RTP_3

city: Pamplona

first: Eneko

last: Garate

address: Avenida de Pío XII, 55

institute: CIMA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM33 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: tumor

extract_protocol:
RNA was extracted using RNA Easy Midi Kit. 1µg of RNA was used for sequencing
Truseq stranded mRNA library + NovaSeq6000 150PE (150x2bp) 80M total reads/samples

value: tumor

value: TS/A+CAF

value: breast cell line+cancer associated fibroblast

value: WT

value: Radiotherapy


title: HET_M_01_OD2

value: Lung

value: BKS.Cg-Dock7m +/+ Leprdb/J

value: 10-week old

value: lean

value: Heterozygote for Leprdb


title: Nebulized_FLAMOD_24h_BLD_biol_rep1

description: Library name: Library-225

value: Blood


title: MIA PaCa-2 DMSO_Myc

data_processing:
Basecalling was performed using bcl2fastq 2 (Illumina).
Reads were trimmed using Trimmomatic 0.39 with options ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 MINLEN:30.
Trimmed, paired reads were aligned to the human reference genome using bwa mem 0.7.17 with options -5 -S -P -T 0.
Alignments were sorted and filtered for mapping quality >= 20 using samtools 1.9.
Read duplicates were removed using Picard MarkDuplicates 2.26.0.
Non-primary alignments were removed using samtools view (option -F 0x900) and converted to BED format using bedtools bamtobed 2.27.1.
Peaks were called from filtered alignments using MACS2 2.2.7.1 with default settings and the -B option to generate bedGraph coverage files.
Peaks were filtered using the ENCODE Unified GRCh38 Exclusion List (https://www.encodeproject.org/files/ENCFF356LFX/).
Coverages captured via MACS2 were converted to bigWig using wigToBigWig 2.4.
Assembly: hg38
Supplementary files format and content: Signal files are in bigWig format (*.bw).
Supplementary files format and content: Peak files (*.bed) are in narrowPeak format (BED 6+4).

growth_protocol: MIA PaCa-2 cells were grown in Gibco DMEM + 10% FBS (ThermoFisher).

extract_protocol:
The iDeal ChIP-seq kit for Transcription Factors (Diagenode) was used for ChIP-seq.  Genomic DNA was sonicated for 30 seconds on/30 seconds off (easy mode) for 4 cycles using a Biorupter (Diagenode) to achieve an average fragment size of 200bp. 4ug of cMYC antibody (Abcam ab32072) was used for immunoprecipitation.
1-20 ng ChIP DNA from each sample was end repaired and A-tailed, then ligated with NEB adapters, following by 2xKAPA HiFi HotStart mix and NEB dual indexes PCR to enrich fragments between 200-500 bp. Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on an Illumina NovaSeq 6000 (150-nucleotide paired-end reads).

treatment_protocol: 5 million MIA PaCa-2 cells were treated with DMSO, AMG510 (100nM), or trametinib (10nM) for 8 hours.

value: DMSO

tag: treatment time_(h)


title: MIA PaCa-2 AMG510_Myc

value: MIA PaCa-2

tag: concentration (nm)


title: MIA PaCa-2 Tram_Myc

tag: cell line

value: pancreatic ductal adenoarcinoma cells

value: trametinib


title: Nebulized_buffer_24h_L1_biol_rep1

description: Library name: Library-287

value: Lung 1

tag: genotype

value: LRxLW TOPIGS 20

value: Buffer


title: Nebulized_FLAMOD_4h_BLD_biol_rep4

description: Library name: Library-224

value: Flagellin


title: Nebulized_FLAMOD_24h_BLD_biol_rep2

description: Library name: Library-226


title: SMC3_K365T_ID_rep2

description:
SMC3_K365T_ID_rep2
SMC3_K365T_ID_rep1_rep2.bin1.rpkm.bw
SMC3_K365T_ID_rep1_rep2.peaks.bed

value: mESC

value: IAA+Doxyxycline

value: replicate 2


title: SMC3_K365T_ID_rep1

description:
SMC3_K365T_ID_rep1
SMC3_K365T_ID_rep1_rep2.bin1.rpkm.bw
SMC3_K365T_ID_rep1_rep2.peaks.bed

value: replicate 1


title: SMC3_Q418R_ID_rep2

description:
SMC3_Q418R_ID_rep2
SMC3_Q418R_ID_rep1_rep2.bin1.rpkm.bw
SMC3_Q418R_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_4h_BLD_biol_rep3

description: Library name: Library-223


title: RTP_1

value: tumor

value: TS/A+CAF

value: breast cell line+cancer associated fibroblast

value: WT

value: Radiotherapy


title: SMC3_H455R_ID_rep2

description:
SMC3_H455R_ID_rep2
SMC3_H455R_ID_rep1_rep2.bin1.rpkm.bw
SMC3_H455R_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_4h_BLD_biol_rep2

description: Library name: Library-222

value: Blood


title: RTmasFAP41BBLP_3

value: Radiotherapy and muFAP-4-1BBL


title: HEK293, DMSO WT rep 3

city: Nottingham

first: Keith

last: Spriggs

state: Notts

address: University Park

department: Pharmacy

institute: University of Nottingham

data_processing:
Adapter sequences and quality of FastQ files were assessed via FastQC (Babraham Bioinformatics)
Mapping and alignment to hg38 performed through Rsubread
Mapped counts used to generate RPKM values by within-normalisation methods
RPKM normalised through Upper Quartile normalisation.
differential expression through calculating Log2FC
Assembly: hg38 (Human Genome; GRCh38.p13)
Supplementary files format and content: format = csv; content = Log2FC from RPKM values

growth_protocol: HEK293 cells (both with and without AMPK KO) were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep in 5% CO2 at 37 degrees, and passaged when 70-80% confluency reached.

extract_protocol:
Reliaprep RNA Cell Miniprep System protocol (including 1-hour DNase treatment) was used to extract total RNA from HEK293 samples. 2 ug of RNA per sample were sent for RNA sequencing.
Illumina stranded RNA-seq libraries with ribo-depletion. 150 bp paired end, run on a NovaSeq6000

treatment_protocol: HEK293 cells were serum starved (DMEM + 0.1% FBS + 1% Pen/Strep) for 24 hours prior to treatment. Treatment conditions were DMSO (0.025% v/v) or Cordycepin (25uM) for 20-minutes prior to EGF stimulation for a further 30-minutes (total 50-minute treatment incubation period), and for comparison, HEK293 cells were also treated with DMSO (0.025% v/v) for 20-minutes without EGF stimulation.

value: Wild type,  DMSO 50 mins


title: SMC3_H455R_ID_rep1

description:
SMC3_H455R_ID_rep1
SMC3_H455R_ID_rep1_rep2.bin1.rpkm.bw
SMC3_H455R_ID_rep1_rep2.peaks.bed


title: FLAG_CTCF_WT_UN_rep2

description:
FLAG_CTCF_WT_UN_rep2
FLAG_CTCF_WT_UN_rep1_rep2.bin1.rpkm.bw

value: Untreated

value: FLAG (CTCF)


title: MIA PaCa-2 DMSO_IgG

value: MIA PaCa-2

value: pancreatic ductal adenoarcinoma cells

value: DMSO


title: RTmasFAP41BBLP_2


title: HEK293, DMSO WT rep 2


title: RTP_2


title: Nebulized_FLAMOD_4h_BLD_biol_rep1

description: Library name: Library-221

value: LRxLW TOPIGS 20

value: Flagellin


title: RTmasFAP41BBLP_1


title: Nebulized_buffer_24h_BLD_biol_rep4

description: Library name: Library-220

value: Buffer


title: FLAG_CTCF_WT_ID_rep2

description:
FLAG_CTCF_WT_ID_rep2
FLAG_CTCF_WT_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_WT_ID_rep1_rep2.peaks.bed

value: mESC

value: IAA+Doxyxycline

value: replicate 2


title: NTP_3

value: tumor

value: TS/A+CAF

value: breast cell line+cancer associated fibroblast


title: HEK293, DMSO EGF WT rep 3

value: Wild type,  DMSO 50 mins, 15 μM EGF 30 mins


title: NTP_2

value: WT


title: HEK293, DMSO EGF WT rep 2


title: FLAG_CTCF_WT_UN_rep1

description:
FLAG_CTCF_WT_UN_rep1
FLAG_CTCF_WT_UN_rep1_rep2.bin1.rpkm.bw

value: replicate 1


title: FLAG_CTCF_WT_ID_rep1

description:
FLAG_CTCF_WT_ID_rep1
FLAG_CTCF_WT_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_WT_ID_rep1_rep2.peaks.bed


title: Nebulized_buffer_24h_BLD_biol_rep2

description: Library name: Library-218

value: Blood


title: Nebulized_buffer_24h_BLD_biol_rep3

description: Library name: Library-219


title: HEK293, DMSO EGF AMPK KO rep 3

value: AMPK knockout,  DMSO 50 mins, 15 μM EGF 30 mins


title: Nebulized_buffer_24h_BLD_biol_rep1

description: Library name: Library-217


title: NTP_1


title: HEK293, DMSO EGF AMPK KO rep 2


title: FLAG_CTCF_S354F_ID_rep2

description:
FLAG_CTCF_S354F_ID_rep2
FLAG_CTCF_S354F_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_S354F_ID_rep1_rep2.peaks.bed

value: FLAG (CTCF)


title: FAP_4_1BBLP_3


title: FAP_4_1BBLP_2


title: Nebulized_FLAMOD_24h_B_biol_rep3

description: Library name: Library-215

source_name: Bronchus

value: Bronchus


title: FLAG_CTCF_S354F_ID_rep1

description:
FLAG_CTCF_S354F_ID_rep1
FLAG_CTCF_S354F_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_S354F_ID_rep1_rep2.peaks.bed


title: HEK293, DMSO AMPK KO rep 2

value: AMPK knockout,  DMSO 50 mins


title: FLAG_CTCF_R448Q_ID_rep2

description:
FLAG_CTCF_R448Q_ID_rep2
FLAG_CTCF_R448Q_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R448Q_ID_rep1_rep2.peaks.bed


title: FAP_4_1BBLP_1


title: Nebulized_FLAMOD_24h_B_biol_rep4

description: Library name: Library-216

value: LRxLW TOPIGS 20


title: HEK293, DMSO AMPK KO rep 3


title: HEK293, Cordycepin EGF WT rep 2

value: Wild type,  25μM cordycepin 50 mins, 15 μM EGF 30 mins


title: FLAG_CTCF_R448Q_ID_rep1

description:
FLAG_CTCF_R448Q_ID_rep1
FLAG_CTCF_R448Q_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R448Q_ID_rep1_rep2.peaks.bed


title: HEK293, Cordycepin EGF WT rep 3


title: Nebulized_FLAMOD_24h_B_biol_rep2

description: Library name: Library-214

value: Flagellin


title: HEK293, Cordycepin EGF AMPK KO rep 3

value: AMPK knockout,  25μM cordycepin 50 mins, 15 μM EGF 30 mins


title: IgG_Rep3

city: Madison

first: Daniel

last: Matson

address: 1111 Highland Avenue

institute: University of Wisconsin

data_processing:
ENCODE ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/, v2.2.1) was used to align sequencing reads to human genome (hg38), call peaks, and generate signals.
Assembly: hg38
Supplementary files format and content: bw: bigWig file of ChIP-seq signals represented by fold change of GATA2 over IgG
Supplementary files format and content: bb: bigBed file of GATA2 ChIP-seq peaks called from all replicates

source_name: Tumor

growth_protocol: RPMI-1640 media with 10% FBS and 1% penicillin/streptomycin

extract_protocol:
150 million Ark1 cells were incubated in serum free media with 1% paraformaldehyde for 10 minutes at room temperature, then quenched with 125 mM glycine. Cells were scraped from the plate, pelleted for 5 minutes at 700xG, then resuspended in 9 mL of Buffer A (50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, and 1 tablet Pierce protease inhibitor cocktail mini) and incubated on ice for 10 minutes. The cells were then pelleted for 5 min at 1400xG, the supernatant was aspirated, and the pellet resuspended in 3 mL Buffer A. After incubation on ice for 5 minutes, cells were pelleted for 5 minutes at 1400xG and the supernatant was aspirated. The pellet was resuspended in 900 µL Buffer A, after which 100 µL of Buffer B (10 mM EGTA, 800 mM NaCl, 1% SOC, and 2% SDS) was added. The lysate was then split between two 1.5 mL Eppendorf tubes, and each lysate sonicated for 5 cycles at 30% amplitude for 15 seconds on and 30 seconds off in an ice water bath, using a Branson SLPe Digital Sonifier and 1/8-inch probe tip. Sonicated lysates were then spun at 14,000xG for 10 minutes and the supernatant transferred to a new 1.5 mL tube and glycerol added to 5% final concentration. For immunoprecipitations, 25 µg of chromatin was added to each tube to which 1 µg of rabbit anti-GATA2 or rabbit IgG control was added, followed by RIPA buffer up to 1 mL. For input, 2.5 µg of chromatin was added and antibody omitted. The tubes were then rotated overnight at 4 C. The next day, 30 µL of protein G magnetic beads (NEB) were washed with RIPA buffer and then split equally across IgG and GATA2 tubes, which were then rotated for 4 hours at 4 C. Using a magnetic tube rack, the beads were then washed 3X with 1 mL of RIPA buffer, 2X with 1 mL of RIPA buffer + 300 mM NaCl, 2X with 1 mL of LiCl buffer (250 mM LiCl, 0.5% NP-40, 0.5% DOC), and 1X with 1 mL TE buffer (10 mM Tris pH 8.0, 1 mM EDTA, 50 mM NaCl). Beads then received 200 µL of ChIP Elution Buffer and tubes were heated overnight at 65 C shaking at 800 rpm with 30 seconds on and 10 second off. Using a magnetic rack, the supernatant was then collected and 20 µg RNase A was added followed by 1 hour incubation at 37 C. The samples then received 20 µg Proteinase K and were incubated for 55 C for 2 hours, followed by clean up using Qiagen PCR cleanup kit and elution into 50 µL EB buffer.
Purified immunoprecipitated and input DNA was submitted to the University of Wisconsin-Madison Biotechnology Center. DNA concentration and sizing were verified using the Qubit® dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity D1000 ScreenTape (Agilent Technologies, Inc.), respectively. Samples were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England Biolabs) with minor modifications from the manufacturer’s protocol. Quality and quantity of the finished libraries were assessed using Agilent D1000 ScreenTape and Qubit® dsDNA HS Assay Kit, respectively. Libraries were standardized to 2nM. Paired end, 150 bp sequencing was performed using the Illumina NovaSeq X Plus (Illumina).

treatment_protocol: Lipofection of 20 nM anti-GATA2 or anti-Scramble siRNA Smartpool using Lipofectamine RNAiMAX and manufacturer's recommended protocol. Cells were incubated for 48 hours after siRNA treatment.

value: Tumor

value: Uterine serous carcinoma

tag: chip antibody

value: Non-specific Rabbit IgG

value: anti-Scramble siRNA


title: FLAG_CTCF_R377H_ID_rep1

description:
FLAG_CTCF_R377H_ID_rep1
FLAG_CTCF_R377H_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R377H_ID_rep1_rep2.peaks.bed

value: mESC

value: IAA+Doxyxycline

tag: replicate


title: FLAG_CTCF_R377H_ID_rep2

description:
FLAG_CTCF_R377H_ID_rep2
FLAG_CTCF_R377H_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R377H_ID_rep1_rep2.peaks.bed

value: replicate 2


title: IgG_Rep1


title: HEK293, Cordycepin EGF AMPK KO rep 2


title: FLAG_CTCF_R342C_ID_rep2

description:
FLAG_CTCF_R342C_ID_rep2
FLAG_CTCF_R342C_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R342C_ID_rep1_rep2.peaks.bed


title: Nebulized_FLAMOD_24h_B_biol_rep1

description: Library name: Library-213


title: Nebulized_FLAMOD_4h_B_biol_rep2

description: Library name: Library-210


title: Nebulized_FLAMOD_4h_B_biol_rep4

description: Library name: Library-212


title: Nebulized_FLAMOD_4h_B_biol_rep3

description: Library name: Library-211


title: FLAG_CTCF_R342C_ID_rep1

description:
FLAG_CTCF_R342C_ID_rep1
FLAG_CTCF_R342C_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R342C_ID_rep1_rep2.peaks.bed

value: replicate 1


title: GATA2_Rep2

value: Custom rabbit anti-GATA2 polyclonal

value: anti-GATA2 siRNA


title: Nebulized_FLAMOD_4h_B_biol_rep1

description: Library name: Library-209


title: scc15sh-22

city: Guangzhou, Guangdong

first: Siqi

address: No.56 Lingyuanxi Road

institute: Sun Yat-sen University

data_processing:
After the completion of the library construction, the quality of the library was tested, and on-machine sequencing could be carried out only after the test results met the requirements. The detection methods were as follows :(1) The Qubit dye method was used for preliminary quantification, the fragment analyzer was used to detect the insert size of the library, and the next experiment could be carried out only after the insert size met the expectations; (2) The effective concentration of the library was accurately quantified by Q-PCR method (the effective concentration of the library was >2nM), and the library examination was completed. After the library test is qualified, different libraries are pooled according to the target data volume and sequenced by Illumina platform. Filter the offline Data to get Clean Data, sequence match with the specified reference genome, and carry out variable splicing analysis on the Mapped Data obtained; According to the expression levels of genes in different samples or different sample groups, differential expression analysis, functional annotation and functional enrichment of differential expression genes were performed.
Assembly: Homo_sapiens.GRCh38.109
Supplementary files format and content: count, FPKM, differential expression

extract_protocol:
scc15si-NCs and scc15sh-NCs are negative control,scc15si-1s were knockdown with IGF2BP3,scc15 sh-2s were knockdown with circPRMT5,and collect total RNA for RNA-seq.
mRNA with polyA tail was enriched by Oligo(dT) magnetic beads. Then the RNA was broken into short fragments by fragmentation buffer, and the first cDNA was synthesized with six-base random hexamers based on the fragment RNA template. Buffer solution, dNTPs(dTTP, dATP, dGTP and dCTP) and DNA polymerase were then added to synthesize the double-stranded cDNA, which was then purified by DNA purification magnetic beads. The purified double-stranded cDNA was then end-repaired, A tail was added and a sequencing joint was connected. Then the fragment size was selected by DNA purification magnetic beads, and the final cDNA library was obtained by PCR enrichment.

value: squamous cell carcinoma

value: circPRMT5 knockdown with shRNA(replication2)


title: FLAG_CTCF_R339Q_ID_rep2

description:
FLAG_CTCF_R339Q_ID_rep2
FLAG_CTCF_R339Q_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R339Q_ID_rep1_rep2.peaks.bed

value: FLAG (CTCF)


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-01

city: Burnaby

first: Antoine

middle: Etienne

last: Simond

state: BC

address: 8888 university drive

department: Biological Sciences

country: Canada

institute: Simon Fraser University

description: Total RNA were extracted from TRIzol then reverse-transcripted into cDNA, the library used was rRNA-depleted stranded (HMR) and the adapter used was NEBNext_dual

data_processing:
Total RNA extraction using TRIzol
RNA cleaning
Library preparation using the library preparation kit NEBNext® rRNA Depletion (Human/Mouse/Rat)
Analyses were carried out by Genome Quebec (Montreal, QC, Canada) using an Illumina NovaSeq 6000 S4 system, with an average of 37 million reads per sample
Sequencing reads were processed using the genPipes framework. Briefly, adaptor sequences and low-quality score containing bases (Phred score < 30) were trimmed from reads using Trimmomatic.
Assembly: The resulting Reads were aligned to the beluga ASM228892v3 genome, using 2 passes of STAR.
Supplementary files format and content: The file "raw_counts.csv" contains the raw counts obtained using HTSeq.
Supplementary files format and content: The file "traits.csv" contains traits data of each samples, i.e., contaminant data (ng/g lw), population, sampling date, RNA quality (RIN number)
Supplementary files format and content: The file "gene_IDs.tsv" contains the IDs of the genes that were measured. Identified genes are originally given in ENSEMBL IDs. This file allows the conversion of ENSEMBL IDs into others such as Symbol IDs (abbreviations and full names) and Entrez IDs.

organism: Delphinapterus leucas

source_name: skin

extract_protocol:
TRIzol
Library preparation kit NEBNext® rRNA Depletion (Human/Mouse/Rat)

value: skin

tag: population

value: EBS

tag: Sex

value: M


title: Nebulized_buffer_24h_B_biol_rep4

description: Library name: Library-208

value: Bronchus

value: LRxLW TOPIGS 20

value: Buffer


title: scc15sh-NC3

tag: cell type


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-02


title: FLAG_CTCF_R339Q_ID_rep1

description:
FLAG_CTCF_R339Q_ID_rep1
FLAG_CTCF_R339Q_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_R339Q_ID_rep1_rep2.peaks.bed


title: IgG_Rep2

value: Tumor

value: Uterine serous carcinoma

value: Non-specific Rabbit IgG


title: Nebulized_buffer_24h_B_biol_rep3

description: Library name: Library-207


title: scc15sh-23

value: circPRMT5 knockdown with shRNA(replication3)


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-03


title: FLAG_CTCF_Q418R_ID_rep2

description:
FLAG_CTCF_Q418R_ID_rep2
FLAG_CTCF_Q418R_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_Q418R_ID_rep1_rep2.peaks.bed

value: mESC

value: IAA+Doxyxycline

value: replicate 2


title: GATA2_Rep1

value: Custom rabbit anti-GATA2 polyclonal

value: anti-GATA2 siRNA


title: Nebulized_buffer_24h_B_biol_rep2

description: Library name: Library-206


title: scc15si-13

value: squamous cell carcinoma

value: IGF2BP3 knockdown with siRNA(replication3)


title: FLAG_CTCF_K365T_ID_rep2

description:
FLAG_CTCF_K365T_ID_rep2
FLAG_CTCF_K365T_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_K365T_ID_rep1_rep2.peaks.bed

value: FLAG (CTCF)


title: scc15sh-NC2


title: scc15sh-NC1

value: negative control for sh-circPRMT5(replication1)


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-06

value: skin

value: EBS

value: M


title: FLAG_CTCF_Q418R_ID_rep1

description:
FLAG_CTCF_Q418R_ID_rep1
FLAG_CTCF_Q418R_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_Q418R_ID_rep1_rep2.peaks.bed

value: replicate 1


title: FLAG_CTCF_K365T_ID_rep1

description:
FLAG_CTCF_K365T_ID_rep1
FLAG_CTCF_K365T_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_K365T_ID_rep1_rep2.peaks.bed


title: scc15si-12

value: IGF2BP3 knockdown with siRNA(replication2)


title: Nebulized_FLAMOD_24h_L3_biol_rep3

description: Library name: Library-203

source_name: Lung 3

value: Lung 3

value: LRxLW TOPIGS 20

value: Flagellin


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-04


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-05


title: Nebulized_FLAMOD_24h_L3_biol_rep4

description: Library name: Library-204


title: Nebulized_buffer_24h_B_biol_rep1

description: Library name: Library-205

value: Bronchus

value: Buffer


title: FLAG_CTCF_H455R_ID_rep2

description:
FLAG_CTCF_H455R_ID_rep2
FLAG_CTCF_H455R_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_H455R_ID_rep1_rep2.peaks.bed

value: mESC

value: IAA+Doxyxycline

value: replicate 2


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-07


title: scc15sh-21

value: squamous cell carcinoma

value: circPRMT5 knockdown with shRNA(replication1)


title: scc15si-11

value: IGF2BP3 knockdown with siRNA(replication1)


title: FLAG_CTCF_H455R_ID_rep1

description:
FLAG_CTCF_H455R_ID_rep1
FLAG_CTCF_H455R_ID_rep1_rep2.bin1.rpkm.bw
FLAG_CTCF_H455R_ID_rep1_rep2.peaks.bed

value: FLAG (CTCF)


title: Nebulized_FLAMOD_24h_L3_biol_rep2

description: Library name: Library-202


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-08

value: skin


title: scc15si-NC3

value: negative control for si-IGF2BP3(replication3)


title: Skin, post hunt sampling, RNAlater ice, ARHI-18-09

value: EBS

value: M


title: totalRNASeq_WT_ID_rep1

data_processing:
Data were processed using Seq-N-Slide pipeline.
The Illumina adaptor and the T overhang were trimmed as per Illumina recommendation using TrimGalore.
Reads were aligned against the mouse reference genome (mm10) using the STAR aligner.
Read count extraction and normalization were performed using the Seq-N-Slide pipeline.
Differentially expressed genes were called using DESeq2 with an adjusted p-value of 0.05 and a fold change cutoff of 1.5
Assembly: mm10
Supplementary files format and content: counts.tpm.csv, comma-separated TPM matrix
Supplementary files format and content: counts.normalized.csv, comma-separated normalized count matrix

extract_protocol:
mESCs were dissociated using TrypLE, washed in 1X PBS, pelletted and 2.5 million cells were used for extracting RNA with RNeasy plus kit (Qiagen #74134) in each case.
RNA quality was checked in Tapestation (Agilent High Sensitivity RNA ScreenTape) and quantified by Nanodrop. 500ng were used for Total RNA libraries preparation using Illumina kit (Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus #20040529). Libraries were then sequenced with the Novaseq6000 Illumina technology according to the standard protocols and with around 100 million 150bp paired-end total per sample.

value: WT

value: replicate 1


title: scc15si-NC2

value: negative control for si-IGF2BP3(replication2)


title: Nebulized_FLAMOD_4h_L3_biol_rep4

description: Library name: Library-200

data_processing:
Genome index was generated using genome Sus_scrofa.Sscrofa11.1 and annotation file Sus_scrofa.Sscrofa11.1.113.gtf through STAR-2.7.10a (sjdbOverhang 149)
Sequence reads were mapped to generated genome using STAR-2.7.10a (-quantMode using bidirectional input (R1/R2))
Assembly: Sscrofa11.1 (GCA_000003025.6)
Supplementary files format and content: ReadsPerGene.out.tab file with four columns (gene ID, counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA, counts for the 2nd read strand aligned with RNA)  was generated by STAR for each sample
Supplementary files format and content: TAB files include read counts for each sample (only first two columns were used :Gene ID and read counts for unstranded RNA-seq)

extract_protocol:
Nasal, tracheal, bronchial, lung tissues and blood samples were collected for RNA extraction and sequencing. Tissues were preserved in NucleoProtect® RNA (Macherey-Nagel, Duren, Germany) at -80°C until ready for processing. Tissue was dried on paper towels and any visible cartilage was removed. The remaining tissue was weighed and depending on size of tissue was added to 1-3 ml RA1 lysis buffer (Macherey-Nagel) supplemented with 2% TCEP (Sigma) and disintegrated with an UltraTurrax homogenizer (IKA-Werke, Staufen, Germany). For nasal, bronchial and tracheal samples, a pretreatment with proteinase K was performed to remove collagen. Briefly, 350 l of lysate was added to 595 l water substituted with 10 l proteinase K (20 mg/ml) and incubated at room temperature for 10 min, followed by 10 min incubation at 55 °C and centrifugation at 10,000 rpm for 3 min. The supernatant was then mixed with 490 l of 100% ethanol and the mixture was loaded onto the NucleoSpin® RNA Plus extraction kit columns, and RNA was extracted as per manufacturer’s instructions (Macherey-Nagel) and eluted in 30 l RNAse-free water. Lung samples were eluted in 60 l RNAse-free water.
RNA libraries for RNA-seq were prepared using QIAseq stranded mRNA library kit (Qiagen) as well as QIAseq FastSelect-Globin Kit for blood samples (Qiagen). 200 ng of total RNA.

value: Lung 3

value: LRxLW TOPIGS 20

value: Flagellin


title: Nebulized_FLAMOD_24h_L3_biol_rep1

description: Library name: Library-201


title: scc15si-NC1

value: negative control for si-IGF2BP3(replication1)


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-03


title: AsiSI_U2OS_Input_NS_Seq_Figure3abc_EDF8a_replicate 2

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

data_processing:
BAM files were filtered using alignmentSieve to remove reads shorter than 40bp
For peak calling the MACS2 algorithm was used.
Nascent strand reads were called by comparison to genomic DNA.
Peaks were filtered to accept the top 40% by q-value based on the raw output
Assembly: hg19
Supplementary files format and content: Bed file format showing: AsiSI TADs and random TADs AsiSI cut sites in U2OS NS-seq peaks AsiSI cut sites in LIG4-/- AID RAD21 AsiSI-HCT116 replication timing in U2OS
Supplementary files format and content: BigWig file format of BrdU-seq NS-seq and ChIP-seq

source_name: Bone

growth_protocol: AsiSI-U2OS cells were grown in DMEM medium 10% FBS. AID RAD21 HCT116 and AID RAD21 AsiSI HCT116 are grown in McCoy's 5A medium with 10% FBS

extract_protocol:
DNA from cell cultures was isolated size fractionated and subject to exunuclease digestion as described in Aladjem et al. Science 281 1005 1998. and Wang et al. Molecular and Cellular Biology 24:3373-86 2004. For ChipSeq DNA molecules were enriched using antibodies against proteins of interest. For BrdU seq extraction was performed using a protocol modified from Marchal et al. 2018
Samples were eluted and then purified by Monarch PCR & DNA Cleanup Kit (NEBT1030S). 100 ng of samples were used to generate the library. The kits used for the library were NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7805S) and NEBNext Multiplex Oligos for Il-lumina (Index Primers Set 1 and Set 2) (NEB E7335S and E7500S).

treatment_protocol: 4OHT was added at a concentration of 300 nM for 4h to induce DNA DSBs. Where relevant WEE1i was added at a concentration of 10 uM for 1h.

value: Bone

value: Osteosarcoma

value: Wild-type AsiSI_U2OS

value: No treatment


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-04


title: totalRNASeq_WT_IAA_rep2

value: mESC

value: IAA

value: replicate 2


title: Nebulized_FLAMOD_4h_L3_biol_rep2

description: Library name: Library-198


title: totalRNASeq_WT_IAA_rep1


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-02

value: skin


title: Nebulized_FLAMOD_4h_L3_biol_rep3

description: Library name: Library-199


title: Nebulized_buffer_24h_L3_biol_rep4

description: Library name: Library-196

value: Buffer


title: Nebulized_FLAMOD_4h_L3_biol_rep1

description: Library name: Library-197


title: totalRNASeq_S354F_ID_rep2

value: IAA+Doxyxycline


title: totalRNASeq_S354F_ID_rep1


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-06

value: EBS

value: M


title: Nebulized_buffer_24h_L3_biol_rep3

description: Library name: Library-195


title: AsiSI_U2OS_control_NS_Seq_Figure3abc_EDF8a_replicate 1


title: AsiSI_U2OS_control_NS_Seq_Figure3abc_EDF8a_replicate 2


title: AsiSI_U2OS_Input_NS_Seq_Figure3abc_EDF8a_replicate 1


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-09


title: totalRNASeq_R448Q_ID_rep2


title: AsiSI_U2OS_4OHT_NS_Seq_Figure3abc_EDF8a_replicate 2


title: Nebulized_buffer_24h_L3_biol_rep2

description: Library name: Library-194


title: totalRNASeq_WT_ID_rep2

value: WT


title: totalRNASeq_R448Q_ID_rep1

value: replicate 1


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-11


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-12


title: AsiSI_U2OS_4OHT_NS_Seq_Figure3abc_EDF8a_replicate 1


title: totalRNASeq_R377H_ID_rep2


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-13


title: PD JAK2V617F sAML 100 nM SY5609 2

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data FASTQ files were generated by standard illumina base calling pipeline. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, Reads were aligned to hg38 reference genome using STAR with default parameters
STAR was used to generate the "raw count" from an aligned bam againt transcript file
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: patient derived sAML

growth_protocol: sAML HEL92.1.7 cells were cultured in 20% FBS containing RPMI media.

extract_protocol:
Total RNA was isolated with a kit from Ambion, Inc. The RNA was DNAse I treated to eliminate genomic DNA, then the purified RNA was utilized to make libraries for next generation sequencing.
Bulk RNA Libraries were constructed following standard Illumina protocols for RNA sequencing in a sequencing and microarray core facility. Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.

treatment_protocol: AML cells were treated with SY-1365 or SY-5609 (100 nM) for 16 hours at 37°C and harvested into RNA lysis buffer. Lysed cells were frozen at -80°C until they were processed for total RNA.

value: patient derived sAML

value: PD JAK2-V617F sAML

value: PD JAK2V617F sAML 100 nM SY5609 2


title: Viral Female P24

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL

address: 1207 W. Gregory Dr.

institute: University of Illinois

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Reads of length 100 nt were recorded in FASTQ files that were demultiplexed with the bcl2fastq v2.20 conversion software (Illumina Inc, San Diego, CA, USA)
Reads were processed according to manufacturer instructions with reads trimmedusing trim_galore v0.6.10. The remaining reads at least 25nt in length after adaptor trimming were retained.
Reads were mapped to the Sus scrofa UCSC (susScr11_2) reference genome using Bismark version 0.22.3 (Krueger & Andrews, 2011) with the HISAT2 short read aligner with default options.
Assembly: Sus scrofa genome (version 11.1)
Supplementary files format and content: cvs format, number of methylated (numC) and non-methylated (numT) positions for each 100,000 bp genome segment for each sample

source_name: Hypothalamus

extract_protocol:
DNA was extracted from all samples using EZNA isolation kit (Omega Biotek, Norcross, GA, USA)  following standards protocols.
Libraries were prepared with Ovation Reduced Representation Bisulfite (RRBS) Methyl-Seq system (NuGEN, now Tecan Genomics, Redwood City, CA) according to manufacturers instructions. The libraries were quantitated by qPCR and NovaSeq 6000 using a NovaSeq SP reagent kit (Illumina Inc, San Diego, CA, USA).

value: Hypothalamus

tag: sampleID

tag: age

value: 21 day old

tag: mia

value: Viral

value: Female


title: Viral Male P23

tag: tissue

value: Male


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-15


title: PD JAK2V617F sAML 100 nM SY5609 1

value: PD JAK2V617F sAML 100 nM SY5609 1


title: totalRNASeq_R377C_ID_rep2

source_name: mESC

value: mESC

value: replicate 2


title: PD JAK2V617F sAML Control 2

value: PD JAK2V617F sAML Control 2

value: Control


title: totalRNASeq_R377C_ID_rep1

value: IAA+Doxyxycline


title: Viral Male P20


title: Viral Female P22


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-16

value: skin

value: EBS

value: M


title: PD JAK2V617F sAML Control 1

value: patient derived sAML

value: PD JAK2V617F sAML Control 1


title: totalRNASeq_R342C_ID_rep2


title: HEL92.1.7 100 nM SY5609 1

source_name: cell line

value: cell line


title: HEL92.1.7 100 nM SY5609 2


title: Viral Male P21

value: Hypothalamus


title: totalRNASeq_R339Q_ID_rep2


title: Skin, post hunt sampling, RNAlater, ARHI-21-04


title: Skin, post hunt sampling, RNAlater, ARHI-21-06


title: Viral Female P18

value: 21 day old


title: Skin, post hunt sampling, RNAlater, ARHI-21-03


title: Nebulized_buffer_24h_L3_biol_rep1

description: Library name: Library-193

value: Lung 3

value: LRxLW TOPIGS 20

value: Buffer

tag: animal id

tag: time


title: totalRNASeq_R377H_ID_rep1

tag: strain

tag: treatment

value: replicate 1


title: totalRNASeq_R339Q_ID_rep1

value: mESC


title: HEL92.1.7 100 nM SY1365 1


title: Skin, post hunt sampling, RNAlater, ARHI-21-07


title: Viral Male P17

value: Viral

value: Male


title: totalRNASeq_Q418R_ID_rep2

value: replicate 2


title: Skin, post hunt sampling, RNAlater ice, ARHI-20-14


title: Skin, post hunt sampling, RNAlater, ARHI-21-08


title: HEL92.1.7 Control 2

value: HEL92.1.7 Control 2

value: Control


title: Viral Female P16

value: Female


title: Skin, post hunt sampling, RNAlater, ARHI-21-11

value: skin

value: EBS

value: M


title: totalRNASeq_R342C_ID_rep1

value: IAA+Doxyxycline


title: Viral Male P19

value: Hypothalamus


title: Skin, post hunt sampling, RNAlater, ARHI-21-12


title: Viral Female P15

value: 21 day old


title: totalRNASeq_K365T_ID_rep2


title: Skin, post hunt sampling, RNAlater, ARHI-21-13


title: HEL92.1.7 100 nM SY1365 2

value: cell line


title: C28/I2 cells, DPP4OE2 + 4,5-Dicaffeoylquinic acid

city: chengdu

first: li

last: xinyu

address: renmin south road

institute: westchina hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismatch cost: 2, insertion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
mm10
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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

value: chondrocytes

value: DPP4 overexpression

value: 4,5-Dicaffeoylquinic acid


title: totalRNASeq_Q418R_ID_rep1

value: mESC

value: replicate 1


title: Control Male P13

value: Male


title: totalRNASeq_H455R_ID_rep2


title: totalRNASeq_H455R_ID_rep1


title: Lacrimal gland, wild-type female mouse #6852, 8 weeks of age

first: Cintia

middle: Sade

last: de Paiva

address: One Baylor Plaza

department: Ophthalmology

institute: Baylor College of Medicine

data_processing:
Data were analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, California). Reads were trimmed using cutadapt and quality scores were assessed using FastQC. Reads were aligned to the Mus musculus genome build GRCm38 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using the DESeq2 R library. Read distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC.  DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. The clustering of genes for the final heatmap of differentially expressed genes was done using the partitioning around medoids method using the fpc R library. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library, was used to determine local similarities and dependencies between GO terms to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro3, NCBI, MSigDB REACTOME, and WikiPathways. A single-read 75 base pair cycle run was used to sequence the flow cell. An average of 34 million reads per sample was sequenced. The FastQ file generation was executed using Illumina’s cloud-based informatics platform, BaseSpace Sequencing Hub (Illumina).
Assembly: GRCm38
Supplementary files format and content: Text file of raw counts in matrix
Supplementary files format and content: Text file of normalized counts in matrix

source_name: Extraorbital Lacrimal Gland

extract_protocol:
A Qiagen Plus Mini Kit was used to extract RNA from total excised lacrimal gland lysates, per manufacturer protocol.
A double-stranded DNA library was created at Baylor College of Medicine’s Genomics and RNA Profiling Core. Briefly, using 100ng of total RNA (measured by pico green), an oligodT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA, and reverse transcription was performed using a Lexogen kit. Second-strand synthesis was initiated by a random primer containing an Illumina-compatible linker sequence at its 5’ end. The purified double-stranded library was then amplified and purified. The resulting libraries were quantitated using Qubit 2.0 (ThermoFisher) and fragment size was assessed with the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, California).

value: Extraorbital Lacrimal Gland

value: wild-type


title: Skin, post hunt sampling, RNAlater, ARHI-21-15


title: Skin, post hunt sampling, RNAlater, ARHI-21-14


title: Viral Male P14

value: Viral


title: Control Male P12

value: Control


title: C28/I2 cells, DPP4OE1 + 4,5-Dicaffeoylquinic acid


title: Control Female P10

value: Female


title: Skin, post hunt sampling, RNAlater, ARHI-21-16

value: skin

value: EBS


title: Lacrimal gland, CD25KO female mouse #6826, 8 weeks of age


title: Lacrimal gland, CD25KO female mouse #6822, 8 weeks of age


title: Skin, post hunt sampling, RNAlater, ARHI-21-18

value: M


title: C28/I2 cells, DPP4OE1


title: Control Male P09

value: Hypothalamus


title: HEL92.1.7 Control 1

value: HEL92.1.7 Control 1


title: Skin, post hunt sampling, RNAlater, ARHI-21-19


title: Control Male P08

value: 21 day old


title: C28/I2 cells, DPP4OE3 + 4,5-Dicaffeoylquinic acid

value: chondrocytes


title: totalRNASeq_K365T_ID_rep1

value: IAA+Doxyxycline


title: C28/I2 cells, OEControl3

value: WT


title: Lacrimal gland, CD25KO female mouse #6891, 8 weeks of age


title: C28/I2 cells, OEControl2


title: Control Male P11


title: C28/I2 cells, DPP4OE3

value: DPP4 overexpression


title: C28/I2 cells, DPP4OE2


title: Control Female P07


title: Skin, biopy sampling, bulk, DLB-1507

value: SLE


title: Control Female P06


title: Skin, biopy sampling, bulk, DLB-1513


title: C28/I2 cells, OEControl1


title: Skin, post hunt sampling, RNAlater, ARHI-21-17


title: Control Female P05


title: Lacrimal gland, CD25KO female mouse #6893, 8 weeks of age


title: siTRIP12+siOTUD5, rep. 3

city: Shinagawa-ku

first: Fumiaki

last: Ohtake

state: Tokyo

country: Japan

institute: Hoshi University

data_processing:
Trimmed reads are mapped to reference genome with HISAT2.
After the read mapping, Stringtie was used for transcript assembly. Expression profile was calculated for each sample and transcript/gene as read count, FPKM (Fragment per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million).
Assembly: In order to map cDNA fragments obtained from RNA sequencing, GRCh38 was used as a reference genome.
Supplementary files format and content: Excel file containing FPKM and TPM for each sample

source_name: HT1091 cells

extract_protocol:
Total RNA was isolated using Rneasy mini plus kit (QIAGEN).
RNA libraries for RNA-seq was prepared using TruSeq Stranded mRNA LT Sample Prep Kit following the manufacturer's protocol (TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E).

value: HT1091 cells

value: human sarcoma cell


title: siTRIP12+siOTUD5, rep. 2

source_name: HT1090 cells

value: HT1090 cells


title: Skin, biopy sampling, bulk, DLB-1515


title: Lacrimal gland, CD25KO female mouse #6918, 8 weeks of age

value: Extraorbital Lacrimal Gland


title: Control Female P04

value: Control


title: siTRIP12+siOTUD5, rep. 1

source_name: HT1089 cells

value: HT1089 cells


title: Lacrimal gland, wild-type female mouse #6824, 8 weeks of age

value: wild-type


title: siOTUD5, rep. 3

source_name: HT1088 cells

value: HT1088 cells


title: Control Male P02

value: Male


title: Skin, biopy sampling, bulk, DLB-1517

value: skin

value: M


title: Skin, biopy sampling, bulk, DLB-1519


title: Lacrimal gland, wild-type female mouse #6921, 8 weeks of age


title: siOTUD5, rep. 2

source_name: HT1087 cells

value: HT1087 cells


title: Skin, biopy sampling, bulk, DLB-1534


title: thrombus, Model3

city: Beijing

first: Zhenguo

last: Zhai

address: No.2 East yinghua road

department: Department of Pulmonary and Critical Care Medicine

institute: China-japan Friendship Hospital

data_processing:
High-quality reads were compared to the reference genome/transcriptome using STAR software (v2.5.1b), and cyclic RNA was detected and characterized using DCC software (v0.4.4).
The identified circular RNAs were annotated using the circBase database and Circ2Traits.
Data normalization and differential expression circRNA screening were then performed using edgeR software (v3.16.5). GO and KEGG analyses were also performed on the genes of origin of the differentially expressed circRNAs.
Assembly: mm10
Supplementary files format and content: Gene Expression Profiling.xlsx

source_name: thrombus

extract_protocol:
Use the GenSeq® rRNA Removal Kit (GenSeq, Inc.) to remove ribosomal RNA (rRNA) from the samples. After rRNA removal, construct sequencing libraries using the GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer's instructions.
After sequencing on Illumina NovaSeq 6000 sequencer, bipartite reads were harvested.Q30 was utilized for quality control, and cutadapt software (v1.9.3) was used to de-join and remove low-quality reads to obtain high-quality reads.Cloud Sequencing Bio used different methods to respectively analyze circRNA, LncRNA and mRNA.

value: thrombus


title: Lacrimal gland, CD25KO female mouse #6819, 8 weeks of age


title: siOTUD5, rep. 1

source_name: HT1086 cells

value: HT1086 cells


title: Skin, biopy sampling, bulk, DLB-1538


title: thrombus, Model2


title: Skin, biopy sampling, bulk, DLB-1546


title: siTRIP12, rep. 2

source_name: HT1084 cells

value: HT1084 cells


title: Skin, biopy sampling, bulk, DLB-1540


title: siTRIP12, rep. 3

source_name: HT1085 cells

value: HT1085 cells


title: Control Female P03

value: Hypothalamus

value: 21 day old

value: Female


title: thrombus, Model1


title: Lacrimal gland, wild-type female mouse #6924, 8 weeks of age


title: ATACseq-MORC-KD-IAA_replicate-3

city: La Tronche

first: Christopher

last: Swale

address: Batiment Jean Roger

department: U1209 - Institute of Advanced Biosciences

institute: INSERM

description: ATACseq-MORC-IAA-merged.bw

data_processing:
Following the demultiplexing of raw reads by bcl2fastq V3, trimming, quality control, alignment to the ME49 reference genome (using bwa2).
Aligned reads were used for peak calling of the ChIP enriched peaks using Generich with a cutoff p-value of 0.1. Reads were counted on annotated peaks by featureCounts and counts were processed by DeSeq2 to generate global statistical analysis of peak intensities in between conditions using biological triplicates.
Assembly: Assembly: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" dowloaded from the ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary files format and content: Supplementary files format and content: Data visualization:  Merged bam files were converted to bigWig file format using a bin size of 5 by bamCoverage (Deeptools).

organism: Toxoplasma gondii

source_name: RH

growth_protocol: Toxoplasma gondii type I strains were maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Diagenode ATAC-SEQ kit protocol (C01080002)
Diagenode ATAC-SEQ kit protocol (C01080002) in 100 000 tachyzoites

treatment_protocol: HFF cells were grown to confluence and infected with HK80 SNF2h KD, RHK80 RFTS KD, RHK80 SNF2L KD or RHK80  MORC KD strains. Genome-wide Tn5 transposase accessiblity profiles in each strain left untreated (UT) and treated with IAA (indole-3-acetic acid) for 24 hours.

value: RH

value: Intracellular tachyzoites

value: IAA treated for 24h


title: Skin, biopy sampling, bulk, DLB-1548

source_name: skin

value: SLE


title: thrombus, Control3


title: siTRIP12, rep. 1

source_name: HT1083 cells

value: HT1083 cells

value: human sarcoma cell


title: thrombus, Control2


title: Skin, biopy sampling, bulk, DLB-1549


title: Scrambled, rep. 2

source_name: HT1081 cells

value: HT1081 cells

value: Scrambled


title: Skin, biopy sampling, bulk, DLB-1551

value: skin

value: M


title: ATACseq-MORC-KD-IAA_replicate-1

description: ATACseq-MORC-IAA-merged.bw


title: Control Female P01

source_name: Hypothalamus

value: Control


title: Scrambled, rep. 3

source_name: HT1082 cells

value: HT1082 cells


title: ATACseq-MORC-KD-UT_replicate-3

description: ATACseq-MORC-UT-merged.bw

value: untreated sample


title: Wnt2-CreERT2 driven EYFP lineage, E12.5, sequencing lane 2

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Reads from L1 and L2 from each experimental condition were simultaneously aligned to the GRCm39 genome using STAR-solo to generate gene by cell counts matrices, using the parameters soloUMIdedup=”1MM_CR”, soloUMIfiltering=”MultiGeneUMI_CR”, and soloCellFilter=”EmptyDrops_CR”.
Counts matrices processed using anndata and scanpy
Assembly: GRCm39
Supplementary files format and content: h5ad anndata-readable annotated scRNA-seq dataset processed with scanpy

source_name: lung/heart

extract_protocol:
Single cell suspensions were made from tissue dissected from the thoracoabdominal area of two litters of whole embryos at E10.5, combined heart and lung dissected out from four embryos at E12.5, and four separated hearts that included the pulmonary vein and artery up to the hilum of the lung at E17.5, and four separated lungs containing only intrapulmonary tissue at E17.5. EYFP+ cells were isolated via FACS .
10Xv3 GEX

value: lung/heart


title: Skin, biopy sampling, bulk, DLB-1554


title: TW2.6 cells_knockdown_ALDH2

type: RNA

city: Kaohsiung

first: Yi-Fang

last: Yang

address: No. 386, Dajhong 1st Rd., Zuoying Dist., Kaohsiung City 813414, Taiwan.

department: Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C onAaffymetrix-calvin-array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: buccal squamous cell carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: TW2.6/shluc and TW2.6/shALDH2  cells were cultured in 5% CO2 incubator at 37℃

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

value: head and neck cancer cell

value: TW2.6 cells

tag: knockdown


title: TW2.6 cells_knockdown_control

value: control


title: Skin, biopy sampling, bulk, DLB-1560


title: ATACseq-MORC-KD-UT_replicate-2

description: ATACseq-MORC-UT-merged.bw

value: RH


title: Scrambled, rep. 1

source_name: HT1080 cells

value: HT1080 cells


title: Wnt2-CreERT2 driven EYFP lineage, E12.5, sequencing lane 1


title: ATACseq-MORC-KD-IAA_replicate-2

description: ATACseq-MORC-IAA-merged.bw

value: Intracellular tachyzoites

value: IAA treated for 24h


title: Skin, biopy sampling, bulk, DLB-1564

value: SLE


title: Wnt2-CreERT2 driven EYFP lineage, E17.5, lung tissue, sequencing lane 2

source_name: lung

value: lung


title: co-culture with fibroblasts replicate 1

city: ann arbor

first: gary

last: luker

address: 109 zina pitcher place

department: radiology

institute: university of michigan

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: gene_expected_count.annot.txt

growth_protocol: Cancer cells cultured as organoids without or with carcinoma associated fibroblasts

extract_protocol:
Separate cancer cells from fibroblasts with EpCAM beads and prepare RNA with Qiagen kit
poly A enrichment

value: Colon cancer patient-derived cell

tag: batch

value: co-cultured with CAFs


title: colon cancer monoculture replicate 2

tag: cell line

value: monoculture


title: thrombus, Control1

value: thrombus


title: ATACseq-SNF2L-KD-IAA_replicate-3

tag: genotype


title: colon cancer monoculture replicate 1


title: co-culture with fibroblasts replicate 2


title: Skin, biopy sampling, bulk, DLB-1566

value: skin

value: M


title: Wnt2-CreERT2 driven EYFP lineage, E17.5, lung tissue, sequencing lane 1


title: Wnt2-CreERT2 driven EYFP lineage, E17.5, heart tissue, sequencing lane 2

source_name: heart

value: heart


title: ATACseq-SNF2L-KD-IAA_replicate-2


title: Skin, biopy sampling, bulk, DLB-1637


title: Skin, biopy sampling, bulk, DLB-1568


title: Wnt2-CreERT2 driven EYFP lineage, E17.0, Wnt2KO/KO, sequencing lane 1

value: lung/heart


title: ATACseq-SNF2L-KD-IAA_replicate-1


title: Skin, biopy sampling, bulk, DLB-1640


title: Skin, biopy sampling, bulk, DLB-1629


title: Wnt2-CreERT2 driven EYFP lineage, E17.5, heart tissue, sequencing lane 1


title: ATACseq-SNF2L-KD-UT_replicate-3

value: untreated sample


title: Control1, ST

first: Raghuveer

last: Kavarthapu

address: 10 Center Dr, Bldg 10, Room 1E3340

department: NICHD

institute: National Institutes of Health (NIH)

data_processing:
Raw sequencing files generated by Illumina sequencing were demultiplexed & processed using the Space Ranger default pipeline to obtain fastq files for each sample.
Alignment of reads (genome hg38), filtering and UMI counting was performed to obtain gene barcode matrix file (gene counts per nucleus) using Space Ranger software from 10x Genomics.
Assembly: hg38
Supplementary files format and content: filtered_feature_bc_matrix.h5 file : The "matrix.h5 file contains information about the features (genes) and cell-barcodes associated with the matrix rows and columns
Supplementary files format and content: scalefactors_json.json : scale factors in json format
Supplementary files format and content: tissue_positions.csv :  list of barcodes and coordinate specifying visium spots
Supplementary files format and content: tissue_hires_image.png : high-resolution images of the ovarian sections
Library strategy: Visium Spatial Transcriptomics

source_name: ovary tissue from Ewing sarcoma patient

extract_protocol:
FFPE ovary sections (5 microns) were mounted onto a positively charged slide followed by staining with hematoxylin and eosin. Slides were mounted in 70% glycerol and brightfield images were taken using microscope.  The tissue sections were transferred immediately onto 6.5 × 6.5mm or 11mm x 11mm capture areas on a Visium gene expression slide using Visium CysAssist (10x Genomics). The tissue sections were then subjected to permeabilization followed by reverse transcription for cDNA synthesis. Subsequently, the cDNA amplification was performed, and spatial libraries were constructed. The libraries were pooled and paired-end sequencing was performed on S2 flow cell using an Illumina NovaSeq 6000 platform.
Spatial transcriptome sequencing libraries from ovarian tissue were constructed using 10x Genomics Visium spatial gene expression slide & reagent kit

value: Ovary

tag: group


title: Wnt2-CreERT2 driven EYFP lineage, E17.0, Wnt2KO/KO, sequencing lane 2


title: ATACseq-MORC-KD-UT_replicate-1

description: ATACseq-MORC-UT-merged.bw


title: ATACseq-SNF2L-KD-UT_replicate-1


title: ATACseq-SNF2L-KD-UT_replicate-2


title: Skin, biopy sampling, bulk, DLB-1643


title: CG5, ST

source_name: ovary tissue from CG patient

value: CG


title: Wnt2-CreERT2 driven EYFP lineage, E17.0, Wnt2+/KO, sequencing lane 2


title: Wnt2-CreERT2 driven EYFP lineage, E17.0, Wnt2+/KO, sequencing lane 1


title: Wnt2-CreERT2 driven EYFP lineage, E10.5, sequencing lane 2


title: Control5, ST

source_name: ovary tissue from Medullablastoma patient

value: control


title: Skin, biopy sampling, bulk, DLB-1653


title: ATACseq-RFTS-KD-IAA_replicate-2

description: ATACseq-RFTS-IAA-merged.bw

value: RH