title: sample_39

value: Retina Periphery

value: >15 years

value: Plavix, metoprolol,dyrenium, gabapentin, multivitamin

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: Phaco, trabeculectomy

value: OD

value: Water


title: sample_24

status: Public on Apr 19 2021

type: SRA

city: Biberach an der Riß

first: Kolja

last: Becker

address: Birkendorfer Str. 65

department: Global Computational Biology and Digital Sciences

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co. KG

library_source: transcriptomic

data_processing:
Filtered reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR aligner software (STAR version 2.5.2b) allowing for soft clipping of adapter sequences. For quantification of transcript levels the annotation files from Ensembl version 86 were used, which corresponds to GENCODE 25. Samples were quantified with the above annotations, using RSEM (RSEM version 1.3.0) and featureCount (featureCount version 1.5.1). Quality controls were implemented using FastQC (FastQC version 0.11.5), picardmetrics (picardmetrics version 0.2.4), and dupRadar (dupRadar version 1.0.0) at the respective steps.
Normalized log2 Counts Per Million (CPM) mRNA expression values were calculated using the voom function provided by the limma R package (limma version 3.42.0).
mRNA were filtered by minimum read counts using the filterByExpr function of the edgeR package (edgeR version 3.26.5) and. In addition, a Gaussian mixture model (mclust version 5.4.5) was applied, fitting two Gaussian distributions to mean CPM expression data. mRNA assigned to the cluster with higher mean were retained.
Surrogate variables describing a technical confounder effect were estimated using the sva R package (sva version 3.34.0). mRNA expression was corrected for donor age as well as the estimated surrogate variable. In more detail, we designed linear models with mRNA expression of each individual transcript as response, and donor age as well as the estimated surrogate variable as covariates. For each linear model, a t-test was performed on the covariate to assess its statistical significance. In case the p-value for a transcript was below 0.05, the expression values of that transcript were replaced by the residuals of the linear model plus the intercept of the model.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: human_retina_DR_totalRNA_normalized_cpm.txt - normalized cpm values for each gene

molecule: total RNA

organism: Homo sapiens

source_name: Retina Macula

extract_protocol:
Post-mortem human eyes from 43 donors were obtained through the Iowa Lions Eye Bank (Coralville, IA) after written informed consent of the next-of-kin was obtained and preserved within 6 hours post-mortem. Donors were categorized into one of four disease groups: a) diabetic donors with no apparent visual impairment or visible pathology of the retina at last eye exam, b) donors diagnosed with non-proliferative diabetic retinopathy (NPDR) but without diabetic macular edema (DME), c) patients diagnosed with NPDR with additional indication of DME, or d) donors diagnosed with proliferative diabetic retinopathy (PDR) and DME. The diagnosis was based on the early treatment diabetic retinopathy study Diabetic Retinopathy Severity Score (ETDRS-DRSS). Additional retinal samples were taken from healthy donors to serve as the control group. The study was designed such that donors of all groups approximately matched in age and gender distribution. Note that none of the donors received treatment for their retinal indication. The study design was reviewed by the University of Iowa Institutional Review Board and found not to involve human subjects research. From each donor group (healthy control, diabetic, NPPR, and NPDR/PDR + DME), 10 tissue samples were collected from the macula region as well as the retinal periphery. All tissue samples were taken with a 6mm biopsy punch, snap frozen in liquid nitrogen, and preserved at -80C until use. Both miRNA and total RNA was extracted using miRNeasy kits (Qiagen) after homogenization of the retina with Qiashredders (Qiagen). RNA was eluted into 30 μl of dH2O. RNA was quantitatively and qualitatively assessed using the fluorescence-based Broad Range Quant-iT RNA Assay Kit (ThermoFisher) and the Standard Sensitivity RNA Analysis DNF-471 Kit on a 48-channel Fragment Analyzer (Agilent), respectively. Concentrations averaged at 100ng/µL while RIN ranged from 4 to 9.
Retina-derived RNA samples were normalized on the MicroLab STAR automated liquid platform (Hamilton). Total RNA input of 240ng was used for library construction with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext rRNA depletion Kit #E6310 upstream and the NEXNext Multiplex Oligos for Illumina #E7600 downstream (all New England Biolabs). The only deviation from the manufacturer’s protocol was the use of Ampure XP beads (Beckman Coulter) at the double-stranded cDNA purification step, instead of the recommended SPRIselect Beads. Final sequencing libraries were quantified by the fluorescence dye-based methodology High Sensitivity dsDNA Quanti-iT Assay Kit (ThermoFisher) on a Synergy HTX (BioTek). Total RNA libraries were also assessed for size distribution and adapter dimer presence by the High Sensitivity NGS Fragment DNF-474 Kit on a 48-channel Fragment Analyzer (Agilent). Sequencing libraries were normalized on the MicroLab STAR (Hamilton), pooled as two 40-plex pools and spiked in with PhiX Control v3 (Illumina). The two individual pools were then separately clustered on a cBot instrument with a HiSeq 3000/4000 PE Cluster Kit and subsequently sequenced on a HiSeq 4000 Sequencer (all Illumina) with dual index, paired-ends reads at 75 bp length (Read parameters: Rd1: 76, Rd2: 8, Rd3: 8, Rd4: 76) to reach a minimum depth of 50 million Pass-filter reads per sample.

tag: tissue

value: Retina Macula

tag: sampleID

tag: samplenumber

tag: donor

tag: gender

value: male

tag: age

value: 9 years

value: Insulin (Humalin)

value: digoxin, prednisone, coumarin

tag: comorbidities

value: cholecystectomy, prostrate surgery

value: PVD, cataracts

value: Diabetic

tag: dme

value: FALSE

tag: eye

value: Macula

tag: buffer

value: ul

value: ng/ul

tag: rin

value: min


title: sample_22

value: >12 years

value: glyburide, insulin

value: atenolol, lisinopril

value: pancreatic cancer, dyspnea from pleural effusion, DM, Afib.

value: cataract


title: sample_23

value: Retina Macula

value: male

value: >25 years

value: Glimepiride, Novolin

value: isosorbide, metoprolol, allopurinol, lisinopril, lasix, ASA, Crestor,  Zetia, sulfasalazine, digoxin

value: ischemic cardiomyopathy, CAD, aortic stenosis, DM, renal insufficiency, hyperlipidemia, HTN, TIA, spinal stenosis, ulcerative colitis, left ulnar palsy,

value: OD

value: Water


title: Series#1: mmu-miR-124-3p(MC10691)-3

city: Fujisawa

first: MASAHIRO

last: NOGAMI

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Research

country: Japan

institute: Takeda Pharmaceutical Company Limited

description: biological replicate #3

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic_ver.0.36 PE -phred 33 -trimlog ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10
Sequenced reads were masked for low-complexity or low-quality sequence with PRINSEQ_ver. 2.20.4 -fastq -fastq2 -out_good -out_bad -out_format 3 -trim_left 5 -trim_tail_right 5 -trim_qual_right 30 -ns_max_p 20 -min_len 30
Mapping to GRCm38.p6 whole genome using STAR_ver.2.5.4b --runMode alignReads --runThreadN 9 --genomeDir --sjdbScore 1 --sjdbGTFfile --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonical --readFilesCommand zcat --readFilesIn --outFileNamePrefix --outFilterMultimapNmax 8 --outFilterMismatchNmax 4 --outFilterType BySJout --outFilterMismatchNoverReadLmax 0.04 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignMatesGapMax 1000000
The number of reads count in the exons of were counted. featureCounts_ver. 1.61 -T 9 -F GTF -O -p -t exon -g gene_id -a gencode.vM17.chr_patch_hapl_scaff.annotation.gtf -o
Genome_build: GRCm38.p6, gencode.vM17.chr_patch_hapl_scaff.annotation.gtf

organism: Mus musculus

source_name: NSC-34 cell treated with mmu-miR-124-3p mimic and RNAiMAX.

growth_protocol: NSC-34 cells were maintained in DMEM (Sigma; # D5796-500ML) with 10% FBS (ATCC, #30-2020) and 100 U/ml Penicillin-Streptomycin (Invitrogen, #15140122) in 5% CO2 at 37 °C.

extract_protocol:
After 48 hours from miRNA mimic transfection, total RNA were extracted from the cells by miRNeasy Kit with QIAzol (QIAGEN).
Illumina Strand-Specific RNA library preparation with polyA selection

treatment_protocol: 400,000 NSC-34 cells/well (6 well plate) were plated on collagen coated plate and 60 nM miRNA mimics and siNC#2 were transfected with Lipofectamine RNAiMAX reagent.

value: NSC-34 cells

tag: cell type

value: mouse motor neuron-like cells


title: Series#1: mmu-miR-124-3p(MC10691)-2

description: biological replicate #2


title: sample_26

value: female

value: 8 years

value: metformin

value: allopurinol, aspirin, ferrous sulfate,  neurontin, omeprazole, KCl, PreserVision, Restasis, Demadex, Tyvaso inhaler, Zetia

value: breast CA, CHF, A-fib, HTN, pulmonary artery fibrillation/flutter-unsuccessful R atrial ablation; non ischsmic dilated cardiomyopathy, hysterectomy 1992; bowel obstruction

value: asteroid hyalosis, choroiodal nevus

value: Diabetic

value: FALSE

value: OS

value: Macula

value: ul

value: ng/ul


title: Series#1: miR-125b-5p mimic(MC10148)-3

description: biological replicate #3

source_name: NSC-34 cell treated with miR-125b-5p mimic and RNAiMAX.


title: sample_21

value: Retina Macula

value: 10 yrs

value: atenolol/chlorthalidone, monopril, synthroid, ambien, tylenol .3, amitriptyline

value: DM, HTN, hypothyroidism, depression CHF, osteoarthritis

value: cataracts, Fuchs., glaucoma suspect, corneal dystrophy

value: min


title: Series#1: mmu-miR-124-3p(MC10691)-1

description: biological replicate #1

value: NSC-34 cells

value: mouse motor neuron-like cells


title: sample_20

source_name: Retina Periphery

value: Retina Periphery

value: female

value: Haldol, lorazepam, melatonin, nystatin, omeprazole, Zofran, oxycodone

value: metastatic duodenal cancer, chemotherapy, small bowel obstruction, hernia repair, hyponatremia, hypertension hyperlipidemia,

value: Control

value: OD

value: Periphery

value: Water


title: sample_02

value: male

value: isoptin, imdur, prozac, trazodone, ASA

value: CAD, s/p coronary angioplasties, HTN, COPD, hyperlipidemia, anxiety, depression, s/p appendectomy, s/p hemorrhoidectomy.

value: cataracts

value: FALSE

value: Macula

value: ul

value: ng/ul


title: Series#1: miR-125b-5p mimic(MC10148)-1

description: biological replicate #1

value: NSC-34 cells

value: mouse motor neuron-like cells


title: Series#1: miR-125b-5p mimic(MC10148)-2

description: biological replicate #2


title: Series#1: siNC#2-3

description: biological replicate #3

source_name: NSC-34 cell treated with siNC#2 and RNAiMAX.


title: sample_19

value: Retina Periphery

value: Levaquin, zosyn, Flomax, hydrochlorothiazide, Compazine, lorazepam, nystatin, warfarin, gabapentin, librax, tarceva,

value: metastatic adenocarcinoma of lung, lung cancer, pulmonary embolism, Waldenstrom macroglobulinemia, hypertension, familial tremor, gastroesophageal disease, asthma, recurring pneumonia

value: cataract extraction

value: OS

value: min


title: Series#1: siNC#2-2

description: biological replicate #2


title: sample_17

value: female

value: Protonix, methotrexate, prednisone, folic acid, captopril, Fosamax, calcium

value: failure to thrive, COPD, hypertension arthritis, osteoporosis, coronary artery disease, CHF, fractures

value: corneal dystrophy

value: Control

value: OD

value: Periphery

value: Water


title: Series#2: siRNA (-)

source_name: NSC-34 cell treated with RNAiMAX only.

treatment_protocol: 400,000 NSC-34 cells/well (6 well plate) were plated on collagen coated plate and 60 nM siNC#1, siNC#2, miR-125b-5p-mimics and pre-miR-125b were transfected with Lipofectamine RNAiMAX reagent.


title: sample_18

value: Tylenol, haldol, ativan, morphine,mylicon

value: Cholangiocarcinoma, sepsis, diabetes type II, coronary artery disease, diverticulitis, liver disease,

value: FALSE

value: ul

value: ng/ul


title: Series#1: siNC#2-1

description: biological replicate #1

value: NSC-34 cells

value: mouse motor neuron-like cells


title: Series#1: (-) siRNA-3

description: biological replicate #3


title: sample_16

value: Retina Periphery

value: male

value: Heparin, lasix, lactulose, protonix, paroxetine, vitamin K

value: liver cirrhosis, alpha-1-AT deficiency diagnosed 2 yrs ago, UTI, HTN, nephrolithiasis, OSA on CPAP at night


title: sample_15

value: female

value: unknown

value: ovarian CA, mitral regurg, choesystectomy, tonsillectomy

value: corneal stromal scar, cataract

value: min


title: sample_14

value: Plavix, demadex, levothyroxine, folic acid, metoprolol, amlodipine, hydralzine, ASA, fosamax, isosorbide, Douvent nebulizer, PULMICORT INHALER,

value: CAD, s/p MI, angina, CHF, COPD, pulmonary HTN, hypothyroidism, breast CA, osteoprosis/OA, vocal cord paralysis, RA, PUD, vitiligo, HTN

value: pseudophakia, Fuchâ€™s endo dystrophy, choroidal nevi

value: Control

value: OD

value: Periphery

value: Water


title: Series#1: (-) siRNA-1

description: biological replicate #1

value: NSC-34 cells

value: mouse motor neuron-like cells


title: sample_13

value: Retina Periphery

value: male

value: atenolol, DECADRON (STEROIDS), paroxetine, ASA, Aricept, folic acid

value: metastatic lung CA, HTN, depression

value: cataract extraction

value: FALSE

value: ul

value: ng/ul


title: sample_11

value: female

value: ASA, levoxyl, verpamil, aldactone, nasonex nasal srapy, vicodin, toprol, mirtazapine, pulmicort puff (glucocorticoid), albuterol inhaler 2 puff, home oxygen, Mg tablets,

value: hypertension (HTN), congestive heart failure (CHF), asthma, history of Vfib with MI x 2 s/p AICD placement in 1999.  Atrial fib, hypothyroidism

value: pseudophakia with YAG

value: min


title: sample_12

value: laspofunginin, posacandozole, neupogen, heparin, coumadin, zosyn, vancomycin

value: ulcerative colitis, bone marrow failure, rhizopus lung infection, refractory anemia with myelodysplasia, pulmonary embolus, HTN, myelodysplasia, dyslipidemia

value: pterygium removed, glasses

value: Control

value: OS

value: Periphery


title: sample_01

value: Retina Macula

value: OD

value: Macula

value: Water


title: sample_10

value: Haldol, lorazepam, melatonin, nystatin, omeprazole, Zofran, oxycodone

value: metastatic duodenal cancer, chemotherapy, small bowel obstruction, hernia repair, hyponatremia, hypertension hyperlipidemia,

value: FALSE

value: ul


title: BCC6

city: Brisbane

first: Valentine

last: Murigneux

state: QLD

address: 37 Kent St, Woolloongabba

country: Australia

institute: The University of Queensland Diamantina Institute, Faculty of Medicine

data_processing:
The RNA-seq reads were mapped to the human reference hg19 genome with STAR v2.5.2b (Dobin et al., 2013) using Ensembl annotation (GRCh37, release 85).
Gene level read counts were obtained with HTSeqcount v0.6.1 (Anders et al., 2015) using the attribute gene_id from the Ensembl GTF file GRCh37 release 85 as feature ID.
Read count normalization and differential gene expression analysis was performed using DESeq2 v1.14.1 (Love et al., 2014). Genes with significant expression changes were filtered using the cutoff of adjusted p-value 0.05.
Genome_build: hg19 (NCBI build GRCh37)
Supplementary_files_format_and_content: Comma-separated values files include raw read counts for each sample and differential expression results from DESeq2 (superficial or solid BCCs as compared to infiltrating BCC)

source_name: Basal Cell Carcinoma

extract_protocol:
Tissue samples were collected, stored in RNAlater, then RNA extracted using Clonetech Laboratories SMARTer® Stranded RNA-Seq Kit
Libraries were constructed according to manufacturers protocol, for Illumina TruSeq protocol

tag: bcc subtype

value: Solid


title: BCC4


title: BCC67

value: Infiltrating


title: Series#1: (-) siRNA-2

description: biological replicate #2

value: NSC-34 cells

value: mouse motor neuron-like cells


title: BCC66


title: BCC9


title: BCC58


title: BCC8


title: BCC2

value: Superficial


title: BCC12


title: CS171_H3K9MK14R_input

city: New York

first: Songtao

last: Jia

state: New York

address: 116th & Broadway

department: Biological Sciences

country: USA

institute: Columbia University

description: ChIP-seq

library_source: genomic

data_processing:
Sequencing reads were de-multiplexed and aligned to the S. pombe reference genome (ASM294v2), obtained from Pombase (Lock et al., 2019) with Bowtie2 using default parameters (Langmead and Salzberg, 2012). Genome-wide coverage was calculated with deepTools2 (Ramirez et al., 2016) and normalized to counts per million (CPM). The coverage plot was visualized with IGV (Robinson et al., 2011). ChIP-seq experiments were performed in duplicates for each genotype.
Genome_build: ASM294v2.29
Supplementary_files_format_and_content: bigwig:coverage tracks

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: Cells were grown in YEA until mid-log phase

extract_protocol:
Log-phase yeast cells were crosslinked with 1% formaldehyde for 20 minutes with shaking at room temperature, followed by 5 minutes quenching with 125mM glycine. Cells were harvested, washed with PBS (phosphate-buffered saline) and flashfrozen with liquid nitrogen. The thawed pellet was washed and then resuspended in ChIP lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1% Triton X-100, 0.1% Deoxycholate, 1mM PMSF). Ice-cold glass beads were added and the mixtures were vigorously disrupted in a bead-beater with four 30-seconds rounds. The lysates were collected and NP buffer was added (10 mM Tris, pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2). MNase was added to the reaction and the reactions were incubated at 37°C for 20 minutes. MNase amount was titrated empirically so that the chromatin was digested to yield mainly mono- and di-nucleosomes. The reaction was stopped by the addition of 0.5 M EDTA, and the tubes were placed on ice. 5X ChIP lysis buffer was added to the reaction, mixed by short vertexing, and the tubes were incubated on ice for 30 minutes. The reactions were then cleared by centrifugation at 16,000 x g for 10 minutes. A small fraction of the cleared supernatant was reserved as input and the rest was used for immunoprecipitation. The protocols for immunoprecipitation, reverse-crosslinking, and DNA precipitation are the same as in the previous ChIP section. The precipitated DNA was treated with RNAase A (EN0531, Thermo Fisher Scientific) for 1 hour at 37°C. DNA concentration was determined with the Qubit dsDNA HS Assay Kit (Q33230, Thermo Fisher Scientific). 1-5 ng of ChIP and input DNA were used for library construction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB). Libraries were pooled and sequenced with single-end sequencing on a NextSeq500/550 at the JP Sulzberger Genome Center at Columbia University.
1-5 ng of ChIP and input DNA were used for library construction using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB).

tag: genotype

tag: media

value: YEA

tag: antibody


title: BCC5


title: CS171_H3K9MK14R_K9me3_rep2

description: ChIP-seq

value: H3K9me3 (Active Motif, 39161)


title: BCC40


title: BCC59


title: CS171_H3K9MK14R_K9me3_rep1

description: ChIP-seq


title: BCC50


title: BCC49


title: Boar frozen-thawed sperm-rep2

city: Chengdu

first: Han

middle: Yi

last: Wang

state: Sichuan

address: GongPing

department: Institute of Animal Genetics and Breeding

country: China

institute: Sichuan Agricultural University

data_processing:
Clean reads were obtained by removing reads that contained adapter, poly-N, low-qualities reads and sequences <18 nt or >34 nt. The designated reference genome of giant panda (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/335/GCF_000004335.2_AilMel_1.0) and Sus scrofa (ftp://ftp.ensembl.org/pub/release-75/fasta/sus_scrofa/) were used for sequence alignment.
Comparison of clean reads to Silva database, GtRNAdb database, Rfam database and Repbase were performed with Bowtie
Known piRNAs and novel piRNAs were identified by comparing sequences with known piRNAs from miRbase using proTRA
DESeq R package (1.10.1), based on Reads Per Kilobase Million (TPM) and Fragments Per Kilobase Million (FPKM) algorithm was used for analyzing the differential expression of piRNAs between fresh and frozen-thawed sperm
The piRNAs between fresh and frozen-thawed sperm were analyzed by IDEG[23], and the adjusted p < 0.01 and absolute value of log2 (Fold change) >1 was classified as DE piRNAs.
Then, hierarchical clustering analysis was performed on the selected differentially expressed piRNAs, and the piRNAs with the same or similar expression behaviors were clustered.
Genome_build: Ailmel 1.0，Sscrofa11.1
Supplementary_files_format_and_content: abundance measurements

organism: Sus scrofa

source_name: Boar frozen-thawed sperm

growth_protocol: All ejaculates from giant panda and boar were pooled and then equally divided into two groups (Fresh sperm and cryopreserved sperm), respectively. The fresh sperm was directly used for RNA extraction.

extract_protocol:
The total RNA of fresh and frozen-thawed sperm was extracted using the TRIzol LS Reagent kit (Invitrogen, Carlsbad, CA, USA).
After total RNA extraction, purity, concentration, and integrity of RNA were determined by Nanodrop (Thermo Fisher Scientific, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara,CA, USA), respectively. Then, the mRNA was isolated by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, E7490, Ipswich, MA, USA). The cDNA library was constructed using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, E7530, Ipswich, MA, USA) and NEBNext Multiplex Oligos for Illumina (NEB, E7500, Ipswich, MA, USA) following the manufacturer’s instructions.

treatment_protocol: Another group was cryopreserved according to the previous procedure. Briefly, giant panda sperm was diluted with TEST egg yolk buffer (Irvine Scientific, Santa Ana, CA) to a final concentration of 5% glycerol. The mixer was loaded into 0.25 mL straws and slowly cooled to 4 °C for 4 hours, then placed at 7.5 cm above liquid nitrogen (LN) for 1 min (cryopreservation rate of -40 ℃ /min), followed by 2.5 cm above LN for 1 min (-100 ℃ /min), and finally immersed in LN till use. During thawing, the straws were immersed into a 37 ℃ water bath for 30 seconds and diluted with equal volume of HF10 (Ham’s F10 medium with 5% fetal calf serum and 25mM HEPES). For boar sperm cryopreservation, after centrifugation (5 min, 1800 rpm, 17℃), boar sperm were diluted with lactose-egg yolk (LEY) extender (40 mL 11% β-lactose, and 10 mL hen’s egg yolk) and cooled to 4℃ at a rate of approximately 0.2°C /min. Then, the mixer was further diluted with LEY extender to yield a final concentration of 3% glycerol. Finally, the mixtures were packaged into 0.25 mL straws (FHK, Tokyo, Japan) and equilibrated in approximately 3 cm above LN vapor for 10 min, then plunged into LN till further use.

value: Boar mature sperm

tag: treatment

value: treated by frozen protocol


title: Boar fresh sperm-rep1

source_name: Boar fresh sperm

tag: tissue


title: BCC29


title: H3K9me2 for CK1750 with UNC0638

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with -k 1 option
Wiggle files with a 1000bp resolution for H3K9me1/2 enrichment were regenerated from size shifted wiggle files by MACS v1.4.2 and then rescaled with wigmath.Scale function of Java-Genomics-Toolkit.
Genome_build: mm10
Supplementary_files_format_and_content: Wiggle files

source_name: Lung adenocarcinoma cells

growth_protocol: CK1750 were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei with Covaris M220 and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext Ultra DNA Library preparation kits from 2-10 ng immunoprecipitated DNA according to manufacturer’s protocol. The finished double strand DNA (dsDNA) libraries were quantified by PicoGreen and Agilent Bioanalyzer according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single or paired-end 75bp reads.

treatment_protocol: CK1750 cells were cultured in the presence of DMSO or  1 μM UNC0638 in DMEM supplemented with 10% FBS

tag: drugs treated

tag: chip-antibody

value: H3K9 dimethylation (Abcam, ab1220)


title: BCC61

value: Mixed


title: BCC28


title: H3K9me2 for CK1750 with DMSO

value: DMSO


title: WT KPC irradiation

type: RNA

city: Atlanta

first: zhen

last: bian

state: Georgia

address: Department of Biology, 161 Jesse Hill Jr. Dr

institute: Georgia State University

description: Gene expression analysis using Nanostring nCounter Mouse Immunology Panel

hyb_protocol: Hybridization was done according to the manufacturer's instructions.

scan_protocol: Gene expression was quantified on the nCounter Digital AnalyzerTM.

data_processing: All data was normalized to 14 housekeeping genes (nSolver). Background was deducted using spiked-in negative controls.

label: Capture probe-3'biotin, Reporter probe-5' barcode signal

source_name: WT KPC irradiation

label_protocol: RNA samples of different time points were pooled and 100 ng of each total RNA sample was labeled according to the manufacturer's instructions.

extract_protocol: Wild-type mice and Sirpα-KO mice bearing MC38, Pan02 and KPC tumors were irradiated when their tumors exceeded 200mm3. Twelve and eighteen hours after irradiation, irradiated and non-irradiated tumors were resected to isolate total RNA using the Trizol extraction protocol.

value: wild type

value: KPC tumor

tag: strain

value: 6-8 weeks

tag: therapy

value: 8Gy radiation on tumor


title: Sirpα-KO KPC irradiation

source_name: Sirpα-KO KPC irradiation

value: Sirp{alpha}-KO

tag: age


title: BCC27

value: Solid


title: H3K9me1 for CK1750 with UNC0638

value: H3K9 monomethylation (Abcam, ab8896)


title: Sirpα-KO KPC no irradiation

source_name: Sirpα-KO KPC no irradiation

value: No radiation on tumor


title: GES1_CBS.deficient_Clone_2_p30

type: genomic

city: Singapore

first: Arnoud

last: Boot

state: Singapore

address: 8 college road

country: Singapore

institute: Duke-NUS Medical School

hyb_protocol: According to manufacturers specifications

data_processing: Array analysis and normalization was performed using the preprocessFunnorm function from the minfi package

label: cy3, cy5

growth_protocol: GES1 and HFE145 cells were grown as recommended by the laboratories in which they were established

extract_protocol: Qiagen DNA isolation kit

treatment_protocol: CRISPR/cas9 editing was used to knockout CBS. Clones were derived, and cultured for up to 31 passages. Sampling was performed at multiple time-points

tag: experiment group

value: CBS-deficient

tag: passage


title: GES1_CRISPR_control_p30

scan_protocol: According to manufacturers specifications

value: CRISPR control


title: BCC26


title: GES1_CBS.deficient_Clone_1_p30

label_protocol: According to manufacturers specifications


title: HFE145_CBS.deficient_Clone_1_p25


title: GES1_CBS.deficient_Clone_2_p20


title: GES1_CRISPR_control_p25


title: HFE145_parental_p25

value: Parental


title: H3K9me1 for CK1750 with DMSO


title: WT Pan02 irradiation

source_name: WT Pan02 irradiation

value: Pan02 tumor


title: HFE145_CRISPR_control_p25


title: GES1_CRISPR_control_p15


title: GES1_parental_p25


title: Sirpα-KO Pan02 irradiation

source_name: Sirpα-KO Pan02 irradiation


title: GES1_parental_p20


title: BCC35

value: Infiltrating


title: WT Pan02 no irradiation

source_name: WT Pan02 no irradiation


title: GES1_parental_p15


title: GES1_CBS.deficient_Clone_1_p8


title: HFE145_CBS.deficient_Clone_2_p25


title: Sirpα-KO Pan02 no irradiation

source_name: Sirpα-KO Pan02 no irradiation


title: WT KPC no irradiation

source_name: WT KPC no irradiation


title: GES1_CRISPR_control_p20


title: GES1_CBS.deficient_Clone_2_p15


title: Input DNA for CK1750 with UNC0638


title: Input DNA for CK1750 with DMSO


title: BCC34

value: Superficial


title: WT MC38 irradiation

source_name: WT MC38 irradiation

value: MC38 tumor


title: BCC36


title: GES1_CBS.deficient_Clone_1_p15


title: GES1_parental_p8


title: GES1_parental_p30


title: Sirpα-KO MC38 no irradiation

source_name: Sirpα-KO MC38 no irradiation


title: BCC25


title: WT MC38 no irradiation

source_name: WT MC38 no irradiation


title: pCREB_4D_training_Corticosterone

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Reads were aligned to rn6 with short read aligner bwa-mem (version 0.7.10).
Peaks were called using MACS2 (version 2.1.1.20160309) subcommand "callpeak", settings: effective genome size = 2.00e+09; q-value cutoff = 0.05; bdg = true. An input sample was provided for each treatment group. Resulting in a bed file with narrowPeaks for each sample.
Separately for GR and pCREB, the corresponding BED files were merged using mergeBed (version 2.26.0), resulting in a list of all peak locations. Overlapping peak regions were replaced by unions of the regions providing a single bed file for GR and pCREB. For these calculated regions the read counts were generated per sample using HTSeq-count (version 0.6.1-1.), settings: -s no, -m intersection-strict, -f bam. This resulted in a count matrix containing both GR and pCREB data.
bw files were created for visualisation of the ChIP-seq data
Genome_build: rn6
Supplementary_files_format_and_content: Matrix table with raw read counts of GR and pCREB for all read counts.
Supplementary_files_format_and_content: BW files the of ChIP-seq reads to rn6 genome.

organism: Rattus norvegicus

source_name: brain

extract_protocol:
The snap-frozen, disected hippocampi were fixated with 1% formaldehyde and homogenized in Jiang buffer using a glass douncer (Kimble-Chase). Chromatin of 4 hippocampi of 2 rats was pooled and suspended in NP-50 containing lysis buffer for fragmentation by sonication. Input aliquots were taken and chromatin samples were split in two for paired GR and pCREB ChIP, using anti-GR antibody H-300 (sc-8992X, Santra Cruz) and anti-phospho-CREB Ser133 antibody (17-10131, Millipore), respectively. Transcription factor bound DNA was collected, decrosslinked and purified by phenolization.
Adapters (Agilent) were ligated and samples were subjected to 15 rounds of PCR for DNA library preparation (KAPA Biosystems). Single-end sequencing was performed on a Illumina HiSeq 2500 at High Output. Two runs were performed to obtain sufficient data, first 51bp and secondly 65bp sequencing.

value: Sprague-Dawley

tag: training

value: training

value: Corticosterone

value: Hippocampus

tag: chip antibody


title: BCC18


title: pCREB_4C_training_Corticosterone

value: anti-phospho-CREB Ser133 antibody (17-10131, Millipore)


title: pCREB_4B_training_Corticosterone


title: AD169 3 dpi UL84-ChIP

city: Reno

first: Cyprian

last: Rossettto

state: NV

address: 1664 North Virginia Street

department: Microbiology & Immunology

institute: University of Nevada, Reno

description: AD169 3 dpi UL84-ChIP

data_processing:
CLC genomics workbench 8.5.1
Sequencing reads were aligned to the HCMV genome using CLC genomics workbench map reads to reference tool
Genome_build: HCMV assesion number (GU179289)
Supplementary_files_format_and_content: Data was aligned to reference genome (GU179289) using CLC genomics workbench

source_name: HCMV DNA

extract_protocol:
ChIP was performed using Diagenode iDeal ChiP-seq kit for Transcription Factors (Diagenode, cat. C01010055).
Libraries were created from ChIP DNA and input DNA samples using the NEXTflex Illumina ChIP-Seq Library Preparation Kit (Bioo Scientific cat. 5143-01).

tag: dose

value: 3 dpi

tag: agent

value: HCMV (HHV-5) stain AD169


title: TB40E 3 dpi UL84 input

description: TB40E 3 dpi UL84 input

value: HCMV (HHV-5) stain TB40E


title: GR_4D_training_Corticosterone

value: anti-GR antibody H-300 (sc-8992X, Santra Cruz)


title: AD169 3 dpi UL84 input

description: AD169 3 dpi UL84 input


title: HFE145_parental_p5


title: BCC20

source_name: Basal Cell Carcinoma

tag: bcc subtype

value: Solid


title: GR_4C_training_Corticosterone


title: GR_4B_training_Corticosterone


title: pCREB_4A_training_Corticosterone


title: BCC3


title: TB40E 3 dpi IE2-ChIP

description: TB40E 3 dpi IE2-ChIP


title: GR_4A_training_Corticosterone


title: BCC55


title: Input 4_training_Corticosterone

value: Input


title: pCREB_3D_training_Vehicle

value: Vehicle


title: TB40E 3 dpi IE2 input

description: TB40E 3 dpi IE2 input


title: HFE145_CRISPR_control_p5

value: CRISPR control


title: BCC54


title: pCREB_3C_training_Vehicle


title: Sirpα-KO MC38 irradiation

source_name: Sirpα-KO MC38 irradiation

tag: genotype

value: Sirp{alpha}-KO

value: 6-8 weeks

value: 8Gy radiation on tumor


title: BCC53

value: Superficial


title: pCREB_3A_training_Vehicle

value: Sprague-Dawley


title: GR_3D_training_Vehicle

value: training


title: GR_3C_training_Vehicle


title: AD169 3 dpi IE2-ChIP

description: AD169 3 dpi IE2-ChIP


title: GR_3A_training_Vehicle


title: GR_3B_training_Vehicle


title: GES1_CRISPR_control_p8


title: AD169 3 dpi IE2 input

description: AD169 3 dpi IE2 input


title: GES1_CBS.deficient_Clone_1_p20

value: CBS-deficient


title: AD169 20 hpi IE2-ChIP

description: AD169 20 hpi IE2-ChIP

value: 20 hpi


title: TB40E 3 dpi UL84-ChIP

description: TB40E 3 dpi UL84-ChIP


title: Input 3_training_Vehicle

value: Hippocampus


title: pCREB_2D_no training_Corticosterone

value: no training

value: Corticosterone

value: anti-phospho-CREB Ser133 antibody (17-10131, Millipore)


title: GR_2D_no training_Corticosterone

value: anti-GR antibody H-300 (sc-8992X, Santra Cruz)


title: pCREB_2A_no training_Corticosterone


title: pCREB_2B_no training_Corticosterone


title: AD169 20 hpi IE2 input

description: AD169 20 hpi IE2 input

value: HCMV (HHV-5) stain AD169


title: GES1_CBS.deficient_Clone_1_p25


title: pCREB_2C_no training_Corticosterone


title: HFE145_CBS.deficient_Clone_1_p5


title: GR_2C_no training_Corticosterone


title: A049_Hela_G2-24

city: Helsinki

first: Marco

last: Savarese

address: Topeliuksenkatu 20

department: Samfundet Folkhälsan i svenska Finland r.f.

country: Finland

institute: Folkhälsan Research Center

description: Parental unedited cell line

data_processing:
Sequence read were mapped using STAR while clipping the adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC from the forward stranded reads and the adapter sequence AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT from the reverse strand reads.
The mapped sequence reads were summarized on intron/exon levels using IntEREst. As a result reads mapping to introns, read mapping to intron-eonx junctions and reads spanning the introns were counted.
Significantly differentially retained introns were estimated using deseqInterest function from IntEREst R package.
Genome_build: HG36
Supplementary_files_format_and_content: tab-delimited text file that includes raw counts of fragments that map and span the introns. The results of differential intron retention analyses are also included.

source_name: Cultured Hela cells (adherent)

growth_protocol: DMEM with 10% FBS (Tet-free), 1% glutamax, 1% P/S. Seeded in 6 well-plate wells at 50% confluency and immediately treated with siRNA/IAA

extract_protocol:
Total RNA was harvested using Trizol reagent, rRNA was removed using Illumina ribo-zero kit. Illumina TruSeq Stranded Total RNA kit for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For CENATAC depletion cells were treated with 20 nM siRNA and 1 mM IAA for 24 or 48 hours. Control cells were treated only with siGAPDH

tag: annotation

value: Untagged Control

tag: cenatac locus genotype

value: wt

tag: cenatac depletion

value: 0 hr


title: A048_Hela_G2-24

description: Parental unedited cell line


title: Input 2_no training_Corticosterone

tag: treatment

tag: tissue

value: Input


title: A047_Hela_G2-24

description: Parental unedited cell line


title: A009_C48

description: Cell line ontaining homozygous AID-Tag inserted to CENATAC locus

value: CENATAC depeltion 48h

value: AID-tag

value: 48 hr


title: GR_1D_no training_Vehicle

value: Sprague-Dawley

value: Vehicle


title: pCREB_1A_no training_Vehicle


title: pCREB_1C_no training_Vehicle


title: pCREB_1B_no training_Vehicle


title: TB40E 20 hpi IE2 input

description: TB40E 20 hpi IE2 input

value: HCMV (HHV-5) stain TB40E


title: GES1_CBS.deficient_Clone_2_p25

value: CBS-deficient


title: GR_1B_no training_Vehicle

value: Hippocampus


title: A007_C48


title: A006_C24

value: CENATAC depeltion 24h

value: 24 hr


title: GR_1A_no training_Vehicle

value: no training


title: Input 1_no training_Vehicle


title: GR_2A_no training_Corticosterone

value: Corticosterone

value: anti-GR antibody H-300 (sc-8992X, Santra Cruz)


title: Colon_SeqScope_1st

city: Ann Arbor

first: Jun Hee

last: Lee

state: MI

address: 109 Zina Pitcher Pl

institute: University of Michigan

description: Synthetic ssDNA library

data_processing:
Library strategy: Seq-Scope
Sequencing by Illumina HiSeqX, HiSeq4000 and NovaSeq platforms .
Tissue Boundary Detection: The HiSeq data were joined into MiSeq data according to their HDMI sequence. For each of HiSeq data whose HDMI is found from MiSeq, tile number and XY coordinates were assigned.  A density plot was generated to visualize the density of HiSeq reads in a given XY space of each tile. The density plots were manually assigned to the corresponding H&E images. The process is done with customized codes written in Python 3.7.1.
Alignment: From MiSeq data, HDMI sequences of clusters located on the bottom tile were extracted and used as a “whitelist” for the cell (HDMI) barcode. First 9 basepairs of HiSeq data Read 2 were copied to Read 1 and used as the unique molecular identifier (UMI). Read 2 was trimmed at the 3’end to remove polyA tails of length 10 or greater, then aligned to mouse genome (mm10) using GeneFull and Velocyto option with no length threshold and no cell filtering using Star/StarSolo 2.7.5c
Data Binning and Collapsing: The digital expression matrix generated by STARsolo with GeneFull option were combined with spatial information, and further the imaging space were divided into into 100 μm2 (10 μm-sided) square grids and collapsing all HDMI-UMI information into one barcode per grid. Alternatively, data binning was also performed with square 25 μm2 (5 μm-sided) square grids. After data binning, gene types were filtered to only contain protein_coding genes, lncRNA genes, or immunoglobulin/T cell receptor genes, to contain only the first-appearing splicing isoform, and to exclude hypothetical gene models (genes designated as Gm-number).
Clustering: The binned and processed DGE matrix was analyzed in the Seurat v4 package. Feature number threshold was applied to remove the grids that corresponded to the area that was not overlaid by the tissue or was extensively damaged through scratches. Data were normalized using regularized negative binomial regression implemented in Seurat’s SCTransform function. Clustering was performed using the shared nearest neighbor modularity optimization implemented in Seurat’s FindClusters function
Subcellular analysis: Genes from digital expression matrix generated by STARsolo Velocyto option were devided into three groups , and three groups of spliced and unspliced read counts were obtained and then independent images were produced. By plotting spliced and unspliced read counts in each group were compared with each other.
Genome_build: mm10

organism: synthetic construct

source_name: HDMI-Oligo

growth_protocol: Standard Mouse rearing condition

extract_protocol: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. 2nd-Seq of Seq-scope begins with overlaying the tissue section slice onto the HDMI-array.

value: HDMI-Oligo


title: A005_C24


title: GES1_CBS.deficient_Clone_2_p8


title: Liver_SeqScope_1st

description: Synthetic ssDNA library


title: GR_2B_no training_Corticosterone


title: A008_C48


title: AKI6_CD8_Day-2_Rep2

city: San Francisco

first: Ruby

last: Yu

state: CA

address: 513 Parnassus Ave

institute: UCSF

description: day negative 2

data_processing:
ATAC-seq reads trimmed using cutadapt v1.18 to remove Nextera transposase
Reads were aligned to hg19 using Bowtie2 v2.3.4.3.
Low-quality reads were removed using samtools v1.9 view function (samtools view -F 1804 -f 2 -q 30 -h -b).
Duplicates were removed using picard v2.18.26
Reads were converted to BED format using bedtools bamtobed function and normalized to reads per million
Reads mapping within 500bp on either side of a CRISPR gRNA cut site for a set of genes of interest were counted using the bedtools intersect function.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file with number of mapped reads within 500bp on either side of a CRISPR gRNA cut site.

source_name: whole blood

growth_protocol: Primary human T cells were isolated from either fresh whole blood from healthy donors. Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood samples by Ficoll centrifugation using SepMate tubes (STEMCELL, per manufacturer’s instructions). T cells were isolated from PBMCs from all cell sources by magnetic negative selection using an EasySep Human T Cell Isolation Kit (STEMCELL, per manufacturer’s instructions). XVivo15 medium (STEMCELL) supplemented with 5% fetal bovine serum, 50 µM 2-mercaptoethanol, and 10 µM N-acetyl L-cystine was used to culture primary human T cells. In preparation for electroporation, T cells were stimulated for 2 days at a starting density of approximately 1 million cells per mL of media with anti-human CD3/CD28 magnetic Dynabeads (ThermoFisher), at a bead to cell ratio of 1:1, and cultured in XVivo15 media containing IL-2 (500 U ml−1; UCSF Pharmacy), IL-7 (5 ng ml−1; ThermoFisher), and IL-15 (5 ng ml−1; Life Tech).

extract_protocol:
ATAC-seq library were prepared following the Omni-ATAC protocol. Briefly, frozen cells were thawed and stained for live cells using Ghost-Dye 710 (Tonbo Biosciences, CA, USA). 50,000 lived cells were FACS sorted and washed once with cold PBS. Technical replicates were done for most of the samples. Cell pellets were resuspended in 50µl cold ATAC-Resuspension buffer (10mM Tris-HCl (Sigmal Aldrich, MO, USA) pH 7.4, 10mM NaCl, 3mM MgCl2 (Sigma Aldrich,) containing 0.1% NP40 (Life Technologies, Carlsbad, CA), 0.1% Tween-20 (Sigma Aldrich) and 0.01% Digitonin (Promega, WI, USA) for 3 mins. Samples were washed once in cold resuspension buffer with 0.1% Tween 20, and centrifuged for 4C for 10 min. Extracted nuclei were resuspended in 50µl of Tn5 reaction buffer (1x TD buffer (Illumina, CA, USA), 100nM Tn5 Transposase (Ilumina), 0.01% Digitonin, 0.1% Tween-20, PBS and H20), and incubated at 37C for 30 min at 300rpm. Transposed samples were purified using MinElute PCR purification columns (Qiagen, Germany) as per manufacturer’s protocol.
Purified samples were amplified and indexed using custom Nextera barcoded PCR primers as described in (Buenrostro JD et al., Transposition of native chromatin for fast and sensitive epigenomic profile of open chromatin, DNA-binding proteins ad nucleosome position. Nature Methods, 2013). DNA libraries were purified using MinElute columns and pooled at equal molarity. To remove primer dimers, pooled libraries were further cleaned up using AmPure beads (Beckman Coulter, CA, USA).

treatment_protocol: ATAC-seq was performed on cell samples on the day of processing from whole blood, prior to anti-CD3/CD28 stimulation, or 48 hours post-processing and stimulation

tag: donor

value: Donor 6

tag: anti-cd3/cd28 stimulation

value: whole blood

tag: cell type

value: CD8+ T cell


title: pCREB_1D_no training_Vehicle

tag: strain

value: anti-phospho-CREB Ser133 antibody (17-10131, Millipore)


title: AKI6_CD8_Day-2_Rep1

description: day negative 2


title: AKI6_CD4_Day-2_Rep2

description: day negative 2

value: CD4+ T cell


title: Alveolar Macrophage Nitrogen Mustard 28 d 1

city: Gainesville

first: Ley

middle: Cody

last: Smith

state: FL

address: 2187 Mowry Rd

institute: University of Florida

data_processing: Fold changes were calculated using the ∆∆Ct method. miRNA expression was normalized to Snord72 as its expression not affected by NM administration. miRNA array data were analyzed using the QIAGEN GeneGlobe Data Analysis Center.

label: Sybr

label_protocol: Purified miRNA was reverse transcribed using a QIAGEN QuantiTect Reverse Transcription kit and analyzed using a QIAGEN miScript Rat Inflammatory Response and Autoimmunity miRNA PCR Array or by RT-qPCR using a QIAGEN miScript SYBR Green kit according to the manufacturer’s protocol. Amplification was performed using a 7300HT Real Time PCR system (Applied Biosystems, Grand Island, NY).

extract_protocol: Total mRNA was collected from lung macrophages by phenol-chloroform extraction.  Samples were enriched for miRNAs using an RNeasy MinElute Cleanup kit (QIAGEN Inc., Valencia, CA).

value: Wistar

tag: Sex

value: Male

value: Nitrogen Mustard 28 d

value: Alveolar macrophages collected by lung lavage plus gentile massage


title: p65PulldownRep3

city: Aurora

first: Matthew

last: Taliaferro

state: CO

address: 12801 E 17th Ave, RC1 South Room 10403D

department: Biology

institute: University of Colorado Anschutz Medical Campus

description: rRNA-depleted RNA

data_processing:
Adapters were trimmed from the 3' end of reads using cutadapt.
Transcript abundances were calculated using salmon or kallisto against hg38 genome.
Gene abundances were calculated from transcript abundances using tximport.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *quant.sf: Salmon transcript quantifications in text format.

source_name: HeLa cell line

extract_protocol:
Trizol RNA extraction.
KAPA RNA hyperprep.

tag: cell line

value: HeLa

tag: fraction

value: Pulldown

value: untreated


title: p65InputRep3

description: rRNA-depleted RNA

value: Input


title: AKI6_CD4_Day-2_Rep1

description: day negative 2


title: p65InputRep2

description: rRNA-depleted RNA


title: p65PulldownRep2

description: rRNA-depleted RNA


title: T623 (d10-16)-3

city: Kyoto

first: Yoshinori

last: Yoshida

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

institute: Kyoto University

description: 50_HTseq_tophat2.DESeq2_normalized  51_HTseq_STAR.DESeq2_normalized

data_processing:
Illumina bcl2fastq (v2.17.14) were performed for converting fastq files and separation by samples with default setting
Too short (<20base) reads were removed and adapter sequence were trimmed by cutadapt (v1.15) with parameters -m 20 --nextseq-trim=20.
For removing human rRNA tRNA mapped reads, bowtie2 (v2.2.5), with parameters --very-sensitive --score-min L,0,-0.6.
The reads were mapped by STAR  (v2.5.3a)
The reads were mapped by tophat2 (v2.1.1) with parameter -p 4 --library-type fr-firststrand --b2-very-sensitive, and with the GENCODE (version 27) annotation gtf file.
HTSeq (v0.9.1) were perfomed for counting reads with the GENCODE (version 27) annotation gtf file.
To normalized read counts, R (v3.4.3) and its package DESeq2 (v1.18.1) were performed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 nomalized count values for each Sample.

source_name: day16 hiPSC-CMs

growth_protocol: For hPSCs, AK02N (Ajinomoto) at 37 ºC in a humidified incubator with 5% CO2. For cardiomyocytes, StemPro-34 supplemented with 2 mM L-glutamine, 4x10-4 M monothioglycerol (MTG), 50 mg/ml ascorbic acid (AA), 150 mg/ml transferrin, 0.5% penicillin/streptomycin, bFGF (10 ng/ml, final 5 ng/ml), activin A (12 ng/ml, final 6 ng/ml) and BMP4 (18 ng/ml, final 10 ng/ml)

extract_protocol:
RNA was prepared using the miRNeasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).
TruSeq Standed Total RNA (Illumina)

treatment_protocol: hiPSCs were differentiated to cardiac lineage cells using ActivinA and BMP4.

value: Cardiomyocytes derived from hiPSCs

tag: differentiation date


title: H2BplusLMBPulldownRep3

description: rRNA-depleted RNA

value: treated


title: p65PulldownRep1

description: rRNA-depleted RNA


title: p65InputRep1

description: rRNA-depleted RNA


title: GR_1C_no training_Vehicle

value: Sprague-Dawley

tag: training

value: no training

value: Vehicle

value: Hippocampus

tag: chip antibody

value: anti-GR antibody H-300 (sc-8992X, Santra Cruz)


title: Alveolar Macrophage Nitrogen Mustard 28 d 3


title: A003_G48

value: AID-tag control

value: AID-tag

value: 0 hr


title: H2BplusLMBPulldownRep2

description: rRNA-depleted RNA


title: AKI5_CD8_Day-2_Rep1

description: day negative 2

value: Donor 5

value: whole blood

value: CD8+ T cell


title: AKI5_CD8_Day-2_Rep2

description: day negative 2


title: Alveolar Macrophage Nitrogen Mustard 28 d 2

value: Wistar

value: Male

value: Nitrogen Mustard 28 d

value: Alveolar macrophages collected by lung lavage plus gentile massage


title: T112 (d8-16) + T623 (d10-16)-3

value: Cardiomyocytes derived from hiPSCs


title: A004_C24

value: CENATAC depeltion 24h

value: 24 hr


title: Alveolar Macrophage Nitrogen Mustard 7 d 1

value: Nitrogen Mustard 7 d


title: AKI5_CD4_Day-2_Rep2

description: day negative 2

value: CD4+ T cell


title: T112 (d8-16)-3


title: TB40E 20 hpi IE2-ChIP

description: TB40E 20 hpi IE2-ChIP

tag: dose

value: 20 hpi

tag: antibody

tag: agent

value: HCMV (HHV-5) stain TB40E


title: Alveolar Macrophage Nitrogen Mustard 7 d 3


title: A002_G48

tag: annotation

value: AID-tag control

tag: cenatac locus genotype


title: A001_G48

value: AID-tag

tag: cenatac depletion


title: AKI5_CD4_Day-2_Rep1

description: day negative 2

tag: tissue


title: H2BplusLMBInputRep3

description: rRNA-depleted RNA

value: HeLa

value: Input

value: treated


title: Alveolar Macrophage Nitrogen Mustard 7 d 2

tag: treatment


title: HFE145_CBS.deficient_Clone_2_p5

tag: experiment group

value: CBS-deficient

tag: passage


title: AKI4_CD8_Day-2_Rep2

description: day negative 2

tag: donor

value: Donor 4

tag: anti-cd3/cd28 stimulation

value: whole blood

tag: cell type

value: CD8+ T cell


title: pCREB_3B_training_Vehicle

tag: strain

value: Sprague-Dawley

value: training

value: Vehicle

value: Hippocampus

value: anti-phospho-CREB Ser133 antibody (17-10131, Millipore)


title: Alveolar Macrophage Nitrogen Mustard 3 d 2

value: Wistar

tag: Sex

value: Male

value: Nitrogen Mustard 3 d

value: Alveolar macrophages collected by lung lavage plus gentile massage


title: T623 (d10-16)-2

value: Cardiomyocytes derived from hiPSCs

tag: differentiation date


title: Alveolar Macrophage Nitrogen Mustard 3 d 1


title: DMSO-3

value: DMSO


title: H2BplusLMBInputRep1

description: rRNA-depleted RNA

tag: cell line

value: HeLa

tag: fraction

value: Input


title: AKI4_CD4_Day-2_Rep2

description: day negative 2

value: CD4+ T cell


title: T112 (d8-16)-2


title: H2BPulldownRep4

description: rRNA-depleted RNA

value: Pulldown

value: untreated


title: Alveolar Macrophage Nitrogen Mustard 3 d 4


title: Alveolar Macrophage Nitrogen Mustard 1 d 1

value: Nitrogen Mustard 1 d


title: H2BplusLMBPulldownRep1

description: rRNA-depleted RNA

value: treated


title: H2BPulldownRep2

description: rRNA-depleted RNA


title: H2BPulldownRep3

description: rRNA-depleted RNA


title: AKI3_CD8_Day-2_Rep2

description: day negative 2

value: Donor 3

value: whole blood

value: CD8+ T cell


title: Alveolar Macrophage Nitrogen Mustard 1 d 2


title: T623 (d10-16)-1


title: DMSO-2


title: AKI3_CD8_Day-2_Rep1

description: day negative 2


title: H2BPulldownRep1

description: rRNA-depleted RNA


title: T112 (d8-16) + T623 (d10-16)-1


title: H2BplusLMBInputRep2

description: rRNA-depleted RNA


title: Alveolar Macrophage Nitrogen Mustard 1 d 3


title: T112 (d8-16) + T623 (d10-16)-2


title: Alveolar Macrophage PBS Control 3

source_name: Alveolar Macrophage PBS Control

value: PBS Control


title: AKI4_CD8_Day-2_Rep1

description: day negative 2

value: Donor 4


title: H2BInputRep4

description: rRNA-depleted RNA


title: T112 (d8-16)-1


title: AKI3_CD4_Day-2_Rep1

description: day negative 2


title: DMSO-1


title: AKI2_CD8_Day-2_Rep2

description: day negative 2

value: Donor 2


title: H2BInputRep2

description: rRNA-depleted RNA


title: AKI4_CD4_Day-2_Rep1

description: day negative 2


title: H2BInputRep3

description: rRNA-depleted RNA


title: Alveolar Macrophage PBS Control 1

value: Wistar

value: Male


title: Alveolar Macrophage PBS Control 4

value: Alveolar macrophages collected by lung lavage plus gentile massage


title: AKI2_CD8_Day-2_Rep1

description: day negative 2


title: H2BInputRep1

description: rRNA-depleted RNA


title: AKI2_CD4_Day-2_Rep2

description: day negative 2


title: FibrillarinPulldownRep3

description: rRNA-depleted RNA

value: Fibrillarin


title: AKI2_CD4_Day-2_Rep1

description: day negative 2


title: FT282_siWT1_Replicate2

city: Los Angeles

first: Robbin

last: Nameki

address: 8700 Beverly Blvd

department: Obstetrics and Gynecology

institute: Cedars-Sinai Medical Center

data_processing:
hisat2-2.1.0(reference genome: hg38, gencodev26 + ERCC92)
htseq-count (v0.5.4.p3)
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

growth_protocol: FT282: DMEM:F12 Supplemented with 10% FBS and 1x Penicillin/streptomycin. OVCAR4:RPMI-1640 supplemented with 10% FBS, 1x NEAA, 11.4 μg/ml of insulin, and 1x penicillin/streptomycin. All maintained at 37°C with 5% CO2

extract_protocol:
Nucleospin RNAplus Kit
Prepared using standard BGI-seq protocol

treatment_protocol: 300000 cells were reverse transfected with 120nM of siRNA, refeeded 24 hours later, and harvested total 72 hours later for total RNA

value: Fallopian Tube Secretory Epithelial Cell Line

tag: passages

value: 1-12 (0 being STR profiled)

tag: transfection agent


title: FibrillarinPulldownRep2

description: rRNA-depleted RNA

value: HeLa


title: AKI1_CD8_Day-2_Rep2

description: day negative 2

value: Donor 1


title: FT282_siWT1_Replicate1


title: AKI3_CD4_Day-2_Rep2

description: day negative 2

value: CD4+ T cell


title: FibrillarinPulldownRep1

description: rRNA-depleted RNA

value: Pulldown

value: untreated


title: Alveolar Macrophage PBS Control 2


title: FT282_siMECOM_Replicate2


title: AKI1_CD8_Day-2_Rep1

description: day negative 2


title: FibrillarinInputRep3

description: rRNA-depleted RNA

value: Input


title: AKI1_CD4_Day-2_Rep2

description: day negative 2

value: whole blood


title: FT282_siDual_Replicate2


title: FibrillarinInputRep2

description: rRNA-depleted RNA


title: FT282_siMECOM_Replicate1


title: AKI1_CD4_Day-2_Rep1

description: day negative 2


title: FT282_siDual_Replicate1


title: FibrillarinInputRep1

description: rRNA-depleted RNA


title: AKI6_CD8_Day0_Rep2

value: Donor 6

value: 48 hours

value: CD8+ T cell


title: FT282_siSOX17_Replicate2


title: FT282_siSOX17_Replicate1


title: AKI6_CD4_Day0_Rep2


title: genome-edited iPSC 409B2-Ho3, 4wks, biological rep1

description: Gene expression data from iPSC-MN

hyb_protocol: Following fragmentation, 5μg of Single-Stranded cDNA was hybridized for 16 hr at 45˚C on GeneChip Human Transcriptome Array 2.0. Arrays was washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

label: Biotin

source_name: genome-edited iPSC 409B2-Ho3, 4wks

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit（Thermo Fisher Scientific) following the manufacturer's instructions.

extract_protocol: Total RNA were extracted by miRNeasy Kit with QIAzol (QIAGEN)

value: iPSC-MN

tag: genotype

tag: time (differentiation from motor neuron precursor)

value: 4 weeks


title: iSLK BAC16 WT induction (2)

city: Daejeon

first: Yun Hee

last: Kang

address: 77 Gyeryong-ro 771 beon-gil, Jung-gu

department: Eulji Biomedical Science Research Institute

country: South Korea

institute: Eulji University School of Mdicine

data_processing:
HISAT v2.1.0(1).1000000019358 v02 software used for basecalling.
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using Fastx_trimmer), then mapped to mm10 whole genome using Tophat.
Read count extraction and normalization were performed using edgeR.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited excel files inclued read count values for each sample.

molecule: polyA RNA

source_name: Renal carcinoma

growth_protocol: iSLK BAC16 cultured in Dulbecco`s modified Eagle`s medium, supplemented with 10% Fetal bovine serum, 1% antibiotics. iSLK BAC16 were maintained by adding 1.2 mg/ml hygromycin B, 250 ug/ml geneticin, 1 ug/ml puromycin.

extract_protocol:
Total RNA was collected from cultured cells using Ribospin II (geneall).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit.

treatment_protocol: HMGB1 wild type and Knock-out iSLK BAC16 cells were induced for 24 hours by 1.2 mM sodium butyrate(sigma) and 50 ug/ml Doxycycline(sigma).

value: Renal carcinoma

value: HMGB1 WT

tag: viral replication state

value: lytic


title: iSLK BAC16 KO induction (2)

tag: tissue

value: HMGB1 KO


title: FT282_siPAX8_Replicate2

value: Fallopian Tube Secretory Epithelial Cell Line

value: 1-12 (0 being STR profiled)


title: AKI6_CD4_Day0_Rep1


title: genome-edited iPSC 409B2-Ho3, 4wks, biological rep2

first: MASAHIRO

last: NOGAMI

address: 26-1, Muraoka-Higashi 2-Chome

institute: Takeda Pharmaceutical Company Limited

description: Gene expression data from iPSC-MN


title: iSLK BAC16 WT no tx (2)

value: latent


title: FT282_siPAX8_Replicate1


title: genome-edited iPSC 409B2-Ho3, 4wks, biological rep3

description: Gene expression data from iPSC-MN


title: AKI5_CD8_Day0_Rep2

value: Donor 5


title: genome-edited iPSC 409B2-Ho2, 4wks, biological rep2

description: Gene expression data from iPSC-MN

source_name: genome-edited iPSC 409B2-Ho2, 4wks


title: genome-edited iPSC 409B2-Ho2, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: genome-edited iPSC 409B2-Ho1, 4wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: genome-edited iPSC 409B2-Ho1, 4wks


title: genome-edited iPSC 409B2-Ho2, 4wks, biological rep3

description: Gene expression data from iPSC-MN


title: AKI6_CD8_Day0_Rep1


title: FT282_siNT2_Replicate2

value: Dharmacon Custom None-targeting Control Pool (D-0012-03, D-001210-04, D-001210-05)


title: AKI5_CD8_Day0_Rep1


title: iSLK BAC16 KO no tx (2)


title: FT282_siNT2_Replicate1

value: Dharmacon Custom None-targeting pool (D-0012-03, D-001210-04, D-001210-05)


title: NFs circCUL2-overexpression vector rpt3

city: Guangzhou

first: Shangyou

last: Zheng

state: Guangdong

address: Guangzhou

institute: Guangdong Provincial People's Hospital

data_processing:
Clean reads were mapped to the genome (for example: Homo sapiens) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml，v2.1.1)
The expression level of mRNA were calculte using RSEM (RNA-Seq by Expectation Maximization) (v1.3.1) by normalized to FPKM (Fragments Per Kilobase Per Million reads)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic Ductal Adenocarcinoma paired non-cancerous tissues

extract_protocol:
Primary normal fibroblasts (NFs) were isolated from pancreatic ductal carcinoma paired non-cancerous tissues. The Human Tumor Dissociation Kit (Miltenyi Biotec 130-095-929) was used for the generation of single cells from dissociated tissues. Fibroblast populations were isolated by differential velocity adherent technique. 48 hours after transfection, RNA was isolated and sent for total RNA sequencing.
After the quality inspection of Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and NanoPhotometer® (Implen, cat.N60, Munich, Germany), mRNA with poly(A) is purified from 1μg total RNA using VAHTS® mRNA Capture Beads with Oligo (dT) (Vazyme, cat.N401-01, Nanjing, China) through two rounds of purification. Subsequently, mRNA fragment was interrupted using VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China) under 94℃ 8min and reversed transcription into cDNA which would use to synthesise U-labeled second-stranded DNAs. An A-base was added to the blunt ends of each strand to ligase the indexed adapters which contains a T-base at the tail end. After UDG enzyme treatment of the U-labeled double-strand DNA, size selection was performed with VAHTS® DNA Clean Beads (Vazyme, cat.N411, Nanjing, China). Then the ligated products are amplified with PCR by the following conditions: initial denaturation at 98℃ for 5 min; 12-17 cycles of denaturation at 98℃ for 10 sec, annealing at 60℃ for 30 sec, and extension at 72℃ for 30 sec; final extension at 72℃ for 5 min. The average insert size of cDNA library was 280±80 bp. After purification by VAHTS® DNA Clean Beads (Vazyme,cat.N411-02, Nanjing, China), quality control of concentration and fragment size is performed by Agilent 2100 Bioanalyzer (Agilent, cat.G2939AA, CA, USA) and Qubit assay tubes (Life, cat. 1604220, CA, USA). At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 system (Illumina Corporation ， San Diego ， USA) following the vendor's recommended protocol by Guangzhou Huayin Health Medical Group CO.,Ltd. (Guangzhou, China).

value: primary normal fibroblasts

tag: treatment

value: transfected with circCUL2-overexpression vector


title: NFs circCUL2-overexpression vector rpt2


title: NFs circCUL2-overexpression vector rpt1


title: AKI5_CD4_Day0_Rep2

value: whole blood

value: CD4+ T cell


title: AKI5_CD4_Day0_Rep1

value: 48 hours


title: FT282_siNT1_Replicate2

value: Dharmacon ON-TARGETplus Non-targeting Control Pool


title: genome-edited iPSC 409B2-Ho1, 4wks, biological rep2

city: Fujisawa

description: Gene expression data from iPSC-MN

value: iPSC-MN

value: 4 weeks


title: NFs Empty vector rpt3

value: transfected with empty vector


title: fALS-2e3, 4wks, biological rep2

description: Gene expression data from iPSC-MN

source_name: fALS-2e3, 4wks


title: genome-edited iPSC 409B2-Ho1, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: fALS-2e3, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: FT282_siNT1_Replicate1


title: NFs Empty vector rpt2


title: fALS-e54, 4wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: fALS-e54, 4wks


title: OVCAR4_siWT1_Replicate2_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550651

value: High-Grade Serous Ovarian Cancer


title: AKI4_CD8_Day0_Rep1

value: Donor 4

value: CD8+ T cell


title: NFs Empty vector rpt1


title: OVCAR4_siWT1_Replicate1_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550650

value: 1-12 (0 being STR profiled)


title: OVCAR4_siMECOM_Replicate2_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550649


title: OVCAR4_siMECOM_Replicate1_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550648


title: fALS-e48, 4wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: fALS-e48, 4wks


title: ATAC-Seq Ad Cor/Conj 246Z

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

description:
Ad Cor/Conj 246Z
peaks.csv

data_processing:
scRNAseq samples were de-multiplexed and aligned to human reference genome GRCh38 before being quantified using CellRanger version 3.0
Quality control filtering was applied to remove any cells where fewer than 1000 reads or 500 genes or greater than 15% mitochondrial reads.
CellRanger version 1.2  was used to process the ATACseq data.  Cellranger-atac agrr module was used to create a set of shared peaks present across all four samples.
data was filtered using thresholds to remove cells where the number of fragments within peaks was less than 1000 or greater than 50000
or with a blacklist ration of greater than 5% or a nucleosome signal of greater than 10 and a TTS enrichment of  , greater than 2
Genome_build: GRCh38
Supplementary_files_format_and_content: The filtered counts from both experiments are provided as a csv file.

source_name: Cornea/Conjunctiva

extract_protocol:
Cornea-conjunctival tissue was excised from donated eyes and dissociated to single cells using a multi tissue dissociation kit (Miltenyi Biotec). Dissociation time varied from 15 to 45 minutes depending on the age of the tissue and a gentleMACS Dissociator (Miltenyi Biotec) was used to aid dissociation of the adult tissue.
For scRNA-Seq libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit, version 3 (10x Genomics). For scATAC-Seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit, version 1 (10x Genomics).
RNA-Seq & ATAC-Seq

tag: developmental stage

value: Adult


title: fALS-e54, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: fALS-2e3, 4wks, biological rep3

description: Gene expression data from iPSC-MN


title: AKI4_CD8_Day0_Rep2


title: ATAC-Seq Ad Cor/Conj 719I

description:
Ad Cor/Conj 719I
peaks.csv


title: ATAC-Seq Ad Cor/Conj 283P

description:
Ad Cor/Conj 283P
peaks.csv


title: AKI3_CD8_Day0_Rep2

value: Donor 3


title: OVCAR4_siDual_Replicate2_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550647


title: ATAC-Seq Ad Cor/Conj 257T

description:
Ad Cor/Conj 257T
peaks.csv


title: AKI4_CD4_Day0_Rep1


title: AKI3_CD4_Day0_Rep2


title: RNA-Seq Ad Kera Cor 43

description:
Ad Kera Cor 43
additional1.csv

source_name: Keratoconus Cornea


title: AKI3_CD8_Day0_Rep1


title: OVCAR4_siDual_Replicate1_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550646


title: fALS-e48, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: fALS-e48, 4wks, biological rep2

description: Gene expression data from iPSC-MN


title: fALS-e46, 4wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: fALS-e46, 4wks


title: fALS-e54, 4wks, biological rep2

description: Gene expression data from iPSC-MN


title: fALS-e46, 4wks, biological rep2

description: Gene expression data from iPSC-MN


title: fALS-e46, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: OVCAR4_siSOX17_Replicate2_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550645


title: OVCAR4_siSOX17_Replicate1_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550644


title: OVCAR4_siPAX8_Replicate2_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550643


title: RNA-Seq Ad Cor Limbal Dysplasia 782T

description:
Ad Cor Limbal Dysplasia 782T
additional2.csv

source_name: Cornea with Limbal Dysplasia


title: RNA-Seq LSC Culture on Feeders C-4046

description:
LSC Culture on Feeders C-4046
additional3.csv

source_name: Limbal Ring


title: AKI2_CD8_Day0_Rep1

source_name: whole blood

value: Donor 2


title: AKI2_CD8_Day0_Rep2


title: AKI2_CD4_Day0_Rep2


title: AKI3_CD4_Day0_Rep1


title: OVCAR4_siNT2_Replicate2_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550641

value: Dharmacon Custom None-targeting Control Pool (D-0012-03, D-001210-04, D-001210-05)


title: OVCAR4_siPAX8_Replicate1_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550642


title: AKI2_CD4_Day0_Rep1


title: Control iPSC EKA03, 4wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: Control iPSC EKA03, 4wks

value: FUSWT/WT


title: RNA-Seq Ad Limbal Ring C-4046

description:
Ad Limbal Ring C-4046
additional3.csv


title: RNA-Seq LSC Culture on HAM C-4046

description:
LSC Culture on HAM C-4046
additional3.csv


title: RNA-Seq Ad Kera Cor 18

description:
Ad Kera Cor 18
additional1.csv


title: AKI1_CD8_Day0_Rep2

value: Donor 1


title: OVCAR4_siNT2_Replicate1_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550640

value: Dharmacon Custom None-targeting pool (D-0012-03, D-001210-04, D-001210-05)


title: Control iPSC EKA03, 4wks, biological rep2

description: Gene expression data from iPSC-MN


title: OVCAR4_siNT1_Replicate2_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550639


title: AKI1_CD8_Day0_Rep1

value: whole blood


title: RNA-Seq Ad Cor/Conj 283P

description:
Ad Cor/Conj 283P
counts_adult_cornea.txt


title: RNA-Seq Ad Cen Cor C-4046

description:
Ad Cen Cor C-4046
additional1.csv

source_name: Central Cornea


title: Control iPSC 409B2, 4wks, biological rep2

description: Gene expression data from iPSC-MN

source_name: Control iPSC 409B2, 4wks


title: Control iPSC 409B2, 4wks, biological rep3

description: Gene expression data from iPSC-MN


title: Control iPSC 201B7, 4wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: Control iPSC 201B7, 4wks


title: Control iPSC 409B2, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: Control iPSC EKA03, 4wks, biological rep1

description: Gene expression data from iPSC-MN


title: OVCAR4_siNT1_Replicate1_reanalyzed

description:
Re-analysed GEO Accession: GSE150443
GSM4550638


title: RNA-Seq Ad Cor/Conj 719I

description:
Ad Cor/Conj 719I
counts_adult_cornea.txt


title: AKI1_CD4_Day0_Rep2

value: 48 hours

value: CD4+ T cell


title: AKI4_CD4_Day0_Rep2


title: OVCAR4_siWT1_Replicate2

data_processing:
typecounts_geo_1.txt Alignment: Aligned with STAR-2.5.1b
typecounts_geo_1.txt Read counts: # Program:featureCounts v1.6.3; Command:"featureCounts" "-T" "8" "-B" "-O" "-C" "-p" "-a" "gencode.v26.annotation.gtf" "-o" "typecounts.txt" <BAMs>
Genome_build: ref_genome_hg38_gencodev26
Supplementary_files_format_and_content: text file representing counts

growth_protocol: OVCAR4:RPMI-1640 supplemented with 10% FBS, 1x NEAA, 11.4 μg/ml of insulin, and 1x penicillin/streptomycin and maintained at 37°C with 5% CO2


title: RNA-Seq Ad Cor/Conj 257T

description:
Ad Cor/Conj 257T
counts_adult_cornea.txt


title: Control iPSC 201B7, 4wks, biological rep2

description: Gene expression data from iPSC-MN

value: iPSC-MN


title: shMCU-exo3

first: Xianchong

address: No.651, Dongfengdonglu, Yuexiu District

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The comparison of sRNA to Genbank and Rfam was performed using blast or bowtie, rRNA, scRNA, snoRNA, snRNA and tRNA were then screened and removed.
The mapping of sequencing reads to the human genome (hg19) was performed using miRDeep2 software package.
Genome_build: hg 19
Supplementary_files_format_and_content: Excel 97-2003 files include RPKM values for each Sample.

growth_protocol: Approximately 5.5 × 106 of MDA-MB-231 cells (shNC or shMCU stable clones) were cultured in DMEM containing 10% exosome-free FBS with a 150 mm dish for 48 hrs.

extract_protocol:
The exosomes were isolated and purified using a PEG6000-based enrichment and ultracentrifugation. Exosomal miRNA was isolated using miRNeasy Mini Kit (#217004, QIAGEN) according to the user's instructions.Preparation of small RNA libraries was done using the CleanTag Small RNA library prep kit (TriLink Biotechnologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: human breast carcinoma cell line

tag: genotype/variation

value: shMCU

tag: sample type

value: exosomes


title: RNA-Seq Ad Cor/Conj 246Z

description:
Ad Cor/Conj 246Z
counts_adult_cornea.txt


title: shMCU-exo2


title: AKI1_CD4_Day0_Rep1

tag: donor

tag: anti-cd3/cd28 stimulation


title: shMCU-exo1

tag: cell type


title: OVCAR4_siWT1_Replicate1

value: High-Grade Serous Ovarian Cancer


title: RNA-Seq Dev Cor/Conj 20PCW 15183

description:
Dev Cor/Conj 20PCW 15183
counts_20_21PCW.txt

value: 20 PCW


title: OVCAR4_siMECOM_Replicate1

value: 1-12 (0 being STR profiled)


title: OVCAR4_siDual_Replicate2


title: shNC-exo3

value: shNC


title: OVCAR4_siMECOM_Replicate2


title: shNC-exo2


title: RNA-Seq Dev Cor/Conj 18PCW 14954

description:
Dev Cor/Conj 18PCW 14954
counts_17_18PCW.txt

value: 18 PCW


title: OVCAR4_siDual_Replicate1


title: Control iPSC 201B7, 4wks, biological rep1

description: Gene expression data from iPSC-MN

value: 4 weeks


title: shNC-exo1


title: RNA-Seq Dev Cor/Conj 17PCW 14613

description:
Dev Cor/Conj 17PCW 14613
counts_17_18PCW.txt

value: 17 PCW


title: OVCAR4_siSOX17_Replicate1


title: OVCAR4_siSOX17_Replicate2


title: genome-edited iPSC 409B2-Ho3, 2wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: genome-edited iPSC 409B2-Ho3, 2wks

value: 2 weeks


title: RNA-Seq Dev Cor/Conj 16PCW 15232

description:
Dev Cor/Conj 16PCW 15232
counts_16PCW.txt

value: 16 PCW


title: OVCAR4_siPAX8_Replicate2


title: RNA-Seq Dev Cor/Conj 20PCW 14556

description:
Dev Cor/Conj 20PCW 14556
counts_20_21PCW.txt


title: S17_bronchial_lymph_node_BRSV

city: Dunsany

first: Dayle

last: Johnston

state: Ireland

address: AGRIC

department: Animal and Bioscience Research Department

country: Ireland

institute: Teagasc

data_processing:
The 3' end of the sequence reads were trimmed for quality scores less than 20 and (because of NextSeq technology) for artificial poly-Gs, using cutadapt version 1.18. Reads which contained fewer than 15 bases, greater than 30 bases, or ambiguous nucleotides (N's), were discarded.
Contaminant short RNA sequences including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs) (downloaded from https://rnacentral.org/) were filtered out using Bowtie version 1.2.2.
The cleaned sequence reads were evaluated for quality using FastQC (version 0.11.7).
Read counts for known miRNAS were generated using the miRDeep2 package (version 2.00.8) with the UMD 3.1 version of the bovine genome and the and the bovine mature and precursor miRNA sequences from the miRBase database (release 22).
Genome_build: UMD3.1
Supplementary_files_format_and_content: TXT file of raw counts table of sequenced reads for miRNAs

organism: Bos taurus

source_name: bronchial lymph node

extract_protocol:
Total RNA (including miRNAs) was extracted using the Qiagen RNeasy Plus Universal Mini Kit (Qiagen LTD, Manchester, UK), according to the manufacturer's instructions including Appendix C of the manufacturer's protocol.
Small RNA-Seq library preparation was performed using the TruSeq Small RNA Library Prep Kit (Illumina, San Diego, California, USA), according to the manufacturer's protocol.

treatment_protocol: Holstein-Friesian calves were either inoculated with BRSV (103.5 TCID50/ml x 15 ml) (n=12) or mock challenged with phosphate buffered saline (n=6). Clinical signs were scored daily until euthanasia at day 7 post-challenge.

value: bronchial lymph node

value: BRSV challenged

tag: breed

value: Holstein-Friesian

tag: shed

value: C


title: S16_bronchial_lymph_node_BRSV


title: RNA-Seq Dev Cor/Conj 16PCW 15057

description:
Dev Cor/Conj 16PCW 15057
counts_16PCW.txt


title: RNA-Seq Dev Cor/Conj 14PCW 15357

description:
Dev Cor/Conj 14PCW 15357
counts_14PCW.txt

value: 14 PCW


title: OVCAR4_siPAX8_Replicate1

tag: cell line


title: RNA-Seq Dev Cor/Conj 21PCW 15184

description:
Dev Cor/Conj 21PCW 15184
counts_20_21PCW.txt

value: 21 PCW


title: S18_bronchial_lymph_node_BRSV


title: genome-edited iPSC 409B2-Ho3, 2wks, biological rep1

description: Gene expression data from iPSC-MN

value: iPSC-MN


title: OVCAR4_siNT2_Replicate2

value: Dharmacon Custom None-targeting Control Pool (D-0012-03, D-001210-04, D-001210-05)


title: S15_bronchial_lymph_node_BRSV


title: RNA-Seq Dev Cor/Conj 14PCW 15208

description:
Dev Cor/Conj 14PCW 15208
counts_14PCW.txt


title: genome-edited iPSC 409B2-Ho2, 2wks, biological rep2

description: Gene expression data from iPSC-MN

source_name: genome-edited iPSC 409B2-Ho2, 2wks


title: OVCAR4_siNT2_Replicate1

value: High-Grade Serous Ovarian Cancer

value: Dharmacon Custom None-targeting pool (D-0012-03, D-001210-04, D-001210-05)


title: genome-edited iPSC 409B2-Ho2, 2wks, biological rep3

description: Gene expression data from iPSC-MN


title: genome-edited iPSC 409B2-Ho1, 2wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: genome-edited iPSC 409B2-Ho1, 2wks


title: S14_bronchial_lymph_node_BRSV


title: RNA-Seq Dev Cor/Conj 13PCW 15205

description:
Dev Cor/Conj 13PCW 15205
counts_13PCW.txt

value: 13 PCW


title: fALS-2e3, 2wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: fALS-2e3, 2wks


title: OVCAR4_siNT1_Replicate2

value: 1-12 (0 being STR profiled)

value: Dharmacon ON-TARGETplus Non-targeting Control Pool


title: S13_bronchial_lymph_node_BRSV


title: genome-edited iPSC 409B2-Ho1, 2wks, biological rep1

description: Gene expression data from iPSC-MN


title: genome-edited iPSC 409B2-Ho1, 2wks, biological rep2

description: Gene expression data from iPSC-MN


title: genome-edited iPSC 409B2-Ho2, 2wks, biological rep1

description: Gene expression data from iPSC-MN


title: RNA-Seq Dev Cor/Conj 13PCW 15176

description:
Dev Cor/Conj 13PCW 15176
counts_12PCW.txt


title: RNA-Seq Dev Cor/Conj 12PCW 15210

description:
Dev Cor/Conj 12PCW 15210
counts_12PCW.txt

value: 12 PCW


title: S12_bronchial_lymph_node_BRSV

value: B


title: fALS-2e3, 2wks, biological rep2

description: Gene expression data from iPSC-MN

value: 2 weeks


title: RNA-Seq Dev Cor/Conj 12PCW 15209

description:
Dev Cor/Conj 12PCW 15209
counts_12PCW.txt


title: Liver_SeqScope_2nd

description: SeqScope 2nd-Seq library

source_name: Mouse liver

value: OCT-frozen liver

tag: condition

value: Normal and Injured liver tisssues from mice. Normal liver was collected from 8 week-old control (Depdc5F/F/Tsc1F/F, male) mouse. Injured liver was collected from TD (Alb-Cre/Depdc5F/F/Tsc1F/F, female) mouse.


title: fALS-2e3, 2wks, biological rep1

description: Gene expression data from iPSC-MN


title: OVCAR4_siNT1_Replicate1

tag: passages


title: ATACseq_ThrbNeg_rep2

city: BOSTON

first: CHANGHEE

last: LEE

state: MA

address: 77 AVENUE LOUIS PASTEUR

department: Genetics

institute: Harvard Medical School

data_processing:
The sequenced reads were aligned to the galgal5 genome assembly using Bowtie2 with -X 1000
MACS2 was perfomed to detect ATAC-seq peaks and generate the reads normalized bogwigle files with parameter -B --SPMR --nomodel --extsize 146
Genome_build: galgal5
Supplementary_files_format_and_content: processed bigWig files and peaks in narrowPeak format were obtained from MACS2

organism: Gallus gallus

source_name: Retina

growth_protocol: Retina were harvested at E5 and explanted for 2 days on floating membranes. Culture media was composed of 45% DMEM, 45% F12, 10% fetal bovine serum and penicillin

extract_protocol: ATAC-seq libraries for each conditions were prepared using the standard protocol (Buenrostro et al. 2013).

treatment_protocol: Retina were co-electroporated with ThrbCRM1-GFP and CAG-Cherry plasmids and cultured for 2 days. Retina were dissociated with papain, cells were sorted by FACS into Cherry+/GFP+ (ThrbCRM1+) and Cherry+/GFP- (ThrbCRM1-) populations.

value: Developing retinal cells

tag: treatment/condition

tag: Stage

value: E5 + 48h culture


title: RNA-Seq Dev Cor/Conj 12PCW 15192

description:
Dev Cor/Conj 12PCW 15192
counts_12PCW.txt

source_name: Cornea/Conjunctiva


title: S11_bronchial_lymph_node_BRSV

value: bronchial lymph node

value: BRSV challenged

value: Holstein-Friesian


title: fALS-e54, 2wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: fALS-e54, 2wks

value: iPSC-MN

tag: genotype

tag: time (differentiation from motor neuron precursor)


title: S9_bronchial_lymph_node_BRSV

tag: tissue


title: S10_bronchial_lymph_node_BRSV

tag: treatment


title: RNA-Seq Dev Cor/Conj 12PCW 14823

description:
Dev Cor/Conj 12PCW 14823
counts_12PCW.txt

tag: developmental stage


title: fALS-e54, 2wks, biological rep2

description: Gene expression data from iPSC-MN


title: fALS-e54, 2wks, biological rep1

description: Gene expression data from iPSC-MN


title: fALS-e48, 2wks, biological rep3

description: Gene expression data from iPSC-MN

source_name: fALS-e48, 2wks


title: S8_bronchial_lymph_node_BRSV


title: S7_bronchial_lymph_node_control


title: RNA-Seq Dev Cor/Conj 10PCW 14849

description:
Dev Cor/Conj 10PCW 14849
counts_10PCW.txt

value: 10 PCW


title: RNA-Seq Dev Cor/Conj 10PCW 14615

description:
Dev Cor/Conj 10PCW 14615
counts_10PCW.txt


title: ATACseq_ThrbPos_rep2


title: ATACseq_ThrbPos_rep1


title: fALS-e48, 2wks, biological rep2

description: Gene expression data from iPSC-MN


title: genome-edited iPSC 409B2-Ho3, 2wks, biological rep2

description: Gene expression data from iPSC-MN


title: ATACseq_ThrbNeg_rep1


title: S6_bronchial_lymph_node_control

value: control

value: A


title: HEK293 YS mutant FUS-HOXA9 rep1

city: Chapel Hill

first: Gang

middle: Greg

last: Wang

state: NC

address: 450 West Drive

department: Dept of Biochemistry and Biophysics

institute: UNC Lineberger Comprehensive Cancer Center

data_processing:
All reads were mapped to the human genome (hg19) or mouse genome (mm10) using the BWA alignment software. Unique reads mapped to a single best-matching location with no more than two mismatches were kept using Samtools. We filter out reads with a mapping quality score < 20 for downstream analysis
Then the quantification was done by salmon (ver 0.14.1). Different expression analysis was done using DESeq2.
Genome_build: GRCh37/hg19 or GRCm38/mm10
processed data files format and content: Excel spread sheet of DEseq2 result

source_name: HEK 293 cells

growth_protocol: HEK 293 cells were grown in DMEM plus 10% FBS and 1% antibiotics. mouse HSPC cells were grown in Opti-medium plus 10% FBS, 2% mSCF, 1% FLT3L, 1% antibiotics and 0.1% beta-mercaptoethanol

extract_protocol:
Total RNAs were purified using RNeasy Plus kit (Qiagen, #74136) and further processed with Turbo DNA-free kit (Thermo Fisher, #AM1907) to ensure the purity of RNA sample.
For RNA-seq, the RNA samples were either sent to Novogene or processed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490) and NEBNext Ultra II RNA library Prep kit (NEB, #E7770) following the instructions of the manufacture’s product manual.

treatment_protocol: HEK293 cells and mouse HSPCs were first infected with virus produced with either MSCV empty vector or that with 3XHA-3XFLAG-tagged NUP98-HOXA9 or FUS-HOXA9, and subject to drug selection and examination by western blotting for chimera expression. Stable HEK293 cells with comparable expression levels of IDR-WT and IDR-mutated fusion were maintained in the above DMEM medium. The mouse HSPCs were collected for RNA isolation 7 days after infection and drug selection in the OptiMEM medium supplemented with the HSPC-supporting cytokines.

value: HEK 293 cells

tag: expression

value: YS mutant FUS-HOXA9


title: HEK293 YS mutant FUS-HOXA9 rep2


title: HEK293 FS mutant NUP-HOXA9 rep2

value: FS mutant NUP-HOXA9


title: S5_bronchial_lymph_node_control


title: S3_bronchial_lymph_node_control


title: IgG_CUT&RUN_30

data_processing:
Library strategy: Cut&Run
The sequenced reads were aligned to the galgal5 genome assembly using Bowtie2 with the parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 and processed with SAMtools to remove duplicates and MT reads.
BigWig coverage tracks were generted using deepTools bamCoverage with the following parameters: -binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 1046932099. MACS2 was perfomed to detect CUT&RUN peaks with the IgG control of the corresponding digestion time as the background, using the parameter -g 1.03e9
Genome_build: galgal5
Supplementary_files_format_and_content: processed bigWig files and peaks in narrowPeak format were obtained from deepTools and MACS2

extract_protocol:
CUT&RUN was performed according to the protocol from (Meers et al., 2019) and available at dx.doi.org/10.17504/protocols.io.zcpf2vn.
Libraries were prepared with NEBNext Ultra II DNA Library Prep kit (E7645S), following the protocol available at dx.doi.org/10.17504/protocols.io.wvgfe3w, except for samples treated with IgG and H3K27me3 antibodies that were prepared following NEB protocol, as recommended.

treatment_protocol: E5 WT retina were dissociated as described previously (Shekhar et al., 2016)

value: 30 minutes digestion time point

tag: cut&run antibody


title: H3K27me3_CUT&RUN_30

value: H3K27me3 (Cell Signaling Technology 9733T)


title: HEK293 FS mutant NUP-HOXA9 rep1


title: ATACseq_ThrbPos_rep3


title: Oc1_CUT&RUN_30

value: Oc1 (Santa Cruz Biotechnology, sc-13050)


title: S4_bronchial_lymph_node_control


title: Otx2_CUT&RUN_30

value: Otx2 (Proteintech, 13497-1-AP)


title: S2_bronchial_lymph_node_control


title: IgG_CUT&RUN_25

value: 25 minutes digestion time point


title: S1_bronchial_lymph_node_control


title: HEK293 wildtype NUP-HOXA9 rep2

value: wildtype NUP-HOXA9


title: H3K27me3_CUT&RUN_25

value: Developing retinal cells


title: Giant panda frozen-thawed sperm-rep2

city: Chengdu

first: Han

address: GongPing

institute: Sichuan Agricultural University

data_processing:
Clean reads were obtained by removing reads that contained adapter, poly-N, low-qualities reads and sequences <18 nt or >34 nt. The designated reference genome of giant panda (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/004/335/GCF_000004335.2_AilMel_1.0) and Sus scrofa (ftp://ftp.ensembl.org/pub/release-75/fasta/sus_scrofa/) were used for sequence alignment.
Comparison of clean reads to Silva database, GtRNAdb database, Rfam database and Repbase were performed with Bowtie
Known piRNAs and novel piRNAs were identified by comparing sequences with known piRNAs from miRbase using proTRA
DESeq R package (1.10.1), based on Reads Per Kilobase Million (TPM) and Fragments Per Kilobase Million (FPKM) algorithm was used for analyzing the differential expression of piRNAs between fresh and frozen-thawed sperm
The piRNAs between fresh and frozen-thawed sperm were analyzed by IDEG[23], and the adjusted p < 0.01 and absolute value of log2 (Fold change) >1 was classified as DE piRNAs.
Then, hierarchical clustering analysis was performed on the selected differentially expressed piRNAs, and the piRNAs with the same or similar expression behaviors were clustered.
Genome_build: Ailmel 1.0，Sscrofa11.1
Supplementary_files_format_and_content: abundance measurements

organism: Ailuropoda melanoleuca

source_name: Giant panda frozen-thawed sperm

extract_protocol:
The total RNA of fresh and frozen-thawed sperm was extracted using the TRIzol LS Reagent kit (Invitrogen, Carlsbad, CA, USA).
After total RNA extraction, purity, concentration, and integrity of RNA were determined by Nanodrop (Thermo Fisher Scientific, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara,CA, USA), respectively. Then, the mRNA was isolated by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, E7490, Ipswich, MA, USA). The cDNA library was constructed using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, E7530, Ipswich, MA, USA) and NEBNext Multiplex Oligos for Illumina (NEB, E7500, Ipswich, MA, USA) following the manufacturer’s instructions.

value: Giant panda mature sperm

value: treated by frozen protocol


title: HEK293 wildtype FUS-HOXA9 rep2

value: wildtype FUS-HOXA9


title: Oc1_CUT&RUN_25


title: HEK293 wildtype FUS-HOXA9 rep1


title: HEK293 MSCV Empty vector rep2

value: MSCV Empty vector


title: Otx2_CUT&RUN_25


title: dAdG-2

city: State College

first: Paul

last: Babitzke

state: PA

address: 203 Althouse Laboratory

institute: Pennsylvania State University

description: NusA depletion nusG deletion

data_processing:
base calling and quality scoring conducted via BaseSpace
adaptor trimming and low quality read removal via Trimmomatic v. 0.38 for RNA-seq .fastq dataset
all reads containing custom oligo were extracted via Cutadapt v. 1.16 for Term-seq .fastq dataset
both RNA-seq and Term-seq .fastq files were mapped to B. subtilis genome using bwa-mem v.0.7.12-r1034
sam -> bam, and bam files split by strand via samtools v. 0.1.19-44428cd
coverage files (.cov) for 3' end mapping and .bedgraph files to illustrate coverage were generated using bedtools v. 2.26.0
2 custom python (python v. 3.8.3) scripts were used to identify 3' ends from Term-seq .fastq derived .cov files (located at: https://github.com/zfmandell/Term-seq)
RNA-seq coverage files generated using bedtools v. 2.26.0
Genome_build: Refseq : NC_000964.3
Supplementary_files_format_and_content: .bedgraph files, containing either RNA-seq coverage information, and list of called 3' ends with associated Cv values

organism: Bacillus subtilis

source_name: NusA depletion nusG deletion

growth_protocol: cells were plated on LB plates at 37°C +2 mM IPTG +20 µg/ml chloramphenicol -> single colonies isolated and grown O/N at 37°C standing culture in +0.4 mM IPTG +20 µg/ml chloramphenicol -> next day, cells were grown at in 25 mL of LB at 37°C +20 µg/ml chloramphenicol and +2 mM IPTG in cases where NusA production was to be sustained

extract_protocol:
Total RNA was extracted from collected cell paste via RNeasy mini-kit (Qiagen, cat # 74104)
total RNA was dephosphorylated using CIP (NEB, discontinued), rRNA was depleted via ribo-zero Gram-positive rRNA depletion kits (Illumina, discontinued), remaining RNA was ligated to custom unique 2', 3’ dideoxy RNA oligonucleotide (IDT), Illumina sequencing libraries were generated from ligation products using TruSeq Stranded mRNA kit (Illumina, cat # 20020594)
Term-seq

value: rpoC-10His nusG::kan amyE::Physpank-nusA lacIq nusA::Spr

tag: iptg

value: 0 mM


title: HEK293 MSCV Empty vector rep1


title: HEK293 wildtype NUP-HOXA9 rep1


title: WT_ACF-S6

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
subread-1.6.1, featurecounts, -s 2 -t exon -g gene_name
Differential expression analysis was performed using DESeq2-1.16.1
Genome_build: GRCm38 + M17 Annotation
Supplementary_files_format_and_content: Raw counts

source_name: Heart

growth_protocol: Primary cardiac fibroblasts were isolated from three pairs of P60 wild type and Fam114a1-/- mice

extract_protocol:
The RNA extraction and purification from the isolated cardiac fibroblasts from WT vs Fam114a1-/- mouse hearts were performed using regular TRIzol reagent (ThermoFisher) according to the instructions in the manual. Then the extracted totoal RNA were treated with DNase I to remove potential genomic DNA followed by purification using phenol:chloroform:isoamyl alcohol for RNA-Seq.
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100-nt are generated for each sample and aligned to the organism specific reference genome.

tag: strain

value: Cardiac cells

value: WT


title: 33_E4_15_C08

first: Kelly

last: Zalocusky

address: 1650 Owens Street, Gladstone Center for Translational Advancement

institute: Gladstone Institutes

description: single nucleus RNA sequencing

data_processing:
Demultiplexed fastq files were aligned to a custom reference genome built from mm10-1.2.0 that includes introns, using the Cellranger v2.0.1 counts function with default parameters, as described in the Cellranger documentation.
UMI counts were also determined using the Cellranger counts function, and count matrices from different samples were aggregated into a single count matrix using Cellranger’s aggr function with default parameters. This function filters barcodes (potential cells) according to a UMI count threshold.
Genome_build: mm10-1.2.0
Supplementary_files_format_and_content: h5

source_name: hippocampus

growth_protocol: All protocols and procedures followed the guidelines of the Laboratory Animal Resource Center at the University of California, San Francisco (UCSF). Experimental and control mice had identical housing conditions from birth through sacrifice (12 h light/dark cycle, housed 5 animals/cage, PicoLab Rodent Diet 20). ApoE3-KI and apoE4-KI homozygous mouse lines (Taconic)51 were born and aged under normal conditions at the Gladstone Institute/UCSF animal facility. ApoE4-KI/Syn-Cre and apoE3-KI/Syn-Cre mice were generated by cross-breeding apoE-floxed-KI mice, which was generated in our lab52, with Syn-Cre mice11.

extract_protocol:
To isolate single nuclei from adult mouse brains, we combined and adapted the 10x Genomics demonstrated protocol for nuclei isolation from adult mouse brain55 and the Allen Brain Institute protocol for FACS sorting of single nuclei56 as follows. Hippocampi were acutely dissected on ice. Dissected hippocampi were placed in 2mL Hibernate A®/B27®/GlutaMAX™ (HEB) medium in a 5mL tube. The HEB medium was removed to a 15mL conical and kept on ice. 2mL of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Nonidet™ P40 Substitute in Nuclease-Free Water) were added to the tissue, and the hippocampi were homogenized by suctioning 10 times through a 21G needle. After homogenization, the tissue was lysed on ice for 15min, swirling 2–3 times during this incubation period. The reserved chilled HEB media was then returned to the lysed tissue solution, and the tissue was further triturated with 5–7 passes through a 1mL pipette. A 30µm cell strainer (MACS SmartStrainer; Miltenyi Biotech 130-110-915) was washed with 1mL of PBS, and the lysed tissue solution was filtered through the strainer to remove debris and clumps. Filtered nuclei were centrifuged at 500 rcf for 5min at 4°C. The supernatant was removed, and nuclei were washed in 1mL of Nuclei Wash and Resuspension Buffer (1X PBS with 1.0% BSA and 0.2U/µl RNase Inhibitor). Nuclei were again centrifuged at 500 rcf for 5min at 4°C and resuspended in 400µL of Nuclei Wash and Resuspension Buffer. DAPI was added to a final concentration of 0.1ug/mL, and the nuclei were filtered through a 35µm cell strainer. DAPI-positive nuclei were sorted by gating on DAPI-positive events, excluding debris and doublets, using the BD FACSAria-II at the Gladstone Institutes’ Flow Cytometry Core.
cDNA libraries were prepared using the Chromium Single Cell 3′ Library and Gel Bead kit v2 (10x Genomics: 120267) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 sequencer at the UCSF CAT Core.

tag: age (months)


title: E3fKI_Syn_Cre602

description: single nucleus RNA sequencing


title: E4fKI_Syn_Cre475

description: single nucleus RNA sequencing


title: Giant panda fresh sperm-rep1

source_name: Giant panda fresh sperm


title: 32_E3_15_C07

description: single nucleus RNA sequencing


title: Fam114a1-/-_ACF-S4


title: Fam114a1-/-_ACF-S3


title: WT-2

description: Wild Type

source_name: Wild Type

value: rpoC-10His amyE::Physpank-nusA lacIq nusA::Spr

value: 2 mM


title: dA-2

description: NusA depletion

source_name: NusA depletion


title: dAdG-1

description: NusA depletion nusG deletion


title: dG-1

description: nusG deletion

source_name: nusG deletion


title: fALS-e46, 2wks, biological rep1

state: Kanagawa

description: Gene expression data from iPSC-MN

source_name: fALS-e46, 2wks

tag: cell type

value: iPSC-MN

value: 2 weeks


title: 31_E4_10_C06

description: single nucleus RNA sequencing