title: F10_Larval EE2-exposed_rep 10

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
Sequenced reads were trimmed for adaptor sequences then mapped against 620 FHM miRNA sequences using Bowtie (bowtie-1.2.3-linux-x86_64).
Sequenced reads were trimmed for adaptor sequences then mapped against 1.3 million Danio rerio piRNA sequences using Bowtie (bowtie-1.2.3-linux-x86_64).
Count data were filtered for features which had at least 3 samples with at least 10 counts
Filtered piRNA count data were further filtered for duplicate count reports
Differential expression analysis was performed using the R limma package (version 3.40.6. Between sample normalization was conducted using the trimmed mean of M-values method implemented by the calcNormFactors function from the R edgeR package (version 3.26.8). Precision weights were calculated using the voom function from the limma package. The limma lmFit function was used to fit a generalized linear model with a term for chemical treatment effects. Moderated t-statistics were calculated for chemical treatment effects using the limma eBayes function, and the limma topTable function was used to sort features (i.e. genes) based on their nominal p-values.
Genome_build: EPA_FHM_2.0.b
Supplementary_files_format_and_content: miRNA_R_9-16.txt: raw counts for miRNA (reverse strand)
Supplementary_files_format_and_content: miRNA_F_9-16.txt: raw counts for miRNA (forward strand)
Supplementary_files_format_and_content: pi_xx_R.list_edit.txt: raw counts for piRNA (reverse strand alignment)
Supplementary_files_format_and_content: pi_xx_F.list_edit.txt: raw counts for piRNA (forward strand alignment)

source_name: Whole 96h post-hatch larva_EE2-exposed

extract_protocol:
Larvae were removed from exposure vessels, placed into Eppendorf tubes together with a steel bead and frozen in liquid nitrogen.  Direct-zolTM RNA microprep kits were used for total RNA isolation for the small RNA work.
1000 ng of total RNA was used as input for library preparation using the TruSeq Small RNA Library preparation kit (Illumina)

treatment_protocol: 48h post-hatch fathead minnow larvae were statically exposed to 0 or 10 ng ethinyl estradiol /l for 48 hours

value: 10 ng ethinyl estradiol for 48 hours

tag: molecule subtype

value: small RNA


title: [Neuropathology] B6_Brain_Naive_rep1

status: Public on Mar 12 2021

type: RNA

city: Riverside

first: Emma

middle: Harriet

last: Wilson

state: CA

address: 900 University Avenue

country: USA

institute: UC Riverside

description: 50ug RNA was loaded for each sample, Naïve samples were used as reference samples for comparison in analysis

hyb_protocol: Panel codeset probes were hybridized with 150ng of total RNA per brain over 18hr at 65C according to NanoString protocol.

scan_protocol: Hybridized RNA was then diluted in molecular grade water and loaded into nCounter SPRINT cartridge (NanoString), placed into nCounter SPRINT Profiler, and quantified.  RNA-conjugated probes were counted via NanoString Sprint Profiler technology.

data_processing: Results from each panel were merged into one data file for comparative analysis, normalized in nSolver following best practices, and analyzed using nSolver and Advanced Analysis software according to previously published protocols (Danaher et al. 2017). nSolver-generated heat maps were created using normalized (merged) data and agglomerative clustering, a bottom-up form of hierarchical clustering (NanoString User Manual C0019-08). For Advanced Analysis, normalized merged data was used (NanoString User Manual 10030-03). Differential expression (DE) analysis was performed to identify specific targets that exhibit significantly increased or decreased expression in response to naïve control values or, in the case of BALB/c C57BL/6 comparison, to C57BL/6 control values at each time point. Gene set analysis was run to determine the change in direction of regulation within each pre-defined gene set relative to naïve controls. Global significance scores, a summary T-statistic used to measure change (NanoString User Manual 10030-03) were calculated, and the directed global significance scores were expressed via heatmap. Cell type profiling module analysis was conducted to determine the relative abundance in classically activated cell types during infection using genes assigned to each cell type: T cells (CD3e, CD6, CD3g, TRAT1, and CD3d), CD8+ T cells (CD8a), macrophages (CD68 and CD84), and microglia (GPR84, LRRC25, IRF8, NCF1, TNF, TLR2, and TNF.1). NanoString cell type profiling is a validated method to measure relative abundance of up to 24 different immune cell types, with high concordance to flow cytometry (Danaher et al. 2017). Pathway analysis was also conducted to determine overall changes in pathways based on the first principal component of the targets within a pathway as annotated by NanoString (NanoString User Manual 10030-03). Direction of pathway change (up- or downregulated) was determined by cross referencing the pathway score with the corresponding volcano plot for that pathway. Summary pathway score plot colors are based on calculated scores and are represented as downregulation (blue) to upregulation (orange). Statistical significance was determined using R software.

label: codeset probes

molecule: total RNA

organism: Mus musculus

label_protocol: nCounter gene expression assays (NanoString Technologies) were performed for the NanoString Neuropathology panel. Samples were labelled with panel-specific codeset probes.

growth_protocol: The ME49 strain of T. gondii was maintained in cyst form by continuous passaging in SW and CBA background mice. Female 6-8 week old WT C57BL/6 and WT BALB/c mice were infected with 10 ME49 cysts per mouse in 200μl of sterile 1x PBS solution via intraperitoneal (IP) injection. Naïve controls received 200µl of sterile 1x PBS solution via intraperitoneal (IP) injection.

extract_protocol: RNA from brain lysate of naïve, 2 week infected, 4 week infected, and 8 week infected C57BL/6 and BALB/c mice (n=3 for all groups) was collected using Trizol extraction method. Whole brain was dissected and homogenized in 1mL Trizol. Phase separation was completed by adding 200µl of chloroform and incubating at room temperature for 2-3 minutes. Samples were centrifuged at 12,000xg for 15 minutes at 4°C, and upper aqueous phase was collected followed by RNA precipitation using 500µl isopropyl alcohol. Samples incubated at room temperature for 10 minutes followed by centrifugation. RNA pellet was washed with 1mL of 75% ethanol twice. All supernatant was discarded and RNA pellet was dissolved in 100µl of nuclease free water. RNA concentration for each sample was determined using a NanoDrop 2000, and RNA samples normalized to a concentration of 10ng/μL in molecular grade water.

treatment_protocol: At each time point, mice were sacrificed and perfused intracardially with 20mL of sterile 1x PBS.

tag: tissue

value: Brain

tag: mouse strain

tag: infection time point

value: Naive


title: T574.1_P7

type: SRA

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

institute: University of Wisconsin-Madison

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X574.1_S73

library_source: transcriptomic

data_processing:
bcl2fastq v2.20.0.422 was used for basecalling.
Sequencing reads were aligned to mm10 using Bowtie-1.2.2 and quantified using RSEM-1.3.0 under default RSEM parameter settings. single samples and paired-end samples were processed separately.
The expected count (EC) matrice for the single batch and paired-end batch  were combined together.
The combined EC matrix was pre-filtered where genes with average expression less than 1 were removed.
The filtered EC matrix was then normalized using median-by-ratio normalization, implemented in R package EBSeq-1.29.0.
Genome_build: mm10
Supplementary_files_format_and_content: Raw and normalized gene-by-sample count matrices in TXT format

source_name: Pancreatic β cell

extract_protocol:
Mouse islets were digested from pancreatas and purified by Histopague gradient centrifugation. The isolated islets were trypsized and sorted through flow cytometer for  mCherry+ cells (β cells). The RNA extraction was performed on sorted cells via TRIzol phenol-chloroform or Qiagen silica gel spin column.
Ultra-low RNA input libraries are generated using the Takara “SMART-Seq v4 Low Input RNA Kit for Sequencing” (Takara, Mountain View, CA, USA) for cDNA synthesis and the Illumina NexteraXT DNA Library Preparation (Illumina, SanDiego, CA, USA) kit for cDNA dual indexing.  Full length cDNA fragments are generated from 1-10ng total RNA by the Takara SMART (Switching Mechanism at 5’ End of RNA Template) technology.  cDNA fragments are fragmented  and dual indexed in a single step by taking advantage of the Nextera kit’s simultaneous transposon and tagmentation step. Libraries were standardized to 2nM.

tag: strain

value: ICR

value: Pancreas

tag: cell type

value: Pancreatic beta cell

tag: age

value: neonates day 7

tag: Sex

tag: blood glucose (mg/dl)

tag: weight (g)

tag: genotype

value: Cherry/+; Ins2-Cre/+

tag: disease state

value: wild type

tag: rna extraction

value: TRIzol-phenol chloroform


title: T578.1_P1

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X578.1_S76

value: neonates day 1


title: Wild type clone_1

city: Munich

first: Sabrina

last: Weser

address: Marchioninistraße 15

department: Department of Medicine III

country: Germany

institute: University Hospital, LMU

data_processing:
Fastq reads were processed with the zUMIs pipeline. Ensembl annotation GRCh38.84
The read count table generated by zUMIs was analysed for differential expression using the R platform
Genome_build: Hg38
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise read count table

organism: Homo sapiens

source_name: Cell line

growth_protocol: K562 cells were cultured according to the recommendations of the DSMZ

extract_protocol:
RNA was isolated from cell lysates by digestion of residual proteins and DNA using a ProteinaseK and DNAseI digest respectively.
RNA-seq libraries were prepared using prime-seq, a bulk version of the single cell RNA-seq method mcSCRB-seq.

treatment_protocol: EZH2 knockouts were generated by CRISPR/Cas9 mediated genome editing, targeting exon 3 of EZH2

value: bone marrow

tag: cell line

value: Wild type


title: F9_Larval EE2-exposed_rep 9

city: Cincinnati

first: Gregory

middle: Peter

last: Toth

state: OH

address: 26 W ML King Jr. Dr.

department: CCTE

institute: USEPA/ORD

organism: Pimephales promelas

tag: treatment


title: T577_P1

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X577_S20


title: Q204_P1

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X204_S2

value: Qiagen RNeasy Plus Mini Kit


title: BE3:CAA,RB,S1-F,CRA,V2C rep2;NT:PGM3 rep2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

library_source: genomic

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: base subtitutions

molecule: genomic DNA

source_name: 293FT_BE3 | NT

growth_protocol: 293FT, U2OS and N2A cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination. All mice were housed under specific pathogen-free conditions at the animal facilities of Medical Research Institute, Wuhan University. All mouse studies were approved by the Animal Care Committees of Medical Research Institute, Wuhan University.

extract_protocol:
Target genomic sequences were PCR amplified by high-fidelity DNA polymerase PrimeSTAR HS (Clonetech) with primer sets flanking examined sgRNA target sites.
For deep target genimoc DNA sequencing, Indexed DNA libraries were prepared by using the TruSeq ChIP Sample Preparation Kit (Illumina) with minor modifications. Briefly, the PCR products amplified from genomic DNA regions were fragmented by Covaris S220, and then PCR amplified by using the TruSeq ChIP Sample Preparation Kit (Illumina). After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina HiSeq X10 (2×150) at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: 293FT, U2OS and N2A cells were seeded in a 24-well plate at a density of 1E+5 per well and transfected with 250 μl serum-free Opti-MEM that contained LIPOFECTAMINE LTX (Life, Invitrogen), LIPOFECTAMINE plus (Life, Invitrogen) and expression vector. After 24 hr, puromycin (ant-pr-1, InvivoGen) was added to the medium at the final concentration of 4 μg/ml. After another 48 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre) for subsequent sequencing analysis.

value: BE3 | NT

tag: 5'-end trimming of r1

tag: 3'-end trimming of r1


title: PDX_24_SC: DLBCL tissue PR/PDX RNA

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

description:
PR sample for this PDX is Sample_69
PDX_humanreads.csv
PDX_mousereads.csv

data_processing:
Illumina Casava-1.8.2 software used for basecalling
STAR v2.6.1a was used to align
XenofilteR v0.99 used to deconvolute PDX samples
Salmon v1.3.0 used for quantification post deconvolution
Genome_build: hg38, mm10 (for PDX TME reads)
Supplementary_files_format_and_content: csv file includes Salmon TPM values

source_name: DLBCL tumor sample

extract_protocol: trizol extraction and llumina RNA Prep with enrichment, tagmentation kit

value: DLBCL tumor sample


title: F8_Larval EE2-exposed_rep 8

value: 10 ng ethinyl estradiol for 48 hours

tag: molecule subtype


title: BE3:CAA,RB,S1-F,CRA,V2C rep1;NT:PGM3 rep1


title: F7_Larval EE2-exposed_rep 7

value: small RNA


title: A02_Control larvae

data_processing:
Base calling was done by Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
The 50 base long reads in the RNA-Seq fastq(.gz) file for each sample were mapped to indexed transcripts from each of the 47,578 gene models (which include isoforms) from the newly updated FHM genome (WIOS00000000; BioSample SAMN12875914
Differential expression analysis was performed using the R limma package (version 3.40.6. Between sample normalization was conducted using the trimmed mean of M-values method implemented by the calcNormFactors function from the R edgeR package (version 3.26.8). Precision weights were calculated using the voom function from the limma package. The limma lmFit function was used to fit a generalized linear model with a term for chemical treatment effects. Moderated t-statistics were calculated for chemical treatment effects using the limma eBayes function, and the limma topTable function was used to sort features (i.e. genes) based on their nominal p-values.
Count data were filtered for features which had at least 3 samples with at least 10 counts
Genome_build: EPA_FHM_2.0.b
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Whole 96h post-hatch larva

extract_protocol:
Larvae were removed from exposure vessels, placed into Eppendorf tubes together with a steel bead and frozen in liquid nitrogen.  MagMax lysing/binding buffer (100 μl) was added to each tube.
Libraries were prepared from 250 ng RNA using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen, Greenland, NH) according to the supplied protocol.

treatment_protocol: 48h post-hatch fathead minnow larvae were statically exposed to 0, 0.12, 1.2, 2.5, 5 or 10 ng ethinyl estradiol /l for 48 hours

tag: tissue

value: whole larva

tag: experiment

tag: treatment (ng ee2/l)

value: mRNA


title: PDX_18_KK: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: BE3:S4A,D1B,E1A,R2A,RIB rep2


title: F6_Larval EE2-exposed_rep 6


title: F5_Larval EE2-exposed_rep 5


title: BE3:S4A,D1B,E1A,R2A,RIB rep3


title: T575.1_E18.5

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X575.1_S74

tag: strain

value: ICR

value: embryos day 18


title: BE3:S4A,D1B,E1A,R2A,RIB rep1


title: BE3:CAA,RB,S1-F,CRA,V2C rep3;NT:PGM3 rep3


title: SaC9+tBE-V5-mA3:VA1B,Sg4a,FF-OTsgd,VA1B-OTsgc rep3


title: Wild type clone_2


title: F4_Larval EE2-exposed_rep 4


title: T572.1_E18.5

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X572.1_S70

value: Pancreas

tag: cell type

value: Pancreatic beta cell


title: CoCl2_2_IP

city: Beijing

first: Xiao-ning

last: Gao

state: Beijing

address: 28 Fuxing Road

department: Department of Hematology

institute: Chinese PLA General Hospital

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
Then sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genomeHomo sapiens (Version: v101). Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org). MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit.
Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).

source_name: Kasumi-1 cell line

growth_protocol: Kasumi-1cells were maintained in RPMI 1640 medium supplemented with 50 µg/ml streptomycin, 50 IU/ml penicillin and 10% fetal calf serum.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
MeRIP-Seq

treatment_protocol: Kasumi-1 cells was treated with 100uM of CoCl2.6H2O for 24 hours.

value: Kasumi-1 cell line

value: acute myeloblastic leukemia cell line

value: treated with 100 uM CoCl2 for 24 hours

tag: experimental

value: IP


title: CoCl2_3_IP


title: CoCl2_1_IP


title: F3_Larval EE2-exposed_rep 3


title: Q203_E18.5

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X203_S1

tag: age

tag: Sex

value: Cherry/+; Ins2-Cre/+

value: wild type


title: T579.1_E18.5

description:
Raw_Matrix.txt
Normalized_Matrix.txt
X579.1_S77

tag: blood glucose (mg/dl)

tag: weight (g)

value: TRIzol-phenol chloroform


title: ctrol_3_IP

value: untreated control


title: ctrol_2_IP


title: F1_Larval EE2-exposed_rep 1


title: ctrol_1_IP


title: SaC9+tBE-V5-mA3:VA1B,Sg4a,FF-OTsgd,VA1B-OTsgc rep1


title: SaC9+tBE-V5-rA1:VA1B,Sg4a,FF-OTsgd,VA1B-OTsgc rep3


title: A10_Larval control_rep 10

source_name: Whole 96h post-hatch larva_control

value: none (control)


title: A9_Larval control_rep 9


title: Heart  UT-B-KO rep1

city: Changchun

first: yanwei

last: du

state: Jilin

address: No. 218, Ziqiang Street, Nanguan District

department: Department of Respiratory and Critical Care Medicine

institute: The 2nd Hospital of Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: 16 weeks old

tag: genotype


title: Heart  UT-B-KO rep2


title: SaC9+tBE-V5-rA1:VA1B,Sg4a,FF-OTsgd,VA1B-OTsgc rep2


title: Heart  WT rep3


title: SaC9+tBE-V5-rA1:VA1B,Sg4a,FF-OTsgd,VA1B-OTsgc rep1


title: CoCl2_2_input

value: input


title: A8_Larval control_rep 8

value: small RNA


title: CoCl2_3_input


title: Heart  WT rep2


title: SaC9+tBE-V5-mA3:E1,FF,Sg3a,SgVAa,E1-OTsga rep2


title: A7_Larval control_rep 7


title: SaC9+tBE-V5-mA3:VA1B,Sg4a,FF-OTsgd,VA1B-OTsgc rep2


title: F2_Larval EE2-exposed_rep 2

value: 10 ng ethinyl estradiol for 48 hours


title: CoCl2_1_input


title: ctrol_3_input


title: Heart  UT-B-KO rep3


title: SaC9+tBE-V5-mA3:E1,FF,Sg3a,SgVAa,E1-OTsga rep1


title: Het_Phz_DMSO_5

city: London

first: Elspeth

last: Payne

email: a.lubin@ucl.ac.uk, e.payne@ucl.ac.uk

address: 72 Huntley Street

department: Department of Haematology

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
Data QC was conducted using FastQC 0.11.9 and reads trimmed using Trimmomatic 0.39
Reads were aligned to the zebrafish genome (GRCz11) using HISAT2 2.1.0
Alignments were sorted and indexed with samtools 1.9
Reads were counted using featureCounts from subread 2.0.0 and GTF Danio Rerio GRCz11.97
Counts were normalised and differential gene expression was analysed using DESeq2
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix of normalised raw counts for every gene and every sample

organism: Danio rerio

source_name: Tg(Itga2b:GFPlo) cells

growth_protocol: Tg(itga2b:GFP) zebrafish were maintained according to standard procedures and UK Home Office guidelines

extract_protocol:
Embryos were pooled by rps14 genotype, stress and treatment and Tg(Itga2b:GFPlo) cells were sorted directly into Trizol for RNA extraction
Libraries were prepared using the Smart-seq2 protocol

treatment_protocol: Haemolytic stress was induced by exposure of embryos to phenylhydrazine. Embryos were incubated in 1 µg/mL PHZ from 24 hpf to 48 hpf and then washed. Embryos were then incubated 20 µM Imiquimod or DMSO control for 4 days from 48hpf to 6dpf. Rps14 genotypes were determined with tailclips and embryos pooled before sorting.

tag: stress

value: Phz

value: DMSO


title: ctrol_2_input

tag: cell line


title: A5_Larval control_rep 5

tag: treatment


title: ctrol_1_input


title: Het_Phz_DMSO_4


title: SaC9+tBE-V5-rA1:E1,FF,Sg3a,SgVAa,E1-OTsga rep3

tag: 5'-end trimming of r1


title: A4_Larval control_rep 4


title: WT_Phz_DMSO_3


title: SaC9+tBE-V5-mA3:E1,FF,Sg3a,SgVAa,E1-OTsga rep3

tag: 3'-end trimming of r1


title: WT_Phz_DMSO_2


title: SaC9+tBE-V5-rA1:E1,FF,Sg3a,SgVAa,E1-OTsga rep2


title: Heart  WT rep1


title: shPRMT5_3

first: Cen

last: Xie

address: 501 Haike Road

institute: Shanghai Institute of Materia Medica

data_processing:
Sequencing was performed on an Illumina Novaseq 6000 platform using paired-end protocol.Illumina Casava1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by SeqPrep and Sickle, then mapped to GRCh38.p13 whole genome using HISAT2 (Version 2.1.0).
The gene expression quantification was performed using RSEM (Version 1.3.3) tool and generated raw count for all genes individually.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: shPRMT5, JHH-7 cells

extract_protocol:
JHH-7 cells were collected, flash frozen in liquid Nitrogen, and RNA was isolated using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, #74136). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HCC cell line JHH-7

value: PRMT5 shRNA transfection

value: PRMT5 knockdown

tag: case history of originator

value: HBs-Ag positive hepato cellular carcinoma (Ed.III) with liver cirrhosis. HBs-Ag(+), HBs-Ab(-), HBe-Ag(-), HBe-Ab(+), HBc-Ab(+), AFP positive (110,000 ng/ml).


title: SaC9+tBE-V5-rA1:E1,FF,Sg3a,SgVAa,E1-OTsga rep1


title: A6_Larval control_rep 6

tag: molecule subtype


title: hsg(10bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep3


title: A2_Larval control_rep 2


title: Het_Phz_DMSO_3


title: shPRMT5_1


title: shPRMT5_2


title: A1_Larval control_rep 1

tag: developmental stage

value: fathead minnow (FHM) larvae (48 h post-hatch)


title: Vector3

source_name: Vector, JHH-7 cells

value: Empty vector transfection

value: control


title: Het_Phz_DMSO_1


title: hsg(10bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep2


title: hsg(10bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep1


title: Het_Phz_DMSO_2


title: Vector2


title: KO_RISP2

city: Chicago

first: Eva

last: Morgun

state: IL

address: 320 N Superior St

department: Department of Microbiology and Immunology

institute: Northwestern University

data_processing:
Trimmomatic 0.33 was used to trim reads
STAR 2.5.2 was used to align reads to mm10 genome
Reads were counted using htseq-count
EdgeR was used to analyze data for differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Counts for individual samples for every gene. Matrix table with raw gene counts for every gene and every sample. Matrix table with normalized gene expression and associated differential expression analysis results.

source_name: Thymus

extract_protocol:
Single cell suspesion was purified from the thymus and sorted for CD4+/CD8+ DP thymocytes were sorted by FACS BD Aria with a purity more than 98%. RNA was extracted with RNAeasy® Mini Kit according to the protocol of the manufacture (Qiagen).
Libraries were generated using the Illumina TruSeq preparation kit

value: Uqcrfs1fl/fl; CD4-Cre+


title: KO_RISP1


title: Vector1


title: hsg(12bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep3


title: WT_Phz_DMSO_1


title: WT_RISP2

value: WT


title: A3_Larval control_rep 3

value: none (control)


title: RNA-seq of DNTET1 Cas9 rep1

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Number of off-target mutations (Base Substitutions)

source_name: 293FT_DNTET1 Cas9

growth_protocol: 293FT cells from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and regularly tested to exclude mycoplasma contamination. All mice were housed under specific pathogen-free conditions at the animal facilities of Medical Research Institute, Wuhan University. All mouse studies were approved by the Animal Care Committees of Medical Research Institute, Wuhan University.

extract_protocol:
Total RNAs were extracted from human 293FT cells and mouse livers tissues by using TransZol® Up Plus RNA Kit (ER501-01, TransGen)
For total RNA-seq, DNA libraries were prepared by using the NEBNext Ultra II FS DNA Library Prep for Illumina, and sequencing by using the Illumina HiSeq X Ten (2×150) at CAS-MPG Partner Institute for Computational Biology Omics CoreIndexed RNA libraries were prepared by using the TruSeq Stranded Total RNA with Ribo-Zero Globin. RNA-seq libraries were sequenced on an Illumina HiSeq X Ten (2×150) at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: After 40hr after transfection, Cells in the first 15% of the fluorescence intensity were sorted by FACSAriaIII.

tag: cell line/tissue

value: DNTET1 Cas9


title: TrB

city: Hong Kong

first: Yang

last: XUAN

state: Please Select

address: L740 Laboratory Block LKS Faculty of Medicine,21 Sassoon Road, Pokfulam

department: Department of Obstetrics & Gynaecology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Use NanoDropTM One/OneC to detect actual RNA purification, use QubitTM RNA HS Assay Kit to make quantification,  use Agilent 4200 TapeStation to detect RIN value
Size Select the small RNA library using AMPure XP beads, use Kapa qPCR to make quantification,  use Agilent 4200 TapeStation to detect library size
Illumina NovaSeq6000
Hierarchical Indexing for Spliced Alignment of Transcripts, use HTSeq to calculate Reads Count
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: OVCA433 FADS2-/-

growth_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before collect pellet, all the cells were grown in DMEM medium containing 10% FBS, and supplemented with penicillin (50 units/ml), streptomycin (100 mg/ml)

extract_protocol:
SCD1-/-  or FADS2-/- was established in OVCA433 cell line via CRISPER/Cas9, collect pellet on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The vector used in the construction contains the vector PX459 (pSpCas9(BB)-2A-Puro V2.0) Plasmid (Catalog #62988, Addgene)

value: human ovarian carcinoma cell line


title: Het_Phz_Imi_3

value: Imiquimod


title: WT_RISP1

tag: strain


title: PDX_25_BH: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv

tag: tissue

value: DLBCL tumor sample


title: Het_Phz_Imi_2


title: PR_25_BH: DLBCL tissue PR/PDX RNA


title: hsg(12bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep1


title: WT_Phz_Imi_4


title: hsg(14bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep3


title: hsg(14bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep2


title: ALS patient_enrolment [UCH00171]

city: ראשון לציון

first: Iddo

last: Magen

state: Not in US

address: בן אליעזר 32, 17

country: Israel

institute: Weizmann Institute

description:
UCH00171
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv

data_processing:
Data were aligned to the genome using the GeneGlobe pipeline (https://geneglobe.qiagen.com/us/)
Data were filtered using the following specifications: >50 UMIs in >60% of the samples for longitudinal analysis, >100 UMIs on average for other analyses
Data were corrected for batch using the ComBat function in R and then normalized by DESeq2
Supplementary_files_format_and_content: txt files contain raw UMI counts, after alignment
Supplementary_files_format_and_content: xls files contain batch and DESeq2 corrected UMIs, after filtration of low-abundance miRNAs. Related R code are in the same folder
Supplementary_files_format_and_content: csv files contain categorial values for miRNAs and other clinical features, to be run by an R code for calculation of hazard ratios by COX proportional hazard analysis. Related R codes are in the same folder

source_name: Blood plasma

extract_protocol:
Plasma were isolated from blood and total RNA was extracted using the Qiagen miRNeasy micro kit (Cat# 217184)
libraries were prepared from 7.5 ng of total RNA using the QIAseq miRNA library kit and QIAseq miRNA NGS 48 Index IL (Qiagen, Cat# 331505 and 331565), by an experimenter who was blinded to the identity of samples. Samples were randomly allocated to library preparation and sequencing in batches. Libraries with different indices were multiplexed and sequenced on NextSeq 500/550 v2 flow cell or Novaseq SP100 (Illumina), with 75bp single read and 6bp index read.

tag: disease

value: ALS

tag: group

value: enrolment


title: PDX_22_AD: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: WT_Phz_Imi_3

value: Phz


title: hsg(14bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep1


title: ALS patient_enrolment [UCH00164]

address: בן אליעזר 32, 17

description:
UCH00164
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PR_22_AD: DLBCL tissue PR/PDX RNA


title: Het_Phz_Imi_4


title: WT_Phz_Imi_2


title: ALS patient_enrolment [UCH00152]

address: בן אליעזר 32, 17

description:
UCH00152
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: hsg(16bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep3


title: ALS patient_enrolment [UCH00153]

address: בן אליעזר 32, 17

description:
UCH00153
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PDX_21_LG: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: Het_None_DMSO_4

value: DMSO


title: hsg(16bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep2


title: hsg(12bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep2


title: PR_21_LG: DLBCL tissue PR/PDX RNA


title: TrA

source_name: OVCA433 SCD1-/-

tag: cell type


title: Ctrl

source_name: OVCA433 vector control

value: wild type


title: Het_None_DMSO_3


title: ALS patient_enrolment [UCH00150]

address: בן אליעזר 32, 17

description:
UCH00150
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: PDX_20_RN: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: hsg(16bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep1


title: Het_None_DMSO_2


title: hsg(18bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep3


title: PR_20_RN: DLBCL tissue PR/PDX RNA


title: ALS patient_enrolment [UCH00143]

address: בן אליעזר 32, 17

description:
UCH00143
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: ALS patient_enrolment [UCH00138]

address: בן אליעזר 32, 17

description:
UCH00138
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: Patient 1 after IVIG therapy

first: Zhen

last: Wang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

data_processing:
Cell Ranger (v3.0.1, 10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered single-cell gene expression matrix and associated cell barcodes and gene features
Supplementary_files_format_and_content: Filtered BCR contig sequences and annotations, clonotype consensus sequences and annotations, and clonotype abundance
Supplementary_files_format_and_content: Filtered TCR contig sequences and annotations, clonotype consensus sequences and annotations, and clonotype abundance

source_name: PBMCs

extract_protocol:
Venous blood was collected on the 5th days after the onset of fever before IVIG therapy and 24 hours after IVIG therapy and subsidence of fever. PBMCs were isolated by density gradient centrifugation using the Ficoll-Paque medium.
Single-cell capturing and library construction were performed using the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 (10x Genomics) according to the manufacturer’s instructions.

treatment_protocol: The KDs received high-dose IVIG treatment combined with oral aspirin.

value: blood

value: PBMCs

value: after IVIG therapy

tag: disease state

value: acute KD


title: WT_None_DMSO_3


title: hsg(18bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep2


title: PDX_19_RRR: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: hsg(18bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep1


title: WT_None_DMSO_2


title: PR_19_RRR: DLBCL tissue PR/PDX RNA


title: ALS patient_enrolment [UCH00136]

address: בן אליעזר 32, 17

description:
UCH00136
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: Het_None_Imi_3


title: ALS patient_enrolment [UCH00129]

address: בן אליעזר 32, 17

description:
UCH00129
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PR_18_KK: DLBCL tissue PR/PDX RNA


title: ALS patient_enrolment [UCH00119]

address: בן אליעזר 32, 17

description:
UCH00119
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: WT_None_Imi_4


title: hsg(20bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep2


title: ALS patient_enrolment [UCH00101]

address: בן אליעזר 32, 17

description:
UCH00101
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PR_16_RR: DLBCL tissue PR/PDX RNA


title: hsg(20bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep1


title: Het_None_Imi_2


title: BE3:DNE1 rep3


title: WT_None_Imi_3


title: WT_None_Imi_2


title: PDX_15_BSE: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: hsg(20bp):hsgDNE1,sgDNE1,hsgFF,sgFF,hsgV1A,sgV1A rep3


title: BE3:DNE1 rep2


title: PR_15_BSE: DLBCL tissue PR/PDX RNA


title: Het_Phz_Imi_1


title: PDX_16_RR: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: ALS patient_enrolment [UCH00084]

address: בן אליעזר 32, 17

description:
UCH00084
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: BE3:DNE1 rep1


title: WT_Phz_Imi_1


title: PDX_14_YLL: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: ALS patient_enrolment [UCH00092]

address: בן אליעזר 32, 17

description:
UCH00092
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: hsgDNT1(+78):DNT1 rep3;NT:CAA,RB,S1-F,CRA,V2C,CRa,S1c,V2a rep3

source_name: 293FT_hsgDNTET1(+78) | NT

value: hsgDNTET1(+78) | NT


title: PR_14_YLL: DLBCL tissue PR/PDX RNA


title: Het_None_DMSO_1


title: hsgDNT1(+78):DNT1 rep2;NT:CAA,RB,S1-F,CRA,V2C,CRa,S1c,V2a rep2


title: ALS patient_enrolment [UCH00063]

address: בן אליעזר 32, 17

description:
UCH00063
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: ALS patient_enrolment [UCH00062]

address: בן אליעזר 32, 17

description:
UCH00062
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PDX_12_CR: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: WT_None_DMSO_1


title: PR_12_CR: DLBCL tissue PR/PDX RNA


title: hsgDNT1(+78):DNT1 rep1;NT:CAA,RB,S1-F,CRA,V2C,CRa,S1c,V2a rep1


title: ALS patient_enrolment [UCH00095]

address: בן אליעזר 32, 17

description:
UCH00095
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: ALS patient_enrolment [UCH00042]

address: בן אליעזר 32, 17

description:
UCH00042
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: Het_None_Imi_1


title: hsgE1(+41bp),hsgFF(+53bp),hsgDNT1(+21bp):E1,FF,DNT1 rep3;NT:VA1B,V1a,VA1B-OTsgc rep3

source_name: 293FT_hsgEMX1(+41bp), hsgFANCF(+53bp), hsgDNTET1(+21bp) | NT


title: PDX_11_FE: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv

source_name: DLBCL tumor sample


title: WT_None_Imi_1


title: hsgE1(+41bp),hsgFF(+53bp),hsgDNT1(+21bp):E1,FF,DNT1 rep2;NT:VA1B,V1a,VA1B-OTsgc rep2

value: hsgEMX1(+41bp), hsgFANCF(+53bp), hsgDNTET1(+21bp) | NT


title: tBE-V5-mA3:P9-Exon 4 mouse#2 rep4

value: Liver


title: ALS patient_enrolment [UCH00030]

address: בן אליעזר 32, 17

description:
UCH00030
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: hsgE1(+41bp),hsgFF(+53bp),hsgDNT1(+21bp):E1,FF,DNT1 rep1;NT:VA1B,V1a,VA1B-OTsgc rep1


title: PR_11_FE: DLBCL tissue PR/PDX RNA


title: ALS patient_enrolment [UCH00029]

address: בן אליעזר 32, 17

description:
UCH00029
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: tBE-V5-mA3:P9-Exon 4 mouse#2 rep3


title: PDX_10_RA: DLBCL tissue PR/PDX RNA

description:
PR sample for this PDX is Sample_107
PDX_humanreads.csv
PDX_mousereads.csv


title: hsgE1(-26bp),hsgFF(+24bp),hsgDNT1(-46bp):E1,FF,DNT1 rep3


title: hsgE1(-26bp),hsgFF(+24bp),hsgDNT1(-46bp):E1,FF,DNT1 rep2


title: PDX_8_TA23: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: tBE-V5-mA3:P9-Exon 4 mouse#2 rep2


title: PDX_7_WA: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: ALS patient_enrolment [TST0006]

address: בן אליעזר 32, 17

description:
TST0006
All_samples_enrolment.txt


title: ALS patient_enrolment [UCH00005]

address: בן אליעזר 32, 17

description:
UCH00005
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PR_8_TA23: DLBCL tissue PR/PDX RNA


title: ALS patient_enrolment [UCH00061]

address: בן אליעזר 32, 17

description:
UCH00061
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: hsgE1(-26bp),hsgFF(+24bp),hsgDNT1(-46bp):E1,FF,DNT1 rep1


title: hsgE1(-34bp),hsgFF(-40bp),hsgDNT1(-66bp):E1,FF,DNT1 rep3;NT:S4A,D1B,E1A,R2A,RIB,E1a,H4c,R2-b rep3

source_name: 293FT_hsgEMX1(-34bp), hsgFANCF(-40bp), hsgDNTET1(-66bp) | NT


title: Uninjected_kidney:P9-Exon 4 mouse#2 rep4

value: kindey


title: PR_7_WA: DLBCL tissue PR/PDX RNA


title: Uninjected_kidney:P9-Exon 4 mouse#2 rep3


title: ALS patient_enrolment [BUH00429]

address: בן אליעזר 32, 17

description:
BUH00429
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: hsgE1(-34bp),hsgFF(-40bp),hsgDNT1(-66bp):E1,FF,DNT1 rep2;NT:S4A,D1B,E1A,R2A,RIB,E1a,H4c,R2-b rep2

value: hsgEMX1(-34bp), hsgFANCF(-40bp), hsgDNTET1(-66bp) | NT


title: ALS patient_enrolment [BUH00377]

address: בן אליעזר 32, 17

description:
BUH00377
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PDX_6_RE: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: Uninjected_kidney:P9-Exon 4 mouse#2 rep2


title: ALS patient_enrolment [UCH00009]

address: בן אליעזר 32, 17

description:
UCH00009
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: Uninjected_kidney:P9-Exon 4 mouse#2 rep1


title: hsgE1(-47bp),hsgFF(-47bp),hsgDNT1(-91bp):E1,FF,DNT1 rep3


title: PR_6_RE: DLBCL tissue PR/PDX RNA


title: ALS patient_enrolment [BUH00372]

address: בן אליעזר 32, 17

description:
BUH00372
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PDX_5_TE: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: tBE-V5-mA3_kidney:P9-Exon 4 mouse#2 rep4


title: ALS patient_enrolment [BUH00332]

address: בן אליעזר 32, 17

description:
BUH00332
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: hsgE1(-47bp),hsgFF(-47bp),hsgDNT1(-91bp):E1,FF,DNT1 rep2


title: PR_5_TE: DLBCL tissue PR/PDX RNA


title: hsgE1(-34bp),hsgFF(-40bp),hsgDNT1(-66bp):E1,FF,DNT1 rep1;NT:S4A,D1B,E1A,R2A,RIB,E1a,H4c,R2-b rep1


title: ALS patient_enrolment [BUH00331]

address: בן אליעזר 32, 17

description:
BUH00331
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: tBE-V5-mA3_kidney:P9-Exon 4 mouse#2 rep3


title: hsgE1(-47bp),hsgFF(-47bp),hsgDNT1(-91bp):E1,FF,DNT1 rep1


title: tBE-V5-mA3_kidney:P9-Exon 4 mouse#2 rep2


title: PDX_4_HD: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: ALS patient_enrolment [BUH00178]

address: בן אליעזר 32, 17

description:
BUH00178
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: ALS patient_enrolment [BUH00330]

address: בן אליעזר 32, 17

description:
BUH00330
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PR_4_HD: DLBCL tissue PR/PDX RNA


title: hsgE1(-82bp),hsgFF(-56bp),hsgDNT1(-106bp):E1,FF,DNT1 rep3


title: ALS patient_enrolment [BUH00177]

address: בן אליעזר 32, 17

description:
BUH00177
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PDX_3_AL: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: hsgE1(-82bp),hsgFF(-56bp),hsgDNT1(-106bp):E1,FF,DNT1 rep2


title: Uninjected:P9-Exon 4 mouse#2 rep4

value: Uninjected


title: hsgE1(-82bp),hsgFF(-56bp),hsgDNT1(-106bp):E1,FF,DNT1 rep1


title: PR_3_AL: DLBCL tissue PR/PDX RNA


title: ALS patient_enrolment [BUH00101]

address: בן אליעזר 32, 17

description:
BUH00101
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: SaC9+tBE-V5-rA1/ctrl gRNAs:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3

value: nSaCas9/Sa-sgRNA+tBE-V5-rA1/ctrl gRNAs


title: ALS patient_enrolment [BUH00095]

address: בן אליעזר 32, 17

description:
BUH00095
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: Uninjected:P9-Exon 4 mouse#2 rep2


title: SaC9+tBE-V5-rA1/ctrl gRNAs:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep2


title: ALS patient_enrolment [BUH00093]

address: בן אליעזר 32, 17

description:
BUH00093
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: PR_2_PA: DLBCL tissue PR/PDX RNA

value: DLBCL tumor sample


title: SaC9+tBE-V5-rA1/ctrl gRNAs:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep1


title: PDX_1_CJ: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: ALS patient_enrolment [BLT00230]

address: בן אליעזר 32, 17

description:
BLT00230
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv

value: ALS


title: Uninjected:P9-Exon 4 mouse#2 rep1


title: BE4max-YE1:P9-Exon 4 mouse#2 rep4


title: SaC9+tBE-V4-rA1:E1,FF,VA1B,Sg3a,SgVAa,Sg4a,E1-OTsga,FF-OTsgd,VA1B-OTsgc rep3


title: ALS patient_enrolment [BLT00225]

address: בן אליעזר 32, 17

description:
BLT00225
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv

value: enrolment


title: tBE-V5-mA3_kidney:P9-Exon 4 mouse#2 rep1


title: PR_1_CJ: DLBCL tissue PR/PDX RNA


title: NT:SgVAa,E1-OTsga rep3

value: NT


title: BE4max-YE1:P9-Exon 4 mouse#2 rep3


title: ALS patient_enrolment [BLT00160]

address: בן אליעזר 32, 17

description:
BLT00160
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: ALS patient_enrolment [BLT00120]

address: בן אליעזר 32, 17

description:
BLT00120
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: Uninjected:P9-Exon 4 mouse#2 rep3


title: NT:SgVAa,E1-OTsga rep1


title: NT:SgVAa,E1-OTsga rep2


title: PDX_2_PA: DLBCL tissue PR/PDX RNA

description:
PDX_humanreads.csv
PDX_mousereads.csv


title: ALS patient_enrolment [BLT00103]

address: בן אליעזר 32, 17

description:
BLT00103
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: hA3A-Y130F:P9-Exon 4 mouse#2 rep3


title: hA3A-Y130F:P9-Exon 4 mouse#2 rep4


title: B4_Secondary tumor_rep4

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file:
A4B4_US83000181_252665240606_S01_GE2_1200_Dec17_1_1.txt
Secondary tumor, replicate 4
Gene expression from secondary prostate cancer tumor

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from the two cancer nodules were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Normalized background subtracted signal of that feature to the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

source_name: Secondary tumor

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

extract_protocol: RNA was extracted with RNAEasy Minikit (Qiagen, Germantown, MD, USA) following the manufacturer's recommendations. RNA was quantified using a Thermo Fisher Scientific NanoDrop ND-1000 spectrophotometer (Waltham, MA, USA) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: male

tag: age

value: prostate

tag: tissue type

value: secondary prostate cancer tumor


title: hA3A-Y130F:P9-Exon 4 mouse#2 rep2


title: ALS patient_enrolment [BLT00067]

address: בן אליעזר 32, 17

description:
BLT00067
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: BE4max-YE1:P9-Exon 4 mouse#2 rep2


title: hA3A-Y130F:P9-Exon 4 mouse#2 rep1


title: B3_Secondary tumor_rep3

description:
raw data file:
A3B3_US83000181_252665240606_S01_GE2_1200_Dec17_1_2.txt
Secondary tumor, replicate 3
Gene expression from secondary prostate cancer tumor


title: BE3:P9-Exon 4 mouse#2 rep4


title: hA3FCDA1-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep3

tag: cell line


title: BE4max-YE1:P9-Exon 4 mouse#2 rep1

tag: treatment


title: hA3FCDA1-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep2

tag: 5'-end trimming of r1


title: ALS patient_enrolment [BLT00046]

address: בן אליעזר 32, 17

description:
BLT00046
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: ALS patient_enrolment [BLT00102]

address: בן אליעזר 32, 17

description:
BLT00102
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: hA3FCDA1-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep3

tag: 3'-end trimming of r1


title: ALS patient_enrolment [BLT00030]

address: בן אליעזר 32, 17

description:
BLT00030
All_samples_enrolment.txt
Survival_study_replication_cohort.xls
Data_file_related_to_fig_3_5_replication.csv


title: hA3FCDA1-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: ALS patient_enrolment [BLT00099]

address: בן אליעזר 32, 17

description:
BLT00099
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: BE3:P9-Exon 4 mouse#2 rep3


title: hA3FCDA1-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: hA3FCDA1-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: A4_Primary tumor A_rep4

description:
raw data file:
A4B4_US83000181_252665240606_S01_GE2_1200_Dec17_1_1.txt
Primary tumor A, replicate 4
Gene expression from primary prostate cancer tumor

source_name: Primary tumor A

value: primary prostate cancer tumor


title: A3_Primary tumor A_rep3

description:
raw data file:
A3B3_US83000181_252665240606_S01_GE2_1200_Dec17_1_2.txt
Primary tumor A, replicate 3
Gene expression from primary prostate cancer tumor


title: B1_Secondary tumor_rep1

description:
raw data file:
A1B1_US83000181_252665240606_S01_GE2_1200_Jun14_1_4.txt
Secondary tumor, replicate 1
Gene expression from secondary prostate cancer tumor


title: Liver Abcb4-/- Tgr5-Tg rep4

city: Tuebingen

first: Gisela

last: Gabernet

state: BW

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

description: Liver Abcb4-/- Tgr5-Tg

data_processing:
read alignment and UMI counting: CellRanger v5.0.0
Genome_build: mm10
Supplementary_files_format_and_content: barcodes: newline separated UMI barcodes
Supplementary_files_format_and_content: features: tab separated features, containing EnsemblID, gene name and details (gene expression)
Supplementary_files_format_and_content: filtered expression matrix: number of UMIs associated with a feature (row) and a barcode (column) in MatrixMarket Exchange format.

source_name: Liver

extract_protocol:
single-cell FACS sorting for EpCAM.
For the single-cell experiments a total of 10.000 cells were used as input for the single-cell droplet libraries generation on the 10X Chromium Controller system utilizing the Chromium Single Cell 3’ NextGEM Reagent Kit v3.1 (10X Genomics, Pleasanton, CA, USA) according to manufacturer’s instructions.
single-cell RNA-Seq

treatment_protocol: Enrichment on Biliary epithelial cells by EpCAM FACS.

tag: genotype

value: Abcb4-/- Tgr5-Tg

value: BALB/c x C57BL6/J


title: BE3:P9-Exon 4 mouse#2 rep2


title: hA3FCDA1-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep3


title: ALS patient_enrolment [BLT00006]

address: בן אליעזר 32, 17

description:
BLT00006
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: A2_Primary tumor A_rep2

description:
raw data file:
A2B2_US83000181_252665240606_S01_GE2_1200_Dec17_1_3.txt
Primary tumor A, replicate 2
Gene expression from primary prostate cancer tumor


title: A1_Primary tumor A_rep1

description:
raw data file:
A1B1_US83000181_252665240606_S01_GE2_1200_Jun14_1_4.txt
Primary tumor A, replicate 1
Gene expression from primary prostate cancer tumor


title: Liver Abcb4-/- Tgr5-Tg rep3

description: Liver Abcb4-/- Tgr5-Tg


title: BE3:P9-Exon 4 mouse#2 rep1


title: ALS patient_enrolment [BLT00047]

address: בן אליעזר 32, 17

description:
BLT00047
All_samples_enrolment.txt
Survival_study_discovery_cohort.xls
Data_file_related_to_fig_2_3_5_discovery.csv


title: hA3FCDA1-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: MCF7 cells-LSD1 E239K Rescue_rep2

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

data_processing:
The clustering of the index-coded samples was performed on a cBot  Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS  (Illumia) according to the manufacturer’s instructions. After cluster  generation, the library preparations were sequenced on an Illumina  Hiseq Xten platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through  in-house perl scripts. In this step, clean data(clean reads) were  obtained by removing reads containing adapter, reads containing  ploy-N and low quality reads from raw data. At the same time, Q20,  Q30, GC-content and sequence duplication level of the clean data  were calculated. All the downstream analyses were based on clean  data with high quality
Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped(FPKM).
Differential expression analysis of two groups was  performed using the DESeq R package (1.10.1). The resulting P values were adjusted using the Benjamini  and Hochberg’s approach for controlling the false discovery rate.  Genes with an adjusted P-value < 0.01 and absolute value of  log2(Fold change)>1 found by DESeq were assigned as differentially  expressed.
Genome_build: ensembl CRCh38
Supplementary_files_format_and_content: abundance measurements

source_name: MCF7 cells

growth_protocol: MCF7 were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS) and 10 IU/ml penicillin/streptomycin, and the stable cell lines were supplemented with additional 500 ng/ml puromycin or 1000μg/ml G418.

extract_protocol:
The total RNA was harvested using Trizol reagent. Illumina NEBNext Ultra Directional RNA Library Prep Kit(NEB) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast cancer cells

value: stably express LSD1 E239K upon LSD1 KD


title: Liver Abcb4-/- Tgr5-Tg rep2

description: Liver Abcb4-/- Tgr5-Tg

value: Liver


title: tBE-V5-mA3/ctrl gRNAs:P9-Exon 4 mouse#2 rep3

source_name: Liver_tBE-V5-mA3/ctrl gRNAs

value: tBE-V5-mA3/ctrl gRNAs


title: MCF7 cells-LSD1 E239K Rescue_rep1


title: hA3FCDA1-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: SaC9+hA3A:Sg3a,SgVAa,Sg4a rep3


title: MCF7 cells-LSD1 WT Rescue_rep3

value: stably express LSD1 WT upon LSD1 KD


title: tBE-V5-mA3/ctrl gRNAs:P9-Exon 4 mouse#2 rep4


title: Liver Abcb4-/- Tgr5-wt rep4

description: Liver Abcb4-/- Tgr5-wt

value: Abcb4-/- Tgr5-wt


title: tBE-V5-mA3/ctrl gRNAs:P9-Exon 4 mouse#2 rep1


title: B2_Secondary tumor_rep2

description:
raw data file:
A2B2_US83000181_252665240606_S01_GE2_1200_Dec17_1_3.txt
Secondary tumor, replicate 2
Gene expression from secondary prostate cancer tumor


title: MCF7 cells-LSD1 WT Rescue_rep2


title: SaC9+hA3A:Sg3a,SgVAa,Sg4a rep1


title: MCF7 cells-LSD1 E239K Rescue_rep3


title: Liver Abcb4-/- Tgr5-wt rep2

description: Liver Abcb4-/- Tgr5-wt


title: MCF7 cells-LSD1 WT Rescue_rep1


title: SaC9+BE3:Sg3a,SgVAa,Sg4a rep3


title: Liver Abcb4-/- Tgr5-wt rep3

description: Liver Abcb4-/- Tgr5-wt


title: tBE-V5-mA3_28d_4E+12:P9-Exon 4 mouse#1 rep5


title: tBE-V5-mA3_28d_4E+12:P9-Exon 4 mouse#1 rep4


title: Liver Abcb4-/- Tgr5-wt rep1

description: Liver Abcb4-/- Tgr5-wt


title: Liver Abcb4-/- Tgr5-Tg rep1

description: Liver Abcb4-/- Tgr5-Tg


title: MCF7 cells-LSD1 KD_rep3

value: stably express LSD1 shRNA


title: SaC9+BE3:Sg3a,SgVAa,Sg4a rep2


title: Liver Abcb4-/- rep4

description: Liver Abcb4-/-

value: BALB/c


title: tBE-V5-mA3_28d_4E+12:P9-Exon 4 mouse#1 rep3


title: tBE-V5-mA3/ctrl gRNAs:P9-Exon 4 mouse#2 rep2


title: SaC9+hA3A:Sg3a,SgVAa,Sg4a rep2


title: MCF7 cells-LSD1 KD_rep2


title: tBE-V5-mA3_28d_4E+12:P9-Exon 4 mouse#1 rep2


title: SaC9+BE3:Sg3a,SgVAa,Sg4a rep1


title: Liver Abcb4-/- rep2

description: Liver Abcb4-/-


title: Liver Abcb4-/- rep3

description: Liver Abcb4-/-


title: tBE-V5-mA3_28d_4E+12:P9-Exon 4 mouse#1 rep1


title: MCF7 cells-Control_rep3

value: untreated


title: SaC9+dSpCas9:Sg3a,SgVAa,Sg4a rep2


title: SaC9+dSpCas9:Sg3a,SgVAa,Sg4a rep3


title: MCF7 cells-LSD1 KD_rep1


title: Liver Abcb4-/- rep1

description: Liver Abcb4-/-


title: tBE-V5-mA3_28d_8E+11:P9-Exon 4 mouse#1 rep3


title: MCF7 cells-Control_rep2


title: MCF7 cells-Control_rep1


title: tBE-V5-mA3_28d_8E+11:P9-Exon 4 mouse#1 rep2


title: tBE-V5-mA3_28d_8E+11:P9-Exon 4 mouse#1 rep1


title: Liver wt   rep4

description: Liver wt

value: wt


title: Liver wt  rep2

description: Liver wt


title: Liver wt  rep3

description: Liver wt


title: tBE-V5-mA3_28d_1.6E+11:P9-Exon 4 mouse#1 rep3


title: hA3BCDA1-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: hA3BCDA1-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: K562_GAi_H3K27ac_ChIP-Seq

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

data_processing:
ChIP-seq raw reads were trimmed to 36 bp using trim sequences tool. Trimmed reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the hg19 canonical genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files.  Peak regions were identified using MACS2 providing input chromatin data as control.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig, bed

growth_protocol: K562 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (10 ng for H3K27ac, 0.5 ng for CTCF) was processed using NEBNext ChIP-seq library (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. The concentration of adaptors was 1.5 µM for H3K27ac ChIP DNA and 0.6 µM for CTCF ChIP DNA. Adaptor-ligated DNA was selected at 200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (7 cycles for H3K27ac, 12 cycles for CTCF). The fragments are purified using NEBNext sample purification beads.

value: erythroleukemia cells

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: K562_Con_Input_ChIP-Seq


title: Liver wt  rep1

description: Liver wt


title: hA3BCDA1-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep3


title: tBE-V5-mA3:P9-Exon 4 mouse#2 rep1


title: tBE-V5-mA3_28d_1.6E+11:P9-Exon 4 mouse#1 rep2


title: K562_C/pi_H3K27ac_ChIP-Seq


title: u87_ont_grch38

city: San Francisco

first: David

last: Wu

state: California

address: 35 Medical Center Way

institute: UCSF

description: Oxford Nanopore direct RNA-Sequencing of U87 RNA

data_processing:
Quality assessment, adapter and quality trimming using fastp (0.13.1)
Alignment to reference genome (hisat2 2.1.0)
Gene expression quantification (featureCounts 1.5.0)
Differential gene expression analysis (DESeq2 1.22, R 3.5)
Genome_build: GRCh38.84
Supplementary_files_format_and_content: Counts matrix output of featureCounts

growth_protocol: DMEM 10% FBS 1% Antibiotics

extract_protocol:
RNA extracted by Zymo Direct-zol RNA miniprep columns
Illumina TruSeq Stranded mRNA and Nanopore Direct RNA Sequencing protocol for the nanopore sample.

treatment_protocol: Transfection using Lipofectamine RNAiMAX and collected at the respective time-point

tag: clone

value: WT


title: tBE-V5-mA3_28d_1.6E+11:P9-Exon 4 mouse#1 rep1

data_processing:
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh38/hg38 human or GRCm38/mm10 mouse reference genome using BWA-MEM 0.7.9a.
Genome_build: hg38 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: base subtitutions

extract_protocol:
Target genomic sequences were PCR amplified by high-fidelity DNA polymerase PrimeSTAR HS (Clonetech) with primer sets flanking examined sgRNA target sites.
For deep target genimoc DNA sequencing, Indexed DNA libraries were prepared by using the TruSeq ChIP Sample Preparation Kit (Illumina) with minor modifications. Briefly, the PCR products amplified from genomic DNA regions were fragmented by Covaris S220, and then PCR amplified by using the TruSeq ChIP Sample Preparation Kit (Illumina). After quantitated with Qubit High-Sensitivity DNA kit (Invitrogen), PCR products with different tags were pooled together for deep sequencing by using the Illumina HiSeq X10 (2×150) at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.


title: hA3BCDA1-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: SaC9+dSpCas9:Sg3a,SgVAa,Sg4a rep1


title: tBE-V5-mA3_14d_4E+12:P9-Exon 4 mouse#1 rep3


title: tBE-V5-mA3_14d_4E+12:P9-Exon 4 mouse#1 rep2


title: K562_C/pi_CTCF_ChIP-Seq

value: CTCF (Milipore, 07-729)


title: [Neuroinflammation] BALB_Brain_56dpi_rep3

city: Riverside

first: Emma

last: Wilson

address: 900 University Avenue

institute: UC Riverside

description: 50ug RNA was loaded for each sample, Naïve samples were used as reference samples for comparison in analysis

data_processing: Results from each panel were merged into one data file for comparative analysis, normalized in nSolver following best practices, and analyzed using nSolver and Advanced Analysis software according to previously published protocols (Danaher et al. 2017). nSolver-generated heat maps were created using normalized (merged) data and agglomerative clustering, a bottom-up form of hierarchical clustering (NanoString User Manual C0019-08). For Advanced Analysis, normalized merged data was used (NanoString User Manual 10030-03). Differential expression (DE) analysis was performed to identify specific targets that exhibit significantly increased or decreased expression in response to naïve control values or, in the case of BALB/c C57BL/6 comparison, to C57BL/6 control values at each time point. Gene set analysis was run to determine the change in direction of regulation within each pre-defined gene set relative to naïve controls. Global significance scores, a summary T-statistic used to measure change (NanoString User Manual 10030-03) were calculated, and the directed global significance scores were expressed via heatmap. Cell type profiling module analysis was conducted to determine the relative abundance in classically activated cell types during infection using genes assigned to each cell type: T cells (CD3e, CD6, CD3g, TRAT1, and CD3d), CD8+ T cells (CD8a), macrophages (CD68 and CD84), and microglia (GPR84, LRRC25, IRF8, NCF1, TNF, TLR2, and TNF.1). NanoString cell type profiling is a validated method to measure relative abundance of up to 24 different immune cell types, with high concordance to flow cytometry (Danaher et al. 2017). Pathway analysis was also conducted to determine overall changes in pathways based on the first principal component of the targets within a pathway as annotated by NanoString (NanoString User Manual 10030-03). Direction of pathway change (up- or downregulated) was determined by cross referencing the pathway score with the corresponding volcano plot for that pathway. Summary pathway score plot colors are based on calculated scores and are represented as downregulation (blue) to upregulation (orange). Statistical significance was determined using R software.

extract_protocol: RNA from brain lysate of naïve, 2 week infected, 4 week infected, and 8 week infected C57BL/6 and BALB/c mice (n=3 for all groups) was collected using Trizol extraction method. Whole brain was dissected and homogenized in 1mL Trizol. Phase separation was completed by adding 200µl of chloroform and incubating at room temperature for 2-3 minutes. Samples were centrifuged at 12,000xg for 15 minutes at 4°C, and upper aqueous phase was collected followed by RNA precipitation using 500µl isopropyl alcohol. Samples incubated at room temperature for 10 minutes followed by centrifugation. RNA pellet was washed with 1mL of 75% ethanol twice. All supernatant was discarded and RNA pellet was dissolved in 100µl of nuclease free water. RNA concentration for each sample was determined using a NanoDrop 2000, and RNA samples normalized to a concentration of 10ng/μL in molecular grade water.

value: Brain

tag: mouse strain

tag: infection time point


title: hA3BCDA1-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep3


title: K562_GAi_CTCF_ChIP-Seq


title: hA3BCDA1-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep3


title: [Neuroinflammation] BALB_Brain_56dpi_rep2

tag: tissue


title: tBE-V5-mA3_14d_4E+12:P9-Exon 4 mouse#1 rep1


title: K562_Con_CTCF_ChIP-Seq


title: hA3BCDA1-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: tBE-V5-mA3_14d_8E+11:P9-Exon 4 mouse#1 rep3


title: tBE-V5-mA3_14d_8E+11:P9-Exon 4 mouse#1 rep2


title: K562_Con_H3K27ac_ChIP-Seq


title: tBE-V5-mA3_14d_8E+11:P9-Exon 4 mouse#1 rep1


title: mA3CDA2-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: [Neuroinflammation] BALB_Brain_28dpi_rep2


title: tBE-V5-mA3_14d_1.6E+11:P9-Exon 4 mouse#1 rep3


title: hA3BCDA1-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: tBE-V5-mA3_14d_1.6E+11:P9-Exon 4 mouse#1 rep2


title: [Neuroinflammation] BALB_Brain_28dpi_rep1


title: mA3CDA2-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep3


title: 21594 neurocase

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

description:
21594-NEUROCASE-POOL1
neuroCC.vcf

data_processing:
Library strategy: DNA-Seq
Mapping with BWA (-c –l 25 -k 2 -n 10).
Variant calling was done using a custom pipeline identifying variants with at least 10x coverage, a 15% allele frequency as well as support from independent reads (>3).
Minimum sample call rate 80%.
Minimum depth 6x.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: neuroCC.vcf

organism: Canis lupus familiaris

source_name: 21594 neurocase

extract_protocol:
DNA was isolated from EDTA blood samples using a Chemagic MSM1 robot (Perkin Elmer).
TruSeq Nano DNA HT Sample Prep Kit.

tag: breed

value: Markiesje

tag: diagnosis

value: juvenile paroxysmal dyskinesia

value: whole blood


title: 22678 neurocontrol

description:
22678-NEUROCONTROL-POOL2
neuroCC.vcf

source_name: 22678 neurocontrol

value: control


title: 22726 neurocontrol

description:
22726-NEUROCONTROL-POOL3
neuroCC.vcf

source_name: 22726 neurocontrol


title: 16815 neurocase

description:
16815-NEUROCASE-POOL3
neuroCC.vcf

source_name: 16815 neurocase


title: mA3CDA2-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep1

first: Li

last: Yang

institute: Fudan University


title: [Neuroinflammation] BALB_Brain_14dpi_rep3


title: 21662 neurocase

description:
21662-NEUROCASE-POOL1
neuroCC.vcf

source_name: 21662 neurocase


title: mA3CDA2-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: mA3CDA2-hA3A-nSpCas9BE:T1,D1,E1,FF,R2 rep3


title: [Neuroinflammation] BALB_Brain_14dpi_rep1


title: hA3BCDA1-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: [Neuroinflammation] BALB_Brain_28dpi_rep3


title: Uninjected:P9-Exon 4 mouse#1 rep7

value: Liver

value: Uninjected


title: [Neuroinflammation] BALB_Brain_14dpi_rep2


title: [Neuroinflammation] BALB_Brain_56dpi_rep1


title: mA3CDA2-rA1-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: mA3CDA2-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep3


title: [Neuroinflammation] BALB_Brain_Naive_rep3

value: Naive


title: Uninjected:P9-Exon 4 mouse#1 rep6


title: Uninjected:P9-Exon 4 mouse#1 rep5


title: tBE-V5-mA3_14d_1.6E+11:P9-Exon 4 mouse#1 rep1


title: mA3CDA2-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep2


title: hA3A:T1,D1,E1,FF,R2 rep3


title: [Neuroinflammation] BALB_Brain_Naive_rep1


title: hA3A:T1,D1,E1,FF,R2 rep2


title: Uninjected:P9-Exon 4 mouse#1 rep3


title: Uninjected:P9-Exon 4 mouse#1 rep1


title: [Neuroinflammation] B6_Brain_56dpi_rep3


title: RNA-seq of mE4 tBE-V5-mA3 Liver rep4

source_name: mouse liver_mE4 tBE-V5-mA3 Liver

tag: cell line/tissue

value: mouse liver

value: mE4 tBE-V5-mA3 Liver


title: hA3A:T1,D1,E1,FF,R2 rep1


title: [Neuroinflammation] BALB_Brain_Naive_rep2

value: BALB/c


title: RNA-seq of mE4 tBE-V5-mA3 Liver rep3


title: BE3:T1,D1,E1,FF,R2 rep2


title: Uninjected:P9-Exon 4 mouse#1 rep4


title: mA3CDA2-mA3CDA1-nSpCas9BE:T1,D1,E1,FF,R2 rep1


title: Uninjected:P9-Exon 4 mouse#1 rep2


title: [Neuroinflammation] B6_Brain_28dpi_rep2


title: [Neuroinflammation] B6_Brain_28dpi_rep1


title: [Neuroinflammation] B6_Brain_56dpi_rep1


title: [Neuroinflammation] B6_Brain_56dpi_rep2


title: [Neuroinflammation] B6_Brain_28dpi_rep3


title: BE3:T1,D1,E1,FF,R2 rep1


title: RNA-seq of mE4 tBE-V5-mA3 Liver rep2


title: BE3:T1,D1,E1,FF,R2 rep3


title: RNA-seq of mE4 tBE-V5-mA3 Liver rep1


title: [Neuroinflammation] B6_Brain_14dpi_rep2


title: RNA-seq of mE4 Uninjected Liver rep4

source_name: mouse liver_mE4 Uninjected Liver

value: mE4 Uninjected Liver


title: mA3CDA1BE3:T1,D1,E1,FF,R2 rep1


title: RNA-seq of mE4 Uninjected Liver rep2


title: RNA-seq of mE4 Uninjected Liver rep3


title: [Neuroinflammation] B6_Brain_Naive_rep3


title: mA3CDA1BE3:T1,D1,E1,FF,R2 rep2


title: mA3CDA1BE3:T1,D1,E1,FF,R2 rep3


title: [Neuroinflammation] B6_Brain_Naive_rep2


title: RNA-seq of mE4 Uninjected Liver rep1


title: [Neuroinflammation] B6_Brain_14dpi_rep1


title: [Neuroinflammation] B6_Brain_Naive_rep1


title: [Neuroinflammation] B6_Brain_14dpi_rep3


title: TS_Input

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
mm10 Reference Genome was indexed from Bowtie (Langmead B., et al 2009).  And sequence reads were aligned using Bowtie.
PCR/Sequencing duplicates were marked with samtools MarkDuplicates. Peaks were called using HOMER2 software.
Supplementary_files_format_and_content: bigWig file with counts after de-duplication.
Genome_build: Mus sequenced genome GRCm38 (mm10)

source_name: VOT-E36 cell line

extract_protocol:
US/VOT-E36 cells (University of Sheffield/ventral otocyst-epithelial cell line clone 36) were used, derived from the otocyst of Immortomice at embryonic day 10.5 (Lawoko-Kerali et al., 2004). The cells were cultured in minimum essential medium (Gibco) supplemented with 10% fetal bovine serum and 50 U/ml -IFN in a humidified atmosphere with 10% CO2 and at a temperature of 33oC, conditions under which these cells proliferate in the absence of differentiation.
For the ChIP assay, once the cultures had reached 85-90% confluence, the chromatin from the cells in six 75-cm2 flasks was cross-linked in 1% formaldehyde for 10 minutes at room temperature; next, the reaction was quenched by adding glycine to a final concentration of 125mM and mixing during an additional 5 minutes. Following removal of the medium and various washes with phosphate buffer saline, cells were scraped off the tissue culture flasks, pelleted and lysed; the chromatin was then sheared into 200-500 bp fragments by sonication (using pulses of 30 seconds on and 30 seconds off in a water-bath sonicator). Any remaining cellular debris was subsequently removed by centrifugation and the sonicated chromatin was pre-cleared for 4 hours at 4oC with protein A agarose beads (Roche). After this time, the beads were removed by centrifugation; half the volume of the chromatin sample was immunoprecipitated (IP sample) at 4oC overnight with a 1:1 mixture of an antibody against Meis2 (K846) and K830, an antibody that recognizes both Meis 1a and Meis 2a isoforms (Penkov et al., 2013). A volume that was equivalent to one tenth of the volume used for the IP reaction was also at that time set apart and frozen, constituting the Input control sample. Following immunoprecipitation with the Meis1/2 antibodies, beads that had been pre-blocked at 4oC overnight with BSA and a rabbit IgG isotype control (ChromPure Rabbit IgG, Jackson ImmunoResearch Laboratories) were added to each tube; the samples were then incubated at 4oC for 4 hours. Afterwards, a series of washes using multiple buffers were conducted in order to remove any molecule that had bound non-specifically to the beads; the chromatin was finally eluted from the beads and cross-linking to the antibody reversed by incubating the IP sample in the presence of NaCl at 65oC overnight; the Input sample that had been stored at -20oC was also incubated in the same solution at 65oC. The next day, both the IP and the Input chromatin were purified using a PCR purification kit (Qiagen), following manufacturer´s instructions. The samples were then used to carry out ChIP-seq analysis.
0.5 ng of total DNA for both Input and IP were used to generate barcoded libraries using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (New England Biolabs). Basically, adapters are ligrated to DNA followed by an amplification and clean up. The size of the libraries was checked using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip and their concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific).
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: otic cell line VOT-E36

tag: stage of cells

value: proliferating cells

tag: stage of tissue

value: derived from ventral portion of mouse otic vesicle at embryonic stage 10.5

tag: antibody

value: Rabbit IgG


title: TS_IP


title: HDG

status: Public on Mar 11 2021

city: Konya

first: gonca

last: sonmez

address: Akademi Mah

country: Turkey

institute: selcuk university

data_processing:
Illumina Casava 1.8 software used for basecalling.
The impurities of raw data are 5' primer contaminants,no insert tags,oversized insertion,low quality reads,poly A tags and small tags.We will get rid of some contaminant reads from the fq file and get the final clean reads.
After data filtering, reads mapped to oar_v3.1 whole genome using bowtie-0.12.9 with parameters -v 0 -k 1. miRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000.
The available software miREvo_v1.1 (with parameters -i -r -M -m -k -p 10 -g 50000) and mirdeep2_0_0_5 (with parameters quantifier.pl -p -m -r -y -g 0 -T 10) were integrated to predict novel miRNA through exploring the secondary structure.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: tab-delimited text files include Readcount and TPM values for known and novel miRNAs of each group.
Supplementary_files_format_and_content: tab-delimited text files include predicted hairpin sequences.
Supplementary_files_format_and_content: tab-delimited text files include mature and star sequences of the predicted hairpin sequences.

organism: Ovis aries

source_name: PBMC

extract_protocol:
Peripheral blood mononuclear cells (pbmc) were separated from blood samples taken from lambs and RNA was isolated with TRI Reagent (Sigma). miRNA libraries (LDG and HDG groups) were prepared with NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) with 3 ug of total RNA.
NEB 3' SR Adaptor was directly and specifically ligated to 3' end of miRNA, siRNA and piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and 50bp.

tag: cell type

value: PBMC

tag: group

value: high average daily gain (HDG)


title: LDG

value: low average daily gain (LDG)


title: NC5

city: Nanjing

first: Zijuan

state: Jiangsu

address: 300 Guangzhou Road, Nanjing, 210029, China

institute: The First Affiliated Hospital of Nanjing  Medical University, Jiangsu Province Hospital

description: circRNA

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Plasma

label_protocol: cDNA labeled with a fluorescent dye (Cy5-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: gender

value: male

tag: age

tag: disease state

value: Healthy volunteers


title: NC3

description: circRNA

value: whole blood


title: CLL3

description: circRNA

value: Untreated chronic lymphocytic leukemia


title: NC4

description: circRNA


title: NC2

description: circRNA

value: female


title: NC1

description: circRNA


title: CLL1

description: circRNA


title: LivN24_4

city: Chongqing

first: Min-Dian

last: Li

address: 30 Gaotanyan Main Street

department: Cardiology

institute: Southwest Hospital, Third Military Medical University (Army Medical University)

data_processing:
illumina Casava 1.8 software use for base calling.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
Expression levels of genes or transcripts were quantified by featureCounts v1.5.0-p3 (Liao et al., 2014), and represented as transcript per million (TPM).
Genome_build: mm10/GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

molecule: polyA RNA

source_name: adult female liver

growth_protocol: Special pathogen-free (SPF) mice were purchased from Hunan SJT Laboratory Animal Co. and housed in a SPF barrier facility. C57BL/6J female mice at 7 weeks of age were grouped housed, and entrained to a 12h light:12h dark cycle with normal chow food and water ad libitum for 7 days before assigned to daytime-restricted feeding (DRF) and nighttime-restricted feeding (NRF) groups for additional 7 days.

extract_protocol:
Liver was removed, flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent.
A ribosome-depletion workflow was applied to generate the strand-specific cDNA library as described (Parkhomchuk et al., 2009). Specifically, ribosomal RNAs were removed by Epicenter Ribo-Zero Kit (Epicenter). The remaining RNAs were fragmented (250-300 bp), and reversely transcribed using random hexamers and M-MuLV Reverse Transcriptase (RNase H-). After RNA digestion by RNase H, second strand cDNA synthesis was subsequently performed using dNTP (dTTP replaced by dUTP) and DNA polymerase I, followed by purification, terminal repair, polyadenylation, adapter ligation, size selection, and degradation of second-strand U-contained cDNA. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE155) were generated.

treatment_protocol: Animals were subjected to daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF) for 7 days

tag: strain

value: 9 weeks

tag: dietary regimen

value: NRF

tag: zeitgeber time in hours


title: CLL2

description: circRNA


title: LivN20_1


title: LivN16_3


title: LivN20_2


title: LivN20_3


title: LivN16_4


title: LivN20_4


title: LivN24_2


title: LivN12_4


title: LivN16_1


title: LivN12_3


title: LivN16_2


title: LivN12_2


title: LivN08_4


title: LivN08_1


title: LivN08_2


title: LivN24_3


title: LivN04_4


title: LivN24_1


title: LivN08_3


title: LivN12_1


title: LivN00_4


title: LivN04_2


title: LivN00_3


title: LivN04_1


title: LivN00_2


title: LivN00_1


title: LivD24_4

value: DRF


title: LivD24_3


title: LivD24_2


title: LivD24_1


title: LivD20_4


title: LivD20_2


title: genomic DNA from subglottic tissue biopsies [control4]

type: genomic

city: Madison

first: Xudong

last: Shi

address: 1111 Highland ave

department: Surgery

institute: University of Wisconsin-Madison

description: Normal subglottic sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the Minfi package within R. Differentially methylated regions were called using the Bumphunter algorithm; differentially methylated CpG sites were called using the dmpFinder function within Minfi on all 865,859 probes.

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Human tissue biopsy.

extract_protocol: Genomic DNA and protein were extracted using a protocol for simultaneous isolation of these biomolecules.Following processing in an AllPrep DNA spin column, DNA (retained in the column), was eluted and reserved.

treatment_protocol: No special treatment

value: Subglottic tissue biopsies


title: LivD20_1


title: LivD16_1


title: genomic DNA from subglottic tissue biopsies [iSGS10]

description: iSGS  sample


title: LivD12_4


title: LivD20_3


title: LivD04_4


title: LivD08_1


title: LivD16_3


title: LivD16_4


title: LivD16_2


title: LivD04_3


title: genomic DNA from subglottic tissue biopsies [iSGS12]

description: iSGS sample


title: genomic DNA from subglottic tissue biopsies [control1]

description: Normal subglottic sample


title: LivD08_4


title: genomic DNA from subglottic tissue biopsies [control2]

description: Normal subglottic sample


title: LivD04_1


title: LivD04_2


title: LivD00_4


title: LivN04_3


title: genomic DNA from subglottic tissue biopsies [control3]

description: Normal subglottic sample


title: genomic DNA from subglottic tissue biopsies [iSGS5]

description: iSGS sample


title: genomic DNA from subglottic tissue biopsies [iSGS6]

description: iSGS sample


title: genomic DNA from subglottic tissue biopsies [iSGS8]

description: iSGS sample


title: LivD12_3


title: LivD12_2


title: LivD12_1


title: LivD08_3


title: LivD00_3


title: LivD00_2


title: LivD00_1


title: sd1-EASCs-3

first: Chuanxi

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

data_processing:
Tophat 2 software used for basecalling.
expected number of Reads Per Kilobase of transcript sequence per Millions base  pairs sequenced (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: rat(rn5)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: epididymal adipose

growth_protocol: Rats were anesthetized with 2% isoflurane to induce sacrifices, soaked in 75% ethanol for whole body disinfection, removed from alcohol, and placed on a sterile ultra clean table. The limbs were fixed, SAT was obtained from the groin. Perirenal and epididymal adipose tissue were obtained from kidney and testis, and the tissue was rinsed in pre-cooled PBS. The washed adipose tissue was transferred into the cell platform, muscle and lymph tissue were removed, tissue was cut into 1–2 mm pieces, and collagenase type I was added. After digestion, all the suspensions collected were filtered through a nylon filter (Dutscher, 100 µm), centrifuged at 1,000 rpm for 5 minutes, and the supernatant was discarded. DMEM / F12 medium containing 10% fetal bovine serum (FBS) was added to the sample. Then the suspension was evenly spread in culture dishes and cultured into a 37°C incubator for 2 hours. The upper medium was discarded, high glucose medium containing 10% FBS was added, and SASCs, PASCs, and EASCs were obtained.

extract_protocol:
P3 SASCs, PASCs, and EASCs were cultured in 12 well plates with six replicates in each group. Each well was ground with 1 mL Trizol solution, placed at room temperature for 5 minutes, and then aspirated. RNA was separated using chloroform (mixture: chloroform = 5:1) and precipitated by isopropanol and absolute ethanol. Finally, RNA was precipitated with DEPC water, and then stored at -80°C for subsequent transcriptome sequencing (Guangzhou Ruibo company，guangzhou, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: epididymal adipose-derived mesenchymal stem cells


title: sd1-EASCs-2


title: sd1-PASCs-3

source_name: perirenal adipose

value: perirenal adipose-derived mesenchymal stem cells


title: sd1-EASCs-1


title: sd1-PASCs-1


title: genomic DNA from subglottic tissue biopsies [iSGS9]

description: iSGS sample


title: sd1-SASCs-3

source_name: Subcutaneous adipose

value: Subcutaneous adipose-derived mesenchymal stem cells


title: sd1-SASCs-2


title: sd1-SASCs-1


title: genomic DNA from subglottic tissue biopsies [iSGS11]

description: iSGS sample


title: genomic DNA from subglottic tissue biopsies [iSGS7]

description: iSGS  sample


title: genomic DNA from subglottic tissue biopsies [iSGS4]

description: iSGS  sample


title: genomic DNA from subglottic tissue biopsies [iSGS1]

description: iSGS  sample


title: LVAD142

city: Stanford

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

data_processing:
Illumina bcl2fastq version 1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using TrimGalore version 0.4.0 with parameters: --paired, --trim1
Trimmed reads were then aligned with TopHat version 2.0.12 (Bowtie2 version 2.2.3) to UCSC hg19 reference genome with parameters: -r 150, --library-type fr-firststrand, --keep-fasta-order, --transcriptome-index, --rg-id, --rg-sample, --rg-library, --rg-platform-unit, --rg-platform, -o
Cufflinks version 2.2.1 estimated transcript abundances with parameters: --library-type fr-firststrand, -o, -g, -L, -b, -u
Cuffmerge, Cuffquant, Cuffdiff, and Cuffquant were then run to get to final differential expression results
Genome_build: hg19

source_name: RNA from cardiac left ventricle

extract_protocol:
Endocardial samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human Samples taken from left ventricle of patients with end-stage heart failure during Ventricular Assist Device implantation.

tag: race

value: Caucasian American

tag: hypertension

value: Apical left ventricle


title: LVAD157

value: African American

tag: tissue


title: LVAD140


title: LVAD141


title: LVAD130


title: LVAD133


title: LVAD132


title: pregnant (Days 12-13) vs. cyclic (Days 12-13 of the estrous cycle) 1_1

city: Olsztyn

first: Agata

last: Zmijewska

address: Oczapowski 1a

department: Demartment of Animal Anatomy and Physiology

country: Poland

institute: Univeristy of Warmia and Mazury

hyb_protocol: Two differentially labelled samples (from pregnant and cyclic gilts) were placed on each array (one slide, n = 4) in a balanced block design with dye swaps. Hybridization was carried out in an Agilent hybridization oven for 17 h at 65°C. After the hybridization process, the microarrays were washed.

scan_protocol: Microarrays were scanned at 5 μm resolution with an Agilent’s High-Resolution C Microarray Scanner according to the manufacturers' protocol.

data_processing: The TIFF image, generated after the scanning process, was used for: data extraction and detailed analysis, background subtraction from features, and dye normalizations (linear and LOWESS); in the Feature Extraction Software. Gene expression data were analysed in GeneSpring GX 12 software (Agilent Technologies, USA) to identify the genes that were differentially expressed in pregnant and cyclic pigs.

organism: Sus scrofa domesticus

source_name: Anterior pituitary of pregnant pigs

label_protocol: The RNA isolated from the pituitary of pregnant and cyclic females were labelled with Cyanine-3 (Cy-3) and Cyanine-5 (Cy-5), respectively. Quantity and purity of obtained cRNA were measured with NanoQuant plates on the Infinite M200 Pro plate reader. 825 ng of Cy-3 and 825 ng of Cy-5-labeled cRNA were mixed together (for each microarray). According to the microarray manufacturer’s protocol, cRNA was fragmented and mixed with hybridization buffer.

growth_protocol: Eight mature gilts (Large White x Polish Landrace, weighing  ~110 kg) were used in the study (n = 8). All individuals were descended from private breeding farm. Day 0 was a day indicating the beginning of estrus. Cyclic animals (n=4) were sacrificed on days 12-13.  Days of the estrous cycle were confirmed on the morphology of ovaries. Gilts assigned to the early pregnancy group (n = 4) were naturally bred twice on the first and the second days of the estrous  and sacrificed on days 12-13of pregnancy. Pregnancy was confirmed by the presence of conceptuses. Animals were slaughtered by qualified abattoir worker.

extract_protocol: Total RNA was isolated from porcine pituitaries using the RNeasy Mini Kit (Qiagen, USA), according to manufacture procedure.RNA purity and quantity were measured spectrophotometrically. RNA quality was checked using RNA 6000 Nano Assay Kit on an Agilent 2100 Bioanalyzer. RNA integrity number (RIN) score ≥ 8. The obtained nucleic acid was used for microarray analysis and quantitative real-time PCR (qPCR) experiments. RNAs were stored at −80 °C until the microarray analysis.

tag: reproductive status

value: Early pregnancy

value: Large White x Polish Landrace

tag: days

value: days 12 to 13

source_name: Anterior pituitary of cyclic pigs

value: the estrous cycle


title: pregnant (Days 12-13) vs. cyclic (Days 12-13 of the estrous cycle) 1_3