title: EpiSC5 OL

data_processing:
For aligning reads to the genome, reads were quality and adapter trimmed using Trim Galore! Version 0.3.1.
Trimmed reads were aligned to the mouse genome (mm10) with Bowtie2 version 2.3.2 and duplicate reads were removed using Picard MarkDuplicates.
Peaks were called using MACS2 narrowpeak subcommand.
Genome_build: mm10
Supplementary_files_format_and_content: bed files and bigwig files

extract_protocol:
cell preparation: Omni ATAC-Seq was performed on 50,000 OPCs and sorted O1+ oligodendrocytes.
Nuclei were extracted from cells and treated with transposition mixture containing Nextera Tn5 Transposase for 30 minutes at 37oC with 1000 RPM mixing. Transposed fragments were then purified using Qiagen MinElute columns, PCR amplified, and libraries were purified with Agencourt AMPure XP magnetic beads with a sample to bead ratio of 1:1.2.
Samples were submitted to UChicago’s genomics core and sequenced on the HiSeq2500 with single-end 50bp reads with 100 million reads per sample.

value: epiblast stem cell derived OLs


title: Norm48hr-1

status: Public on Sep 01 2023

type: SRA

city: Durham

first: Jarrett

last: Bliton

address: 6 Davis Drive

country: USA

institute: Altis Biosystems

library_source: transcriptomic

data_processing:
Transcript quantification and pseudoalignment: Gene level expression was obtained through pseudo alignment of reads to human genome GRCh38 using Kallisto
Normalization: Expression values for plotting were obtained by TMM normalization across all samples using EdgeR package and differential expression between normoxic and hypoxic samples at each time point was calculated from raw counts with DESeq2
Assembly: GRCh38
Supplementary files format and content: csv - TMM normalized gene expression values per sample
Supplementary files format and content: h5ad - annotated matrix with read counts per gene x sample

molecule: total RNA

organism: Homo sapiens

source_name: 48 hours Normoixa

growth_protocol: Crypts or dissociated monolayers were placed on the top of 1.0 mg/mL collagen hydrogels (1 ml into each well of 6-well plate (T1006; Denville, Holliston, MA)) at a density of 5,000 crypts/ well and overlaid with 4 ml of Expansion Media (EM) containing 10 mmol/L Y-27632 (S1049; SelleckChem). EM contains a mixture of advanced Dulbecco’s modified Eagle medium/F12 medium (12634010; ThermoFisher) and Wnt-3A, R-spondin 3, noggin (WRN) conditioned medium (WRN medium prepared in lab from L-WRN cells (CRL- 3276; ATCC) following a published protocol98 at a volumetric ratio of 1:1, and supplemented with GlutaMAX (35050061; ThermoFisher), B27 supplement without vitamin A (12587010; ThermoFisher), 10 mM HEPES (15630-080; ThermoFisher), 1.25 mM N-acetyl cysteine (194603; MP Bio, Santa Ana, CA), 10 mM nicotinamide (N0636; Sigma-Aldrich), 50 ng/mL epidermal growth factor (315-09; Peprotech), 2.0 nM gastrin (AS-64149; Anaspec), 10 nM prostaglandin E2 (14010; Cayman Chemicals), 3.0 µM SB202190 (S1077; Selleckchem), 100 U/mL penicillin-streptomycin (15140122; ThermoFisher), and 50 mg/mL primocin (ant-pm-1; InvivoGen, San Diego, CA). EM was used to expand the epithelial cell numbers as monolayers or organoids. Y-27632 was present only in the first 48 hours of cell culture and was not added to subsequent media changes. The medium was changed every 48 hours. When the cell coverage was greater than 80% (typically 5 to 7 days), the epithelium was dissociated to fragments to seed onto the intestinal MPS or passaged for further expansion.

extract_protocol:
To investigate the dynamic response of hISC to hypoxia at the whole transcriptomic level, we performed RNA-seq on human intestinal epithelium exposed to 6 hours, 24 hours, or 48 hours of hypoxia inside intestinal MPS, along with normoxic control intestinal MPS which were cultured for each respective time point with no hypoxia exposure. RNA samples were collected from each intestinal MPS, and Total RNA was extracted using RNAqueous-Micro Total RNA Isolation Kit (AM1931; ThermoFisher) according to manufacturer’s protocols and stored at −80°C.
Three technical replicates were collected from each duration of normoxia or hypoxia. RNA was extracted via the RNAqueous-Micro Total RNA Isolation Kit (AM1931; ThermoFisher, Waltham, MA) according to the manufacturer’s protocol. To assess RNA quality prior to submission for sequencing, an RNA integrity number (RIN) was measured using the Agilent 2100 Bioanalyzer. After confirmation that each sample had a RIN of at least 8, integrated fluidic circuits (IFCs) for gene expression and genotyping analysis were prepared using the Advanta™ RNA-Seq NGS Library Prep Kit for the Standard Biotools Juno™. Bulk sequencing was run on a NovaSeq 6000 instrument using one lane of an S4 v1.5 flow cell (Illumina).

tag: tissue

value: Healthy human jejunal epithelium

tag: treatment

value: 48 hours of normoxic culture


title: Hypo6hr-1

source_name: 6 hours Hypoxia

value: 6 hours of hypoxic culture


title: Bisulfite-seq_HSD1

city: Chongqing

first: Peng

last: Gao

state: Chongqing

address: 10 Chang Jiang Zhi Lu

country: China

institute: Daping hospital, Army Medical University

library_source: genomic

data_processing:
Reads were trimmed to remove low quality bases, and were mapped to the mm10 reference genome using Bismark v0.20.0
Methylation data at CG sites were extracted for the downstream analyses
Genome_build: mm10
Supplementary_files_format_and_content: position of CpG (name of scaffold, start position, and end position), methylation ratio.

molecule: genomic DNA

organism: Mus musculus

source_name: liver

growth_protocol: 6-week-old male mice

extract_protocol:
DNA extracted using phenol-chloroform protocol after RNAse treatment. DNA was bisulfite converted with the EZ DNA methylation kit (Zymo).
DNA were spiked with 1% unmethylated lambda phage DNA. Libraries were generated by post bisulfite adaptor tagging method with 8 cycles of library amplification.

treatment_protocol: Mice were fed with high salt diet (HSD, containing 8% NaCl) or normal salt diet (NSD, containing 0.4% NaCl) for 4 months.

tag: strain

value: liver

tag: Sex

value: male

tag: age

value: post natal month 6

tag: genotype

value: wild type

value: post high salt diet weeks 8


title: Bisulfite-seq_NSD2

value: post normal salt diet weeks 8


title: Norm24hr-3

source_name: 24 hours Normoxia

value: 24 hours of normoxic culture


title: EpiSC5 OPCs

city: Cleveland

first: Paul

last: Tesar

state: Ohio

address: 10900 Euclid Ave.

department: Genetics & Genome Sciences

institute: Case Western Reserve University

source_name: oligodendrocyte progenitor cells (OPCs)

growth_protocol: Data were generated using OPCs generated from epiblast stem cell (EpiSC) lines EpiSC5 and 129O1, which were derived from mouse strain 129SvEv and 129S1/SvImJ as described previously except SHH was not used for the maintenance nor differentiation of OPCs (Najm et al., 2011). All OPC and immature oligodendrocyte cultures were maintained on plates or glass coverslips coated with 100 µg/mL poly(L-ornithine), followed by 10 µg/ml laminin. OPC growth media consisted of DMEM/F12 supplemented with N2 Max, B27, 20ng/mL bFGF, and 20ng/mL PDGFA and was changed every 48 hours. After 4 passages, these EpiSC derived OPCs were purified by fluorescence activated cell sorting using conjugated CD140a and NG2-AF488 antibodies. Sorted OPCs were then expanded and purity was verified by staining for markers of OPCs, astrocytes, and oligodendrocytes and frozen down in aliquots.

tag: cell line

tag: cell type

value: epiblast stem cell derived OPCs


title: 129O1 OPCs


title: CKD RASi/SGLT2i/MRA 1

city: München

first: ZHIHUI

last: ZHU

address: Geiselgasteigstr. 62, 2.0G

country: Germany

institute: LMU Klinikum

data_processing:
After QC, Fastq was mapped to the mm39 by hisat2. DESeq2 for downstream analyze.
Assembly: mm39
Supplementary files format and content: count, rpkm matrix

source_name: kidney

extract_protocol:
Total RNA was isolated using an RNA extraction kit (Life Technologies, Darmstadt, Germany) according to the manufacturer´s instructions, and RNA quality was assessed using agarose gels. RNA-seq of total RNA samples was conducted on the Illumina DNBSEQ-G400 platform, producing 100bp paired-end reads.
Strand-specific transcriptome library construction is completed by enriching mRNA from total RNA, sequenced by DNBSEQ high-throughput platform, and followed by bioinformatics analysis.

treatment_protocol: Col4a3-/- mice were treated with food admix of either vehicle, 10 mg/kg ramipril, 10 mg/kg ramipril plus 30 mg/kg empagliflozin, and 10 mg/kg ramipril plus 30 mg/kg empagliflozin plus 10 mg/kg finerenone. The different types of food preparations were marked by different food colors starting from 6 weeks of age for 8 weeks.

value: kidney

value: primary cell

value: Ramipril/Empagliflozin/Finerenone


title: Norm24hr-2


title: KO_Input_NSD

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.05 as cutoff
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: chip antibody

value: none (input)


title: EpiSC5 OL - Sox6

data_processing:
For aligning reads to the genome, reads were quality and adapter trimmed using Trim Galore! Version 0.3.1.
Trimmed reads were aligned to the mouse genome (mm10) with Bowtie2 version 2.3.2 and duplicate reads were removed using Picard MarkDuplicates.
Peaks were called with MACSv2.1.1 with an FDR<0.001 using the broad peaks subcommand for histone marks (H3K27Ac) and narrow peaks subcommand for transcription factors (SOX6) and normalized to background input genomic DNA.
Peaks were visualized using the Interactive Genomics Viewer (IGV, Broad Institute). Aggregate plots were generated using deepTools2 computeMatrix followed by plotHeatmap (https://deeptools.readthedocs.io/en/develop/) (Ramirez et al., 2016).
Peaks were assigned to the nearest expressed gene (TPM>1) using bedtools closest function (Quinlan and Hall, 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bed files and bigwig files

source_name: oligodendrocytes (OLs)

growth_protocol:
Data were generated using OPCs generated from epiblast stem cell (EpiSC) lines EpiSC5 and 129O1, which were derived from mouse strain 129SvEv and 129S1/SvImJ as described previously except SHH was not used for the maintenance nor differentiation of OPCs (Najm et al., 2011). All OPC and immature oligodendrocyte cultures were maintained on plates or glass coverslips coated with 100 µg/mL poly(L-ornithine), followed by 10 µg/ml laminin. OPC growth media consisted of DMEM/F12 supplemented with N2 Max, B27, 20ng/mL bFGF, and 20ng/mL PDGFA and was changed every 48 hours. After 4 passages, these EpiSC derived OPCs were purified by fluorescence activated cell sorting using conjugated CD140a and NG2-AF488 antibodies. Sorted OPCs were then expanded and purity was verified by staining for markers of OPCs, astrocytes, and oligodendrocytes and frozen down in aliquots.
cell preparation: OPCs and purified intermediate O1+ oligodendrocytes were harvested using the autoMACS automated cell sorter. Fixation, nuclei isolation, and chromatin shearing were performed using the Covaris TruChIP protocol following the manufacturer’s instructions for the “high-cell” format (Allan et al., 2020). Sorted OPCs and O1+ oligodendrocytes were crosslinked in “Fixing buffer A” supplemented with 1% fresh formaldehyde for 10 minutes at room temperature with oscillation and quenched for 5 minutes with “Quench buffer E.”

extract_protocol:
ChIP DNA was purified by phenol-chloroform separation
Illumina sequencing libraries were submitted to UChicago’s genomics core and sequenced on the HiSeq2500 or NextSeq with single-end 50bp or 75bp reads respectively with at least 20 million reads per sample.

treatment_protocol: Cells were washed with PBS and immediately proceeded to nuclei extraction. Isolated nuclei were then sonicated using the Covaris S2 with 5% Duty factor, 4 intensity and four 60-second cycles. Sheared chromatin was then cleared and incubated with protein G magnetic DynaBeads that had been pre-incubated with primary ChIP-grade antibodies overnight at 4oC. Primary antibodies used included anti-H3K27Ac (9µg/sample, Abcam, ab4729), and anti-SOX6 (15 µg/sample, Abcam, ab30455). Protein DynaBeads were then washed and DNA was eluted, reverse cross-linked, and treated with RNAse A followed by Proteinase K digestion.

tag: cell line source

value: Sox6 (15 µg/sample, Abcam, ab30455)


title: 129O1 OL

value: epiblast stem cell derived OLs


title: Bisulfite-seq_NSD1


title: CKD RASi 3

value: Ramipril


title: 163360-1L

city: Toronto

first: Andrew

last: Advani

state: Ontario

address: 6-151 61 Queen Street East

department: Medicine

country: Canada

institute: St. Michael's Hospital

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software
Transcript abundances for each sample were estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown
Assembly: GRCm38
Supplementary files format and content: Excel files containing FPKM values for each gene in each sample
Supplementary files format and content: Excel files containing FPKM values for each transcript in each sample

source_name: Left kidney

extract_protocol:
Total RNA from kidney tissue was isolated using Trizol and quantified using NanoDrop ND-1000
Total RNA was used to prepare sequencing libraries with a KAPA Stranded RNA-Seq Library Prep Kit (Illumina)

value: Left kidney

value: Sham Surgey


title: WT_Input_NSD2

value: liver


title: Bisulfite-seq_HSD2

value: male


title: Norm48hr-2

value: Healthy human jejunal epithelium

value: 48 hours of normoxic culture


title: CKD RASi 2

description: CKD_RASi _2


title: Norm24hr-1


title: WT_Input_NSD1

value: post natal month 6

value: wild type


title: Norm6hr-2

source_name: 6 hours Normoxia

value: 6 hours of normoxic culture


title: CKD RASi 1


title: EpiSC5 OPC - H3K27Ac

value: epiblast stem cell derived OPCs

value: H3K27Ac (9µg/sample, Abcam, ab4729)


title: WT_Input_HSD2

value: post high salt diet weeks 8


title: EpiSC5 OL - H3K27Ac


title: EpiSC5 OPC - Sox6


title: CKD veh 3

value: kidney

value: primary cell


title: Norm6hr-3


title: EpiSC5 mouse ESCs - input DNA


title: Norm6hr-1


title: WT_Input_HSD1

value: none (input)


title: KNS42 GBM cells, CPI-613 2

city: New York

first: Markus

last: Siegelin

state: New York

department: Pathology and Cell Biology

institute: Columbia University

data_processing: the Fasq file was processed and gene set analysis was performed by using Scidap software (https://scidap.com/)

growth_protocol: KNS42 cells were cultured in DMEM + 10% FBS + primocin

extract_protocol:
total RNA by using miRNAeasy Mini Kit from QIAGEN (217004)
SIRV-Set 1 (Iso Mix E0, E1, E2) - RNA-seq  (Cat#SKU: 025.03)

treatment_protocol: KNS42 cells were treated with 100 uM CPI-613 for 24h in  DMEM + 1.5% FBS + primocin

value: Gliobalstoma


title: KO_H3_NSD

value: post normal salt diet weeks 8


title: CKD veh 2


title: 129O1 OPC - Sox6

value: Sox6 (15 µg/sample, Abcam, ab30455)


title: KNS42 GBM cells, CPI-613 1


title: 129O1 OL - H3K27Ac

value: epiblast stem cell derived OLs


title: CKD veh 1


title: KNS42 GBM cells, DMSO 1

value: DMSO


title: 129O1 OPC - H3K27Ac


title: KNS42 GBM cells, DMSO 2


title: WT_H3_NSD1

value: male

value: liver


title: 129O1 mouse ESCs - input DNA


title: WT 2

value: WT


title: WT_H3_HSD2

value: post natal month 6


title: WT 1


title: ALI-AO_vehicle, replicate 1, scMultiome

city: Seoul

first: Jong-Il

last: Kim

address: Daehakro 103

country: South Korea

institute: Seoul National University

description: 10x Genomics

library_source: other

data_processing:
Gene counting and peak calling were made using the Cell Ranger (v6.0.1) and Cell Ranger-arc (v2.0.0) softwares.
Assembly: GRCh38
Supplementary files format and content: Tab-separated valued files and matrix files
Library strategy: scMultiome

molecule: other

source_name: primary lung

growth_protocol: We culture human airway organoids derived from freshly removed lung tissue with previously established protocol.

extract_protocol:
Cultured organoids were dissociated with TrypLE for 15min on 37C. Dissociated cells were suspended with 0.04% BSA/PBS solution.
Libraries were generated with the manufacter's instructions (single cell 3' v3.1 and multiome protocols, 10x Genomics).

treatment_protocol: For viral infection, we treat virus (MOI 1.0) for 3 hours on ALI-AO.

value: human airway organoid

tag: culture method

value: ALI-AO

tag: agent

value: vehicle


title: Female_placentae_pooled

city: Columbia

first: Susanta

middle: K.

last: Behura

state: Missouri

address: 920 East Campus Drive

department: Division of Animal Sciences

institute: Univeristy of Missouri

data_processing:
The raw sequence files were first chekced for quality by FASTQC.
The quality control was performed using cutadpat
Bowtie2 was used for read aligment to processd genome sequences
MACS2 was used to call peaks.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: bed file for narrowpeaks

source_name: Placenta

growth_protocol: Gestation day 15 of wildtype mice. The vaginal plug was observed was considered day 0.5 of gestation to detemine gestational age.

extract_protocol:
Freshly collected  day 15 placentae from three biological replicates were pooled that was used to preapre ChIP DNA using Zymo-Spin ChIP Kit (Catalog# D5210).
The REST antibody from Millipore-sigma (Catalog# 17-641) was validated and used to prepare the ChIP DNA.
ChIP-seq approach was adopted for library prepartion, and Illumina Hiseq was used to sequence the libraries.

value: Placenta

tag: gender

value: Female

tag: antibody

value: REST antibody


title: small_RNA_sos2-2_100N_rep3

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

data_processing:
For mRNA-seq, Kallisto_0.46.2 was used for quantification. TPM values were calculated for each transcript of genes.
For mRNA-seq, Differential expression analysis of genes was performed by Sleuth_0.30.0
For small RNA-seq, the adapter sequence was removed by cutadapt.
For small RNA-seq, the clean reads were mapped to Arabidopsis genome by using Bowtie2.2.5
For small RNA-seq, the annotation of Arabidopsis miRNAs was downloaded from https://www.mirbase.org/. FeatureCount_1.6.4 was used for the quantification of each miRNA
Assembly: Tair10
Supplementary files format and content: For mRNA-seq, tab-delimited text files include TPM values for each Sample
Supplementary files format and content: For small RNA-seq, tab-delimited text files include RPM for each Sample

organism: Arabidopsis thaliana

source_name: whole-seedling

growth_protocol: The sterilized seeds of wild-type and sos2-2 were sown on MS medium containing 3% sucrose and 0.6% phytagel. Seeds were kept at 4 ℃ for 2 days and then transferred into a growth chamber under constant illumination at 22 ℃ for 10 days.

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen). The small RNA was extracted by using TRIzol reagent with MgCl2.
Standard mRNA-seq libraries were constructed by using Illumina RNA-seq kit (RS-122-2201). The small RNA-seq libraries were constructed by using Illumina sRNA-seq kit (RS-200-0012).

treatment_protocol: Ten-day-old seedlings of the wild type and sos2-2 mutant were treated in liquid MS medium containing 100 mM NaCl for 12 hours.

value: whole-seedling

value: sos2-2 mutant

value: 100 mM NaCl treatment

tag: molecule subtype

value: small RNA


title: Male_placentae_pooled

value: Male


title: ALI-AO_omicron, replicate 1, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Gene counting and peak calling were made using the Cell Ranger (v6.0.1) and Cell Ranger-arc (v2.0.0) softwares.
Assembly: GRCh38
Supplementary files format and content: Tab-separated valued files and matrix files

molecule: polyA RNA

value: omicron


title: WT_H3_HSD1

value: wild type

value: post high salt diet weeks 8


title: WT_H3k9ac_NSD2

value: male

value: liver

value: post normal salt diet weeks 8


title: ALI-Pn_vehicle, replicate 1, scRNAseq

description: 10x Genomics

value: human airway organoid

value: ALI-Pn


title: KO_H3k27ac_NSD

value: post natal month 6


title: ALI-AO_delta, replicate 1, scRNAseq

description: 10x Genomics

value: ALI-AO

value: delta


title: small_RNA_sos2-2_MS_rep3

value: MS medium


title: WT_H3_NSD2


title: WT_H3k9ac_HSD2


title: WT_H3k9ac_NSD1


title: small_RNA_sos2-2_100N_rep1

value: whole-seedling


title: small_RNA_sos2-2_MS_rep2

value: sos2-2 mutant


title: CoTAC_1 [JP747]

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie version 1.0.0 with parameters ---library-type fr-unstranded -p 6 --no-coverage-search
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cuffdiff v2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: an excel file (RPKM.xlsx) contains RPKM values for each gene.

source_name: TAC cohoused with JAX (CoTAC)

extract_protocol:
Total RNA was extracted from mouse liver tissues using Trizol reagent (Thermo, 15596018). Afterwards, mRNA was extracted from total RNA using  NEBNext® Poly(A) mRNA Magnetic Isolation Module, 24 rxns (NEB, E7490S)
RNA libraries were prepared for sequencing using ThruPLEX-FD-12 kit (Rubicon Genomics)

tag: vendor

value: Taconic (TAC)


title: ALI-AO_beta, replicate 1, scRNAseq

description: 10x Genomics

value: beta


title: CoTAC_3 [JP749]


title: WT 3

value: kidney

value: primary cell

value: WT


title: WT_H3k9ac_HSD1

value: wild type

value: post high salt diet weeks 8


title: CoJAX_2 [JP745]

source_name: JAX cohoused with TAC (CoJAX)

value: Jackson (JAX)

value: liver


title: CoJAX_3 [JP746]


title: small_RNA_sos2-2_MS_rep1

value: small RNA


title: ALI-AO_mers, replicate 1, scRNAseq

description: 10x Genomics

value: human airway organoid

value: mers


title: ALI-AO_influenza, replicate 1, scRNAseq

description: 10x Genomics

value: ALI-AO

value: influenza


title: WT_H3k27ac_NSD2

value: male

value: post natal month 6

value: post normal salt diet weeks 8


title: small_RNA_WT_100N_rep3

value: whole-seedling

value: 100 mM NaCl treatment


title: CoTAC_2 [JP748]

value: Taconic (TAC)


title: small_RNA_WT_100N_rep2


title: CoJAX_1 [JP744]


title: ALI-AO_vehicle, replicate 3, scRNAseq

description: 10x Genomics

value: vehicle


title: small_RNA_sos2-2_100N_rep2

value: sos2-2 mutant


title: ALI-AO_beta, replicate 2, scRNAseq

description: 10x Genomics

value: beta


title: WT_H3k27ac_HSD1

value: wild type

value: post high salt diet weeks 8


title: small_RNA_WT_100N_rep1

value: WT


title: ALI-AO_alpha, replicate 1, scRNAseq

description: 10x Genomics

value: alpha


title: WT_H3k27ac_HSD2

value: liver


title: TAC_1 [JP741]

source_name: TAC cohoused with TAC (TAC)


title: TAC_3 [JP743]


title: ALI-AO_vehicle, replicate 2, scRNAseq

description: 10x Genomics

value: human airway organoid


title: TAC_2 [JP742]


title: WT_H3k4me1_NSD1


title: WT_H3k4me1_NSD2


title: JAX_3 [JP740]

source_name: JAX cohoused with JAX (JAX)

value: Jackson (JAX)


title: 3D-AO_vehicle, replicate 1, scRNAseq

description: 10x Genomics


title: WT_H3k4me1_HSD2


title: ALI-AO_vehicle, replicate 1, scRNAseq

description: 10x Genomics

value: ALI-AO


title: JAX_2 [JP739]


title: small_RNA_WT_MS_rep1

value: MS medium

value: small RNA


title: WT_H3k27ac_NSD1

value: male

value: post natal month 6

value: post normal salt diet weeks 8


title: WT_H3k4me1_HSD1


title: Differentiation day6

city: Shenzhen

first: Fujian

last: Wu

state: Guangdong

address: No.1017, Dongmen North Road, Luohu District

institute: Shenzhen People's Hospital

data_processing:
Illumina NovaSeq 6000.
After the library is qualified, the different libraries are pooling according to the  effective concentration and the target amount of data off the machine, then being  sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is  generated. The basic principle of sequencing is to synthesize and sequence at the same  time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase  and splice primers were added to the sequenced flowcell and amplified. When the  sequence cluster extends the complementary chain, each dNTP labeled by  fluorescence can release the corresponding fluorescence. The sequencer captures the  fluorescence signal and converts the optical signal into the sequencing peak by  computer software, so as to obtain the sequence information of the fragment to be  tested.
The image data measured by the high-throughput sequencer are converted into  sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq  format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000  Assay Kit. total RNA was used for the construction of sequencing libraries.
During the differentiation of cardiac organoids, the cells were harvested on days 0, 2, 3, 4, 6, and 30, and 10 organoids were harvested at each time point.Total amounts and integrity of RNA were assessed using the RNA Nano 6000  Assay Kit of the Bioanalyzer 2100 system.Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in  First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using  random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to  degrade the RNA. Second strand cDNA synthesis was subsequently performed using  DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends  via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA  fragments, Adaptor with hairpin loop structure were ligated to prepare for  hybridization. In order to select cDNA fragments of preferentially 370~420 bp in  length, the library fragments were purified with AMPure XP system (Beckman  Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by  AMPure XP beads, and the library was finally obtained.After  the construction of the library, the library was initially quantified by Qubit2.0  Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by  Agilent 2100 bioanalyzer.After insert size meets the expectation, qRT-PCR is used to  accurately quantify the effective concentration of the library to ensure the quality of the  library

value: Embryonic stem cell

tag: time point

value: day 6


title: JAX_1 [JP738]

tag: tissue


title: Nannochloropsis, mutant M4, rep2

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

description:
17623_2
5.14 Gb

data_processing:
split into subreads
filter unmapped reads
randomly downsampled to 100X
detect modified sites
select 6mA sites
unaligned
Supplementary files format and content: GFF files with 6mA sites
Library strategy: 6mA-Seq

organism: Nannochloropsis oceanica

source_name: Nannochloropsis oceanica

growth_protocol: conventional

extract_protocol:
genomic DNA without amplification
PacBio Sequel II

treatment_protocol: high light, 7 days

value: Nannochloropsis oceanica

tag: treatment

value: high light, 7 days


title: Differentiation day30

value: day 30


title: Nannochloropsis, mutant M4, rep3

description:
17623_3
3.85 Gb, abnormal knockout

tag: strain


title: Nannochloropsis, mutant M4, rep1

description:
17623_1
5.48 Gb


title: KO+APAP rep2

city: Wuhan

first: Yixue

last: Huang

address: Hangkong Road 13

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10（ensembl_mus_musculus_grcm38_p6_gca_000001635_8） whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample ...

growth_protocol: Animals were housed in ventilated microisolator cages with free access to water and food under a 12:12 h light/dark cycle in a temperature-controlled room (22 ± 2°C).

extract_protocol:
Total RNA from each sample was extracted using RNAiso Plus (Takara Biotech), and concentration was measured using an ND-1000 NanoDrop (Thermo Scientific, Wilmington, DE).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Firststrand cDNA wassynthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: mice were fasted for 16 hours before APAP treatment, while APAP (Macklin Biochemical, Shanghai, China) was freshly dissolved in phosphate-buffered saline (PBS), and 300 mg/kg APAP was intraperitoneally injected.

tag: developmental stage

value: adult

value: C57BL/6 x 129S4/SvJae

value: Utx KO


title: small_RNA_WT_MS_rep3

value: whole-seedling

value: WT


title: KO+APAP rep1

value: liver


title: Differentiation day4

value: day 4


title: Differentiation day3

value: day 3


title: 3D-AO_vehicle, replicate 2, scRNAseq

description: 10x Genomics

value: human airway organoid

value: vehicle


title: WT+APAP rep2


title: WT+APAP rep1


title: Nannochloropsis, mutant M3, rep1

description:
17611_1
3.86 Gb


title: Differentiation day2

value: day 2


title: small_RNA_WT_MS_rep2

value: MS medium

value: small RNA


title: SOX6_OL_sg2KO_rep3

description:
20200510.NTCvsSox6KO.DPcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DPabundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.results.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.nofilter.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200405_EpiSC5_DP_NTCvsS6g1vsS6g2_counts.csv
20200405_EpiSC5_DP_NTCvsS6g1vsS6g2_abundance.csv
20200405_DP_NTCvsS6g1vsS6g2_DESEQ.csv
20200405_DP_NTCvsS6g2_DESEQ.csv

data_processing:
Final libraries were pooled evenly and sequenced on the Illumina NovaSeq with paired-end 150bp reads with a read-depth of at least 20 million reads per sample.
For gene expression analysis, reads were aligned to the mm10 genome and quantified in transcripts per million (TPM) values using salmon 0.14.1.
Transcripts were summarized as gene-level TPM abundances with tximport. A gene with TPM>1 was considered expressed.
Differential expression analysis was performed using DESEQ2. Significant genes were called based on p-adj and fold change.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated files including DESEQ2 abundance comparing each sample
Supplementary_files_format_and_content: comma separated files including DESEQ2 counts comparing each sample

growth_protocol:
Data were generated using OPCs generated from epiblast stem cell (EpiSC) lines EpiSC5 (rep 1 OPCs) and 129O1 (rep 2 OPCs), which were derived from mouse strain 129SvEv and 129S1/SvImJ as described previously except SHH was not used for the maintenance nor differentiation of OPCs (Najm et al., 2011). All OPC and immature oligodendrocyte cultures were maintained on plates or glass coverslips coated with 100 µg/mL poly(L-ornithine), followed by 10 µg/ml laminin. OPC growth media consisted of DMEM/F12 supplemented with N2 Max, B27, 20ng/mL bFGF, and 20ng/mL PDGFA and was changed every 48 hours. After 4 passages, these EpiSC derived OPCs were purified by fluorescence activated cell sorting using conjugated CD140a and NG2-AF488 antibodies. Sorted OPCs were then expanded and purity was verified by staining for markers of OPCs, astrocytes, and oligodendrocytes and frozen down in aliquots.
For immature oligodendrocyte formation, OPCs were seeded at 40,000 cells per well in 96-well plates or 50 million cells per 500 cm2 bioassay plate (for generating large quantities of cells for sequencing studies) coated with PO and laminin. OPCs were plated in oligodendrocyte differentiation media consisting of DMEM/F12 supplemented with N2 Max, B27, 100ng/mL noggin, 100ng/mL IGF-1, 10uM cyclic AMP, 10ng/mL NT3, and 40ng/mL T3. Differentiation permissive media is identical to differentiation media except without the addition of T3.

extract_protocol:
OPCs and immature oligodendrocyte cultures were lysed in TRIzol followed by purification and elution of RNA using phenol-chloroform extraction and the RNeasy Mini Kit. Specifically, RNA for defining in vitro OPC and immature oligodendrocyte expression profiles were generated from magnetically sorted OPCs and O1+ oligodendrocytes. For RNA isolated from sgNTC, sgSox6 g1, and sgSox6 g2 OPCs and immature oligodendrocytes, cells were plated into 6-well plates in OPC growth media and differentiation permissive media respectively for 60 hours at which point cells were lysed with TRIzol.
Libraries were prepared following protocols from NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra RNA Library Prep Kit for Illumina. Samples were enriched for mRNA using oligo(dT) beads, which were fragmented randomly and used for cDNA generation and subsequent second-strand synthesis using a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I. cDNA libraries then went through terminal repair, A-base ligation, adapter ligation, size selection, and PCR enrichment.

treatment_protocol: Guides were selected from the Brie library (Doench et al., 2016) including: sgNTC (AAGCCTACTTCACCGGTCGG), sgSox6 g1 (TTGACGGAATGAACTGTACG), and sgSox6 g2 (AGAACACGCTTTGAGAACCT). These were cloned into the linearized CRISPRv2 backbone (Sanjana et al., 2014). Clones were sequence verified by sanger sequencing. 293T cells were then transfected using lenti-X shots following the manufacturer’s protocol. Transfection media was replaced with N2B27 base media after 24 hours. Lentivirus containing N2B27 was then collected after an additional 48 hours days, filtered, supplemented with OPC growth factors PDGFA and FGF2, and added to OPCs at a ratio of 1:2 (v/v) with fresh OPC growth media. The next day, viral media was switched for fresh virus-free OPC growth media for 48 hours. Infected OPCs were then selected for 96 hours in OPC growth media supplemented with a lethal dose of puromycin (500ng/mL). OPCs were allowed to recover in selection free OPC growth media for at least 24 hours prior to being aliquoted and frozen down. For all experiments, infected CRISPR targeting and non-targeting control OPCs were derived from the same original batch of EpiSC-derived mouse OPCs. qPCR was performed to validate a reduction of gene targets for each batch of CRISPR KO OPCs generated.

value: epiblast stem cell derived OLs


title: Nannochloropsis, mutant M2, rep3

description:
17635_3
0.09 Gb

value: Nannochloropsis oceanica


title: Differentiation day0

value: Embryonic stem cell

value: day 0


title: SOX6_OL_sg2KO_rep2


title: Nannochloropsis, mutant M2, rep2

description:
17635_2
4.58 Gb

value: high light, 7 days


title: SOX6_OL_sg2KO_rep1


title: E3assem_scRNAseq

description: 10x Genomics

data_processing:
The gene counting were made using the Cell Ranger software (v6.0.1).
Assembly: GRCh38
Supplementary files format and content: Tab-separated valued files and matrix files

source_name: Brain organoids+microglia

growth_protocol: DIV 100 brain organoids and DIV 35 microglial cells were used

extract_protocol:
Cultured assembloides were dissociated with Adult Brain Dissociation Kit (Miltenyi) with manufacturer's protocol (37C_ABDK_02). Dissociated cells were stained with Fixable Viability Dye eFluorTM 700 (BD) for 30min, 4C for FACS sorting. FACS sorted cells were suspended with 0.04% BSA/PBS solution.
Libraries were generated with the manufacter's instructions (single cell 3' v3.1 protocol, 10x Genomics).

treatment_protocol: APOE3 and APOE4 Microglial cells were treated to APOE3 brain organoids to make brain assembloids

tag: sample type

value: iPSC-derived brain assembloids

value: Brain organoids+microglia

value: APOE3 brain organoids + APOE3 microglia


title: E4assem_scRNAseq

description: 10x Genomics

tag: genotype

value: APOE3 brain organoids + APOE4 microglia


title: Nannochloropsis, mutant M2, rep1

description:
17635_1
9.14 Gb


title: Nannochloropsis, mutant M3, rep2

description:
17611_2
4.03 Gb


title: Pl-EOH4-lame4

type: RNA

city: Rouen

first: Anthony

last: Falluel-Morel

address: 22 Boulevard Gambetta

country: France

institute: Rouen University

description: Gene expression after 5 days of Ethanol treatment in mice placenta

hyb_protocol: 100 ng of Cy3-labelled cRNA was  hybridized to Agilent Whole Mouse Genome Oligo 4_44K Microarray (G2519F-014868, Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid:026655_D_F_20121126) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Placenta, Ethanol, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: RNA was extracted using the NucleoSpin® RNA plus (Macherey-Nagel, Hoerdt, France) following the manufacturer's recommendations.  The quality and quantity of isolated mRNAs were assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA  , USA) and the Nanodrop device (Thermo Scientific, Wilmington, DE  , USA). Pooled samples for microarray study were created with 5 µg of RNA extracted from five control placentas or cerebral cortices and five alcohol-exposed placentas or cere-bral cortices at GD20. Matching between a given placenta and its associated fetal cortex was systematically respected. The experimental design of a typical experiment was as follows: 1 pool of 5 control placentas, 1 pool of 5 matching control cerebral cortices, 1 pool of 5 alcohol-exposed placentas and 1 pool of 5 matching alcohol-exposed cerebral cortices. This design was replicated in four independent experiments.

value: NMRI

value: Placenta

value: Embryonnic day 20


title: Nannochloropsis, mutant M1, rep3

description:
17632_3
3.37 Gb


title: SOX6_OL_sg1KO_rep2

description:
20200510.NTCvsSox6KO.DPcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DPabundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.results.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.nofilter.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200405_EpiSC5_DP_NTCvsS6g1vsS6g2_counts.csv
20200405_EpiSC5_DP_NTCvsS6g1vsS6g2_abundance.csv
20200405_DP_NTCvsS6g1vsS6g2_DESEQ.csv
20200405_DP_NTCvsS6g1_DESEQ.csv


title: dC-dT3

first: Xiaonan

last: Guan

state: NY

address: 1150 St Nicholas Ave, 403

institute: Russ Berrie Medical Science Pavillion

description: dCas9-dTet1 with sgRNA3 edited hESCs, rep3

data_processing:
Adaptor sequences and low-quality reads were removed by Trim Galore.
Using Bismark, the high-quality reads were mapped to human GRCh38 version genome.
The methylation level in overlapped peak regions were called by methylpy.
Assembly: human GRCh38 version genome
Supplementary files format and content: tab-delimited text files including the mean DNA methylation level of each peaks

source_name: hESC

extract_protocol:
29-R hESCs expressing dCas9-Tet1 or dCas9-dead Tet1 with MECP2 target sgRNA-3 were used to extract genomic DNA and subject to sequencing library preparation according to the instructions by Pico Methyl-Seq Library Prep Kit
Pico Methyl-Seq™ Library Prep Kit was used

tag: cell line

value: hESC

value: human embryonic stem cells

value: Dox


title: Pl-EOH1-lame1

source_name: Placenta, Ethanol, replicate 1


title: dC-T3

description: dCas9-Tet1 with sgRNA3 edited hESCs,rep3

tag: cell type


title: Pl-EOH3-lame3

source_name: Placenta, Ethanol, replicate 3


title: Pl-EOH2-lame2

source_name: Placenta, Ethanol, replicate 2


title: Pl-CT3-lame3

description: Gene expression after 5 days of NaCl treatment in mice placenta

source_name: Placenta, Control, replicate 3


title: Nannochloropsis, mutant M1, rep2

description:
17632_2
0.89 Gb


title: nontargeting_OL_control_rep3

source_name: oligodendrocytes (OLs)


title: Pl-CT4-lame4

source_name: Placenta, Control, replicate 4


title: Nannochloropsis, mutant M1, rep1

description:
17632_1
2.36 Gb


title: Nannochloropsis, wild-type, rep3

description:
176_wt3
4.97 Gb

value: WT


title: Nannochloropsis, mutant M3, rep3

description:
17611_3
5.46 Gb


title: dC-T2

description: dCas9-Tet1 with sgRNA3 edited hESCs,rep2


title: nontargeting_OL_control_rep2


title: dC-dT1

description: dCas9-dTet1 with sgRNA3 edited hESCs, rep1


title: nontargeting_OL_control_rep1


title: Pl-CT2-lame2

source_name: Placenta, Control, replicate 2


title: Nannochloropsis, wild-type, rep2

description:
176_wt2
8.32 Gb


title: Cor-EOH3-lame3

description: Gene expression after 5 days of Ethanol treatment in mice cortex

source_name: Cortex, Ethanol, replicate 3

value: Cortex


title: Cor-EOH4-lame4

source_name: Cortex, Ethanol, replicate 4


title: SOX6_OPC_sg2KO_rep3

description:
OPC_EpiSC5_Sox6KO_abundance_RNAseq.csv
OPC_EpiSC5_Sox6KO_counts_RNAseq.csv
EpiSC5_OPC_NTCvsS6g1vsS6g2_DESEQ_all.csv
EpiSC5_OPC_NTCvsS6g2_DESEQ_all.csv
20200510.NTCvsSox6KO.OPC.abundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.counts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.results.g1andg2.mm10.csv

source_name: oligodendrocyte progenitor cells (OPCs)

value: epiblast stem cell derived OPCs


title: Cor-EOH2-lame2

source_name: Cortex, Ethanol, replicate 2


title: dC-C-scramble-3

description: dCpf1-CTCF with scramble RNA, rep3

data_processing:
Using hisat2, the high-quality reads were mapped to hg19 version genome
The read counts were obtained using featureCounts
Reads were normalized with DESeq2
Assembly: hg19
Supplementary files format and content: tab-delimited text file including normalized reads counts

growth_protocol: HEK293T cells were maintained in DMEM supplemented with 10% Cosmic Calf Serum (CCS), L-glutamine, non-essential amino acid and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol and Direct-zol RNA Miniprep kit (Zymo research).  ug of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra II RNA Library Prep by Illumina

treatment_protocol: Cells are transfected with corresponding plasmids. Dox was used to induce the expression for 48 hrs

value: Human Embryonic Kidney cells

value: Transfection + dox induce

tag: time

value: 48 hr


title: dC-T1

description: dCas9-Tet1 with sgRNA3 edited hESCs,rep1


title: dC-C-scramble-2

description: dCpf1-CTCF with scramble RNA, rep2


title: SOX6_OPC_sg2KO_rep2


title: SOX6_OPC_sg2KO_rep1


title: dC-C-scramble-1

description: dCpf1-CTCF with scramble RNA, rep1


title: Pl-CT1-lame1

source_name: Placenta, Control, replicate 1


title: Ptab0_2

city: Tucson

first: David

last: Baltrus

state: AZ

address: 1140 E. South Campus Drive

institute: University of Arizona

description: featureCounts_mapped_results_Ptab_4DE.txt

data_processing:
Alignment: HISAT2 v2.2.1 (plant) or bowtie2 v (bacterial)
Quantification: StringTie v2.2.0 (plant) or featureCounts (bacterial)
Expression Analysis: DESeq2
Assembly: N. benthamiana Genome v1.0.1 with NbD transcriptome, P. syringae B728a (Genbank: CP000075.1), and P. amygdali pv. tabaci (Genbank: NZ_CP042804.1 and NZ_CP042805.1).
Supplementary files format and content: Output from StringTie (plant) or featureCounts (bacterial)

organism: Pseudomonas amygdali pv. tabaci

source_name: bacterial cells

extract_protocol:
Frozen samples were homogenized in 2mL homogenization tubes with high-density zirconium beads (Glen Mills) using a Geno/Grinder (SPEX SamplePrep) for 1 min at 1,750 Hz with a LN2 chilled sample holder. RNA was extracted using the DirectZol RNA miniprep kit (Zymo Research). RNA samples were DNAse treated with the Turbo DNAse (Thermo-Fisher) followed by cleanup with the Monarch RNA Cleanup Kit (NEB). Reagents were used according to the manufacturer’s recommendations.
Plant mRNA sequencing libraries were prepared with the Illumina-compatible KAPA Stranded mRNA-seq Kit (Roche) by the Georgia Genomics and Bioinformatics Core (GGBC). The Psy RNA samples were rRNA depleted using the RiboMinus Bacterial kit (Thermo Fisher) and  libraries were prepared with the Illumina-compatible KAPA Stranded RNA-seq Kit (Roche) by the GGBC. The Pta RNA samples were rRNA depleted using both RiboZero Plant and RiboZero Bacteria (Illumina)  in combination and RNA sequencing libraries were prepared in-house using the TruSeq Stranded Total RNA kit (Illumina). Library prep kits were used according to the manufacturer’s recommendations.

tag: tissue/sample type

value: bacterial cells


title: Cor-EOH1-lame1

source_name: Cortex, Ethanol, replicate 1


title: Cor-CT4-lame4

description: Gene expression after 5 days of NaCl treatment in mice cortex

source_name: Cortex, Control, replicate 4


title: SOX6_OPC_sg1KO_rep2

description:
OPC_EpiSC5_Sox6KO_abundance_RNAseq.csv
OPC_EpiSC5_Sox6KO_counts_RNAseq.csv
EpiSC5_OPC_NTCvsS6g1_DESEQ_all.csv
20200510.NTCvsSox6KO.OPC.abundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.counts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.results.g1andg2.mm10.csv


title: Index_16.E-09

city: Sherbrooke

first: Sophie

last: Roux

state: Quebec

address: 3001, 12th avenue N

department: Division of Rheumatology

institute: Université de Sherbrooke

description: cDNA library generated with RNA-seq

data_processing:
Trimming of paired-end reads was performed using Trimmomatic v0.36 (parameters: ILLUMINACLIP:<fastaWithAdaptersEtc>:2:30:10) in order to remove adapters and low-quality reads.
FastQC v0.11.8 was used before and after trimming to assess the quality of the reads.
Alignment of reads to the reference human genome hg38 (v98) was performed using STAR v2.5.3a (parameters: --outFilterScoreMinOverLread = 0.3  --outFilterMatchNminOverLread = 0.4). The index needed to align reads was generated using STAR v2.5.3a, the reference human genome hg38 (v87) and the annotation file was taken from ENSEMBL (v98) and supplemented with missing miRNA information from mirbase.
Raw count gene expressions were obtained using CoCo v0.2.2.
Assembly: hg38.98
Supplementary files format and content: Tabular-separated value (.tsv) file containing the raw count values of each sample for all the genes detected in the RNA-Seq.

source_name: cell culture (blood)

extract_protocol:
Total RNA was extracted at the end of the cultures by lysing the cells in Qiazol (Qiagen) and stored at -80°C until the experiment. The miRNeasy Micro Kit 217084 was used for RNA extraction.
The library was performed using NEBNext small RNA libraries E7330 protocol.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were differentiated into osteoclasts in 3-week in-vitro cultures in the presence of M-CSF and RANKL.

value: cell culture (blood)

tag: condition

value: erosive rheumatoid arthritis (RA)

tag: Sex

value: male

tag: age


title: dC-C-MeCP2-3

description: dCpf1-CTCF with crRNA targting MECP2, rep3


title: Ptab5_3

source_name: leaf intercellular wash fluid

value: leaf intercellular wash fluid


title: Nannochloropsis, wild-type, rep1

description:
176_wt1
1.71 Gb

source_name: Nannochloropsis oceanica

value: Nannochloropsis oceanica

value: high light, 7 days


title: Index_15.E-08

description: cDNA library generated with RNA-seq

value: female


title: Ptab0_3


title: dC-C-MeCP2-2

description: dCpf1-CTCF with crRNA targting MECP2, rep2


title: Cor-CT3-lame3

source_name: Cortex, Control, replicate 3

value: NMRI

value: Embryonnic day 20


title: dC-dT2

description: dCas9-dTet1 with sgRNA3 edited hESCs, rep2

source_name: hESC

value: hESC

value: human embryonic stem cells

value: Dox


title: Index_14.E-07

description: cDNA library generated with RNA-seq


title: Index_14.E-04

description: cDNA library generated with RNA-seq


title: Mock-3

description: Mock, rep3

value: WT


title: nontargeting_OPC_control_rep2

description:
EpiSC5_OPC_NTCvsS6g1_DESEQ_all.csv
EpiSC5_OPC_NTCvsS6g1vsS6g2_DESEQ_all.csv
EpiSC5_OPC_NTCvsS6g2_DESEQ_all.csv
20200510.NTCvsSox6KO.OPC.abundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.counts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.results.g1andg2.mm10.csv

value: epiblast stem cell derived OPCs


title: nontargeting_OPC_control_rep1


title: SOX6_OL_sg1KO_rep3

value: epiblast stem cell derived OLs


title: Index_13.E-06

description: cDNA library generated with RNA-seq


title: Ptab0_1


title: Cor-CT1-lame1

source_name: Cortex, Control, replicate 1

value: Cortex


title: Index_12.E-05

description: cDNA library generated with RNA-seq


title: Mock-1

description: Mock, rep1

value: Human Embryonic Kidney cells

value: Transfection + dox induce

value: 48 hr


title: pdac_44_after

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus University Medical Center

hyb_protocol: For each sample, a total of 200 ng RNA, in a maximum volume of 7 μL, was subjected to hybridization with the two panels for a duration of 17 h at 65 °C, following the protocol provided by the manufacturer (NanoString Technologies Inc., Seattle, WA, USA).

scan_protocol: The nCounter® FLEX platform was utilized to wash away the unbound probes and to count the genes by scanning 490 fields of view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

source_name: pancreatic ductal adenocarcinoma, blood

extract_protocol: The whole-blood samples intended for targeted gene expression analysis were collected in Tempus tubes (Applied Biosystems, Foster City, CA, USA) and subsequently stored at −80 °C. Tempus tubes are designed to contain an RNA-stabilizing reagent, which effectively preserves RNA quality, enabling the measurement of gene expression profiles without the need to isolate peripheral blood mononuclear cells. To extract total RNA from the blood in Tempus tubes, a Tempus Spin RNA Isolation Kit from Thermo Fisher Scientific (Waltham, MA, USA) was employed, following the manufac-turer’s instructions. Subsequently, RNA quality was assessed using an Agilent 2100 Bi-oAnalyzer (Santa Clara, CA, USA). Samples with RNA concentrations below 35 mg/mL were excluded from further analysis. Corrected RNA concentrations were calculated based on the percentage of fragments within the 300–4000 nucleotide range to account for RNA degradation. An nCounter® PanCancer Immune Profiling (IP) Panel and nCounter® Myeloid Innate Immunity (MII) Panel, each consisting of 730 genes and 40 housekeeping genes, were used for NanoString targeted gene expression analysis of the 88 whole-blood samples

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: gender

value: Male

tag: smoking status

value: Former

tag: alcohol status

value: Current

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

tag: disease stage

value: (borderline) Resectable

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Disease control

tag: overall survival


title: OL_sorted_rep3

source_name: oligodendrocytes (OLs)

tag: cell type


title: pdac_44_before

tag: tissue


title: Ptab5_2

tag: strain

tag: tissue/sample type

value: leaf intercellular wash fluid


title: OL_sorted_rep2


title: dC-C-scramble-Cpf1

description: dCpf1-CTCF with scramble RNA,  anti-Cpf1 IP

data_processing:
High-quality reads were mapped to human hg19 version genome using Bowtie2 with default parameters.
Duplicated reads were removed by Picard (https://broadinstitute.github.io/picard/).
MACS2 was used for peak calling.  For each sample, its own input was used as a control, and q value (adjusted P value for the False Discovery Rate) for peak detection was set as 10-10.
After removed the overlapped peaks with its own mock control, the overlapping peaks between anti-CTCF and anti-Cpf1 ChIP-seq were defined as binding sites for dCpf1-CTCF with MECP2 crRNAs.
Assembly: hg19
Supplementary files format and content: narrowPeak (except for Input sample)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB #E7645). 200 ng of DNA was used as starting material for input and 4-60 ng for ip samples.  length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

value: Human embryonic kidney

tag: chip antibody


title: Ptab5_1


title: Index_11.E-02

description: cDNA library generated with RNA-seq

value: cell culture (blood)

tag: condition

value: erosive rheumatoid arthritis (RA)

tag: Sex

value: female

tag: age


title: Index_10.E-01

description: cDNA library generated with RNA-seq

value: male


title: OL_sorted_rep1

value: epiblast stem cell derived OLs


title: dC-C-MeCP2-1

description: dCpf1-CTCF with crRNA targting MECP2, rep1

value: Human Embryonic Kidney cells

tag: genotype

value: WT

tag: treatment

tag: time


title: pdac_43_after

tag: patient diagnosis

tag: gender

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)


title: OPC_sorted_rep3

tag: cell type

value: epiblast stem cell derived OPCs


title: OPC_sorted_rep2


title: pdac_43_before

tag: tissue

value: blood

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: pdac_42_after

value: Pancreatic Ductal Adenocarcinoma

tag: age

value: Never


title: dC-C-scramble-CTCF

description: dCpf1-CTCF with scramble RNA,  anti-CTCF IP

tag: cell line

tag: chip antibody

value: CTCF (Abcam, #ab128873)


title: Mock-Cpf1

description: Mock, anti-Cpf1 IP


title: pdac_42_before

tag: patient diagnosis

tag: gender

value: Male

tag: smoking status

value: Former


title: Mock-2

description: Mock, rep2

tag: genotype

tag: treatment

value: Transfection + dox induce

tag: time

value: 48 hr


title: pdac_41_after

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

value: (borderline) Resectable

value: No CT-scan evaluation


title: Index_9.NE-07

description: cDNA library generated with RNA-seq

tag: tissue

value: cell culture (blood)

tag: condition

value: no erosive rheumatoid arthritis (RA)

tag: Sex


title: Index_10.NE-08

description: cDNA library generated with RNA-seq

value: female

tag: age


title: Mock-CTCF

description: Mock, anti-CTCF IP

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: chip antibody


title: OPC_sorted_rep1


title: dC-C-MECP2-CTCF

description: dCpf1-CTCF with crRNA targting MECP2,  anti-CTCF IP


title: WT_D1_4

city: Buffalo

first: Scott

last: Olejniczak

address: Elm and Carlton, CGP Rm. L5 306

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Illumina bcl2fastq 2.20 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences.
Quality control for the raw reads was performed with fastqc. STAR aligner was used to create a genome index and BAM files from paired end reads using Genome Reference Consortium Build 38 (mm10). Count matrices were generated using RSEM. Normalization and differential gene expression (DGE) analysis was performed in R using the limma R package. Alternative pre-mRNA splicing changes were detected using the Percent Spliced-In (PSI)-Sigma method. Only genes with average expression across all samples > 10 counts per million (CPM), calculated differential expression changes >/< ± 1 log fold change as compared to WT D0, and adjusted p values < 0.05 were used for DGE. Unique identifiers for splice sites were created by concatenating event region and target exon parameters. Splicing scores were created as the product of the change in PSI and the average CPM. Genes were segregated as up or downregulated depending on whether scores were > or < 0, respectively. Venn diagrams were generated using in-house R scripts and the R package VennDiagram.
Genome_build: Grcm38 (mm10)
Supplementary_files_format_and_content: Matrix table with raw gene counts and all samples

source_name: Spleenic pan T cells

growth_protocol: Cells were isolated via negative selection and cultured in RPMI-1640 supplemented with 10% FBS (Corning) and 10U/ml pen/strep, 2mM L-glutamine, 50μM β-mercaptoethanol and 10mM HEPES (Gibco) at 37°C in a humidified incubator containing 5% CO2

extract_protocol:
Total RNA was isolated from harvested cells using Trizol (Qiagen) using the miRNeasy Mini Kit (Qiagen) according to manufacturer's instructions. Quantity of RNA was evaluated using a Qubit 3.0 fluorometer and QC was performed using TapeStation Analysis Software A.02.02
The sequencing libraries are prepared with the RNA HyperPrep Kit with RiboErase (HMR)kit (Roche Sequencing Solutions), from 100ng total RNA.  Following manufacturer’s instructions, the first step depletes rRNA from total RNA.  After ribosomal depletion, the remaining RNA is DNase digested to remove any gDNA contamination. Samples are then purified, fragmented and primed for cDNA synthesis.  Fragmented RNA is then reverse transcribed into first strand cDNA using random primers.  The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA.  Pure Beads (KAPA BIOSYSTEMS) are used to separate the ds cDNA from the second strand reaction mix resulting in blunt-ended cDNA.  A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments.  Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, are ligated to the ends of the ds cDNA, preparing them for hybridization onto a flow cell.   Adapter ligated libraries are amplified by PCR, purified using Pure Beads, and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.).   The DNA libraries are quantitated using KAPA Biosystems qPCR kit, and are pooled together in an equimolar fashion, following experimental design criteria.  Each pool is denatured and diluted to 350pM with 1% PhiX control library added.  The resulting pool is then loaded into the 200 cycle NovaSeq Reagent cartridge for 100 paired end sequencing, and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: Purified T cells were stimulated with αCD3/αCD28/rIL-2 for 24 or 72 hours

tag: strain

value: 6-12 weeks

tag: day


title: Index_8.NE-06

description: cDNA library generated with RNA-seq

value: male


title: Index_9.NE-04

description: cDNA library generated with RNA-seq


title: dC-C-scramble-Input

description: dCpf1-CTCF with scramble RNA , input


title: pdac_40_after

tag: patient diagnosis

tag: gender

tag: smoking status

value: Current

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Disease control

tag: overall survival


title: DKI_D3_3

tag: genotype

value: DKI


title: Index_11.NE-10

description: cDNA library generated with RNA-seq

tag: tissue

tag: condition


title: Cor-CT2-lame2

source_name: Cortex, Control, replicate 2

value: NMRI

value: Cortex

tag: developmental stage

value: Embryonnic day 20


title: dC-C-MECP2-Cpf1

description: dCpf1-CTCF with crRNA targting MECP2,  anti-Cpf1 IP

tag: cell line


title: pdac_41_before

value: blood

value: Pancreatic Ductal Adenocarcinoma

tag: age

value: Male

value: Never

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)


title: pdac_40_before

tag: patient diagnosis

tag: gender

tag: smoking status

value: Former

tag: baseline crp (mg/l)

value: (borderline) Resectable


title: dC-C-MECP2-Input

description: dCpf1-CTCF with crRNA targting MECP2, input

tag: cell type

tag: chip antibody


title: DKI_D3_2

tag: strain

tag: genotype

tag: day


title: Index_7.NE-02

description: cDNA library generated with RNA-seq

tag: tissue

value: cell culture (blood)

tag: condition

value: no erosive rheumatoid arthritis (RA)

tag: Sex


title: Index_8.NE-03

description: cDNA library generated with RNA-seq

value: female

tag: age


title: Mock-Input

description: Mock, input

tag: cell line

value: Human embryonic kidney


title: pdac_39_after

value: Female

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: No CT-scan evaluation

tag: overall survival


title: Index_5.NE-01

description: cDNA library generated with RNA-seq

value: male


title: DKI_D3_1

value: 6-12 weeks

value: DKI


title: pdac_39_before

tag: patient diagnosis

tag: gender

tag: smoking status

value: Current

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)


title: WT_D3_4

tag: strain

tag: genotype

value: WT

tag: day


title: Human ILC2s, sh-ANXA1, Day 6 [PR1861_06]

city: Tokyo

first: Hiroki

last: Kabata

address: 35 Shinanomachi, Shinjyuku-ku

country: Japan

institute: Keio University School of Medicine

data_processing:
bcl2fastq2 (v2.20) software used for basecalling.
Sequenced reads were mapped to hg38 whole genome using DRAGEN Bio-IT Platform (v3.5.7).
Transcripts per million (TPM) were calculated using DRAGEN Bio-IT Platform (v3.5.7).
Assembly: hg38
Supplementary files format and content: TPM values for each Sample

source_name: Peripheral blood-derived ILC2s

extract_protocol:
RNA was isolated from ILC2s using the RNeasy mini kit (Qiagen).
cDNA libraries were synthesized using SMART-Seq v4 Ultra Low Input RNA Kits (Takara Bio).The amplified cDNA was fragmented and linked with dual-indexed barcodes using Illumina Nextera XT DNA Library Prep Kits, according to the manufacturer’s instructions

tag: tissue

value: Peripheral blood-derived ILC2s

tag: cell line

value: Primary

tag: cell type

value: Lymphoid cells

value: Wild-type

tag: treatment

value: transduced with shRNA for ANXA1


title: Human ILC2s, sh-ANXA1, Day 6 [PR1861_05]


title: DKI_D1_3

tag: age


title: RPI48.RL_93-HSApos-6d [miRNA-seq]

city: Montreal

first: Eric

middle: A

last: Cohen

address: 110 Ave des Pins Ouest

institute: IRCM

data_processing:
Basecalls performed using CASAVA version 1.8
Adaptor sequences and poor quality bases were trimmed with Cutadapt
Alignment of reads was performed using miRDeep2 (mapper.pl) on the hg19 human genome
Quantification of individual microRNAs were performed using miRDeep2
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: hg19
Supplementary_files_format_and_content: normalized count, Diff files with differential expression

source_name: Human monocyte-derived macrophages

extract_protocol:
Samples were resuspended in QIAzol lysis buffer and total RNA isolated from sorted cell populations using the miRNeasy kit from QIAGEN
Illumina TruSeq Small RNA system; sequencing using PE50 on a HiSeq 2000 sequencer (Illumina technologies)

tag: donor

tag: hiv infection

value: 6 days

tag: hsa+ or hsa-

value: HSA+

value: Human monocyte-derived macrophages


title: RPI47.RL_93-HSAneg-6d [miRNA-seq]

value: HSA-


title: Human ILC2s, sh-ANXA1, Day 6 [PR1861_04]


title: pdac_38_after

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

value: Male

tag: alcohol status

value: Former

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: disease stage

value: (borderline) Resectable

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Progressive disease

tag: overall survival


title: DKI_D1_1

tag: strain

value: 6-12 weeks

tag: genotype

value: DKI

tag: day


title: RPI46.RL_93-mock-6d [miRNA-seq]

value: 6 days (MK)

value: Not infected

tag: cell type


title: Human ILC2s, sh-Control, Day 6 [PR1861_03]

tag: tissue

value: Peripheral blood-derived ILC2s

tag: cell line

value: Primary

value: Lymphoid cells

tag: treatment

value: transduced with shRNA for shRNA control


title: pdac_38_before

tag: age

tag: gender

tag: smoking status

value: Current

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)


title: RPI45.RL_93-HSApos-36hr [miRNA-seq]

tag: donor

tag: hiv infection

value: 36 hrs

tag: hsa+ or hsa-

value: HSA+

value: Human monocyte-derived macrophages


title: WT_D0_2

value: WT


title: pdac_37_after

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

value: Female

tag: alcohol status

value: Never

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Disease control

tag: overall survival


title: Human ILC2s, sh-Control, Day 6 [PR1861_02]

tag: tissue

tag: cell line

tag: cell type

tag: genotype

value: Wild-type

tag: treatment


title: WT_D0_1

tag: strain

tag: age

value: 6-12 weeks

tag: day


title: pdac_37_before

tag: patient diagnosis

tag: gender

tag: smoking status

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

value: (borderline) Resectable


title: RPI44.RL_93-HSAneg-36hr [miRNA-seq]

tag: donor

tag: hiv infection

tag: hsa+ or hsa-

value: HSA-


title: Human ILC2s, sh-Control, Day 6 [PR1861_01]

tag: tissue

value: Peripheral blood-derived ILC2s

value: Primary


title: SOX6_OL_sg1KO_rep1

city: Cleveland

first: Paul

last: Tesar

address: 10900 Euclid Ave.

institute: Case Western Reserve University

description:
20200510.NTCvsSox6KO.DPcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DPabundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.results.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.nofilter.g1andg2.mm10.csv
20200510.NTCvsSox6KO.DP.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200405_EpiSC5_DP_NTCvsS6g1vsS6g2_counts.csv
20200405_EpiSC5_DP_NTCvsS6g1vsS6g2_abundance.csv
20200405_DP_NTCvsS6g1vsS6g2_DESEQ.csv
20200405_DP_NTCvsS6g1_DESEQ.csv

value: epiblast stem cell derived OLs


title: WT_D3_1


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_ER l (Sample 52)

city: Durham

first: Christopher

middle: Vincent

last: Nicchitta

state: NC

department: Department of Cell Biology

institute: Duke University School of Medicine

description:
Sample 52
Biological replicate for Sample 16

data_processing:
Run Type: 51PE, Application Name: Ilumina NovaSeq 6000 Control Software, Application Version 1.6.0, RTA Version 3.4.4, Flow Cell: NovaSeq 6000 S-Prime
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RNAseq reads were analyzed using Kallisto. A Kallisto index was built from all RefSeq genes (https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/ on 04.06.2018).  Illumina read files were mapped to the RefSeq index at default settings (single end mapping; parameters of -1 300 -s20). Mapped reads were transformed to transcript per million (TPM), including only annotated mRNAs (NM prefix) and using total transcript length (5’UTR, CDS, 3’UTR) and summed to generate a TPM/gene metric.
Genome_build: https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/
Supplementary_files_format_and_content: RNA-Seq Analysis_rawTPM_Total.xlsx (Excel file include TPM values for each sample and experimental condition)

source_name: HeLa cells

growth_protocol: HeLa cell cultures were maintained in DMEM, 10% FCS, 5% CO2, and all experiments conducted with cultures at 70-80% confluence

extract_protocol:
HeLa cell fractions were extracted in guanidinium thiocyanate-phenol-chloroform and total RNA was isolated.
Following  oligo-dT selection for poly(A) mRNA, mRNAs was processed for deep sequencing library construction using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, E7770).  NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, E7490) was used for poly(A) selection. NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 and Set 2) adapter/primers were used to enable multiplexing.

treatment_protocol: Parental HeLa/Cas9 cells (non-trasnsfected), parental HeLa/Cas9 cells transfected with a non-targeting siRNA, parental,HeLa/Cas9 cells transfected with siRNA targeting SRPRA, HeLa/Cas9 SRB knockout cells (non-transfected), HeLa/Cas9 SRB knockout cells transfected with a non-targeting siRNA, and HeLa/Cas9 SRB knockout cells transfected with siRNA targeting SRPRA, were cultured for 96 hrs in DMEM, 10% FCS, 5% CO2 and at the 96 hour time point fractionated by sequential detergent treatments to yield cytosol and ER fractions.

tag: cell line

value: HeLa

tag: fraction

value: endoplasmic reticulum RNA fraction

value: Cas9 SRB KO cells, transfected with a non-targeting siRNA


title: pdac_36_before

value: Male

value: Current

tag: alcohol status

value: Former

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: pdac_36_after

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: age

tag: gender

tag: smoking status

tag: baseline nlr


title: RPI42.RL_89-HSApos-6d [miRNA-seq]

tag: donor

tag: hiv infection

value: 6 days

tag: hsa+ or hsa-

value: HSA+

tag: cell type

value: Human monocyte-derived macrophages


title: RPI43.RL_93-mock-36hr [miRNA-seq]

value: 36 hrs (MK)

value: Not infected


title: WT_D1_1

tag: strain

value: 6-12 weeks

tag: genotype

value: WT

tag: day


title: DKI_D1_2

value: DKI


title: HeLa Cas9 WT non-targeting siRNA_ER l (Sample 51)

description:
Sample 51
Biological replicate for Sample 15

tag: cell line

tag: fraction

tag: treatment

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: RPI41.RL_89-HSAneg-6d [miRNA-seq]

value: HSA-


title: CD28_KO_D3_2


title: HeLa Cas9 SRB-3-12 untransfected_ER l (Sample 50)

description:
Sample 50
Biological replicate for Sample 14

value: HeLa

value: endoplasmic reticulum RNA fraction

value: parental HeLa Cas9 SRB KO cells, untransfected


title: RPI40.RL_89-mock-6d [miRNA-seq]

value: 6 days (MK)


title: pdac_35_after

tag: tissue

value: Female

value: Never

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

tag: disease stage

value: (borderline) Resectable

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Disease control


title: pdac_34_after

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: age

tag: gender

tag: smoking status

value: Current

tag: baseline nlr

tag: overall survival


title: HeLa Cas9 WT untransfected_ER l (Sample 49)

description:
Sample 49
Biological replicate for Sample 13

tag: cell line

tag: fraction

tag: treatment

value: parental HeLa Cas9 cells, untransfected


title: RPI39.RL_89-HSApos-36hr [miRNA-seq]

tag: donor

tag: hiv infection

value: 36 hrs

tag: hsa+ or hsa-

value: HSA+

tag: cell type

value: Human monocyte-derived macrophages


title: pdac_35_before

tag: tissue

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)


title: HeLa Cas9 SRB-3-12 SRa_siRNA_Cyt l (Sample 48)

description:
Sample 48
Biological replicate for Sample 12

value: cytosol RNA fraction

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: CD28_KO_D1_2

tag: strain

tag: age

value: 6-12 weeks

tag: genotype

tag: day


title: HeLa Cas9 WT SRa_siRNA_Cyt l (Sample 47)

description:
Sample 47
Biological replicate for Sample 11

tag: cell line

value: HeLa

tag: fraction

value: parental Cas9  cells, transfected with SRA targeting siRNA


title: CD28_KO_D1_1


title: pdac_34_before

tag: patient diagnosis

tag: gender

tag: smoking status

tag: baseline nlr

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: CD28_Y170F_D3_3


title: CD28_KO_D3_3


title: CD28_Y170F_D1_3


title: RPI37.RL_89-mock-36hr [miRNA-seq]

tag: donor

tag: hiv infection

value: 36 hrs (MK)

tag: hsa+ or hsa-

value: Not infected

tag: cell type


title: RPI36.RL_84-HSApos-6d [miRNA-seq]

value: 6 days


title: CD28_Y170F_D3_2

tag: strain

tag: age


title: HeLa Cas9 WT non-targeting siRNA_Cyt l (Sample 45)

description:
Sample 45
Biological replicate for Sample 9

tag: treatment

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: pdac_32_after

tag: tissue

value: Female

tag: alcohol status

value: Former

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

value: (borderline) Resectable

value: Disease control


title: RPI35.RL_84-HSAneg-6d [miRNA-seq]

value: HSA-


title: RPI34.RL_84-mock-6d [miRNA-seq]

value: 6 days (MK)


title: pdac_32_before

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: gender

tag: smoking status

value: Current

tag: baseline nlr

tag: disease stage

tag: total cycles of folfirinox


title: CD28_Y170F_D1_2

tag: genotype

tag: day


title: HeLa Cas9 SRB-3-12 untransfected_Cyt l (Sample 44)

description:
Sample 44
Biological replicate for Sample 8

tag: cell line

tag: fraction

value: cytosol RNA fraction

value: Total cytosolic RNA from HeLa Cas9 SRB KO cells, untransfected


title: HeLa Cas9 SRB-3-12 SRa_siRNA_total l (Sample 42)

description:
Sample 42
Biological replicate for Sample 6

value: HeLa

value: total RNA fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: RPI38.RL_89-HSAneg-36hr [miRNA-seq]

tag: donor

tag: hiv infection

value: 36 hrs

tag: hsa+ or hsa-

tag: cell type

value: Human monocyte-derived macrophages


title: HeLa Cas9 WT untransfected_Cyt l (Sample 43)

description:
Sample 43
Biological replicate for Sample 7

value: parental HeLa Cas9 cells, untransfected


title: CD28_Y170F_D3_1

tag: strain

tag: age

value: 6-12 weeks


title: CD28_Y170F_D1_1


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_Cyt l (Sample 46)

description:
Sample 46
Biological replicate for Sample 10

value: Cas9 SRB KO cells, transfected with a non-targeting siRNA


title: HeLa Cas9 WT SRa_siRNA_total l (Sample 41)

description:
Sample 41
Biological replicate for Sample 5

value: parental Cas9  cells, transfected with SRA targeting siRNA


title: RPI33.RL_84-HSApos-36hr [miRNA-seq]

value: HSA+


title: pdac_31_after

tag: tissue

tag: patient diagnosis

value: Male

value: Never

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline bilirubin (micromol/l)

tag: baseline crp (mg/l)

value: (borderline) Resectable

tag: progression after 4 cycles (recist 1.1)

value: Disease control

tag: overall survival


title: pdac_33_after

value: blood

value: Pancreatic Ductal Adenocarcinoma

tag: gender

value: Female

tag: smoking status

tag: baseline nlr

tag: disease stage

tag: total cycles of folfirinox


title: RPI32.RL_84-HSAneg-36hr [miRNA-seq]

tag: donor

tag: hiv infection

tag: hsa+ or hsa-

value: HSA-

tag: cell type


title: pdac_33_before

tag: tissue

tag: patient diagnosis

tag: age

tag: alcohol status


title: pdac_30_after

value: Current

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline bilirubin (micromol/l)

value: Metastatic disease


title: CD28_AYAA_D3_3

tag: strain

tag: genotype

tag: day


title: RPI31.RL_84-mock-36hr [miRNA-seq]

value: 36 hrs (MK)

value: Not infected


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_total l (Sample 40)

description:
Sample 40
Biological replicate for Sample 4

tag: cell line

value: HeLa

tag: fraction

value: total RNA fraction

tag: treatment


title: RPI30.RL_79-HSApos-6d [miRNA-seq]

tag: donor

tag: hiv infection

value: 6 days

value: Human monocyte-derived macrophages


title: HeLa Cas9 WT non-targeting siRNA_total l (Sample 39)

description:
Sample 39
Biological replicate for Sample 3

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: pdac_31_before

tag: gender

value: Male

tag: smoking status

tag: baseline nlr

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: CD28_AYAA_D1_3

tag: age

value: 6-12 weeks


title: RPI29.RL_79-HSAneg-6d [miRNA-seq]

tag: hsa+ or hsa-

tag: cell type


title: CD28_AYAA_D1_2

tag: strain

tag: genotype

tag: day


title: HeLa Cas9 SRB-3-12 untransfected_total l (Sample 38)

description:
Sample 38
Biological replicate for Sample 2

tag: cell line

tag: fraction

tag: treatment

value: parental HeLa Cas9 SRB KO cells, untransfected


title: CD28_AYAA_D3_2


title: nontargeting_OPC_control_rep3

description:
EpiSC5_OPC_NTCvsS6g1_DESEQ_all.csv
EpiSC5_OPC_NTCvsS6g1vsS6g2_DESEQ_all.csv
EpiSC5_OPC_NTCvsS6g2_DESEQ_all.csv
20200510.NTCvsSox6KO.OPC.abundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.counts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.results.g1andg2.mm10.csv

source_name: oligodendrocyte progenitor cells (OPCs)

value: epiblast stem cell derived OPCs


title: HeLa Cas9 WT untransfected_total l (Sample 37)

description:
Sample 37
Biological replicate for Sample 1

value: parental HeLa Cas9 cells, untransfected


title: RPI28.RL_79-mock-6d [miRNA-seq]

tag: donor

tag: hiv infection

value: 6 days (MK)


title: pdac_29_after

tag: tissue

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: gender

value: Female

tag: smoking status

value: Never

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

value: Disease control


title: RPI27.RL_79-HSApos-36hr [miRNA-seq]

value: 36 hrs

tag: hsa+ or hsa-

value: HSA+

tag: cell type


title: pdac_30_before

tag: age

value: Current

tag: baseline crp (mg/l)

tag: disease stage

value: Metastatic disease

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: CD28_AYAA_D3_1

tag: strain

tag: genotype

tag: day


title: HeLa Cas9 SRB-3-12 SRa_siRNA_ER l (Sample 36)

description:
Sample 36
Biological replicate for Sample 18

tag: cell line

value: HeLa

tag: fraction

value: endoplasmic reticulum RNA fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: RPI26.RL_79-HSAneg-36hr [miRNA-seq]

tag: donor

tag: hiv infection

value: HSA-

value: Human monocyte-derived macrophages


title: HeLa Cas9 WT SRa_siRNA_ER l (Sample 35)

description:
Sample 35
Biological replicate for Sample 17

value: parental Cas9 cells, transfected with SRA targeting siRNA


title: pdac_28_after

tag: tissue

tag: patient diagnosis

tag: gender

value: Male

tag: smoking status

value: Former

tag: alcohol status

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)

value: LAPC


title: Ars2_KO_D3_3

tag: strain

tag: age

value: 6-12 weeks

tag: genotype


title: CD28_AYAA_D1_1

tag: day


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_ER l (Sample 34)

description:
Sample 34
Biological replicate for Sample 16

tag: cell line

tag: fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a non-targeting siRNA


title: SOX6_OPC_sg1KO_rep1

description:
OPC_EpiSC5_Sox6KO_abundance_RNAseq.csv
OPC_EpiSC5_Sox6KO_counts_RNAseq.csv
EpiSC5_OPC_NTCvsS6g1_DESEQ_all.csv
20200510.NTCvsSox6KO.OPC.abundance.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.counts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.filterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.NONfilterednormcounts.g1andg2.mm10.csv
20200510.NTCvsSox6KO.OPC.DESEQ2.results.g1andg2.mm10.csv

tag: cell type

value: epiblast stem cell derived OPCs


title: RPI25.RL_79-mock-36hr [miRNA-seq]

tag: donor

tag: hiv infection

value: 36 hrs (MK)

tag: hsa+ or hsa-

value: Not infected


title: S863 BiSulfite-seq

city: ROCHESTER

first: ZHIFU

last: SUN

state: Minnesota

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Illumina’s RTA version 1.13.48.
RRBS reads were aligned to the hg19 genome assembly using the internal SAAP-RRBS pipeline
RRBS was performed at the Mayo Clinic Genotyping Shared Resource facility as previously described.  Briefly, DNA (250ng) was digested with Msp1 (New England Biolabs, Catalog Number:  R0106M) and purified using Qiaquick Nucleotide Removal Kit (Qiagen, Catalog Number: 28004).  End-repair A tailing was performed (New England Biolabs, Catalog Numbers:  M0212L) and TruSeq methylated indexed adaptors (Illumina, Catalog Number:  15025064) were ligated with T4 DNA ligase (New England Biolabs, Catalog Number: M0202L). Size selection was performed with Agencourt AMPure XP beads (Beckman Coulter, Catalog Number:  A63882). Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research, Catalog Number:  D5001) as recommended by the manufacturer with the exception that incubation was performed using 55 cycles of 95 ̊C for 30 sec and 50°C for 15 min.  Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo C Hotstart DNA Polymerase (Agilent Technologies, Catalog Number: 600414). Library quantification was performed using Qubits dsDNA HS Assay Kit (Life Technologies, Catalog Number:  Q32854) and the Bioanalyzer DNA 1000 Kit (Agilent Technologies, Catalog Number:  5067-1504).
Genome_build: hg19
Supplementary_files_format_and_content: methylation ratio file (text)

source_name: Isolated CD4+ cells

extract_protocol: Resection or mucosal biopsies of the terminal ileum and CD4+ cells were isoloated for RNA-seq and RRBS

tag: Sex

value: F

tag: case control

value: Dis


title: Ars2_KO_D1_3


title: pdac_29_before

tag: tissue

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: gender

value: Female

tag: smoking status

value: Never

tag: alcohol status

value: Current

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline crp (mg/l)

tag: disease stage

value: Metastatic disease

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Disease control

tag: overall survival


title: pdac_28_before

tag: age

value: Male

tag: baseline sii

tag: baseline nlr

tag: baseline bilirubin (micromol/l)


title: pdac_27_after


title: Ars2_KO_D3_2

tag: strain

tag: genotype

tag: day


title: HeLa Cas9 WT non-targeting siRNA_ER l (Sample 33)

description:
Sample 33
Biological replicate for Sample 15

tag: cell line

value: HeLa

tag: fraction

value: endoplasmic reticulum RNA fraction

tag: treatment

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: Ars2_KO_D1_2

value: 6-12 weeks


title: HeLa Cas9 SRB-3-12 untransfected_ER l (Sample 32)

description:
Sample 32
Biological replicate for Sample 14

value: parental HeLa Cas9 SRB KO cells, untransfected


title: pdac_26_before

tag: tissue

tag: patient diagnosis

tag: gender

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

value: LAPC


title: S861 BiSulfite-seq

tag: Sex

tag: case control


title: S862 BiSulfite-seq

tag: age


title: HeLa Cas9 WT untransfected_ER l (Sample 31)

description:
Sample 31
Biological replicate for Sample 13

value: parental HeLa Cas9 cells, untransfected


title: pdac_26_after

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: pdac_25_after

tag: tissue

value: Former

tag: baseline bilirubin (micromol/l)


title: Ars2_KO_D3_1

tag: strain

tag: genotype

tag: day


title: S857 BiSulfite-seq

value: M

value: Dis


title: Ars2_KO_D1_1


title: HeLa Cas9 SRB-3-12 SRa_siRNA_Cyt l (Sample 30)

description:
Sample 30
Biological replicate for Sample 12

tag: cell line

tag: fraction

value: cytosol RNA fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: pdac_27_before

value: blood

tag: patient diagnosis

value: Pancreatic Ductal Adenocarcinoma

tag: age

tag: gender

tag: smoking status

value: Never

tag: alcohol status

tag: baseline ca19-9 (u/ml)


title: HeLa Cas9 WT SRa_siRNA_Cyt l (Sample 29)

description:
Sample 29
Biological replicate for Sample 11

value: parental Cas9  cells, transfected with SRA targeting siRNA


title: S856 BiSulfite-seq

tag: Sex

value: F

tag: case control


title: pdac_24_after

value: Female

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Progressive disease

tag: overall survival


title: pdac_25_before

tag: tissue

value: Current

tag: baseline bilirubin (micromol/l)

value: Disease control


title: Sertoli,DMRT1, Santa

city: Yangling

first: Mengfei

last: Zhang

state: Shaanxi

address: No.3rd, Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
The clean reads were mapped to the reference genome using STAR software (version 2.5.3a)  with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis. The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
Peak maps of reads across the genome are described using IGV (v2.4.16). The differentially binding peaks were identified by a python script, using fisher test.
The Homer（version 4.10）was used for motifs analysis. Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for annotated genes were both implemented by KOBAS software (version: 2.1.1) with a corrected P-value cutoff of 0.05 to judge statistically significant enrichment.
Assembly: GCF_001704415.1
Supplementary files format and content: tab-delimited text files include Peaks and RPKM values for each Sample

organism: Capra hircus

source_name: testis

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
The 10% lysis sonicated chromatin was stored and named “Input”, and 80% was used in immunoprecipitation reactions with specific anti-Flag Magnetic Beads (Beyotime Biotechnology, P2115) and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively. The DNA of Input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）.

value: testis

value: male

tag: cell line

value: Primary Sertoli cell

tag: cell type

value: Overexpressing FLAG-tagged Dmrt2

tag: chip antibody

value: DMRT1 (Santa Cruz Biotechnology, #sc-377167)


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_Cyt l (Sample 28)

description:
Sample 28
Biological replicate for Sample 10

value: HeLa

tag: fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a non-targeting siRNA


title: pdac_24_before

tag: patient diagnosis

tag: age

tag: gender

tag: smoking status

tag: alcohol status

tag: baseline ca19-9 (u/ml)

value: LAPC


title: S855 BiSulfite-seq

tag: Sex

tag: case control

value: Dis


title: HeLa Cas9 WT non-targeting siRNA_Cyt l (Sample 27)

description:
Sample 27
Biological replicate for Sample 9

value: cytosol RNA fraction

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: Sertoli,Input

value: Overexpressing FLAG-tagged Dmrt1


title: S854 BiSulfite-seq

value: M


title: S853 BiSulfite-seq


title: HeLa Cas9 SRB-3-12 untransfected_Cyt l (Sample 26)

description:
Sample 26
Biological replicate for Sample 8

value: Total cytosolic RNA from HeLa Cas9 SRB KO cells, untransfected


title: pdac_23_after

value: blood

value: Pancreatic Ductal Adenocarcinoma

value: Male

value: Former

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline crp (mg/l)

tag: disease stage

value: Metastatic disease

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: No CT-scan evaluation


title: pdac_23_before

tag: tissue

tag: baseline bilirubin (micromol/l)

tag: overall survival


title: S850 BiSulfite-seq

tag: age


title: HeLa Cas9 WT untransfected_Cyt l (Sample 25)

description:
Sample 25
Biological replicate for Sample 7

tag: cell line

tag: fraction

tag: treatment

value: parental HeLa Cas9 cells, untransfected


title: HeLa Cas9 SRB-3-12 SRa_siRNA_total (Sample 24)

description:
Sample 24
Biological replicate for Sample 6

value: total RNA fraction

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: S849 BiSulfite-seq

value: F


title: pdac_22_after

tag: patient diagnosis

tag: gender

value: Female

tag: smoking status

value: Current

tag: alcohol status

value: Never

tag: baseline ca19-9 (u/ml)

value: LAPC

value: Disease control


title: pdac_22_before

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr


title: HeLa Cas9 SRB-3-12 non-targeting siRNA_total (Sample 22)

description:
Sample 22
Biological replicate for Sample 4

value: HeLa

value: Cas9 SRB KO cells, transfected with a non-targeting siRNA


title: S846 BiSulfite-seq

tag: Sex

tag: case control

value: Dis


title: HeLa Cas9 WT SRA_siRNA_total (Sample 23)

description:
Sample 23
Biological replicate for Sample 5

value: parental Cas9  cells, transfected with SRA targeting siRNA


title: pdac_20_after

tag: tissue

value: blood

value: Pancreatic Ductal Adenocarcinoma

value: Male

tag: baseline crp (mg/l)

tag: disease stage

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

value: Progressive disease


title: S843 BiSulfite-seq

tag: age


title: pdac_21_after

value: Former

tag: baseline bilirubin (micromol/l)

value: No CT-scan evaluation

tag: overall survival


title: pdac_20_before

tag: patient diagnosis

tag: gender


title: pdac_21_before

tag: smoking status

tag: alcohol status


title: HeLa Cas9 SRB-3-12 untransfected_total (Sample 20)

description:
Sample 20
Biological replicate for Sample 2

tag: cell line

tag: fraction

value: total RNA fraction

tag: treatment

value: parental HeLa Cas9 SRB KO cells, untransfected


title: HeLa Cas9 WT non-targeting siRNA_total (Sample 21)

description:
Sample 21
Biological replicate for Sample 3

value: parental HeLa Cas9 cells, transfected with a non-targeting siRNA


title: S852 BiSulfite-seq

tag: Sex

value: M


title: NZBWF_28_nine_(miRNA-4_0)

city: beijng

first: shipeng

last: Li

address: Nan Li Shi Road No. 56,Beijing

institute: Beijing children's hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0 were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: total RNA

source_name: 28-week-old NZBWF1 kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: strain

value: kidney


title: S839 BiSulfite-seq

value: F

tag: case control


title: HeLa Cas9 WT untransfected_total (Sample 19)

description:
Sample 19
Biological replicate for Sample 1

value: parental HeLa Cas9 cells, untransfected


title: NZBWF_28_six_(miRNA-4_0)

tag: tissue


title: pdac_19_before

value: Current

tag: baseline ca19-9 (u/ml)

tag: baseline cea (µg/l)

tag: baseline sii

tag: baseline nlr

tag: baseline crp (mg/l)

tag: disease stage

value: LAPC

value: Disease control


title: pdac_19_after

tag: patient diagnosis

tag: age

tag: baseline bilirubin (micromol/l)

tag: total cycles of folfirinox

tag: progression after 4 cycles (recist 1.1)

tag: overall survival


title: HeLa Cas9 SRB-3-12 SRa_siRNA_ER l (Sample 18)

description:
Sample 18
Sample 18 provides  a transcriptome for CRISPR SRB KO/SRA knockdown.

tag: cell line

value: HeLa

tag: fraction

value: endoplasmic reticulum RNA fraction

tag: treatment

value: Cas9 SRB KO cells, transfected with a SRA-targeting siRNA


title: S838 BiSulfite-seq

tag: Sex

tag: case control

value: Dis


title: S837 BiSulfite-seq


title: NZBWF_8_four_(miRNA-4_0)

source_name: 8-week-old NZBWF1 kidney

tag: strain

tag: tissue