title: shSYNCRIP_Enz WES_KDCE3

description:
shSYNCRIP_Enz
WES


title: Sftpc-CreERT2 control

status: Public on Jul 20 2023

type: SRA

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

country: USA

institute: City of Hope

description: Fresh frozen spatial transcriptome sequencing

library_source: transcriptomic

data_processing:
Paired-end sequencing (2x100) was performed on an Illumina instrument. Sequencing data was pre-processed using the Space Ranger pipelines (10x Genomics,https://cloud.10xgenomics.com/cloud-analysis).
BCL data was demultiplexed and converted to FASTQ format using the spaceranger mkfastq pipeline.
The spaceranger count pipeline was then used for read alignment to human reference genome mm10, Unique Molecular Identifier (UMI) counting, and generation of feature-spot matrices corresponding to the microscopic tissue image. The pipeline also performs automatic tissue detection and fiducial alignment from the image.
Assembly: mm10
Supplementary files format and content: UMI count matrices
Library strategy: Spatial transcriptomics

molecule: total RNA

organism: Mus musculus

source_name: Lung

growth_protocol: The Sftpc-CreERT2 mouse line has been used previously to track AT2 cell fate. Gramd2-CreERT2 mice were generated by homologous recombination insertion of a cassette including CreERT2- downstream of the endogenous Gramd2 gene stop codon within exon 12. These were separately crossed to heterozygous KrasLSL-G12D mice (Jackson laboratory, Stock: #008179). Gramd2-CreERT2 and Sftpc-CreERT2 mice were in a B6/129 mixed strain background (129 N1), while KrasLSL-G12D mice are in a B6/129S4 mixed strain background (C57BL/6 N10).

extract_protocol:
Spatial transcriptomic profiling was performed at the Molecular Genomics Core, a part of the Norris Comprehensive Cancer Center and under manufacturer’s instructions. Briefly, two biological replicates (one block for each) of Gramd2:KrasG12D and Sftpc:KrasG12D underwent initial 10μM sectioning at the Tissue Pathology Core, part of the Norris Comprehensive Cancer Center. Sections were H&E stained (as above) and underwent pathology review. Regions of Interest (ROIs) then underwent sample preparation including test slide sample sequencing using the Visium Tissue Section Test Slide (PN-2000460, 10X Genomics, Dublin, CA, USA). RNA quality assessment of test slides was determined by first extracting RNA using the Qiagen RNeasy FFPE kit (#73504, Qiagen, Hilden, Germany) and measuring RNA concentration using a Qubit fluorometer (#Q33238, ThermoFisher Scientific, Waltham, MA, USA). To determine The percentage of total fragments >200nt in length was determined by running the samples using a 4200 Tapestation (#G2991AA, Agilent, Santa Clara, CA). Once samples were determined to be of high enough quality to continue, 5μM FFPE sections were then placed in a 42C water bath and once rehydrated adhered to the Visium Spatial Gene Expression Slide (PN-2000233, 10X Genomics). Subsequently, samples were dried at 42C for 3hrs in a desiccation chamber and underwent deparrafinization using Qiagen Deparaffinization Solution (Cat # 19093) at 60C for 2 hr. Subsequently H&E staining (#MHS16, #HT110116 Millipore Sigma, Burlington MA, USA) was performed according to Visium technical parameters (CG000409) and images were captured with a Zeiss Axioscan2 microscope using a 10x objective. Decrosslinking was performed according to 10X standard protocol (CG000407) and immediately hybridized to the Visium Mouse Transcriptome probe set V1.0, which contained 20,551 genes targeted by 20,873 probes.
Post-probe extension, sequencing library construction was performed using unique sample indices using the Dual Index Kit TS, Set A (PN-1000251) for Illumina-compatible sequencing.

treatment_protocol: Tamoxifen (Sigma, CAS: 10540-29-1) powder was first dissolved in 100% ethanol (SHBJ8384, Sigma-Aldrich) and then diluted to a final concentration of 40 mg/mL with corn oil (Sigma, CAS: 8001-30-7). To ensure that tamoxifen was fully dissolved, the mixture was gently shaken in a shaking incubator (SHEL LAB, model: SSI5R; cat: #33-804R) at 55℃ for 2 hours. Six-week-old mice were injected with tamoxifen via intraperitoneal injection. For Gramd2-CreERT2; Sftpc-CreERT2, KrasLSL-G12D and WT mice, 40 mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 200 mg/Kg according to the body weight of each mouse. Tamoxifen was given three times over a period of one week. For Sftpc::KrasLSL-G12D mice, 40mg/mL tamoxifen was injected via intraperitoneal injection. The dosage of tamoxifen was 100 mg/Kg according to the body weight of each mouse. Tamoxifen was given twice over a period of one week.

tag: tissue

value: Lung

tag: genotype

tag: treatment

value: Tamoxifen


title: Chap cells, differentiated 55 days-4

city: Cleveland

first: Ya

last: Chen

state: OH

address: 2109 Adelbert Road, Room 747A

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description: Drop-seq

library_source: transcriptomic single cell

data_processing:
McCarroll laboratory Drop-seq protocol
Assembly: GRCh38

organism: Homo sapiens

source_name: Skin

growth_protocol: iPSC cells were cultured on a feeder layer of iMEF cells in hES medium containing DMEM/F12 (Gibco:11330-032), 20% knockout serum replacement (Gibco:10828-028), 1% GlutaMAX (Gibco: 35050-061), 1% Non-essential AA (Gibco:11140-050). Prior to the experiment, ReleSR media (StemCell Technologies:5872) was used to remove iMEF cells, and the iPSC cells were then plated onto vitronectin-coated culture dish (Life Technology; A31804) and culture in E8 medium (Life Technology:A1517001) until they reached about 60% confluence

extract_protocol:
We followed the McCarroll laboratory Drop-seq protocol. We used barcoded beads (ChemGenes Corporation, Macosko-2011-10(V+)) suspended at 120000 beads/ml in drop-seq lysis buffer containing 200mM Tris pH 7.5, 6% Ficoll PM-400, 0.2% Sarkosyl, 20mM EDTA, 50mM DTT. We dissociated 4 libraries from Chap D55 organoids, 3 libraries from D80 organoids and 4 libraries from D156 organoids (3 organoids/library, repeated one batch), or one time point, D80 (2 libraries) from the other control line, into single-cell suspension using Papain kit (Worthington Biochemical Co. LK003153) (27), then suspended the cells in PBS with 0.01% BSA at 0.2x106 cells/ml. To generate droplets, we injected the cells, beads, and oil (Bio-Rad, 186-4006) at flow rates of 2ml/h, 2ml/h and 7.5ml/h, respectively, using syringe pumps.
After droplet generation, we broke the droplet, washed, and collected the beads. We subjected the beads to reverse transcription using TSO_RNA hybris primer, followed by exonuclease I digestion. The libraries were multiplexed and sequenced on HiSeqX PE150 (Medgenome) to generate ~200M total pair reads per library in gzip-compressed FASTQ files.

treatment_protocol: iPSC cells were plated at a density of 6x103 -1x104 cells per well of V-shape 96-well plate in CDM medium, which contained DMEM/F12 (Gibco:11330-032), 5mg/ml BSA (Sigma: A2153), 15µg/ml apo-transferrin (Sigma:T1147), 39nl/ml 1-thioglycerol (Sigma:M6145), and 7µg/ml insulin (Sigma: I2643). On the first day, half of the CDM medium was replaced with fresh medium containing 50ng/ml Fgf2 (GoldBio:1140-02-1000) and 10µM SB431542 (ED millopore:61646).  On day 7 of the differentiation protocol, fresh CDM medium containing 25ng/ml Fgf2 and 5µM SB431542 was added to the cells. On day 14, the organoids were transferred from the V-shape 96-well plate to a U-shape 96-well plate containing new CDM medium supplemented with 100ng/ml Fgf19 (R&D system:969-FG-025). On day 21, the culture medium was switched to CMM1 medium, which contained neurobasal medium (Thermo Fisher:21103049), N2 supplement (Thermo Fisher: 17502048), and 1% Penicillin- streptomycin. On day 28, fresh CMM1 medium containing 300ng/ml recombinant human SDF-1a (CXCL12) (Pepro TECH:300-28A) was added. From day 35 onwards, all organoids were maintained in CMM1 medium

value: Skin

tag: cell line

value: Chap

tag: cell type

value: induced pluripotent stem cells

value: WT

value: cerebellar differentiation 55 days


title: SREX5

city: Dallas

first: Tao

last: Wang

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: WES

library_source: genomic

data_processing:
Exome-seq reads were aligned to the human reference genome (GRCh38) using BWA-MEM
Picard was used to add read group information and sambamba was used to mark PCR duplicates. The calculation of read coverage was performed after duplicate removal.
The GATK toolkit was used to perform base quality score recalibration and local realignment around Indels.
Various algorithms were used to call SNPs and Indels, including MuTect ,VarScan, Shimmer, SpeedSeq, Manta, and Strelka2  and mutation called by more than 3 of these algorithms was retained.
Annovar was used to annotate SNPs and Indels
Assembly: GRCh38
Library strategy: WES

molecule: genomic DNA

source_name: Prostate

growth_protocol: LNCaP/AR cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, 1% penicillin-streptomycin, 1% HEPES, and 1% sodium pyruvate. Cells were split 1 to 6 every 4 days.

extract_protocol: For RNAseq and WES samples: When treated with 10 µM enzalutamide, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum. For scRNAseq samples: When treated with 10 µM enzalutamide or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum for 5 days or 14 days.

value: Prostate

value: LNCaP/AR

value: prostate cancer cells

value: enzalutamide 10mg for 16 weeks


title: shSYNCRIP_Enz WES_KDCE2

description:
shSYNCRIP_Enz
WES

data_processing:
Bulk RNAseq:
Briefly, Agilent 2100 Bioanalyzer was used to determine the sample degradation level and only high-quality RNA is used (RIN Score 8 or higher). Sample concentration was determined by Qubit fluorometer before starting library preparation. TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina was used to prepare 4 mg DNase treated RNA. Before strand specific cDNA synthesis, poly-A RNA is purified and fragmented. cDNA is then a-tailed and ligated with indexed adapters. Samples are amplified by PCR and purified with Ampure XP beads after adapter ligation, following validation on the Agilent 2100 Bioanalyzer. Qubit is used to quantify samples before they were normalized and pooled. Then all samples were run as paired end read 150 nucleotides in length on the Illumina HiSeq 2500 using SBS v3 reagents. Alignment, quantification, and differential analysis were performed using the QBRC_BulkRnaSeqDE pipeline (https://github.com/QBRC/QBRC_BulkRnaSeqDE). Briefly, Alignment of reads to human reference genome (GRCh38) was done using (v2.7.2b) (Dobin et al., 2013)(Ref: 23104886). FeatureCounts (v1.6.4) (Liao, 2014 #607)[REF: 24227677] was then used gene count quantification.
WES:
Exome-seq reads were aligned to the human reference genome (GRCh38) using BWA-MEM
Picard was used to add read group information and sambamba was used to mark PCR duplicates. The calculation of read coverage was performed after duplicate removal.
The GATK toolkit was used to perform base quality score recalibration and local realignment around Indels.
Various algorithms were used to call SNPs and Indels, including MuTect ,VarScan, Shimmer, SpeedSeq, Manta, and Strelka2  and mutation called by more than 3 of these algorithms was retained.
Annovar was used to annotate SNPs and Indels
scRNAseq:
Single-cell gene expression libraries were generated according to the manufacturer’s instructions and single-cell expression sequencing was run on a NovaSeq 6000 (Novogene Co., Ltd). All the subsequent steps were performed following the standard manufacturer’s protocols. 10x scRNA-seq data was processed using the Cell Ranger software (5.0.0). We used the “mkfastq”, “count” and ‘aggr’ commands to process the 10x scRNA-seq output into one cell by gene expression count matrix, using default parameters.
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized gene counts for every gene and every sample
Supplementary files format and content: HDF5 Feature Barcode Matrix Format

source_name: prostate cancer cells

extract_protocol:
For RNAseq samples: LNCaP/AR cells transduced with different shRNA constructs were treated with enzalutamide or vehicle for 6 days before the total RNA was extracted using Trizol. For scRNAseq samples: Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and cells were counted by Countess II FL automatic cell counter (Invitrogen) and cell viability was above 90%. The concentration of single cell suspensions was adjusted to 900-1100 cells/l. Cells were loaded between 10,000 and 17,000 cells/chip position using the Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V1 barcoding chemistry).
For RNAseq samples: RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA. For scRNAseq samples: Single-cell gene expression libraries were generated according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols.
For RNAseq samples: RNA-Seq. For scRNAseq samples: Single-cell RNA-seq were performed by the 10x Genomic single cell 5’library platform.

treatment_protocol: For RNAseq and WES samples: When treated with 10 µM enzalutamide, or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum. For scRNAseq samples: When treated with 10 µM enzalutamide or equivalent amount of DMSO (veh), LNCaP/AR cells were cultured in RPMI medium supplemented with 10% charcoal-stripped serum for 5 days or 14 days.

value: enzalutamide 10uM


title: DonorD_day22

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

data_processing:
Quality Control: FastQC
Trimming adaptor and low quality seqs: Trim Galore
Alignment: Star-aligner
Read counting: Subread / FeatureCounts
Assembly: hg19
Supplementary files format and content: individual tab-delimited text files per sample

source_name: peripheral blood

growth_protocol: For expansion of T cells with CD2/CD3/CD28-loaded particles, we isolated peripheral blood mononuclear cells (PBMCs), selected CD3+ cells with the MicroBead Kit (Miltenyi Biotec), and confirmed successful enrichment by flow cytometry. T cells (10^6 cells/mL) were resuspended in RPMI (Gibco Thermo Fisher), 10% FCS (Gibco Thermo Fisher), 20 U IL-2 per mL (Miltenyi Biotec), with the T Cell Activation/Expansion Kit, human (containing CD2/CD3/CD28-loaded MACSiBead Particles; Miltenyi Biotec) according to manufacturer’s instructions. Restimulation was performed at day 7 and day 17.

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany).
Library preparation with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Vienna, Austria) and sequencing on the HiSeq 2500v4 platform (Illumina; 10 M 50 bp single-end reads) was performed at Life and Brain GmbH (Bonn, Germany).

value: peripheral blood

value: CD3+ T cells

value: 22 days of in vitro culture


title: Chap cells, differentiated 55 days-2

description: Drop-seq


title: C. elegans-fed-heat shock-Rep3

city: London

first: John

last: Labbadia

address: Darwin Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

description:
FED_HS_C
FAST_HSvsFED_HS_deg_all

data_processing:
Sequenced reads were trimmed for adaptor sequences and polyN and low quality reads were removed before mapping reads to the WBcel235 reference genome using  Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene and FPKM for each gene was then calculated
DESeq2 was then used for differential expression analysis
Assembly: WBcel235
Supplementary files format and content: Table with raw gene counts and normalised abundance for every gene and every sample

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: Worms were grown on standard NGM plates with OP50 at 20degC

extract_protocol:
Worms were lysed in Trizol by vortexing at 4degC for 20 minutes. RNA was then purified using a Qiagen Rneasy Minelute kit as per manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Worms were fasted at the mid-L4 stage by moving worms to plates without food for 24 hours. Following this, worms were allowed to recover for 24 hours and were then exposed to heat shock at 35C for 30 minutes by submerging plates in a water bath.

value: Whole animals

value: N2 - Wild-type

value: Fed heat shock


title: C. elegans-fed-heat shock-Rep2

description:
FED_HS_B
FAST_HSvsFED_HS_deg_all


title: C. elegans-fed-heat shock-Rep1

description:
FED_HS_A
FAST_HSvsFED_HS_deg_all


title: Gramd2-CreERT2 control

value: Lung

value: Tamoxifen


title: C. elegans-fasted-no heat shock-Rep1

description:
FAST_NOHS_A
FAST_NOHSvsFED_NOHS_deg_all

value: Fasted no heat shock


title: SREX2

description: WES


title: SREX1

description: WES


title: shNT_Enz NTCE2

description:
shNT_Enz
RNAseq


title: C. elegans-fed-no heat shock-Rep4

description:
FED_NOHS_D
FAST_NOHSvsFED_NOHS_deg_all

value: Fed no heat shock


title: shNT_Veh NTFS1

description:
shNT_Veh
RNAseq

value: Vehicle DMSO


title: Gramd2:KrasG12D Lung 3

value: Gramd2-CreERT2; Kras-LSL-G12D


title: shNT_Veh NTFS3

description:
shNT_Veh
RNAseq


title: C. elegans-fed-no heat shock-Rep3

description:
FED_NOHS_C
FAST_NOHSvsFED_NOHS_deg_all


title: C. elegans-fed-no heat shock-Rep2

description:
FED_NOHS_B
FAST_NOHSvsFED_NOHS_deg_all


title: DonorC_day22


title: eggd-1 genetically null smRNA sequencing. RNAs treated with sodium periodate. Replicate 1.

city: Columbus

first: Wen

last: Tang

state: Ohio

address: 1060 Carmack Rd

department: Department of Biological Chemistry and Pharmacology

institute: The Ohio State University

data_processing:
Raw reads weer trimmed of adapters and removed of poor quality sequences using TrimGalore. Sequences were then collapsed and transformed into fasta files using cutsom shell scripts.
Reads were aligned to contaminating RNAs (rRNAs, tRNAs, snRNAs…) using Bowtie. Reads that failed to align were aligned to the genome using Bowtie.
Aligned reads were normalized and assigned to genomic features using custom shell scripts. Alignments were converted to BigWig files using UCSC Tools.
Downstream analysis was preformed using R/Python/IGV.
Assembly: WormBase WS279
Supplementary files format and content: Tab Delimmited Counts Matrix
Supplementary files format and content: Unique fasta file of collapsed reads

source_name: whole animal

growth_protocol: Synchronized L1 were platted and maintained at 20 celcius on NGM median supplemented with OP50 E. coli . Animals were then harvested when the population reached adulthood.

extract_protocol:
Approximately 50,000 synchronized adult worms were collected with M9 using a glass Pasteur pipette. The worms were washed once with M9, rocked in fresh M9 for 5 min, washed once in ddH2O, and resuspended suspended in 1ml of TRI Reagent (Sigma). Worms were lysed using the Bead Mill 24 homogenizer (Thermo Fisher Scientific) and the lysate was transferred to a clean tube 1.5 ml centrifuge tube. 0.1 volumes of bromochloropropane were added to the mix and shaken by hand for 30 seconds. The mixture was then centrifuged at 15,000g and the aqueous phase was transferred to a fresh 1.5 ml microcentrifuge tube, followed by the addition of 1 volume of isopropanol. The tube was incubated at -20 °C for 1 hour to precipitate RNA and centrifuged for 15 mins at 14,000rpm at 4°C. The supernatant removed by pipetting and the pellet was washed twice by adding 1 mL 75% ethanol. The pellet of RNA was allowed to dry for 3 minutes to remove remaining ethanol, dissolved in ddH2O and stored at -80°C.
Small RNAs were enriched using MirVana miRNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. β–elimination was performed as described (Pastore et al., (2021)). Small RNA-sequencing libraries were constructed as described (Tang etal., (2016)). Briefly, Small RNA samples were first treated with the polyphosphatase PIR-1 to remove the γ and β phosphates from 5´-triphosphorylated RNAs 4. The monophosphorylated small RNAs were ligated to a 3’ adaptor (5’rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/3’, IDT) using T4 RNA ligase 2 (NEB) at 15 °C overnight. T4 RNA ligase 1 (NEB) was used to ligate the 5’ adaptor (rArCrArCrUrCrUrUrUrCrCrCrUrArCrArCrGrArCrGrCrUrCrUrUrCrCrGrArUrCrU, IDT). The ligated products were converted to cDNA using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific). The cDNAs were further amplified by PCR, and the Small RNA libraries with unique barcodes were pooled and sequenced at the Illumina Novaseq platform (SP 2 X 50 bp).

treatment_protocol: Some samples were treated with NaIO4 to assess methylation status of small RNAs.

value: whole animal

value: eggd-1 null

value: NaIO4 sodium periodate


title: DonorB_day22


title: shNT_Enz NTCE1

description:
shNT_Enz
RNAseq

value: prostate cancer cells


title: shNT_Enz NTCE3

description:
shNT_Enz
RNAseq

value: enzalutamide 10uM


title: snSeqTAC

city: Munich

first: Karin

middle: A.

last: Ziegler

address: Biedersteiner Str. 29

institute: Technical University of Munich

description: 10x Genomics

data_processing:
bcl2fastq for basecalling, fastq conversion and demultiplexing
cellranger v5.0.0 for alignment, filtering, barcode counting, UMI counting
Assembly: mm10
Supplementary files format and content: Feature-Barcode Matrices from cellranger (10x Genomics)
Library strategy: single-nucleus RNA-seq

molecule: polyA RNA

source_name: Sympathetic ganglion

extract_protocol:
After harvest and cleaning, SCGs were homogenized into single nuclei (as previously described by Mathys et al.2019) and proceeded for single nucleus capture, barcoding and library preparation (10x genomics).
Barcoding and library preparation was done using Chromium single cell 3’ (v3, 10x Genomics).

value: Sympathetic ganglion

tag: strain

tag: age

value: 8-12 weeks old

tag: Sex

value: male

tag: disease state

value: early stage heart disease (5d)


title: snSeqSham

description:
10x Genomics
snSeq_integrated_res025_alra.RData


title: Bone marrow Monocyte, DEL, rep2

city: itabashi-ku

first: Daisuke

last: Tsukui

state: tokyo

country: Japan

institute: Teikyo University

description: Sample 5

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver.10.1.1, Qiagen).
Reads were mapped to mouse reference genome (mm10) and quantified for 49585 genes.
Total counts were normalized by quantile method.
Differentially expressed genes were identified using Empirical Analysis of DGE tool in CLC Genomics Workbench.
Assembly: mm10
Supplementary files format and content: Microsoft Excel file format, containing gene name and normalized read counts converted by log2.

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using the TRIZOL (Termo Fisher Scientifc). 500 ng total RNA was used for the construction of sequencing libraries.
RNA-seq library was made using NEB Next Ultra Directional RNA Library Prep Kit (New England Biolabs) after a process with rRNA-depletion kit (New England Biolabs) as manufacturer's protocols.

value: Bone marrow

value: Monocyte

value: Sykdel/del

value: High-fat diet


title: C. elegans-fed-no heat shock-Rep1

description:
FED_NOHS_A
FAST_NOHSvsFED_NOHS_deg_all

value: Whole animals

value: N2 - Wild-type


title: DonorA_day22

value: peripheral blood

value: CD3+ T cells

value: 22 days of in vitro culture


title: DonorD_day0

value: freshly isolated


title: shSYNCRIP_Veh KDFS1

description:
shSYNCRIP_Veh
RNAseq

value: Vehicle DMSO


title: shSYNCRIP_Veh KDFS2

description:
shSYNCRIP_Veh
RNAseq

value: prostate cancer cells


title: Bone marrow Monocyte, DEL, rep1

description: Sample 4


title: control (N2) smRNA sequencing. RNAs treated with sodium periodate. Replicate 1.

value: whole animal

value: wild type

value: NaIO4 sodium periodate


title: eggd-1 null mutant smRNA sequencing rep. 2

value: eggd-1 null


title: Bone marrow Monocyte, DEL, rep3

description: Sample 6


title: DonorC_day0


title: eggd-1 null mutant smRNA sequencing rep. 1


title: DonorB_day0


title: shSYNCRIP_Enz KDCE3

description:
shSYNCRIP_Enz
RNAseq

value: enzalutamide 10uM


title: Bone marrow Monocyte, WT, rep3

description: Sample 3

value: Bone marrow

value: Syk+/+


title: shSYNCRIP_Veh KDFS3

description:
shSYNCRIP_Veh
RNAseq


title: control smRNA sequencing rep. 2


title: DonorA_day0


title: shSYNCRIP_Enz KDCE2

description:
shSYNCRIP_Enz
RNAseq


title: SCG3_region2_cellpose_res03

type: RNA

hyb_protocol: A total of 140 genes were assigned with a binary barcode for MERFISH imaging.

scan_protocol: MERFISH data were generated on the MERSCOPE Platform, services provided by Vizgen, Inc. In Vizgen’s MERSCOPE platform, the raw data files ".inf" and ".dax“  are generated by the system.          1.  .inf: The ".inf" extension typically represents information files or metadata files. It contains metadata or information about the corresponding fields of view (FOV). It includes details such as acquisition parameters, experimental settings, sample information, or any other relevant information related to the raw data.          2.  .dax: The ".dax" extension is commonly used for raw data files acquired from imaging systems. In the MERSCOPE platform, a ".dax" file contains the actual raw image data obtained from the MERSCOPE imaging system. These files are typically binary files that store the pixel values or intensity values of the acquired images.

data_processing: Python package scanpy was applied to perform data preprocessing, dimensionality reduction, and single-cell Leiden clustering.

extract_protocol: Sample preparation of fresh frozen SCG was performed according to manufacturer’s protocol (Vizgen).

value: Sympathetic ganglion

value: wildtype

value: male

tag: disease stage


title: shSYNCRIP_Enz KDCE1

description:
shSYNCRIP_Enz
RNAseq


title: Bone marrow Monocyte, WT, rep2

description: Sample 2

value: Monocyte

value: High-fat diet


title: control smRNA sequencing rep. 1


title: Bone marrow Monocyte, WT, rep1

description: Sample 1


title: M7

status: Public on Jul 19 2023

city: Shanghai

first: Xin

state: None Selected

address: No. 83 Fenyang Road, Xuhui District, Shanghai, China.

country: China

institute: Eye & ENT Hospital of Fudan University

description: Gene expression of microtia

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 15 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: Auricular Cartilage

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The isolated cartilage tissues were rapidly immersed in TRIzol reagent (Invitrogen). RNA was extracted by adding chloroform and then precipitated with isopropyl alcohol. The RNA precipitates were washed twice with 70% ethanol, dried, and resolved in water without RNase. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity and gDNA contamination test were assessed by standard denaturing agarose gel electrophoresis.

value: elastic cartilage

tag: gender

value: Female

tag: diagnosis

value: Microtia


title: C2

description: Gene expression of control

value: Male

value: Cholesteatoma of middle ear


title: M5

description: Gene expression of microtia


title: M9

description: Gene expression of microtia


title: M6

description: Gene expression of microtia


title: C3

description: Gene expression of control


title: High fat diet,  rep 3 [miRNA-Seq]

city: Kiryat Shmona

first: Ari

last: Meerson

address: 2 Tarshish St.

country: Israel

institute: MIGALGalilee Research Institute

data_processing:
Processing was by the Technion Genome Center, Israel and the online CLC Genomics Workbench 20.0.3.
Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench, which included removal of the Qiagen 3' adapter on the 3' end.
Reads without this adapter were discarded, and only sequences between 15 and 54 nucleotides were retained. These trimmed files (read lengths of ~23 bases) were joined.
miR quantify was run on these files, using the reference - miRbase v.22.1 and the preference - Danio rerio.
Normalization was executed using TMM (trimmed mean of M values). Annotation was carried out using Go Mapping RNAcentral v10.
Supplementary files format and content: excel file with Max Group Mean, Log2 Fold change, Fold change, p Value, FDR pvalue, Bonferroni for each miR in each model.

organism: Danio rerio

source_name: whole larvae (30)

growth_protocol: Kept under 14 h light/10 h dark regimen. Water was pH7-7.7, 27.7-28.3 C, 490-510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults.

extract_protocol:
Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle (20-G). Kit used was Nucleospin® miRNA kit (Macherey-Nagel GmbH & Co.)
Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center, Israel.
miRNA-seq, including other small RNAs. 75 nucleotide single-end runs

treatment_protocol: anxiety (induced by a half hour exposure to 100 mg/liter caffeine [CAF], compared to no treatment [NO]) and obesity (induced by feeding 6 dpf larvae a high fat diet  [HFD, egg yolk-based] until 15 dpf, compared to a standard diet [SD]).

value: whole larvae (30)

value: AB strain

value: High fat diet (egg yolk-based)


title: C5

description: Gene expression of control

value: Tympanitis


title: M10

description: Gene expression of microtia


title: M8

description: Gene expression of microtia


title: C4

description: Gene expression of control


title: M1

description: Gene expression of microtia


title: d-hASCs, adipocyte

city: Tsukuba

first: Farhana

last: Ferdousi

state: Ibaraki

address: Tennodai 1-1-1

institute: University of Tsukuba

description: Gene expression data from d-hASCs cultured in adipogenic differentiation medium for 14 days

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S array, Human; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the robust multi-chip analysis (RMA) algorithm. Further, gene-level analysis was performed using the Limma Bioconductor package. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome analysis console software (VALUE). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files). filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 2 (in linear space)
algorithm: robust multi-chip analysis (RMA) algorithm

label: biotin

source_name: d-hASCs cultured in adipogenic differentiation medium for 14 days.

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/ uL total RNA

growth_protocol: Diabitic human adipose stem cells (d-hASCs) were purchased from Lonza (PT-5008, Walkersville, MD, Unitied States). The isolation of cells from human tissue was conducted in accordance with informed consent or legal authorization, solely for the purpose of research. Briefly, the cells were cultured at 37°C in a 5% CO2 humidified incubator using ASC growth medium sourced from Lonza company (ADSC-GM BulletKitTM). The ASC growth medium comprised ASC basal medium supplemented with 10% FBS, 1% L-glutamine, and gentamicin-amphotericin B (GA-1000), following the manufacturer's instructions. To initiate differentiation, preadipocyte growth medium (PGM-2TM BulleKit) was used to seed d-hASC cells, followed by a switch to adipogenic differentiation medium. The entire differentiation process spanned a duration of 14 days.

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol: White adipocyte differentiation of d-hASCs was performed using ASC growth medium. Adipogenic differentiation operated on the confluence greater than 80%. To initiate differentiation, preadipocyte growth medium (PGM-2TM BulleKit) was used to seed d-hASC cells, followed by a switch to adipogenic differentiation medium. The entire differentiation process spanned a duration of 14 days. oleacein were added from the first day of differentiation process.

value: diabetic human adipose-derived stem cells (d-hASC)


title: M2

description: Gene expression of microtia


title: M3

description: Gene expression of microtia


title: C1

description: Gene expression of control

value: Acquired external auditory canal stenosis


title: M4

description: Gene expression of microtia


title: d-hASCs, adipocyte treated with oleacein

description: Gene expression data from d-hASCs cultured in adipogenic differentiation medium treated with 1uM oleacein for 14 days.


title: High fat diet,  rep 1 [miRNA-Seq]


title: High fat diet,  rep 2 [miRNA-Seq]


title: Standard diet, rep 1 [miRNA-Seq]

value: Standard diet


title: Caffeine,  rep 3 [miRNA-Seq]

value: Caffeine (100 mg/l, 0.5 h)


title: Caffeine,  rep 2 [miRNA-Seq]


title: Standard diet, rep 2 [miRNA-Seq]


title: No treatment,  rep 1 [miRNA-Seq]


title: Standard diet, rep 3 [miRNA-Seq]


title: Caffeine,  rep 1 [miRNA-Seq]


title: Standard diet, Rep 3

data_processing:
FastQC, version v0.11.9
BOWTIE2 for read alignment and RSEM software for annotation and expression calculation  (https://bioinformaticshome.com/tools/rna-seq/descriptions/RSEM.html).
Assembly: Danio_rerio.GRCz11.dna.primary_assembly.fa.gz
Supplementary files format and content: result files of RSEM software for each sample, one of genes and one of isoforms
Supplementary files format and content: Result files contain gene id, transcript id(s), length, effective length, expected count, TPM and FPKM.

extract_protocol:
Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle (20-G). Kit used was Nucleospin® miRNA kit (Macherey-Nagel GmbH & Co.)
The  poly(A)+ RNA libraries were generated using TruSeq RNA Library Prep Kit v2 and sequenced at the Technion Genome Center, Israel.
poly(A)+ RNA-seq.  51 nucleotides single-end runs.


title: High fat diet, Rep 2


title: High fat diet, Rep 3


title: No treatment,  rep 2 [miRNA-Seq]


title: Standard diet, Rep 1


title: Caffeine, Rep 3


title: Third Trimester Control_CTB3_36.2weeks

city: Auckland

first: Teena

last: Gamage

state: Scotland

country: New Zealand

institute: Grafton

hyb_protocol: Affymetrix GeneChip PrimeView microarrays using the3' IVT PLUS kit

scan_protocol: Standard Affymetrix protocol

data_processing: Microarray data were quality checked and lacked obvious outliers (Bolstad et al. 2003; Irizarry et al 2003a; Irizarry et al 2003b). Preprocessing and normalaisation of the data using RMA was conducted using R package affy (Gautier et al. 2004). Side-population trophoblast gene expression was compared to that of cytotrophoblasts from the same placenta.  In oder to determine differentially expressed transcripts, the statistical program R and the R package limma were used. (Ritchie et al 2015). Linear models were used to determine Log fold changes between side-population trophoblasts and cytotrophoblast populations from FGR and gestation-matched control placentae and an emperical Bayes method was used to moderate the standard deviation of the estimated Log fold changes. All data were cleaned and reanalysed using the method described to analyse the FGR and gestation-matched control samples to mitigate any bias in the data that may result from differences in the analysis pipelines used in the previous publication from which first trimester samples were obtained (James et al 2015).

source_name: Placental Villi

label_protocol: Standard Affymetrix protocol

growth_protocol: Uncultured

extract_protocol: FACS sorting live MHC Class I negative  Hoechst 33342-low side-population trophoblasts and bete4-integrin positive cytotrophoblasts

tag: sample type

value: Gestation-matched control

tag: time point

value: 36.2 weeks

value: Cytotrophoblast


title: Third Trimester Control_CTB1_38weeks

value: 38 weeks


title: Third Trimester Control_CTB4_36.6weeks

value: 36.6 weeks


title: Third Trimester Control_SP5_40.0weeks

value: 40.0 weeks

value: Side-population


title: Third Trimester Control_CTB2_34.4weeks

value: 34.4 weeks


title: High fat diet, Rep 1


title: No treatment,  rep 3 [miRNA-Seq]


title: Third Trimester Control_SP4_36.6weeks


title: Caffeine, Rep 1


title: Third Trimester Control_SP2_34.4weeks


title: Third Trimester Control_CTB5_40.0weeks


title: Third Trimester Control_SP3_36.2weeks


title: Third Trimester Control_SP1_38weeks


title: No treatment, Rep 1


title: SKSC13

description: WES

value: Prostate

value: LNCaP/AR

value: prostate cancer cells

value: Vehicle DMSO


title: No treatment, Rep 2

value: whole larvae (30)

value: AB strain


title: Caffeine, Rep 2


title: 2xMinikirikou-BLS_12-7F5

city: Paris

first: Caroline

last: Tonnerre-Doncarli

address: 15 rue Hélène Brion

country: France

institute: Institut Jacques Monod, CNRS UMR7592, Université Paris cité

description: MNAse G2 for the βA-globin minimal active origin inserted on chr1

data_processing:
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012).
the βA-globin minimal active origin inserted on chr1 (Figure 4A)

organism: Gallus gallus

source_name: modified DT40

growth_protocol: DT40 cells were grown in RPMI 1640 Glutamax (Thermo Fisher Scientific #61870010) containing 10% FBS, 1% chicken serum, 0.1 mM β-mercaptoethanol, 200 U/mL penicillin, 200 µg/mL streptomycin and 1.75 µg/mL amphotericin B, at 37°C, under an atmosphere containing 5% CO2.

extract_protocol:
We cross-linked 30 x 106 exponential growing cells by incubation for 5 minutes with 1% freshly prepared formaldehyde (Thermo Fisher Scientific, #28908) at room temperature. Fixation was stopped by adding 0.125 M glycine-PBS for five minutes at room temperature. After three ice cold PBS washing, nuclei were extracted in lysis buffer (10mM Tris-HCl, pH7.5, 10mM NaCl, 3mM MgCl2, 0.2% triton X-100, 0.5mM EGTA, 1mM DTT, 1x protease inhibitor cocktail (Sigma, #P8340)) for 5min on ice, 15 centrifuged and resuspended in digestion buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1 mM CaCl2, 1x protease inhibitor cocktail (Sigma, #P8340)). Micrococcal Nuclease (MNase; Thermo Fisher Scientific, #EN0181) digestions were performed for 15 minutes at 37°C, with 160 U/mL of MNase. The reaction was stopped by adding 0.1 volume of stop buffer (200 mM EDTA pH 8.0, 40 mM EGTA pH 8.0). Chromatin was then sonicated during 30 sec at 7°C in a buffer adjusted to a final SDS concentration of 0.1% with a Covaris sonicator using 75W intensity, 200 cycles per burst, 5% of duty cycle. For nucleosome coverage analyses, DNA molecules were recovered after RNAse A and proteinase K digestion and phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared using NEBNext Ultra II DNA library prep Kit for Illumina (NEB #E7645S) according to the manufacturer’s instructions for MNase, ChIp and input libraries. Samples were not subjected to size selection, but only cleaned-up for adaptor-ligated DNA using SPRISelect Reagent kit (Beckman coulter #B23317), to ensure a MNase digested small fragment overall recovery. Libraries were prepared with a starting DNA input of 10 ng. We used a 10 fold diluted adaptor for the adaptor ligation. The library amplification was performed using NEB-Next Multiplex Oligos for Illumina (NEB #E7710S) with different NEB-Next index primers and the NEB-Next Universal PCR Primer (NEB #E6861A) with eight PCR cycles.

value: modified DT40

value: dervived from a Bursal lymphoma

value: DT40Cre1 has been described previously (Arakawa et al. 2001)


title: 2xMinikirikou-G4Inv-BLS_20-9_F2M

description: MNAse G1/S for the βA-globin minimal inactive origin inserted on chr1

data_processing:
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012).
the sequence of the βA-globin minimal inactive origin pG4#1 rev compl inserted on chr1 (Figure 4B)


title: 2xMinikirikou-G4Inv-BLS_20-9_F5

description: MNAse G2 for the βA-globin minimal inactive origin inserted on chr1


title: S4 2x (βA-globin full origin)

description:
Repli-seq
Repli-Seq S4

data_processing:
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012). For each timing fraction, replication timing was computed using 50kb sliding windows at 10kb intervals, normalized by the global and local genomic coverage of the asynchonous cell population, to normalize for total and local coverage variations. Then the centered and standardized timing profiles were smoothed using cubic splines (smooth.spline function of R).
Bed Graph files were generated.
galGal5 chicken genome

extract_protocol:
Exponentially growing cells were pulse-labeled with 5-Bromo-2’-deoxyuridine for 1h and four S-phase fractions (S1 to S4) were collected by flow cytometry or from an asynchronous cell population (AS). The cells were treated with lysis buffer (50 mM Tris pH 8.0; 10 mM EDTA pH 8.0; 300 mM NaCl; 0.5% SDS, 0.2 mg/ml of freshly added proteinase and 0.5 mg/ml of freshly added RNase A), incubated at 65°C for 2 h and stored at -20°C, in the dark. Genomic DNA was isolated from each sample by phenol-chloroform extraction and alcohol precipitation and sonicated four times for 30s each, at 30s intervals, in the high mode at 4°C in a Bioruptor water bath sonicator (Diagenode), to obtain fragments of 500 to 1000 bp in size. The sonicated DNA was denatured by incubation at 95°C for 5 minutes. We added monoclonal anti-BrdU antibody (BD Biosciences #347580) at a final concentration of 3.6 μg/ml in 1x IP buffer (10 mM Tris pH 8.0, 1 mM EDTA pH 8.0, 150 mM NaCl, 0.5% Triton X-100, and 7 mM NaOH). We used 30 μl or 50 µl of protein-G-coated magnetic beads (from Ademtech #4342 or Thermo Fisher Scientific #10004D, respectively) per sample to pull down the anti-BrdU antibody. Beads and BrdU-labeled nascent DNA were incubated for 2-3 hours at 4°C, on a rotating wheel. The beads were then washed once with 1x IP buffer, twice with wash buffer (20 mM M Tris pH 8.0, 2 mM EDTA pH 8.0, 250 mM NaCl, 0.25% Triton X-100) and then twice with 1x TE buffer pH 8.0. The DNA was eluted by incubating the beads at 37°C for 2 h in 250 µl 1x TE buffer pH 8.0, to which we added 1% SDS and 0.5 mg/ml proteinase K. DNA was purified by phenol-chloroform extraction and alcohol precipitation and resuspended in 50 µl TE. Immunoprecipitated NS were amplified by whole-genome amplification (GenomePlex Complete Whole Genome Amplification kit #WGA2; Sigma) according to the manufacturer’s recommendations to obtain sufficient DNA amount.
Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB #E7645S) following the manufacturer’s instructions with minor modifications. For the adaptor ligation, undiluted adaptor and no size selection were used. The library amplification was performed using NEB-Next Multiplex Oligos for Illumina (NEB #E7710S) with nine different NEB-Next index primer and the NEB-Next Universal PCR Primer (NEB #E6861A) with three PCR cycles. Library purification was performed with the SPRI-select Reagent kit (Beckman coulter #B23317), and the final elution step was reduced to 33µl of 0.1×TE. The mean size of the library molecules determined on an Agilent Bio-analyser High Sensitivity DNA chip (Agilent technologies, #5067–4626) was 330-350 bp. Sequencing was performed on a NextSeq 500 Illumina sequencer with a High Output 150 cycles flow cell (paired-end reads of 75 bp) according to standard procedures. For each sample, 15-20 M of reads were generated.


title: ChIp_H2AZ_2xMinikirikou-G4Inv_20-9

description: H2A.Z-3_local analysis on chr1

data_processing:
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012).
These samples were used as a reference for H2AZ peak detection, performed using bowtie2 version 2.3.4.1 and MAC2s version 2.1.2. Coverage plots represent the average number of genomic features in sliding windows of 20 bp, overlapping by 10 bp. Bed Graph files were generated.
the sequence of the βA-globin minimal inactive origin pG4#1 rev compl inserted on chr1 (Figure 4B)

extract_protocol:
We cross-linked 30 x 106 exponential growing cells by incubation for 5 minutes with 1% freshly prepared formaldehyde (Thermo Fisher Scientific, #28908) at room temperature. Fixation was stopped by adding 0.125 M glycine-PBS for five minutes at room temperature. After three ice cold PBS washing, nuclei were extracted in lysis buffer (10mM Tris-HCl, pH7.5, 10mM NaCl, 3mM MgCl2, 0.2% triton X-100, 0.5mM EGTA, 1mM DTT, 1x protease inhibitor cocktail (Sigma, #P8340)) for 5min on ice, 15 centrifuged and resuspended in digestion buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1 mM CaCl2, 1x protease inhibitor cocktail (Sigma, #P8340)). Micrococcal Nuclease (MNase; Thermo Fisher Scientific, #EN0181) digestions were performed for 15 minutes at 37°C. The final concentration of 160 U/mL was used for ChIp coverage analyses. The reaction was stopped by adding 0.1 volume of stop buffer (200 mM EDTA pH 8.0, 40 mM EGTA pH 8.0). Chromatin was then sonicated during 30 sec at 7°C in a buffer adjusted to a final SDS concentration of 0.1% with a Covaris sonicator using 75W intensity, 200 cycles per burst, 5% of duty cycle. For nucleosome coverage analyses, DNA molecules were 25 recovered after RNAse A and proteinase K digestion and phenol-chloroform extraction and ethanol precipitation. Chromatin was then adjusted in 1x IP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton-X100 and 0.1% SDS). Immunoprecipitation was performed overnight at 4°C, in a final volume of 300 μl of 1X IP buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA pH 8.0, 150 mM NaCl, 1% Triton-X100 and 0.1% SDS) on an amount of MNAse digested chromatin corresponding to 10 μg of DNA, with anti-H2A.Z antibody (Active Motif, #39013), according to manufacturer recommendations. Immuno-complexes were pulled down with 50 μl of protein-G coated magnetic beads (Thermo Fisher Scientific, Dynabeads protein G, #10004D) per sample. Beads and immuno-complexes were incubated for 2 h at 4°C, on a rotating wheel. The beads were then washed once with 1× IP buffer, twice with wash B buffer (20 mM Tris pH 8.0, 2mM EDTA pH 8.0, 500 mM NaCl, 0.25% Triton X-100) and then twice with 1× TE buffer pH 8.0. The DNA was eluted by incubating the beads for 2 h at 37°C with 250 μl 1× TE buffer pH 8.0, to which we added 1% SDS and 0.5 mg/ml proteinase K. Cross-linking was reversed by overnight incubation at 65°C, and samples were further treated with 10 μg of RNase A for 15 min at 37°C, and with 20 μg of proteinase K for 1 h at 56°C. DNA was purified by phenol–chloroform 5 extraction, precipitated in alcohol, resuspended in 100 μl TE and quantified by QuBit (dsDNA HS assay kit, Thermo Fisher Scientific, #Q32851). Input samples were obtained from MNAse digested chromatin after RNAse A and proteinase K digestion, phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries were prepared using NEBNext Ultra II DNA library prep Kit for Illumina (NEB #E7645S) according to the manufacturer’s instructions for MNase, ChIp and input libraries. Samples were not subjected to size selection, but only cleaned-up for adaptor-ligated DNA using SPRISelect Reagent kit (Beckman coulter #B23317), to ensure a MNase digested small fragment overall recovery. Libraries were prepared with a starting DNA input of 10 ng. We used a 10 fold diluted adaptor for the adaptor ligation. The library amplification was performed using NEB-Next Multiplex Oligos for Illumina (NEB #E7710S) with different NEB-Next index primers and the NEB-Next Universal PCR Primer (NEB #E6861A) with eight PCR cycles.


title: S2 2x (βA-globin full origin)

description:
Repli-seq
Repli-Seq S2


title: S3 2x (βA-globin full origin)

description:
Repli-seq
Repli-Seq S3


title: 2xMinikirikou-BLS_12-7F2M

description: MNAse G1/S for the βA-globin minimal active origin inserted on chr1


title: Standard diet, Rep 2

value: Standard diet


title: F2-ATAC

data_processing:
ATAC-seq reads were trimmed and then mapped to the chicken gal5 genome using version 2.3.4.1 of bowtie2. We removed discordant pairs (inserts >2000bp) as well as reads with quality score below 40 and reads mapping to mitochondrial DNA. Finally, duplicated reads were removed using Picard Toolkit http://broadinstitute.github.io/picard/). Reads from the three different replicates were pooled together to increase the statistical power. To do so, we first called open regions using macs2 (with option 15 --broad), and peaks close to each other (<30bp) were merged together.
NFRs were called in open regions using the nucleoatac pipeline from Schep et al. 2015. Coverage plots represent the average number of genomic features in sliding windows of 20 bp, overlapping by 10 bp. Bed Graph files were generated.
galGal5 chicken genome

source_name: Wt DT40

extract_protocol:
ATAC experiments were performed as described in Buenrostro, J. D. et al. 2013. Briefly, 1 x 105 asynchronous, G1 and G2/M cells collected by elutriation were washed once with cold PBS. The pellet was resuspended in 50μl of 20 Lysis buffer (0.3M Sucrose, 10mM Tris pH8, 10mM NaCl, 3mM MgCl2, 0.2% Triton X100) and the transposition reaction was incubated for 30 min at 37°C in a thermomixer shaking at 700rpm. Samples were purified with the MinElute PCR purification kit (Qiagen #28004) following manufacturer instructions and eluted in 11μl.
The tagmentation and library preparation was performed with the Nextera DNA Library Preparation Kit with 8 cycles of PCR amplification (Illumina #FC-121-1030) and the libraries were cleaned up with SPRselect beads (Beckman Coulter, #B23317).

value: Wt DT40

value: G1 cells collected by elutriation


title: F6-ATAC

value: G2/M cells collected by elutriation


title: Input_2xMinikirikou_12-7

description: H2A.Z-2 / MNAse_Whole Genome and local analysis on chr1

data_processing:
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012).
These samples were used as a reference for H2AZ peak detection, performed using bowtie2 version 2.3.4.1 and MAC2s version 2.1.2 and for Nucleosome coverage profiles. Coverage plots represent the average number of genomic features in sliding windows of 20 bp, overlapping by 10 bp. Bed Graph files were generated.
galGal5 chicken genome or the sequence of the βA-globin minimal active origin inserted on chr1 (Figure 4A)


title: ChIp_H2AZ_2xMinikirikou_12-7

description: H2A.Z-1_Whole Genome and local analysis on chr1

data_processing:
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012).
These samples were used as a reference for H2AZ peak detection, performed using bowtie2 version 2.3.4.1 and MAC2s version 2.1.2. Coverage plots represent the average number of genomic features in sliding windows of 20 bp, overlapping by 10 bp. Bed Graph files were generated.
galGal5 chicken genome or the sequence of the βA-globin minimal active origin inserted on chr1 (Figure 4A)


title: No treatment, Rep 3


title: MSB1,NaB, 72 hpi (NaB_2_IP)

city: ZHENG ZHOU

first: shuai

last: zhang

address: China Henan Zhengzhou Agricultural Road No. 63 (450002)

institute: Henan Agricultural University

description:
m6A-seq
ExpressionProfile_m6A_NaB_peak
NaB_2_IP

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Supplementary files format and content: tab-delimited text files include RPKM values for RNA-seq Samples, fold_enrichment for m6A-seq Input and IP samples

growth_protocol: MSB1 cells were maintained in RPMI 1640  Medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
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.
RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols.

treatment_protocol: One-day-old chickens were wing-banded at hatch, randomly sorted into two experimental groups, and maintained in modified Horsfall_x0002_Bauer isolators for the duration of animal experiment. One group of chickens was remained as the uninoculated control. The others were inoculated subcutaneously with 2,000 PFUs Md5BAC virus. 3 chickens from each group were euthanatized at 5-,14- and 60- days post infection (dpi). Spleen tissues were collected for splenocytes isolation followed by RNA extraction

value: Lymphoblast

value: sodium butyrate (NaB)-treated

tag: rip antibody


title: MSB1,NaB, 72 hpi (NaB_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_NaB_peak
NaB_3_IP


title: MSB1,NaB, 72 hpi (NaB_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_NaB_peak
NaB_1_IP


title: MSB1,Negative, 72 hpi (M_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_MSB1_peak
M_3_IP

value: untreated


title: Input_2xMinikirikou-G4Inv_20-9

description: H2A.Z-2 / MNAse_local analysis on chr1

data_processing:
Paired-end sequencing data were mapped on the galGal5 chicken genome using bowtie2 (Langmead & Salzberg, 2012).
These samples were used as a reference for H2AZ peak detection, performed using bowtie2 version 2.3.4.1 and MAC2s version 2.1.2 and for Nucleosome coverage profiles. Coverage plots represent the average number of genomic features in sliding windows of 20 bp, overlapping by 10 bp. Bed Graph files were generated.
the sequence of the βA-globin minimal inactive origin pG4#1 rev compl inserted on chr1 (Figure 4B)


title: spleen, Negative, Tumor (Ne_tu_2_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne_Tu_peak
Ne_tu_2_IP

source_name: spleen

value: spleen


title: spleen, Negative, Tumor (Ne_tu_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne_Tu_peak
Ne_tu_3_IP


title: spleen, Md5_infected, Tumor (Tu_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_Tu_peak
Tu_3_IP


title: MSB1,Negative, 72 hpi (M_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_MSB1_peak
M_1_IP


title: spleen, Md5_infected, Tumor (Tu_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_Tu_peak
Tu_1_IP


title: MSB1,Negative, 72 hpi (M_2_IP)

description:
m6A-seq
ExpressionProfile_m6A_MSB1_peak
M_2_IP


title: spleen, Md5_infected, Tumor (Tu_2_IP)

description:
m6A-seq
ExpressionProfile_m6A_Tu_peak
Tu_2_IP


title: spleen, Negative, Tumor (Ne_tu_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne_Tu_peak
Ne_tu_1_IP


title: spleen, Md5_infected, Day14 (Md14_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_Md14_peak
Md14_1_IP


title: spleen, Md5_infected, Day14 (Md14_2_IP)

description:
m6A-seq
ExpressionProfile_m6A_Md14_peak
Md14_2_IP


title: spleen, Negative, Day14 (Ne14_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne14_peak
Ne14_3_IP


title: spleen, Md5_infected, Day14 (Md14_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_Md14_peak
Md14_3_IP


title: spleen, Negative, Day14 (Ne14_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne14_peak
Ne14_1_IP


title: spleen, Negative, Day14 (Ne14_2_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne14_peak
Ne14_2_IP


title: spleen, Md5_infected, Day5 (Md5_2_IP)

description:
m6A-seq
ExpressionProfile_m6A_Md5_peak
Md5_2_IP


title: spleen, Md5_infected, Day5 (Md5_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_Md5_peak
Md5_1_IP


title: spleen, Negative, Day5 (Ne5_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne5_peak
Ne5_3_IP


title: MSB1,NaB, 72 hpi (NaB_2_In)

description:
m6A-seq
ExpressionProfile_m6A_NaB_peak
NaB_2_In


title: MSB1,NaB, 72 hpi (NaB_3_In)

description:
m6A-seq
ExpressionProfile_m6A_NaB_peak
NaB_3_In


title: MSB1,NaB, 72 hpi (NaB_1_In)

description:
m6A-seq
ExpressionProfile_m6A_NaB_peak
NaB_1_In


title: MSB1,Negative, 72 hpi (M_3_In)

description:
m6A-seq
ExpressionProfile_m6A_MSB1_peak
M_3_In


title: S1 2x (βA-globin full origin)

description:
Repli-seq
Repli-Seq S1


title: MSB1,Negative, 72 hpi (M_1_In)

description:
m6A-seq
ExpressionProfile_m6A_MSB1_peak
M_1_In


title: MSB1,Negative, 72 hpi (M_2_In)

description:
m6A-seq
ExpressionProfile_m6A_MSB1_peak
M_2_In


title: spleen, Md5_infected, Tumor (Tu_1_IN)

description:
m6A-seq
ExpressionProfile_m6A_Tu_peak
Tu_1_IN


title: spleen, Md5_infected, Tumor (Tu_3_IN)

description:
m6A-seq
ExpressionProfile_m6A_Tu_peak
Tu_3_IN


title: spleen, Md5_infected, Tumor (Tu_2_IN)

description:
m6A-seq
ExpressionProfile_m6A_Tu_peak
Tu_2_IN


title: spleen, Negative, Tumor (Ne_tu_2_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne_Tu_peak
Ne_tu_2_IN


title: spleen, Md5_infected, Day14 (Md14_3_IN)

description:
m6A-seq
ExpressionProfile_m6A_Md14_peak
Md14_3_IN


title: spleen, Negative, Tumor (Ne_tu_1_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne_Tu_peak
Ne_tu_1_IN


title: spleen, Negative, Tumor (Ne_tu_3_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne_Tu_peak
Ne_tu_3_IN


title: spleen, Md5_infected, Day14 (Md14_2_IN)

description:
m6A-seq
ExpressionProfile_m6A_Md14_peak
Md14_2_IN


title: spleen, Md5_infected, Day5 (Md5_3_IP)

description:
m6A-seq
ExpressionProfile_m6A_Md5_peak
Md5_3_IP


title: spleen, Md5_infected, Day14 (Md14_1_IN)

description:
m6A-seq
ExpressionProfile_m6A_Md14_peak
Md14_1_IN


title: spleen, Negative, Day5 (Ne5_1_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne5_peak
Ne5_1_IP


title: spleen, Negative, Day5 (Ne5_2_IP)

description:
m6A-seq
ExpressionProfile_m6A_Ne5_peak
Ne5_2_IP


title: spleen, Md5_infected, Day5 (Md5_1_IN)

description:
m6A-seq
ExpressionProfile_m6A_Md5_peak
Md5_1_IN


title: spleen, Negative, Day5 (Ne5_2_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne5_peak
Ne5_2_IN


title: spleen, Negative, Day5 (Ne5_3_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne5_peak
Ne5_3_IN


title: spleen, Md5_infected, Day5 (Md5_3_IN)

description:
m6A-seq
ExpressionProfile_m6A_Md5_peak
Md5_3_IN


title: spleen, Negative, Day14 (Ne14_3_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne14_peak
Ne14_3_IN


title: MSB1,NaB, 72 hpi (NaB_2)

description:
ExpressionProfile_MSB1_gene_count
NaB_2


title: spleen, Md5_infected, Day5 (Md5_2_IN)

description:
m6A-seq
ExpressionProfile_m6A_Md5_peak
Md5_2_IN


title: spleen, Negative, Day14 (Ne14_1_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne14_peak
Ne14_1_IN


title: spleen, Negative, Day14 (Ne14_2_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne14_peak
Ne14_2_IN


title: spleen, Negative, Day5 (Ne5_1_IN)

description:
m6A-seq
ExpressionProfile_m6A_Ne5_peak
Ne5_1_IN


title: MSB1,Negative, 72 hpi (M_1)

description:
ExpressionProfile_MSB1_gene_count
M_1


title: spleen, Md5_infected, Tumor (Tu_3)

description:
ExpressionProfile_SP_gene_count
Tu_3


title: spleen, Md5_infected, Tumor (Tu_2)

description:
ExpressionProfile_SP_gene_count
Tu_2


title: MSB1,Negative, 72 hpi (M_3)

description:
ExpressionProfile_MSB1_gene_count
M_3


title: spleen, Md5_infected, Tumor (Tu_1)

description:
ExpressionProfile_SP_gene_count
Tu_1


title: spleen, Negative, Tumor (Ne_tu_3)

description:
ExpressionProfile_SP_gene_count
Ne_tu_3


title: spleen, Negative, Tumor (Ne_tu_1)

description:
ExpressionProfile_SP_gene_count
Ne_tu_1


title: spleen, Negative, Tumor (Ne_tu_2)

description:
ExpressionProfile_SP_gene_count
Ne_tu_2


title: spleen, Md5_infected, Day14 (Md14_3)

description:
ExpressionProfile_SP_gene_count
Md14_3


title: spleen, Md5_infected, Day14 (Md14_2)

description:
ExpressionProfile_SP_gene_count
Md14_2


title: spleen, Md5_infected, Day14 (Md14_1)

description:
ExpressionProfile_SP_gene_count
Md14_1


title: spleen, Negative, Day14 (Ne14_3)

description:
ExpressionProfile_SP_gene_count
Ne14_3


title: spleen, Negative, Day14 (Ne14_2)

description:
ExpressionProfile_SP_gene_count
Ne14_2


title: spleen, Md5_infected, Day5 (Md5_3)

description:
ExpressionProfile_SP_gene_count
Md5_3


title: MSB1,NaB, 72 hpi (NaB_3)

description:
ExpressionProfile_MSB1_gene_count
NaB_3


title: spleen, Md5_infected, Day5 (Md5_1)

description:
ExpressionProfile_SP_gene_count
Md5_1


title: spleen, Md5_infected, Day5 (Md5_2)

description:
ExpressionProfile_SP_gene_count
Md5_2


title: spleen, Negative, Day5 (Ne5_1)

description:
ExpressionProfile_SP_gene_count
Ne5_1


title: MSB1,NaB, 72 hpi (NaB_1)

description:
ExpressionProfile_MSB1_gene_count
NaB_1


title: spleen, Negative, Day5 (Ne5_3)

description:
ExpressionProfile_SP_gene_count
Ne5_3


title: spleen, Negative, Day14 (Ne14_1)

description:
ExpressionProfile_SP_gene_count
Ne14_1


title: spleen, Negative, Day5 (Ne5_2)

description:
ExpressionProfile_SP_gene_count
Ne5_2


title: MSB1,Negative, 72 hpi (M_2)

description:
ExpressionProfile_MSB1_gene_count
M_2


title: INPUT_SPOT4_R1_2

first: Folkert

last: van Werven

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters "--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC".
BWA (version 0.5.9-r16) (Li & Durbin, 2009) using default parameters was used to perform the read mapping independently to  the S. cerevisiae (SK1)
Genomic alignments were filtered to only include those that were primary, properly paired, uniquely mapped, not soft-clipped, maximum insert size of 2kb and fewer than 3 mismatches using BamTools (version 2.4.0; (Barnett et al, 2011)).
Read counts relative to protein coding genes were obtained using the featureCounts tool from the Subread package (version 1.5.1) (Liao et al, 2014). The parameters used were “-O --minOverlap 1 --nonSplitOnly --primary -s 2 -p -B -P -d 0 -D 1000 -C --donotsort”.
Assembly: Genome_build: SK1 assembly from Keeney lab (http://cbio.mskcc.org/public/SK1_MvO/)
Supplementary files format and content: bw

organism: Saccharomyces cerevisiae

source_name: yeast strains in small batch culture

growth_protocol: Cells were grown in yeast extract-peptone-dextrose (YPD) medium in conical flasks at 30 °C, shaking at 300 RPM in incubators, then switched to pre-sporulation medium for 17 h and further to sporulation medium for 4 h. For mating cells were grown in YPD and treated with alpha factor.

extract_protocol:
Samples were snap-frozen and lysed by beadsbeating and the DNA was fragmented by sonication. IP was performed using agarose beads. Protein was removed by using Proteinase K and DNA was purified over column.
Libraries were prepared using the KAPA hyper prep kit

treatment_protocol: Samples for formaldehyde fixed for ChIP

value: FW8216 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG Kar4-v5::KAN)

tag: gene deletion

tag: condition

value: Sporulation medium 4h

tag: molecule type

value: Input DNA


title: INPUT_MATING_R2

value: FW8199 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG Kar4-v5::KAN)

value: YPD + alpha factor


title: INPUT_MATING_R1


title: INPUT_SPOT4_R1_1


title: INPUT_SPOT0_R2_1

value: Sporulation medium 0h


title: INPUT_SPOT0_R1_1


title: INPUT_SPOT0_R1_2


title: INPUT_EXP_R2_2

value: YPD


title: INPUT_EXP_R1_2


title: KAR4_IP_MATING_R1_2

value: IP DNA


title: KAR4_IP_MATING_R2_2


title: KAR4_IP_MATING_R1_1


title: INPUT_EXP_R1_1


title: INPUT_EXP_R2_1


title: KAR4_IP_SPOT4_R2_2


title: KAR4_IP_SPOT4_R1_1


title: KAR4_IP_SPOT4_R1_2


title: KAR4_IP_SPOT0_R2_1


title: INPUT_SPOT4_R2_1


title: KAR4_IP_SPOT0_R1_2


title: INPUT_SPOT4_R2_2


title: INPUT_SPOT0_R2_2


title: KAR4_IP_EXP_R1_2


title: KAR4_IP_SPOT0_R1_1


title: KAR4_IP_EXP_R2_2


title: KAR4_IP_EXP_R1_1


title: KAR4_IP_MATING_R2_1


title: Mum2-V5_input1

value: FW6500 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG Mum2-v5::KAN)


title: Slz1-V5_input2

value: FW6502 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG Slz1-v5::KAN)


title: Slz1-V5_input1


title: Mum2-V5_input2


title: Ime4-V5_input2

value: FW6057 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG Ime4-v5::KAN)


title: Ime4-V5_input1


title: WT_input2

value: FW1511 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG)

value: wild type


title: WT_input1


title: Slz1-V5_repeat2


title: KAR4_IP_SPOT4_R2_1


title: Slz1-V5_repeat1


title: Mum2-V5_repeat2


title: Mum2-V5_repeat1


title: Ime4-V5_repeat2


title: WT_repeat2


title: WT_repeat1


title: Ime4-V5_repeat1


title: MS_W31

city: Qingdao

first: Hao

last: Zhang

address: 38 Dengzhou, Qingdao Shandong China

institute: Qingdao University School of Pharmacy

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) 脳 exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text files includes RPKM for each sample

source_name: brain

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

tag: tissue

value: brain

tag: genotype

value: WT

value: CUMS-water


title: MS_O13

tag: treatment

value: CUMS-krill oil


title: MS_W95


title: MS_O78


title: MS_O46


title: MS_W75


title: C_O30

value: krill oil


title: C_W70

value: water


title: C_O15


title: C_W1


title: C_W64


title: V2-4-10

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Base-pair quality is examined running fastqc (v0.11.8)
Sequenced reads were mapped to GRCh38 reference GENCODE (p13) annotation (v38) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4) at the gene level; --fractionOverlap 1
Assembly: GRCh38.p13 GENCODE v38
Supplementary files format and content: comma-separated text file raw counts for each sample; first column includes gene symbols

source_name: PDAC Tumor

growth_protocol: Syngeneic KPC tumor chunks (~0.55 mm3, p3) were subcutaneously implanted into the left flank of female C57BL/6 mice and were collected 2 hr post-dosing, 17 days post-enrollment

extract_protocol:
RNA was extracted by using an miRNeasy mini kit.
RNA-Seq libraries were prepared from 500 ng total RNA by using an RNA HyperPrep Kit along with RiboErase (HMR) kit.

treatment_protocol: 0.5 mg/kg lorazepam (50 ug/mL LOR working solution in saline, .01mL/g mouse weight) or DMSO control, I.P, QD, mice were enrolled when tumors reached 100-250 mm3

value: PDAC Tumor

value: DMSO


title: L2-3-3

value: Lorazepam


title: L2-2-1


title: L2-2-10-outlier


title: V2-4-3


title: L2-4-NT


title: V2-2-30


title: C_O72


title: V2-1-1


title: 9F_M_3053

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region


title: 9F_M_3065

tag: strain


title: 9F_M_3054

tag: age


title: 9F_M_3063


title: 9F_M_3061


title: 9F_M_3058


title: 9F_M_3064


title: 9F_M_3060


title: 9F_M_3062


title: 9F_M_3059


title: 9F_M_3052


title: 9F_M_3055


title: 9F_M_3057


title: 9F_M_3050


title: 9F_M_3051


title: 9F_M_3049


title: 9F_M_3046


title: KAR4_IP_SPOT0_R2_2

value: FW8216 (MATa/alpha, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG Kar4-v5::KAN)

value: Sporulation medium 0h


title: 9F_M_3067


title: 9F_M_3047


title: 9F_M_3042


title: 9F_M_3045


title: 9F_M_3044


title: 9F_M_3043


title: 9F_M_3066


title: 9F_M_3056


title: 9F_M_3041


title: 9F_M_3037


title: 9F_M_3035


title: 9F_M_3038


title: 9F_M_3048


title: 9F_M_3040


title: 9F_M_3036


title: 9F_M_3034


title: 9F_M_3033


title: 9F_M_3029


title: 9F_M_3024


title: 9F_M_3022


title: 9F_M_3039


title: 9F_M_3030


title: 9F_M_3028


title: 9F_M_3019


title: 9F_M_3032


title: 9F_M_3020


title: 9F_M_3018


title: 9F_M_3021


title: 9F_M_3023


title: 9F_M_3017


title: 9F_M_3014


title: 9F_M_3015


title: 9F_M_3031


title: 9F_M_3027


title: 9F_M_3025


title: 9F_M_3026


title: 9F_M_3012


title: 9F_M_3008


title: 9F_M_3011


title: 9F_M_3007


title: 9F_M_3006


title: 9F_M_2939


title: 9F_M_3009


title: 9F_M_2938


title: 9F_M_2937


title: 9F_M_2929


title: 9F_M_2934


title: 9F_M_2930


title: 9F_M_3005


title: 9F_M_2935


title: 9F_M_3016


title: 9F_M_2933


title: KAR4_IP_EXP_R2_1

value: FW8199 (MATa, ho::LYS2, lys2, ura3, leu2::hisG, his3::hisG, trp1::hisG Kar4-v5::KAN)

value: YPD

value: IP DNA


title: 9F_M_2932


title: 9F_M_2928


title: 9F_M_2927


title: 9F_M_2926


title: 9F_M_3004


title: 9F_M_2925


title: 9F_M_2924


title: 9F_M_2936


title: 9F_M_2923


title: 9F_M_3010


title: 9F_M_2922


title: 9F_M_2920


title: 9F_M_2918


title: 9F_M_2915


title: 9F_M_2919


title: 9F_M_2931


title: 9F_M_2917


title: 9F_M_2921


title: 9F_M_2910


title: 9F_M_2912


title: 9F_M_2911


title: 9F_M_2908


title: 9F_M_2913


title: 9F_M_2906


title: 9F_M_2914


title: 9F_M_2904


title: 9F_M_2903


title: 9F_M_2909


title: 9F_M_2905


title: 9F_M_2900


title: 9F_M_2901


title: 9F_M_3013


title: 9F_M_2899


title: 9F_M_2897


title: 9F_M_2896


title: 9F_M_2895


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