title: IleumSingleCells - iPGC1a-/-_CHOW - Rep6


title: Rbbp5_Young_Rep2

status: Public on Nov 02 2023

type: SRA

city: Shantou

first: Chengyang

middle: Peter

last: Huang

address: 22 Xinling Street

country: China

institute: Shantou University Medical College

library_source: genomic

data_processing:
ChIP-Seq reads were aligned to the mm10 genome using Bowtie software (for single-end) or Bowtie2 (for paired-end) with default settings. Only uniquely mapping reads with at most two mismatches were retained. The reads of repeated samples were merged in the BAM file for peak calling analysis. Peaks were called using MACS2 with default settings. Bedgraph (Bdg) files were generated using MACS2.
Assembly: mm10
Supplementary files format and content: Bedgraph files with peaks (except for input samples)

molecule: genomic DNA

organism: Mus musculus

source_name: Neural stem cells

growth_protocol: Primary NSCs were isolated from the brain SVZs of young (2 months) and aged (18 months) mice, respectively (Nat Protoc. 2012 Nov; 7(11):2005-2012). Briefly, microdissection of the brain SVZ was performed on ice. The tissue pieces of SVZ from 6 mice were pooled and dissociated into single cells using Neural Tissue Dissociation kit (Miltenyi Biotec). The NSCs were maintained in the initial proliferation medium at 37°C at 5% CO2.

extract_protocol:
NSCs were fixed with 1% formaldehyde for 10 min and quenched with glycine solution for 20 min at room temperature. The fixed NSCs were lysed in ChIP lysis buffer on ice. Chromatin was released during cell lysis and sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-Seq libraries were prepared based on the protocol of KAPA HyperPrep Kit (Roche) complemented with the NEXTflex DNA Barcodes (Bioo Scientific).

tag: cell type

value: Neural stem cells

tag: tissue type

value: Brain SVZ

tag: antibody

value: Rbbp5 (Cell Signaling, D316P)

tag: condition

value: Young


title: eIF4E2_CLIPseq_rep3

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

country: USA

institute: Indiana University School of Medicine

library_source: transcriptomic

data_processing:
sequencing adapters from read2 were removed with CutAdapt (5'adapt: CTCTTCCGATCT, 3'adapt:GATCGTCGGACT); UMI extracted with UMI-tools (pattern "NNNNNNNNNN" located at 3'end)
mapped with RNA-STAR to TgME49 genome (v58). Settings: –outFilterMismatchNoverLmax=0.1, –outFilterScoreMinOverLread=0.75, –outFilterMatchNminOverLread=0.75, –alignIntronMin50, –alignIntronMax=5000
mapped reads deduplicated with UMI-tools
peaks called with Peakachu (options -adaptive mode; -min_cluster_expr_frac = 10-6, -min_block_overlap = 0.8; -min_max_block_expr = 0.8; -mad_multiplier) = 0; -fc_cutoff = 1; -padj_threshold = 0.05)
Assembly: Toxoplasma gondii (TGME49) v58 from toxodb.org
Supplementary files format and content: eIF4E1 & 2 binding profiles across genome (bigwig)
Supplementary files format and content: eIF4E1 & 2 enriched peaks (bed)

molecule: cytoplasmic RNA

organism: Toxoplasma gondii

source_name: RH::TIR1 parental strain

growth_protocol: parasites innoculated and grown in confluent human foreskin fibroblasts in DMEM+10%FBS (no antibiotic) for 48h prior to harvest

extract_protocol:
monolayers were rinsed with PBS, UV-crosslinked 2x 175mJ/cm2 with 254nm.  Monolayers were syringe lysed and parasites were pelleted twice with PBS washes. Parasites were lysed in (50mM Tris pH7.4, 100mM NaCl, 1% NP40, 0.1% SDS, 0.5% sodium deoxycholate) and HA tag was immunoprecipated for 6h after saving an aliquot for size-matched input
library was generated according to eCLIP protocol PMID: 27018577
eCLIP

tag: cell line

value: RH::TIR1 parental strain

value: tachyzoites


title: eIF4E2_CLIPseq_rep2


title: IleumSingleCells - iPGC1afl/fl_HFD - Rep5

type: RNA

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 microarray (8X60K, Design 074809  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 074809_D_F_20150624). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 20 out of 24 microarrays or with a minimal weight of 4 per group from at least one experimental group. At this step, 35743 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 33095 rows each corresponding to a unique ProbeName (provided as data Matrix).

molecule: total RNA

source_name: IleumSingleCells

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

extract_protocol: RNA was extracted using Qiazol reagent, following the protocol.B2

treatment_protocol: For ileum section, the isolation of single cells was performed by a modification of Weiser method, as previously described 27,28. Briefly, the ileum was harvested, washed with cold saline solution and cut longitudinally. To remove luminal content, ileum was transferred into Hank’s balanced salt solution with 0.5mM-DTT. Then, ileum was placed into 20 ml of Chelating Buffer (Na2PO4 5mM, NaCl 96mm, Na Citrate27mM, KH2PO4 8mM, KCl 1.5 mm, D-Sorbitol 55mM, Sucrose 44mM, DTT 0.5 mM), and incubated at 4˚C with constant stirring for 20 minutes and supernatant was collected. After, ileum was transferred into a 50ml tube with 15 ml of Chelating buffer, gently shaken by hand (30 inversions) and supernatant was collected. This operation was repeated eight time. All collected supernatant were centrifuged at 1000g, washed with cold saline buffer and then stored at -80°C.

tag: genotype

tag: diet

value: HFD


title: Animal C2 Deep White Matter ROI 73

city: Minneapolis

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description:
GeoMx DSP
ROI_73_DWM_C2

data_processing:
library strategy: GeoMx DSP
Reads were trimmed, merged, and aligned to retrieve probe identity, and the unique molecular identifier of each read was used to remove PCR duplicates converting reads to digital counts for each target within an individual AOI
Supplementary files format and content: CountsROI_matrix.csv - ontains raw counts for the 94 samples that passed  min limit of quantification of 2
Supplementary files format and content: normROI_matrix.csv -  contains log2 Q3 normalized counts for 94 samples
Supplementary files format and content: countsAOI_matrix.csv - contains raw counts for the 18 samples that passed the minimum limit of quantification 2
Supplementary files format and content: normAOI_matrix.csv - contains log2 Q3 normalized counts for 18 samples

organism: Macaca nemestrina

source_name: Fetal brain

extract_protocol:
Unstained 5 µm-thick tissue sections cut from PFA-fixed, paraffin-embedded specimens were mounted on Colorfrost microscope slides
In situ hybridizations with the GeoMx Whole Transcriptome Atlas Panel (WTA, 18,676 total targets) were performed in Buffer R
Rabbit polyclonal anti-Olig2 antibody was incubated first at 1:100 in Buffer W, followed by Goat anti-rabbit AF647 for visualization. The remaining morphology markers were collectively diluted in Buffer W at the following concentrations: 1:50 RBFOX3 (NeuN), 1:400 GFAP, and STYO 83 for nuclei visualization
Each slide was scanned with a 20X objective and default scan parameters on a GeoMx Digitial Spatial Profiler
ROI placement: Geometric 500 µm diameter circle ROIs were placed in the subcortex (Superficial WM; n=3/section), WM tracts (Deep WM; n=3/section), and cortical layers IV-VI (GM; n=3/section). One maximum area (660 µm X 785 µm) ROI was placed at the GM/WM interface on each section
ALOI segmentation: Segmentation mask was applied to the GM/WM interface maximum area to select Olig2+, GFAP+, and NeuN+ areas of interest (AOI).
Sequencing libraries were generated by PCR from the photo-released indexing oligos and ROI-specific Illumina adapter sequences and unique i5 and i7 sample indices were added
Total target counts per DSP collection plate for sequencing were calculated from the total samples areas (µm2). For WTA libraries, the target sequencing depth was 100 counts/µm2. Pooled libraries were sequenced at 2×27 base pairs and with the dual-indexing workflow on an Illumina NovaSeq

tag: tissue

value: Fetal brain

tag: brain reigion

value: DWM

tag: zika infection

value: mock

tag: animal id

tag: region of interest (roi) identifer


title: eIF4E2_CLIPseq_rep1


title: Input_Young_Rep2

value: none (input)


title: Animal Z8 Gray Matter ROI 69

description:
GeoMx DSP
ROI_69_GM_Z8

value: GM

value: ZIKV


title: Kmt2d_Aged_Rep2

value: Kmt2d (Millipore, ABE1867)

value: Aged


title: Kmt2d_Young_Rep2


title: eIF4E1_input_rep3


title: Animal Z8 Gray Matter ROI 68

description:
GeoMx DSP
ROI_68_GM_Z8


title: eIF4E1_input_rep1


title: Animal Z8 Gray Matter ROI 67

description:
GeoMx DSP
ROI_67_GM_Z8


title: eIF4E1_input_rep2


title: IleumSingleCells - iPGC1a-/-_HFD - Rep2


title: IleumSingleCells - iPGC1a-/-_CHOW - Rep5

value: CHOW


title: Animal Z8 Superficial White Matter ROI 66

description:
GeoMx DSP
ROI_66_SWM_Z8

value: SWM


title: Animal Z8 Superficial White Matter ROI 65

description:
GeoMx DSP
ROI_65_SWM_Z8


title: sp7 mutant 5.8 mm

city: Boston

first: Shannon

last: Fisher

state: MA

address: 700 Albany Street

institute: Boston University

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoded processing, gene counting, and aggregation were performed using Cell Ranger software version 3.1.0 (10X Genomics)
Assembly: danRer11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: craniofacial skeletal tissues

extract_protocol:
Fish were euthanized and transferred to ice-cold PBS. In <2 min, we cut off the head just above the pectoral fins, and removed the eyes and brain to enrich for musculoskeletal tissue.The remaining skull was rinsed 2X in PBS, and transferred to a dissociation buffer containing 0.25% trypsin-EDTA and 10mg/mL collagenase at 30°. Alternating between pipetting and incubation at 30°, the tissue was fully dissociated, again in <2 min. Digestion was stopped by addition of DMEM w/ 10% BSA. After centrifugation at 700g for 5min, cells were resuspended in PBS, centrifuged again to wash, and the final pellet resuspended in 100μL of FACS buffer (1x PBS, 2% BSA and 1mM EDTA). Single cells were isolated by filtration through a 40μm nylon mesh.
Cells were loaded onto 10X Genomics microfluidic chips and processed for scRNAseq according to manufacturer's instructions.

value: craniofacial skeletal tissues


title: eIF4E1_CLIPseq_rep3


title: eIF4E1_CLIPseq_rep2


title: IleumSingleCells - iPGC1a-/-_HFD - Rep5


title: corneal epithelial cells 8% O2 rep 3

city: Wuhan

first: Ming-Feng

last: Wu

address: 1277 Jiefang Avenue

institute: Wuhan Union Hospital

data_processing:
Quality control was performed by FastQC v 0.11.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v 1.9.1
Trimmed sequence reads were mapped tomm10 using HISAT2 v 2.0.4
StringTie v 1.3.4d was used to assemble reads and calculate gene transcript expression level (FPKM).
Assembly: mm10
Supplementary files format and content: Excel file including FPKM values for all samples

source_name: cornea

extract_protocol:
RNA was harvested using TRIzol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

value: cornea

value: corneal epithelial cells

value: WT

tag: treatment

value: 8% oxygen


title: sp7 mutant  7.0 mm


title: Animal Z8 Superficial White Matter ROI 64

description:
GeoMx DSP
ROI_64_SWM_Z8


title: WT 7.0 mm


title: IleumSingleCells - iPGC1a-/-_CHOW - Rep2


title: corneal epithelial cells 21% O2 rep 1

value: 21% oxygen


title: IleumSingleCells - iPGC1afl/fl_HFD - Rep2

value: HFD


title: Animal Z8 Supe White Matter ROI 63

description:
GeoMx DSP
ROI_63_DWM_Z8

value: Fetal brain


title: corneal epithelial cells 8% O2 rep 2


title: corneal epithelial cells 21% O2 rep 3


title: WT 5.8 mm


title: corneal epithelial cells 21% O2 rep 2


title: Control, Lbr and Lmna Barcode Library

city: Ottawa

first: José Alex

last: Lourenço Fernandes

state: ON

address: 501 Smyth Rd

country: Canada

institute: Ottawa Hospital Research Institute

description: 10x Genomics

data_processing:
Fastq files were aligned to the mm10 genome using CellRanger version 6.1.2 (Cell Ranger software, 10x Genomics). Output files were filtered and analyzed using Scanpy version 1.9.1 in Python (Python Core Team n.d.). Genes detected in less than 3 cells were removed from the analysis. Low-quality cells (less than 200 genes detected, more than 2500 genes detected or more than 18% of mitochondrial genes) were also excluded. Scrublet version 0.2.2 was used to detect doublets. Replicates were demultiplexed with using the MULTI-seq workflow. To annotate cell types, we trained a deep learning model grounded on previously published retinal single cell expression data30 using scDeepSort version 1.0. Mitochondrial gene regression and initial gene expression analysis was performed using scVI-tools version 0.19.0. Differential gene expression analyses were performed using MAST version 1.24.0. Data integration was carried out on PostgreSQL version 14.3 (PostgreSQL Core Team n.d.) and Python’s library Pandas version 1.5.2 (Pandas Core Team n.d.).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Adult retinas were dissected and placed in StemPro Accutase (Gibco) for 30 minutes at 37 °C. Cells were triturated manually, incubated with Dapi as a viability marker, and then sorted by the OHRI Flow Cytometry and Cell Sorting Facility using a Beckman Coulter MoFlo XDP.
After flow cytometric sorting, cells were barcoded with ‘anchor’ and ‘co-anchor’ lipid-modified oligonucleotides generously provided by the Zev Gartner lab. Barcode oligonucleotides were purchased from Integrated DNA Technologies as follows. Barcode 1: F: 5′- CCTTGGCACCCGAGAATTCCAGGAGAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′; Barcode 2: F: 5′- CCTTGGCACCCGAGAATTCCACCACAATGAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′; Barcode 3: F: 5′- CCTTGGCACCCGAGAATTCCATGAGACCTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA-3′;  Each replicate was incubated with barcode oligonucleotides for 10 minutes. Cells were pelleted and washed 3 times with PBS. Replicates were pooled and processed in a single 10X Genomics Chromium run.

value: Retina

value: Rods


title: MO-994.1G.A

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

data_processing:
Paired-end reads were aligned to rat genome build Rn7 with STAR v2.6.1
Kallisto was used to generate TPM which were then processed through NOISeq v2.42.0 for batch correction. One outlier sample was identified from the Control treatment group (MO2) and was removed from further analysis.
AltAnalyze v2.1.4.4 (EnsMart106 database) was then used for differential expression analysis on the batch corrected data matrix.
The AltAnalyze supplied empirical Bayes moderated t-test was performed followed by Benjamini-Hochberg adjustment for false discovery (FDR).
Final threshold cutoffs were an adjusted p-value < 0.05 (FDR) and fold change ≥ 1.5. GO and KEGG pathway enrichment was also performed in AltAnalyze using the integrated GO-Elite pathway analysis tool
Assembly: Rn7
Supplementary files format and content: TPM_NPC.txt tab delimited file containing Gene-level Transcript Per Million (TPM) estimates before outlier removal
Supplementary files format and content: TPM_NPC_outlierRemoved.txt tab delimited file containing Gene-level Transcript Per Million (TPM) estimates after outlier removal

organism: Rattus norvegicus

source_name: brain

growth_protocol: Neural progenitor cells were isolated from the brain of E15 Sprague Dawley rat fetuses and cultured in NeuroCult basal medium supplemented with 1% Pen/Strep, 1X N-2 supplement, 1X B-27 supplement, 20ng/mL human epidermal growth factor, 20ng/mL human fibroblast growth factor, and 1:500 dilution of 0.2% heparin solution in ultra-low attachment microplates where they spontaneously form spheroids (neurospheres)

extract_protocol:
RNA was extracted from Neurospheres using TRIzol and pipet homogenization. Glycogen was added to the TRIzol sample after homogenization to aid in RNA recovery.  RNA quantification was assessed using Epoch Biotek spectrophotometer (Biotek Instruments, Winooski, Vermont)
RNA was QC analyzed by Bioanalyzer (Agilent, Santa Clara, CA). To isolate polyA RNA for library preparation, NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used with 1 µg good quality total RNA as input.
The polyA RNA was enriched using SMARTer Apollo automated NGS library prep system (Takara Bio USA, Mountain View, CA). Next, NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs) was used for library preparation under PCR cycle number of 8

treatment_protocol: The effect of radiation on NSp growth and differentiation was measured after 0 and 1 Gy photon radiation (day=3 after NPCs seeding) with a CellRad+ benchtop X-ray irradiator (Precision). 5uM of Noggin and 200uM Ascobic Acid as tretament pre and post radiation exposure

value: brain

value: brain primary cell line

value: Neural Progenitor Cell

tag: strain

value: Sprague Dawley

value: 1Gy 200 uM Ascorbic Acid


title: corneal epithelial cells 1% O2 rep 3

value: 1% oxygen


title: MO-970.1G.A

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt


title: Input_for_Cbx3_Aged_Rep2

value: Neural stem cells

value: Brain SVZ

value: none (input)

value: Aged


title: Animal Z8 Deep White Matter ROI 62

description:
GeoMx DSP
ROI_62_DWM_Z8

value: DWM

value: ZIKV


title: MO-946.1G.A

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt


title: IleumSingleCells - iPGC1afl/fl_CHOW - Rep1

value: CHOW


title: Input_for_Cbx3_Young_Rep2

value: Young


title: eIF4E1_CLIPseq_rep1

value: RH::TIR1 parental strain

value: tachyzoites


title: corneal epithelial cells 1% O2 rep 1

value: cornea

value: corneal epithelial cells

value: WT


title: Animal Z5 Gray Matter ROI 43

description:
GeoMx DSP
ROI_43_GM_Z5

value: Fetal brain

value: GM


title: Cbx3_Aged_Rep2

value: Cbx3 (Millipore, 05-690)


title: Animal Z8 Deep White Matter ROI 61

description:
GeoMx DSP
ROI_61_DWM_Z8


title: Animal Z5 Gray Matter ROI 42

description:
GeoMx DSP
ROI_42_GM_Z5


title: MO-1066.1G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: brain

value: brain primary cell line

value: Neural Progenitor Cell

value: Sprague Dawley

value: 1Gy 5uM Noggin


title: corneal epithelial cells 1% O2 rep 2

value: 1% oxygen


title: Aged NSC, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (10x Genomics)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

source_name: Brain SVZ

extract_protocol:
Primary NSCs were isolated from the brain SVZ of the young (2 months) and aged (15-18 months) mice, respectively (Nat Protoc. 2012 Nov; 7(11):2005-2012). Briefly, microdissection of the brain SVZ was performed on ice. The tissue pieces of SVZ from 5 mice were pooled and dissociated into single cells using Neural Tissue Dissociation kit. The isolated cells were maintained in the initial proliferation medium before used in scRNAseq library generation.
scRNAseq library was prepared according to the protocol of 10x Genomics (single cell 3’ v3 protocol). Briefly, the primary NSCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Neural stem cells

value: Brain SVZ

tag: age

value: 15-18 months old


title: Animal Z5 Gray Matter ROI 41

description:
GeoMx DSP
ROI_41_GM_Z5

value: ZIKV


title: Young NSC, scRNAseq

description: 10x Genomics

value: 2 months old


title: Input_for_Cbx3_Aged_Rep1

value: none (input)

value: Aged


title: MO-1065.1G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt


title: mESC_BRM014_8h_PRO-seq_rep2

first: Karen

last: Adelman

address: 45 Shattuck St. LHRRB-201a

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description:
8h BRM014 2
PRO-seq

data_processing:
Reads were trimmed for a minimum quality score of 20 using a custom script (https://github.com/AdelmanLab/NIH_scripts/tree/main/trim_and_filter_PE), adapter sequences were removed using cutadapt version 1.14.
Data was mapped to mm10 using bowtie 1.2.2
Strand-specific Bedgraphs were generated from dedpulicated SAM files.
Assembly: mm10
Supplementary files format and content: All files with the .bw suffix are normalized BigWig files containing combined data from all replicates of the indicated treatment condition.

source_name: Mouse embryonic stem cells

growth_protocol: Cells were grown in serum-free ES media supplemented with glutamine (Gibco), monothioglycerol (Sigma), MEK inhibitor (Reprocell), GSK3 inhibitor (Reprocell) and LIF (Cell Guidance Systems). Cells were passaged onto new gelatin-coated plates every other day, and received fresh media on other days.

extract_protocol: For nascent RNA, cells were permeabilized and run on mostly as described (Reimer et al, 2021), but with a few changes. For permeabilization, buffers W and P were supplemented with 1 mM EGTA, and buffer F was supplemented with 1 mM EDTA. Cells were resuspended in 500 µL Buffer W, 10 mL Buffer P was added, and this was incubated on a Nutator for 1 minutes, then 6 minutes on ice. Cells were washed once with 10mL buffer W, before being resuspended in Buffer F. Run-on was performed on 30M permeabilized cells, and in the 2X run-on reaction mix MgCl2 was present at 10 mM, SUPERase-In at 0.4 U/µL and (biotin-)rNTPs are at 50 µM each. Run-on was performed at 37°C for 15 minutes, and Biotin-11-C/UTP (Perkin-Elmer) were mixed with regular rGTP and rATP (New England BioLabs). After RNA isolation using the Total RNA Purification Kit (Norgen Biotek Corp), biotinylated RNAs were immediately bound to Streptavidin M-280 magnetic beads (ThermoFisher) and binding and washing was done as described.

treatment_protocol: Cells were treated with 1µM BRM014 (in 0.1% DMSO) for 8h.

value: F121-9 wt mESCs

value: 1µM BRM014, 8h

tag: assay

value: PRO-seq


title: Control, Lbr and Lmna scRNA-seq Library

description: 10x Genomics

value: Retina

value: Rods


title: MO-1041.1G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: brain

value: brain primary cell line


title: Animal Z5 Superficial White Matter ROI 40

description:
GeoMx DSP
ROI_40_SWM_Z5

value: Fetal brain

value: SWM


title: Input_for_Cbx3_Young_Rep1

value: Young


title: Animal Z5 Superficial White Matter ROI 39

description:
GeoMx DSP
ROI_39_SWM_Z5


title: MO-1017.1G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: Neural Progenitor Cell

value: Sprague Dawley

value: 1Gy 5uM Noggin


title: Input_Aged_Rep1

value: Neural stem cells

value: Brain SVZ


title: mESC_BRM014_8h_PRO-seq_rep1

description:
8h BRM014 1
PRO-seq


title: mESC_BRM014_4h_PRO-seq_rep2

description:
4h BRM014 2
PRO-seq

treatment_protocol: Cells were treated with 1µM BRM014 (in 0.1% DMSO) for 4h.

value: 1µM BRM014, 4h


title: Animal Z5 Superficial White Matter ROI 38

description:
GeoMx DSP
ROI_38_SWM_Z5

value: ZIKV


title: MO-1064.1G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: 1Gy none


title: MO-32.1G.A

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: 1Gy 200 uM Ascorbic Acid


title: Input_Young_Rep1

value: none (input)


title: Animal Z5 Deep White Matter ROI 37

description:
GeoMx DSP
ROI_37_DWM_Z5

value: DWM


title: mESC_BRM014_4h_PRO-seq_rep1

description:
4h BRM014 1
PRO-seq

value: F121-9 wt mESCs

value: PRO-seq


title: Cbx3_Aged_Rep1

value: Cbx3 (Millipore, 05-690)

value: Aged


title: Cbx3_Young_Rep1


title: Animal Z5 Deep White Matter ROI 36

description:
GeoMx DSP
ROI_36_DWM_Z5

value: Fetal brain


title: MO-1063.1G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: brain

value: brain primary cell line


title: MO-1039.1G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: Neural Progenitor Cell

value: Sprague Dawley


title: Cbx3_Young_Rep2

value: Neural stem cells

value: Young


title: mESC_BRM014_2h_PRO-seq_rep2

description:
2h BRM014 2
PRO-seq

treatment_protocol: Cells were treated with 1µM BRM014 (in 0.1% DMSO) for 2h.

value: 1µM BRM014, 2h


title: Animal Z5 Deep White Matter ROI 35

description:
GeoMx DSP
ROI_35_DWM_Z5

value: ZIKV


title: MO-1015.1G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: 1Gy none


title: MO-982.0G.A

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: 0Gy 200 uM Ascorbic Acid


title: Animal C3 Gray Matter ROI 31

description:
GeoMx DSP
ROI_31_GM_C3

value: GM

value: mock


title: mESC_DMSO_8h_PRO-seq_rep2

description:
DMSO 2
PRO-seq

treatment_protocol: Cells were treated with 0.1% DMSO for 8h.

value: F121-9 wt mESCs


title: mESC_BRM014_2h_PRO-seq_rep1

description:
2h BRM014 1
PRO-seq

value: PRO-seq


title: Animal C3 Gray Matter ROI 30

description:
GeoMx DSP
ROI_30_GM_C3


title: MO-958.0G.A

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt


title: mESC_DMSO_8h_PRO-seq_rep1

description:
DMSO 1
PRO-seq


title: Wdr5_Young_Rep1

value: Brain SVZ

value: Wdr5 (Proteintech, 15544-1-AP)


title: MO-934.0G.A

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt


title: mESC_DMSO_4h_PRO-seq_rep2

description:
4h DMSO 2
PRO-seq

treatment_protocol: Cells were treated with 0.1% DMSO for 4h.


title: Wdr5_Aged_Rep1

value: Aged


title: Rbbp5_Young_Rep1

value: Rbbp5 (Cell Signaling, D316P)


title: Animal C3 Gray Matter ROI 29

description:
GeoMx DSP
ROI_29_GM_C3

value: Fetal brain


title: mESC_DMSO_4h_PRO-seq_rep1

description:
4h DMSO 1
PRO-seq


title: MO-26.0G.A

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: brain

value: brain primary cell line

value: Neural Progenitor Cell


title: Rbbp5_Aged_Rep1

value: Neural stem cells


title: Kmt2d_Aged_Rep1

value: Kmt2d (Millipore, ABE1867)


title: Animal C3 Superficial White Matter ROI 28

description:
GeoMx DSP
ROI_28_SWM_C3

value: SWM


title: Animal C3 Superficial White Matter ROI 27

description:
GeoMx DSP
ROI_27_SWM_C3


title: Kmt2d_Young_Rep1

value: Young


title: Input_Aged_Rep2

data_processing:
ChIP-Seq reads were aligned to the mm10 genome using Bowtie software with default settings. Only uniquely mapping reads with at most two mismatches were retained. The reads of repeated samples were merged in the BAM file for peak calling analysis. Peaks were called using MACS2 with default settings. Bedgraph (Bdg) files were generated using MACS2.
Assembly: mm10
Supplementary files format and content: Bedgraph files with peaks (except for input samples)

growth_protocol: Primary NSCs were isolated from the brain SVZs of young (2 months) and aged (18 months) mice, respectively (Nat Protoc. 2012 Nov; 7(11):2005-2012). Briefly, microdissection of the brain SVZ was performed on ice. The tissue pieces of SVZ from 6 mice were pooled and dissociated into single cells using Neural Tissue Dissociation kit. The NSCs were maintained in the initial proliferation medium at 37°C at 5% CO2.

value: 18 months


title: MO-1053.0G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: Sprague Dawley

value: 0Gy 5uM Noggin


title: Animal C3 Superficial White Matter ROI 26

description:
GeoMx DSP
ROI_26_SWM_C3

value: mock


title: Animal C3 Deep White Matter ROI 25

description:
GeoMx DSP
ROI_25_DWM_C3

value: DWM


title: mESC_BRM014_2h_ChIP-seq_BRG1_rep1

description: BRG1 BRM014 1

data_processing:
Reads were trimmed for a minimum quality score of 20 using a custom script (https://github.com/AdelmanLab/NIH_scripts/tree/main/trim_and_filter_PE), adapter sequences were removed using cutadapt version 1.14.
Data was mapped to mm10 using bowtie 1.2.2
Bedgraphs were generated in 50bp bins from dedpulicated SAM files.
Assembly: mm10
Supplementary files format and content: All files with the .bw suffix are normalized BigWig files containing combined data from all replicates of the indicated treatment condition.

extract_protocol:
After the indicated treatment interval, cells were fixed for 1 h in 2 mM DSG with the addition of 1% formaldehyde for the final 12.5 min, as described in.86 Crosslinking was quenched by the addition of glycine to a final concentration of 0.125 M. Cells were collected and washed with ice-cold 1X PBS before being resuspended in Sonication Buffer (20 mM Tris, pH 8.0, 2 mM EDTA, 0.5 mM EGTA, 1X Complete Mini EDTA-free Protease Inhibitor Cocktail [Roche 11836170001], 0.5% SDS, and 0.5 mM PMSF) at a concentration of 1 x 108 cells per mL. Chromatin was sheared to an average fragment size of ∼200 bp using a QSonica sonicator, flash-frozen in liquid nitrogen, and stored at -80°C until use. ChIP material was diluted into IP buffer (20 mM Tris pH 8.0, 2 mM EDTA, 0.5% Triton X-100, 150 mM NaCl, 10% Glycerol, 5% BSA) and pre-cleared with 30 μL of Protein A agarose beads (Millipore Cat No. 16-125) for 1 h at 4°C. Cleared samples were collected and combined with primary antibody before overnight incubation at 4°C with rotation. Subsequently, 200 μL Protein A beads were added to each IP reaction, and samples were rotated for 2 h at 4°C. Samples were washed once with Low-Salt Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 150 mM NaCl, 0.1% SDS), three times with High-Salt Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 1% Triton X-100, 500 mM NaCl, 0.1% SDS), once with Lithium Chloride Buffer (20 mM Tris pH 8.0, 2 mM EDTA, 250 mM LiCl, 1% IGEPAL CA-630, 1% sodium deoxycholate), and twice with TE Buffer (10 mM Tris-HCl, 1mM EDTA). Each wash was performed by rotating samples for 3 minutes with 1 mL volume of ice-cold wash solution. Two elutions were performed by resuspending beads in Elution Buffer (100 mM NaHCO3, 1% SDS) and rotating for 15 min at room temperature (22°C). The combined eluate was supplemented with 200 mM NaCl and incubated overnight in a 65°C water bath. Samples were treated with Proteinase K (New England Biolabs P8107), extracted with phenol:chloroform:isoamyl alcohol (25:24:1, Sigma P3803), and resuspended in 65 μl H2O. To enable accurate sample normalization, an equal amount of fragmented D. melanogaster DNA was added to the eluate of each sample.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions.

value: F121-9 wt mESCs

value: 1µM BRM014, 2h

value: ChIP-seq


title: MO-1029.0G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt


title: mESC_DMSO_2h_ChIP-seq_BRG1_rep2

description: BRG1 DMSO 2

treatment_protocol: Cells were treated with 0.1% DMSO for 2h.


title: Input_Aged_Rep1

value: Brain SVZ


title: Animal C3 Deep White Matter ROI 24

description:
GeoMx DSP
ROI_24_DWM_C3

value: Fetal brain


title: MO-1005.0G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: brain


title: mESC_DMSO_2h_ChIP-seq_BRG1_rep1

description: BRG1 DMSO 1


title: Input_Young_Rep2

value: 2 months


title: MO-25.0G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: brain primary cell line

value: Neural Progenitor Cell

value: 0Gy none


title: Animal C3 Deep White Matter ROI 23

description:
GeoMx DSP
ROI_23_DWM_C3


title: mESC_siEP400_BRM014_4h_ATAC-seq_rep3

description: siEP400 BRM014 3

extract_protocol:
Harvested cells were resuspended in 50µL CSK Lysis Buffer (10 mM PIPES, pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton-X-100), incubated on ice for 5 min, and centrifuged for 5 min at 500 ´ g and 4ºC.
Samples were tagmented for 30 min at 37ºC using TDE1 Tagment DNA Enzyme (Illumina).

treatment_protocol: Cells were treated with siEP400 for 72h, then treated with 1µM BRM014 (in 0.1% DMSO) for 4h.

value: siEP400, 72h and 1µM BRM014, 4h

value: ATAC-seq


title: Input_Young_Rep1

value: Neural stem cells


title: MO-1051.0G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: Sprague Dawley


title: mESC_siEP400_BRM014_4h_ATAC-seq_rep2

description: siEP400 BRM014 2


title: Animal Z2 Gray Matter ROI 108

description:
GeoMx DSP
ROI_108_GM_Z2

value: GM

value: ZIKV


title: mESC_siEP400_BRM014_4h_ATAC-seq_rep1

description: siEP400 BRM014 1


title: H3K27me3_Aged_Rep1

value: H3K27me3 (Active motif, #39055)

value: 18 months


title: Animal Z2 Gray Matter ROI 107

description:
GeoMx DSP
ROI_107_GM_Z2


title: MO-1027.0G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt


title: MO-1054.0G.N

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: 0Gy 5uM Noggin


title: mESC_BRM014_2h_ChIP-seq_BRG1_rep2

description: BRG1 BRM014 2

value: F121-9 wt mESCs

value: 1µM BRM014, 2h

value: ChIP-seq


title: MO-1003.0G.C

description:
TPM_NPC.txt
TPM_NPC_outlierRemoved.txt

value: brain


title: H3K27me3_Young_Rep2

value: Brain SVZ

value: 2 months


title: Animal Z2 Superficial White Matter ROI 105

description:
GeoMx DSP
ROI_105_SWM_Z2

value: Fetal brain

value: SWM


title: mESC_siEP400_DMSO_4h_ATAC-seq_rep2

description: siEP400 DMSO 2

treatment_protocol: Cells were treated with siEP400 for 72h, then treated with 0.1% DMSO for 4h.

value: siEP400, 72h and 0.1% DMSO, 4h


title: H3K27me3_Young_Rep1


title: Fetal Brain Animal CTRL003 mock Brain region 1

data_processing:
Sequenced reads were trimmed with Trim galore using default parameters version 0.6.4
Globin and rRNA reads filtered out with bowtie2 version 2.4.2
Reads aligned to Macaca nemestring genome version1 ensembl annotaiton version 106
Gene counts obtained using HTSeq version 0.13.5
Assembly: Macaca nemestring genome version1 ensembl annotaiton version 106
Supplementary files format and content: tab-delimited text file including all gene count values for each sample

source_name: fetal brain

extract_protocol:
Brain samples were immersed immediately in RNALater, stored at 4°C for 24 h, and subsequently frozen at -80°C. RNA was isolated from TRIzol homogenates following the QIAGEN RNeasy protocol
Ribosomal RNA (rRNA) was depleted from each RNA sample using the Ribo-ZerorRNA Removal Kit (Epicentre). Libraries were prepared from 150 ng of rRNA-depleted RNA following the KAPA Stranded RNA-Seq with RiboErase workflow for Total RNA-Seq libraries (KAPA Biosystems)

treatment_protocol: Pregnant pigtail macaques received subcutaneous (s.c.) administration of 1x10^7 PFU of either ZIKV/Cambodia or ZIKV/Brazil in five separate 100 ul injections adminsitered into the bilateral forearm at different sites. Control animals received s.c. administration of media alone following the same protocol. Cesarean section was performed at least 10 days before the natural due date (~172 days gestation) and fetal brains were sectioned to collect tissue samples for Total RNA-seq

value: fetal brain

value: mock


title: Animal Z2 Superficial White Matter ROI 104

description:
GeoMx DSP
ROI_104_SWM_Z2


title: Fetal Brain Animal CTRL003 mock Brain region 3


title: H3K27ac_Aged_Rep2

value: Neural stem cells

value: H3K27ac (Abcam, #ab4729)


title: Animal Z2 Superficial White Matter ROI 103

description:
GeoMx DSP
ROI_103_SWM_Z2

value: ZIKV


title: mESC_siNT_BRM014_4h_ATAC-seq_rep2

description: siNT BRM014 2

treatment_protocol: Cells were treated with siNT for 72h, then treated with 1µM BRM014 (in 0.1% DMSO) for 4h.

value: siNT, 72h and 1µM BRM014, 4h

value: ATAC-seq


title: H3K27ac_Aged_Rep1

value: 18 months


title: Animal Z2 Deep White Matter ROI 99

description:
GeoMx DSP
ROI_99_DWM_Z2

value: DWM


title: H3K27me3_Aged_Rep2

value: H3K27me3 (Active motif, #39055)


title: mESC_siNT_BRM014_4h_ATAC-seq_rep1

description: siNT BRM014 1

value: F121-9 wt mESCs


title: Fetal Brain Animal CTRL003 mock Brain region 7


title: Animal Z2 Deep White Matter ROI 98

description:
GeoMx DSP
ROI_98_DWM_Z2


title: Fetal Brain Animal CTRL003 mock Brain region 9


title: mESC_siNT_DMSO_4h_ATAC-seq, rep2

description: siNT DMSO 2

treatment_protocol: Cells were treated with siNT for 72h, then treated with 0.1% DMSO for 4h.

value: siNT, 72h and 0.1% DMSO, 4h


title: Fetal Brain Animal CTRL003 mock Brain region 5


title: Animal Z2 Gray Matter ROI 106

description:
GeoMx DSP
ROI_106_GM_Z2

value: GM


title: Fetal Brain Animal zika003 ZIKVB Brain region 1


title: H3K27ac_Young_Rep2

value: Brain SVZ

value: 2 months


title: mESC_siEP400_DMSO_4h_ATAC-seq_rep3

description: siEP400 DMSO 3


title: mESC_siNT_DMSO_4h_ATAC-seq_rep1

description: siNT DMSO 1


title: H3K27ac_Young_Rep1


title: Animal Z3 Gray Matter ROI 97

description:
GeoMx DSP
ROI_97_GM_Z3

value: Fetal brain


title: H3K4me3_Aged_Rep2

value: H3K4me3 (Abcam, #ab8580)


title: mESC_BRM014_8h_ATAC-seq_rep3

description: 8h BRM014 3

value: 1µM BRM014, 8h


title: H3K4me3_Aged_Rep1


title: Animal Z3 Gray Matter ROI 96

description:
GeoMx DSP
ROI_96_GM_Z3


title: Fetal Brain Animal zika003 ZIKVB Brain region 3

value: fetal brain


title: mESC_siEP400_DMSO_4h_ATAC-seq_rep1

description: siEP400 DMSO 1

value: siEP400, 72h and 0.1% DMSO, 4h


title: Fetal Brain Animal zika003 ZIKVB Brain region 5


title: H3K4me3_Young_Rep2

value: Neural stem cells


title: mESC_BRM014_8h_ATAC-seq_rep2

description: 8h BRM014 2


title: Animal Z2 Deep White Matter ROI 95

description:
GeoMx DSP
ROI_95_DWM_Z2

value: ZIKV


title: Animal Z3 Superficial White Matter ROI 94

description:
GeoMx DSP
ROI_94_SWM_Z3

value: SWM


title: mESC_BRM014_8h_ATAC-seq_rep1

description: 8h BRM014 1

value: ATAC-seq


title: H3K4me3_Young_Rep1


title: Fetal Brain Animal zika003 ZIKVB Brain region 9


title: MV411_ATACseq_8h_DMSO_rep3

library_source: other

data_processing:
All custom scripts described here are accessible at zenodo (doi:10.5281/zenodo.5519915).
Reads were trimmed for a minimum quality score of 20 using a custom script trim_and_filter_PE. Cutadapt 1.14 was used to remove adaptor sequences and low-quality reads.
In order to identify spike-in reads, read pairs were next aligned to the D. melanogaster genome (dm6) using bowtie 1.2.2 (-k1 -v2 -X1000, --best --p 5 --allow-contain).
All reads that failed to align to the spike genome were subsequently aligned to the H. sapiens genome (hg38) using bowtie 1.2.2 (-k1 -v2 -X1000 --best -p 5 -S --allow-contain).
Fragments were deduplicated and filtered to retain unique reads between 10 and 150 bp, representing regions of accessible chromatin, which were then converted to bedGraph format using the custom script extract_fragments.pl. As spike returns were consistently elevated in BRM014 and AU-5330 treated conditions, samples were spike-normalized using the custom script normalize_bedGraph.pl. As the replicate samples were highly correlated across ATAC-seq peaks, biological replicates were merged using the custom scripts bedgraphs2stdBedGraph.pl. Data was binned in 50 bp windows to generate bedGraph files for UCSC Genome Browser visualization and downstream analysis.
Assembly: hg38
Supplementary files format and content: All files with the .bw suffix are normalized BigWig files containing combined data from all replicates of the indicated treatment condition.

molecule: other

organism: Homo sapiens

growth_protocol: Cells were maintained in RPMI medium consisting of RPMI 1640 with L-glutamine (Corning MT 10-040-CV), 10% fetal bovine serum (Fisher Scientific 16-000-044) and Penicillin-Streptomycin (Thermo Fisher 15140163).

extract_protocol:
ATAC-seq was performed as described in Grandi et al., (PMID: 35478247) with some modifications. Briefly 100,000 cells were mixed with 10,000 S2 Drosophila cells, and pelleted at 500g for 5 minutes at 4°C. Cells were washed with 100 µL ice cold DPBS (Corning 21-031-CV), and pelleted at 500g for 5 minutes at 4°C. The cell pellet was resuspended in 50 µL of ATAC-seq Lysis Buffer (0.1% NP40, 0.1% Tween-20, 0.01% digitonin, 10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2) and incubated on ice for 3 minutes. Then 1 mL of ATAC-seq Wash Buffer (0.1% Tween-20, 10 mM Tris–HCl pH 7.5, 10 mM NaCl and 3 mM MgCl2) was added to dilute the lysis reagents, and nuclei were pelleted by spinning at 500g for 19 minutes at 4°C. Nuclei were then resuspended in 50 µL Transposition Mix (1X Tagment DNA Buffer, 0.33X DPBS, 0.01% digitonin, 0.1% Tween-20) treated with 3 µL TDE1 Tagment DNA Enzyme (Illumina 20034197). The reaction was incubated at 37°C for 30 minutes shaking at 1,000 rpm. Tagmented DNA was subsequently purified using the DNA Clean and Concentrator-5 Kit (Zymo Research, cat. no. D4014).
Purified samples were combined with NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs M01541) for amplification. As described in Grandi et al., (PMID: 35478247), custom primers were used to incorporate Illumina adaptors and index sequences into sample fragments.

value: AML

value: wt


title: mESC_DMSO_8h_ATAC-seq_rep3

description: 8h DMSO 3


title: Animal Z3 Superficial White Matter ROI 93

description:
GeoMx DSP
ROI_93_SWM_Z3


title: MV411_ATACseq_8h_DMSO_rep2


title: mESC_DMSO_8h_ATAC-seq_rep2

description: 8h DMSO 2


title: Animal Z3 Deep White Matter ROI 91

description:
GeoMx DSP
ROI_91_DWM_Z3

value: DWM


title: Animal Z3 Superficial White Matter ROI 92

description:
GeoMx DSP
ROI_92_SWM_Z3


title: mESC_DMSO_8h_ATAC-seq_rep1

description: 8h DMSO 1

value: F121-9 wt mESCs


title: Animal Z3 Deep White Matter ROI 90

description:
GeoMx DSP
ROI_90_DWM_Z3


title: MV411_ATACseq_8h_DMSO_rep1


title: Fetal Brain Animal zika004 ZIKVB Brain region 5


title: mESC_BRM014_4h_ATAC-seq_rep2

description: 4h BRM014 2

value: 1µM BRM014, 4h


title: Fetal Brain Animal zika004 ZIKVB Brain region 3


title: MV411_ATACseq_8h_BRM014_rep3


title: MV411_ATACseq_8h_BRM014_rep2


title: mESC_BRM014_4h_ATAC-seq_rep1

description: 4h BRM014 1


title: Animal Z3 Gray Matter ROI 86

description:
GeoMx DSP
ROI_86_GM_Z3

value: GM


title: Animal Z3 Deep White Matter ROI 85

description:
GeoMx DSP
ROI_85_DWM_Z3


title: Fetal Brain Animal zika004 ZIKVB Brain region 9


title: Fetal Brain Animal zika003 ZIKVB Brain region 7


title: MV411_ATACseq_8h_AU15330_rep3


title: Fetal Brain Animal zika004 ZIKVB Brain region 7


title: mESC_DMSO_4h_ATAC-seq_rep2

description: 4h DMSO 2


title: Fetal Brain Animal zika005 ZIKVB Brain region 1


title: mESC_DMSO_4h_ATAC-seq_rep1

description: 4h DMSO 1


title: MV411_ATACseq_8h_AU15330_rep2


title: Animal Z4 Gray Matter ROI 19

description:
GeoMx DSP
ROI_19_GM_Z4


title: Fetal Brain Animal zika005 ZIKVB Brain region 3


title: Animal Z4 Gray Matter ROI 18

description:
GeoMx DSP
ROI_18_GM_Z4


title: Fetal Brain Animal zika004 ZIKVB Brain region 1


title: mESC_BRM014_2h_ATAC-seq_rep2

description: 2h BRM014 2

value: 1µM BRM014, 2h


title: mESC_BRM014_2h_ATAC-seq_rep3

description: 2h BRM014 3


title: Fetal Brain Animal zika005 ZIKVB Brain region 5


title: Animal Z4 Gray Matter ROI 17

description:
GeoMx DSP
ROI_17_GM_Z4


title: corneal epithelial cells 8% O2 rep 1

value: cornea

value: corneal epithelial cells

value: WT

value: 8% oxygen


title: MV411_ATACseq_4h_DMSO_rep3


title: Fetal Brain Animal zika005 ZIKVB Brain region 7

value: fetal brain


title: mESC_BRM014_2h_ATAC-seq_rep1

description: 2h BRM014 1


title: Animal Z4 Superficial White Matter ROI 16

description:
GeoMx DSP
ROI_16_SWM_Z4

value: Fetal brain


title: Animal Z4 Superficial White Matter ROI 15

description:
GeoMx DSP
ROI_15_SWM_Z4


title: mESC_DMSO_2h_ATAC-seq_rep3

description: 2h DMSO 3


title: Animal Z4 Superficial White Matter ROI 14

description:
GeoMx DSP
ROI_14_SWM_Z4


title: MV411_ATACseq_4h_DMSO_rep1


title: MV411_ATACseq_4h_DMSO_rep2


title: Fetal Brain Animal CTRL002 mock Brain region 1

value: mock


title: Fetal Brain Animal CTRL002 mock Brain region 3


title: mESC_DMSO_2h_ATAC-seq_rep1

description: 2h DMSO 1


title: mESC_DMSO_2h_ATAC-seq_rep2

description: 2h DMSO 2


title: MV411_ATACseq_4h_BRM014_rep3


title: Animal Z4 Deep White Matter ROI 13

description:
GeoMx DSP
ROI_13_DWM_Z4

value: ZIKV


title: Animal Z4 Deep White Matter ROI 12

description:
GeoMx DSP
ROI_12_DWM_Z4


title: mESC_WT_ATAC-seq_rep4

description: WT 4

value: Untreated


title: Fetal Brain Animal CTRL002 mock Brain region 5


title: MV411_ATACseq_8h_AU15330_rep1


title: mESC_WT_ATAC-seq_rep3

description: WT 3

value: ATAC-seq


title: Animal Z4 Deep White Matter ROI 11

description:
GeoMx DSP
ROI_11_DWM_Z4


title: MV411_ATACseq_4h_AU15330_rep3

value: AML


title: Fetal Brain Animal zika005 ZIKVB Brain region 9


title: MV411_ATACseq_4h_AU15330_rep2

value: wt


title: Animal Z1 Gray Matter ROI 57

description:
GeoMx DSP
ROI_57_GM_Z1


title: Fetal Brain Animal CTRL002 mock Brain region 7


title: mESC_WT_ATAC-seq_rep1

description: WT 1


title: Animal Z1 Gray Matter ROI 56

description:
GeoMx DSP
ROI_56_GM_Z1


title: Fetal Brain Animal Zika002 ZIKVF Brain region 9

value: Zika infection strain FSS13025


title: MV411_ATACseq_4h_AU15330_rep1


title: Fetal Brain Animal Zika002 ZIKVF Brain region 7


title: NSC Aged, Rep3

data_processing:
RNAseq reads were aligned to mm10 genome using TopHat with default parameters. Aligned reads were converted to sam format. Cuffdiff software was used to determine the transcript FPKM (Fragments Per Kilobase of transcript per Million mapped reads).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

growth_protocol: Primary NSCs were isolated from the brain SVZ of the young (2 months) and aged (15-18 months) mice, respectively (Nat Protoc. 2012 Nov; 7(11):2005-2012). Briefly, microdissection of the brain SVZ was performed on ice. The tissue pieces of SVZ from 5 mice were pooled and dissociated into single cells using Neural Tissue Dissociation kit. The isolated NSCs were maintained in the initial proliferation medium.

extract_protocol:
Total RNA extraction of the primary NSCs was performed using TRIzol Reagent following manufacturer’s instructions (Thermo Fisher).
1 ug of total RNA was used for rRNA depletion (rRNA depletion kit, MGI) and RNAseq library generation using MGIEasy RNA Library Prep Set (Item No.：1000006383)

value: Neural stem cells

value: Brain SVZ

value: 15-18 months old


title: Fetal Brain Animal Zika002 ZIKVF Brain region 5


title: MV411_ATACseq_4h_BRM014_rep2

value: 1µM BRM014, 4h


title: MV411_ATACseq_2h_DMSO_rep3


title: MV411_ATACseq_2h_DMSO_rep2


title: MV411_ATACseq_4h_BRM014_rep1


title: Animal Z1 Superficial White Matter ROI 54

description:
GeoMx DSP
ROI_54_SWM_Z1

value: SWM


title: NSC Aged, Rep1


title: Animal Z1 Gray Matter ROI 55

description:
GeoMx DSP
ROI_55_GM_Z1

value: GM


title: MV411_ATACseq_2h_DMSO_rep1


title: NSC Young, Rep3

value: 2 months old


title: Fetal Brain Animal CTRL002 mock Brain region 9


title: Fetal Brain Animal Zika002 ZIKVF Brain region 1


title: Animal Z1 Superficial White Matter ROI 52

description:
GeoMx DSP
ROI_52_SWM_Z1


title: mESC_WT_ATAC-seq_rep2

description: WT 2

value: F121-9 wt mESCs


title: Animal Z1 Superficial White Matter ROI 53

description:
GeoMx DSP
ROI_53_SWM_Z1


title: MV411_ATACseq_2h_BRM014_rep3

value: 1µM BRM014, 2h


title: Fetal Brain Animal CTRL001 mock Brain region 9

value: fetal brain


title: NSC Young, Rep2


title: Animal Z1 Deep White Matter ROI 48

description:
GeoMx DSP
ROI_48_DWM_Z1

value: Fetal brain

value: DWM


title: NSC Young, Rep1


title: Fetal Brain Animal CTRL001 mock Brain region 7

value: mock


title: MV411_ATACseq_2h_BRM014_rep2


title: MV411_ATACseq_2h_BRM014_rep1


title: Fetal Brain Animal CTRL001 mock Brain region 5


title: Animal Z1 Deep White Matter ROI 46

description:
GeoMx DSP
ROI_46_DWM_Z1

value: ZIKV


title: Fetal Brain Animal Zika002 ZIKVF Brain region 3


title: NSC Aged, Rep2


title: MV411_ATACseq_2h_AU15330_rep3

value: AML


title: Fetal Brain Animal CTRL001 mock Brain region 3


title: Fetal Brain Animal CTRL001 mock Brain region 1


title: Control for AT1 cell ablation

city: Durham

first: Purushothama Rao

last: Tata

email: pt93@duke.edu, tata.lab@yahoo.com

state: NC

address: 303 Research Dr., Alexander Sands Building, Room- 451, BOX 3709

department: Department of Cell Biology

institute: Duke University School of Medicine

data_processing:
FASTQ files were processed using dropSeqPipe v0.3 (https://hoohm.github.io/dropSeqPipe) and mapped on the GRCm38 genome reference with annotation version 91 to get UMI expression matrix files.
Assembly: GRCm38.91
Supplementary files format and content: .tsv

source_name: Lung

extract_protocol:
lungs were inflated with an enzyme dissociation solution (450U/mL Collagenase I (Worthington, LS004197), 5U/mL Dispase (Corning, 354235), and 0.33U/mL DNase I (Roche, 10104159001), in DMEM). Separated lung lobes were minced and incubated in enzyme solution at 37°C for 25-35 minutes. Dissociation was quenched with equivalent volume 10% FBS/DMEM and strained through a 100 µm strainer. Cell pellet was resuspended in red blood cell lysis buffer (100 µm EDTA, 10 mM KHCO3, 155 mM NH4Cl) for 2 minutes, followed by quenching with 10% FBS/DMEM and filtration through a 40 µm strainer. Cell pellet was resuspended in 500µL 2%FBS/DMEM and split into three fractions: CD45/31/140a, CD45, and bulk sample. For MACS, cells were incubated for 30 minutes with the following antibodies: CD45 (MiltenyiBiotech, 130-052-301), CD31 (MiltenyiBiotech, 130-097-418), and CD140a (MiltenyiBiotech, 130-101-547). MACS depletion was performed as per manufacturer protocol using LD columns (MiltenyiBiotech, 130-042-901). Lung cell suspensions were first enriched for epithelial and mesenchymal cell populations as follows: 11,200 cells from CD31/CD45/CD140a-depleted cells, 3200 cells from CD45-depleted cells, and 1600 cells from bulk fractions, and resuspended in PBS supplemented with 0.01% BSA.
We used Drop-seq S3 (Second-Strand Synthesis), the method optimized by adopting S3 procedure from Seq-well S3 (Hughes et al., Immunity 2020 ). Briefly, cells at a concentration of 100 cells/μl were run through microfluidic channels at 3,000 μl/h, together with mRNA capture beads at 3,000 μl/h and droplet-generation oil at 13,000 μl/h. Captured mRNA on the beads were reverse-transcribed using Maxima H Minus RTase (Thermo Fisher, #EP0753) with a series of incubation at 25°C for 30 min, 42°C for 90 min and 50°C for 30 min followed by Exonuclease I treatment. The beads were treated with fresh 0.1M NaOH at room temperature for 5 min followed by second-strand synthesis using Klenow fragment (3'→5' exo minus, New England Biolabs, #M0212L) with incubation at 37°C for 60 min. DNA polymerase for The beads were then used for pre-amplification step (1 cycle of 985°C for 3 min, 4 cycles of 98°C for 15 sec, 55°C for 45 sec, 68°C for 4min, 10-1445–17 cycles of 98°C for 15 sec, 5765°C for 30 sec, 68°C for 4 min and 1 cycle of 72°C for 10 min) using was replaced by Terra PCR Direct Polymerase (#639271, Takara) which was ranked #1 polymerase in several studies (Sasagawa et al., Genome Biology 2013; Bagnoli et al., Nature Communications 2018). The rest of theother processes were performed as described in the original Drop-seq protocol.
Drop-seq S3

treatment_protocol: Ager-CreER;Rosa26R-DTA mice treated with Tamoxifen followed by Diphtheria Toxin

value: Lung

value: Lung cells

value: WT


title: MV411_ATACseq_2h_AU15330_rep1

value: wt


title: ste12_LL_2

city: Tulln

first: Miriam

last: Schalamun

address: Konrad Lorenz Strasse 24

country: Austria

institute: Austrian Institute of Technology

data_processing:
quality filtering and trimming bbduk version 38.18 (Q30)
Mapping using HISAT2 version 2.2.1
Read count extraction by feautreCounts version 2.0.1
Supplementary files format and content: tab-delimited text file include raw counts

organism: Trichoderma reesei QM6a

growth_protocol: Trichoderma reesei WT (QM6a) and deletion mutant QM6aΔste12 were grown in minimal medium with celluloseas carbon source at 28°C at for 96h

extract_protocol:
RNA was extracted using Rneasy plant mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using RNA stranded kit, NEB, rRNA depletion  by the Next Generation Sequencing Facility (Vienna Biocenter Core Facilities)

treatment_protocol: cultivation under at constant light or constant darkness

value: mycelium

value: ste12 deletion

value: growth on cellulose in light

tag: time


title: AT1 cell ablation day 10

tag: cell type


title: Fetal Brain Animal 5627 mock Brain region 10


title: QM6a_LL_3


title: MV411_ATACseq_1h_DMSO_rep3


title: AT1 cell ablation day 6


title: MV411_ATACseq_1h_DMSO_rep2


title: Lung cells, AT2-specific Mdm2 knock out-1

description: 10X genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: polyA RNA

extract_protocol:
lungs were inflated with an enzyme dissociation solution (450U/mL Collagenase I (Worthington, LS004197), 5U/mL Dispase (Corning, 354235), and 0.33U/mL DNase I (Roche, 10104159001), in DMEM). Separated lung lobes were minced and incubated in enzyme solution at 37°C for 25-35 minutes. Dissociation was quenched with equivalent volume 10% FBS/DMEM and strained through a 100 µm strainer. Cell pellet was resuspended in red blood cell lysis buffer (100 µm EDTA, 10 mM KHCO3, 155 mM NH4Cl) for 2 minutes, followed by quenching with 10% FBS/DMEM and filtration through a 40 µm strainer. Cell pellet was resuspended in 500µL 2%FBS/DMEM. For MACS, cells were incubated for 30 minutes with the following antibodies: CD45 (MiltenyiBiotech, 130-052-301) and CD31 (MiltenyiBiotech, 130-097-418). MACS depletion was performed as per manufacturer protocol using LD columns (MiltenyiBiotech, 130-042-901). Lung cell suspensions were enriched for epithelial and mesenchymal cell populations and resuspended in PBS supplemented with 0.01% BSA.
We used 10X genomics, 3'-GEX scRNA-seq (V3.1) protocol to capture cells and prepare libraries.
3'-GEX v3.1 (10X genomics)

treatment_protocol: Sftpc-creER;Rosa26-lsl-tdTomato (Ai9); Mdm2 fl/fl mice were treated with Tamoxifen (3 doses) followed by tissue harvest on day-8

value: 3doses of Tamoxifen


title: Animal Z1 Deep White Matter ROI 47

description:
GeoMx DSP
ROI_47_DWM_Z1


title: Fetal Brain Animal 5627 mock Brain region 8


title: AT1 cell ablation day 3


title: Fetal Brain Animal 5627 mock Brain region 6


title: QM6a_LL_2


title: QM6a_LL_1


title: MV411_ATACseq_1h_DMSO_rep1


title: Fetal Brain Animal 5627 mock Brain region 4


title: ste12_DD_3

value: growth on cellulose in darkness


title: Fetal Brain Animal 5627 mock Brain region 2


title: ste12_LL_3


title: MV411_ATACseq_2h_AU15330_rep2


title: ste12_DD_2


title: MV411_ATACseq_1h_BRM014_rep2

value: 1µM BRM014, 1h


title: ATAC-Seq_Aged_Rep3

data_processing:
ATAC-Seq reads were aligned to the mm10 genome using Burrows-Wheeler Aligner (BWA) with default settings. Only uniquely mapping reads with at most two mismatches were retained. The reads of repeated samples were merged for peak calling. All the reads were shifted +4 bp at the + strand and -5 bp at the - strand in the BAM file before peak calling. Peaks were called using MACS2 with --nomodel and --extsize 200 options. Bedgraph (Bdg) files were generated using MACS2.
Assembly: mm10
Supplementary files format and content: Bedgraph files with peaks

extract_protocol:
Primary NSCs were dissociated into single cells and examined for cell viability using trypan blue staining. About 2×104 NSCs with cell viability > 90% were added in cell lysis on ice (lysis buffer: 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630). Cell nuclei were collected in a tube by centrifugation at 500 g at 4 °C and used for the tagmentation reaction in ATAC-Seq assay.
ATAC-Seq libraries were prepared based on the protocol of TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme #TD501).

value: Neural stem cells

tag: tissue type

value: Brain SVZ

value: 18 months


title: ste12_LL_1


title: ATAC-Seq_Aged_Rep2


title: MV411_ATACseq_1h_BRM014_rep1


title: ste12_DD_1


title: Fetal Brain Animal zika001 infected ZIKVF Brain region 7

value: fetal brain

value: Zika infection strain FSS13025


title: ATAC-Seq_Aged_Rep1


title: MV411_ATACseq_1h_AU15330_rep3


title: ATAC-Seq_Young_Rep3

value: 2 months


title: QM6a_DD_3


title: QM6a_DD_2


title: MV411_ATACseq_1h_AU15330_rep2

value: AML


title: Fetal Brain Animal zika001 infected ZIKVF Brain region 5


title: ATAC-Seq_Young_Rep2


title: Fetal Brain Animal zika001 infected ZIKVF Brain region 3


title: ATAC-Seq_Young_Rep1


title: MV411_ATACseq_1h_AU15330_rep1


title: MV411_ATACseq_1h_BRM014_rep3


title: DCA-treated Pmel-1 T cells, Day 7, mouse 3, experiment 2

status: Public on Nov 01 2023

city: Pittsburgh

first: Greg

last: Delgoffe

state: PA

address: 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
RNA-seq reads went through quality control, base correction, poly-x and quality filtering, and quality trimming using fastp v0.23.2.
Library strand information was verified using gffutils v0.11.1 and RSeqC v5.0.1.
Trimmed maximum read length per sample was determined for alignment using BBMap readLength v39.01.
Read alignment and count quantification were performed using STAR v2.7.10a in two-pass mode with ENCODE options against the GENCODE mouse M30 (GRCm39) reference genome and gene annotations. STAR first-pass novel splice junctions that were non-canonical, mitochondrial, or not supported by least one unique read mapper were filtered before the second pass.
Read counts were evaluated for outlier and batch effects using EDASeq v2.28.0 and edgeR v3.36.0.
Differential gene expression analysis was performed using edgeR. Model-based technical batch effect correction, glmQLFit quasi-likelihood negative binomial linear model fitting, and glmTreat testing of differential expression relative to a fold-change threshold of 1.1 were performed. An FDR < 0.1 was used to determine differential expression significance.
Assembly: GENCODE M30 (GRCm39)
Supplementary files format and content: dca_in_vitro_count_matrix.tsv: Gene count matrix tab-delimited file.
Supplementary files format and content: dca_in_vitro_edger_dge_results.tsv: edgeR differential gene expression results table tab-delimited file.

source_name: splenocytes

growth_protocol: T cells were maintained in RPMI supplemented with 10% FBS and 50ug/mL IL-2 at 37°C with 5% CO2.

extract_protocol:
Two technical batches of CD8+ T-cell samples were sorted into lysis buffer and went through direct cDNA extraction.
cDNA was generated using the Takara SmartSeq Kit (Takara: 634438) using 15 cycles of whole genome amplification.

treatment_protocol: 1) whole spleens were stimulated with cognate antigen (250nM SIINFEKL peptide for OT-1 or 1uM gp100 for pmel-1) for 24 hours then 2) expanded in the presence or absence of 5mM DCA for 6 days further and 3) sorted for CD8 purity on day 7 of expansion.

value: splenocytes

value: CD8+ T cell

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

value: dichloroacetate (DCA)

value: Day 7


title: DCA-treated Pmel-1 T cells, Day 7, mouse 1, experiment 2


title: QM6a_DD_1

value: mycelium

value: WT


title: Fetal Brain Animal zika001 infected ZIKVF Brain region 1


title: untreated Pmel-1 T cells, Day 7, mouse 1, experiment 2

value: untreated


title: DCA-treated Pmel-1 T cells, Day 7, mouse 2, experiment 2


title: Fetal Brain Animal zika001 infected ZIKVF Brain region 9


title: DCA-treated Pmel-1 T cells, Day 7, mouse 1, experiment 1


title: untreated Pmel-1 T cells, Day 7, mouse 3, experiment 1


title: DCA-treated Pmel-1 T cells, Day 7, mouse 2, experiment 1


title: untreated Pmel-1 T cells, Day 7, mouse 1, experiment 1


title: DCA-treated Pmel-1 T cells, Day 7, mouse 3, experiment 1


title: TF3

city: Wuxi

first: Jun

last: Qiang

state: Jiangsu

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

description: Tilapia ovarian tissue after SF1 gene suppression

data_processing:
Using the Illumina paired-end RNA-seq approach
we aligned reads of  all samples to the reference genome using HISAT package
StringTie and Ballgown was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM
The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown.
Genome_build: http://asia.ensembl.org/Oreochromis_niloticus/Info/Index
Supplementary_files_format_and_content: xls include FPKM values for each Sample

organism: Oreochromis niloticus

source_name: Ovarian tissue

growth_protocol: The newly-hatched larvae were placed and fed in a small water circulating system for 30 days, then the feeding larvae were transferred to a large water circulating system for culturing. The culture cycle was a 150-day period. The fish were stopped feeding for 1 day before the end of the experiment, and then the body shape of the fish, sexual organs, and gonads were photographed. The blood was drawn from tail vein to extract serum for hormone determination, and gonadal weight was weighed. At the same time, gonadal tissues were selected for HE staining, related gene quantification and protein level determination.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Introduction of antisense RNA fragments: First, 1.5 mL solution for promoting the opening of fertilization hole (each liter of water contained 6 g of sodium chloride, 0.1 g of potassium chloride, 0.1 g of calcium chloride, and 0.1 g of sodium bicarbonate, 0.1 g of sodium dihydrogen phosphate and 1.2 g of glucose) was added respectively into the stainless steel basin where the eggs were placed. The opening time of the egg fertilization hole could be prolonged and the antisense RNA fragments could be fully introduced by using the chemical solution that obtained above. Then 0.8 mL of transfection reagent was added. The stainless steel basin was gently shaken for 15 min to make the antisense RNA fragment enter the eggs through the fertilization hole. In negative control group, 0.8 mL of transfection reagent containing blank plasmid was added according to the above operation. In control group, 0.8 mL of transfection reagent containing ultrapure water was added according to the above operation.

value: Ovarian tissue

value: SF1 gene suppression


title: CM1

description: Testis tissue of tilapia during sexual maturity

source_name: Testis tissue

value: Testis tissue

value: control


title: untreated Pmel-1 T cells, Day 7, mouse 2, experiment 1


title: untreated Pmel-1 T cells, Day 7, mouse 2, experiment 2


title: untreated Pmel-1 T cells, Day 7, mouse 3, experiment 2


title: 221209L24_exp221207_MS96_SCGEuri-7hr-G1-arrest_00uM-EU_polyA-EU-enrich-RNA-seq

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr.

data_processing:
read alignment, ChIP-seq and gDNA data Bowtie (version 1.0.1)
read alignment, RNA-seq data STAR (version 2.5.3a
bigWig file generation custom code
Assembly: sacCer3
Supplementary files format and content: bigWig

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

growth_protocol:
S. pombe: Standard yeast cell culture practices were followed. Cells were cultured at 30C  in Edinburgh Minimal Media (EMM).
C. Glabrata: Standard yeast cell culture practices were followed. Cells were cultured at 30C  in synthetic complete media with either 2% glucose (SCD) or 2% glycerol + 1% ethanol (SCGE) as a carbon source.
S. cerevisiae: Standard yeast cell culture practices were followed. Cells were cultured at 30C  in synthetic complete media with either 2% glucose (SCD) or 2% glycerol + 1% ethanol (SCGE) as a carbon source.

extract_protocol:
S. cerevisiae and S. pombe cells were separately pelleted and snap-frozen in liquid nitrogen. Pellets were thawed in ice-cold PBS and mixed. 30 µl of cells in PBS were added to 300 µl TRI Reagent (Zymo Research) and lysed by bead beating using a Fastprep 24. Cell debris was pelleted (14k rpm, 1 minute) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research). mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). EU-mRNA was then enriched using the Click-iT Nascent RNA Capture Kit (invitrogen) with the following modifications to the kit protocol. 5 µl Dynabeads MyOne Streptavidin T1 (invitrogen) per sample were washed 1x 50 µl wash buffer 2 (kit component J) and then resuspended in the 50 µl wash buffer 2 + 5% (v/v) Denhardt's reagent and incubated at room temperature (10 minutes). Blocked beads were then washed 3x in 50 µl wash buffer 2 and resuspended in 5 µl wash buffer 2. 12.5 µl Click-iT RNA binding buffer (kit component G) and 0.2 µl RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen) was then added to 12.3 µl mRNA, mixed, and incubated at 70 °C (5 minutes). 5 µl of blocked and washed beads were then added to each 25 µl mRNA reaction, mixed, and incubated (room temperature, 30 minutes). Beads were then washed 4x with 100 µl wash buffer 1 (kit component I), 2x 100 µl SDS wash buffer (1% SDS, 5 mM TRIS-HCL, 1 mM EDTA), 4x with 100 µl wash buffer 2 and resuspended in 5 µl wash buffer 2.
Indexed sequencing libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, #E7775). Biotin-EU-mRNA bound to 5 µl streptavidin beads was immediately used as the input for cDNA synthesis on the beads. cDNA synthesis reactions were pipetted every 10 minutes on the thermocycler to keep Streptavidin beads in suspension. Beads were removed prior to the cDNA clean-up step. Libraries were pooled and then sequenced by paired-end (2x150bp) Illumina sequencing.
spike-in normalised polyA EU-enriched RNA-seq

tag: sample

value: yeast

tag: chip-antibody


title: 221209L20_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-06min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 06min after EU washout from media.


title: 221209L19_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-00min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 00min after EU washout from media.


title: 221209L22_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-24min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 24min after EU washout from media.


title: 221209L18_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_00uM-EU_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr.


title: 221209L15_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-12min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 12min after EU washout from media.


title: 221209L13_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-00min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 00min after EU washout from media.


title: TM1

description: Tilapia testis tissue after SF1 gene suppression


title: TF1


title: CM2


title: 221209L12_exp221207_MS96_SCGEuri-7hr-G1-arrest_00uM-EU_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr.

extract_protocol:
S. cerevisiae and S. pombe cells were separately pelleted and snap-frozen in liquid nitrogen. Pellets were thawed in ice-cold PBS and mixed. 30 µl of cells in PBS were added to 300 µl TRI Reagent (Zymo Research) and lysed by bead beating using a Fastprep 24. Cell debris was pelleted (14k rpm, 1 minute) and the supernatant recovered. RNA was then extracted using the direct-zol RNA microprep kit (Zymo Research). mRNA was enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
Indexed sequencing libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, #E7775), pooled, and then sequenced by paired-end (2x150bp) Illumina sequencing.
spike-in normalised polyA RNA-seq


title: CF3

description: Ovarian tissue of tilapia during sexual maturity


title: TM2


title: TM3


title: TF2


title: CF2


title: 221209L21_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-12min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 12min after EU washout from media.


title: 221209L17_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-36min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 36min after EU washout from media.


title: 221209L14_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-06min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 06min after EU washout from media.


title: 221209L11_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-36min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 36min after EU washout from media.


title: 221209L10_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-24min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 24min after EU washout from media.


title: CF1


title: 221209L23_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-36min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 36min after EU washout from media.


title: CM3

description: Testis tissue of tilapia during sexual maturity


title: 221209L08_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-06min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 06min after EU washout from media.


title: 221209L06_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_00uM-EU_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr.


title: 221209L16_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-24min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 24min after EU washout from media.


title: 221209L07_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-00min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 00min after EU washout from media.


title: 221209L05_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-36min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 36min after EU washout from media.


title: 221209L04_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-24min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 24min after EU washout from media.


title: 221209L03_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-12min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 12min after EU washout from media.


title: 221209L02_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-06min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 06min after EU washout from media.


title: 221209L01_exp221207_MS96_SCGEuri-1.5hr-G1-arrest_10uM-EU-00min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 1.5 hr and then was collected 00min after EU washout from media.


title: 221205L36_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-32min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 32min after EU washout from media.


title: 221205L35_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-32min-chase_polyA-EU-enrich-RNA-seq

value: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 32min after EU washout from media.


title: 221205L34_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-20min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 20min after EU washout from media.


title: 221205L14_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-05min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 05min after EU washout from media.


title: 221205L16_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-20min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 20min after EU washout from media.


title: 221205L17_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-32min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 32min after EU washout from media.


title: 221205L18_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-32min-chase_polyA-input-RNA-seq

value: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 32min after EU washout from media.


title: 221205L19_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-00min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 00min after EU washout from media.


title: 221205L24_exp221129_MS95_SCGEuri-00nM-BE_00uM-EU_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597).


title: 221205L31_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-00min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 00min after EU washout from media.


title: 221205L15_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-10min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 10min after EU washout from media.


title: 221205L32_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-05min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 05min after EU washout from media.


title: 221205L33_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-10min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 10min after EU washout from media.


title: 221205L13_exp221129_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-00min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 00min after EU washout from media.


title: 221205L21_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-10min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 10min after EU washout from media.


title: 221209L09_exp221207_MS96_SCGEuri-7hr-G1-arrest_10uM-EU-12min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was arrested in G1 for 7.5 hr and then was collected 12min after EU washout from media.


title: 221205L30_exp221129_MS95_SCGEuri-20nM-BE_00uM-EU_polyA-EU-enrich-RNA-seq

value: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597).


title: 221205L20_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-05min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 05min after EU washout from media.


title: 221205L12_exp221129_MS95_SCGEuri-20nM-BE_00uM-EU_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597).


title: 221205L23_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-32min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 32min after EU washout from media.


title: 221205L22_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-20min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 20min after EU washout from media.


title: 221205L06_exp221129_MS95_SCGEuri-00nM-BE_00uM-EU_polyA-input-RNA-seq

value: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597).


title: 221205L04_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-20min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 20min after EU washout from media.


title: 221205L05_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-32min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 32min after EU washout from media.


title: 221205L03_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-10min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 10min after EU washout from media.


title: 221205L01_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-00min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 00min after EU washout from media.


title: 221205L02_exp221129_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-05min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 05min after EU washout from media.


title: 221122L32_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-20min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 20min after EU washout from media.


title: 221122L30_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-05min-chase_polyA-EU-enrich-RNA-seq

value: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 05min after EU washout from media.


title: 221122L31_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-10min-chase_polyA-EU-enrich-RNA-seq

value: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 10min after EU washout from media.


title: 221122L29_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-00min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 00min after EU washout from media.


title: 221122L28_exp221120_MS95_SCGEuri-20nM-BE_00uM-EU_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597).


title: 221122L21_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-32min-chase_polyA-EU-enrich-RNA-seq

value: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 32min after EU washout from media.


title: 221122L22_exp221120_MS95_SCGEuri-00nM-BE_00uM-EU_polyA-EU-enrich-RNA-seq


title: 221122L02_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-05min-chase_polyA-input-RNA-seq

value: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 05min after EU washout from media.


title: 221122L01_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-00min-chase_polyA-input-RNA-seq

value: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 00min after EU washout from media.


title: 221122L14_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-05min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 05min after EU washout from media.


title: 221122L16_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-20min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 20min after EU washout from media.


title: 221122L06_exp221120_MS95_SCGEuri-00nM-BE_00uM-EU_polyA-input-RNA-seq


title: 221122L17_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-00min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 00min after EU washout from media.


title: 221122L15_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-10min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 10min after EU washout from media.


title: 221122L12_exp221120_MS95_SCGEuri-20nM-BE_00uM-EU_polyA-input-RNA-seq


title: 221122L03_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-10min-chase_polyA-input-RNA-seq

value: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 10min after EU washout from media.


title: 221122L04_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-20min-chase_polyA-input-RNA-seq

value: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 20min after EU washout from media.


title: 221122L18_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-05min-chase_polyA-EU-enrich-RNA-seq

value: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 05min after EU washout from media.


title: 221122L20_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-20min-chase_polyA-EU-enrich-RNA-seq

value: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 20min after EU washout from media.


title: 221122L19_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-10min-chase_polyA-EU-enrich-RNA-seq

description: cDNA of polyA-enriched EU-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 10min after EU washout from media.


title: 200216L20_exp200205_MS249_SCD-RAPA_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS249) and S. pombe (MSsp109). MS249 was treated with rapamycin before collection.

extract_protocol:
S. cerevisiae cultures were combined with spike-in cultures (C. glabrata or S. pombe) and immediately fixed  with formaldehyde at a final concentration of 1% for 15 minutes. Cells were then quenched with 0.125 M glycine (5 minutes), washed twice in cold PBS, pelleted, snap-frozen, and stored at −80 °C. Pellets were thawed and lysed in 300 µl FA lysis buffer (50 mM HEPES–KOH pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF) with ∼1 ml ceramic beads on a Fastprep-24 (MP Biomedicals). The entire lysate was then collected and adjusted to 1 ml before sonication with a 1/8” microtip on a Q500 sonicator (Qsonica) for 8-16 minutes (cycles of 10 seconds on and 20 seconds off). The sample tube was held suspended in a −20 °C 80% ethanol bath to prevent sample heating during sonication. Cell debris was then pelleted, and the supernatant was retained for ChIP or input. For each ChIP reaction, 20 µl Protein G Dynabeads (Invitrogen) were blocked (PBS + 0.5% BSA, incubate 40 minutes at room temperature), pre-bound with 5 µl of antibody in PBS (incubate 40 minutes at room temperature), and washed 2x with PBS before being incubated with supernatant (4°C overnight). Dynabeads were then washed (5 minutes per wash) 2x in FA lysis buffer and 3x in high-salt FA lysis buffer (50 mM Hepes-KOH pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF) and DNA was then eluted in ChIP elution buffer (50 mM TrisHCl pH 7.5, 10 mM EDTA, 1% SDS) at 65 °C for 20 minutes. 15 µl of input was mixed directly with 115 µl of ChIP elution buffer for input samples. Crosslinks were then reversed (65 °C, 5hr) before treatment with RNAse A (37 °C, 1 hour) and then Proteinase K (65 °C, 2 hours). DNA was then purified using the ChIP DNA Clean & Concentrator kit (Zymo Research).
Indexed sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep kit (NEB Cat # E7645), pooled, and then sequenced by paired-end (2x150bp) Illumina sequencing.
spike-in normalised ChIP-seq


title: 200216L19_exp200205_MS207_SCD-RAPA_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS207) and S. pombe (MSsp109). MS207 was treated with rapamycin before collection.


title: 200917L24_exp200205_MS249_SCD-RAPA_anti-FLAG

description: Eluted Rpb1-FLAG ChIP DNA from a mixture S. cerevisiae (MS249) and S. pombe (MSsp109). MS249 was treated with rapamycin before collection.

value: anti-FLAG (M2; Sigma-Aldrich #F3165)


title: 200917L26_exp200205_MS297_SCD-RAPA_anti-FLAG

description: Eluted Rpb1-FLAG ChIP DNA from a mixture S. cerevisiae (MS250) and S. pombe (MSsp109). MS250 was treated with rapamycin before collection.


title: 200917L23_exp200205_MS207_SCD-RAPA_anti-FLAG

description: Eluted Rpb1-FLAG ChIP DNA from a mixture S. cerevisiae (MS207) and S. pombe (MSsp109). MS207 was treated with rapamycin before collection.


title: 200526L37_exp200205_MS207_SCD-RAPA_input

value: Input ChIP DNA from a mixture S. cerevisiae (MS207) and S. pombe (MSsp109). MS207 was treated with rapamycin before collection.


title: 200526L40_exp200205_MS297_SCD-RAPA_input

description: Input ChIP DNA from a mixture S. cerevisiae (MS250) and S. pombe (MSsp109). MS250 was treated with rapamycin before collection.


title: 200526L38_exp200205_MS249_SCD-RAPA_input

value: Input ChIP DNA from a mixture S. cerevisiae (MS249) and S. pombe (MSsp109). MS249 was treated with rapamycin before collection.


title: 200216L22_exp200205_MS297_SCD-RAPA_input

value: Input ChIP DNA from a mixture S. cerevisiae (MS250) and S. pombe (MSsp109). MS250 was treated with rapamycin before collection.

value: yeast


title: 221122L13_exp221120_MS95_SCGEuri-20nM-BE_1hr-5uM-EU-00min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was cultured in the prescence of 20nM beta-estradiol and was collected 00min after EU washout from media.


title: 200216L44_exp200205_MS249_SCD-RAPA_anti-FLAG

value: Eluted Rpb1-FLAG ChIP DNA from a mixture S. cerevisiae (MS249) and S. pombe (MSsp109). MS249 was treated with rapamycin before collection.


title: 200216L46_exp200205_MS297_SCD-RAPA_anti-FLAG

value: Eluted Rpb1-FLAG ChIP DNA from a mixture S. cerevisiae (MS250) and S. pombe (MSsp109). MS250 was treated with rapamycin before collection.


title: 221122L05_exp221120_MS95_SCGEuri-00nM-BE_1hr-5uM-EU-32min-chase_polyA-input-RNA-seq

description: cDNA of polyA-enriched RNA from a mixture S. cerevisiae (MS95) and S. pombe (PN10597). MS95 was collected 32min after EU washout from media.


title: Simu_AV-2

city: Anseong-si,

first: Sang Woo

last: Lee

address: 4726 Seodong-daero, Daedeok-myeon

department: Plant Science and Technology

country: South Korea

institute: CHUNG-ANG UNIVERSITY

description: replicate 2

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software.
The raw reads were trimmed and quality-filtered before genome alignment using Trimmomatic (ver0.36) with more than 90% portion (Q>30) were only used in the mapping.
Reference genome of Brassica rapa plants was obtained from Ensembl (https://plants.ensembl.org/info/website/ftp/index.html) and mapped using TopHat2 software with default parameters.
Aligned reads were converted to digital counts using FeatureCounts and analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a p-value < 0.05 and two-fold difference cut-off.
Assembly: Raphanus sativus L. reference genome was obtained from Radish Genome Database (http://radish-genome.org/)
Supplementary files format and content: tab-delimited text files with raw gene counts for individual samples

organism: Raphanus sativus

source_name: whole plant

extract_protocol:
Total RNA was extracted from whole seedling samples using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions.

value: whole plant

tag: line

value: Simu

value: Wild type

value: AV


title: Simu_AV-3

description: replicate 3

tag: genotype


title: Simu_V40-2

description: replicate 2


title: 200526L28_exp200118_MS297_SCD-RAPA_input


title: 200917L20_exp200118_MS297_SCD-RAPA_anti-FLAG


title: 200526L52_exp200118_MS297_SCD-RAPA_anti-FLAG


title: 200216L43_exp200205_MS207_SCD-RAPA_anti-FLAG

value: Eluted Rpb1-FLAG ChIP DNA from a mixture S. cerevisiae (MS207) and S. pombe (MSsp109). MS207 was treated with rapamycin before collection.


title: 200526L25_exp200118_MS207_SCD-RAPA_input


title: 200526L26_exp200118_MS249_SCD-RAPA_input


title: 200917L18_exp200118_MS249_SCD-RAPA_anti-FLAG


title: 200224L82_exp200118_MS249_SCD_input


title: 200526L49_exp200118_MS207_SCD-RAPA_anti-FLAG


title: 200526L50_exp200118_MS249_SCD-RAPA_anti-FLAG


title: 200224L84_exp200118_MS297_SCD-RAPA_input


title: Simu_V40-3

description: replicate 3


title: Simu_NV-2

description: replicate 2

value: NV


title: Simu_V40-1

description: replicate 1


title: Simu_NV-1

description: replicate 1


title: Jinjudaepyung_AV-3

description: replicate 3

value: Jinjudaepyung


title: Jinjudaepyung_AV-2

description: replicate 2


title: 200224L81_exp200118_MS207_SCD_input


title: TNBC 2

city: Guangzhou

first: Huang

middle: Shan

last: Shan

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: PiRNA expression profiles in triple negative breast cancer

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agllent fragmentation buffer and 2x Agilent blocking agent following the manufacturers'instructions. On completian of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arraystar Human piRNA Array in Agilent's SureHyb Hybridization Chambers for 17 hours at 65C in a rotating Agilent hybridization oven.After hybridization,microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agllent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agllent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set data processing to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagged as Detectedwere maintained.

source_name: Triple negative breast tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,Valencia,CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacture's instructions

value: breast tissue

tag: gender

value: female


title: Adjacent 1

source_name: Adjacent normal breast tissue

tag: tissue


title: TNBC 3


title: Adjacent 3


title: 200917L17_exp200118_MS207_SCD-RAPA_anti-FLAG


title: Adjacent 2


title: Simu_AV-1

description: replicate 1


title: Simu_NV-3

description: replicate 3