title: UT_6

value: prostate cancer cell line PPC1

value: parental/mitotic


title: UBV PHH at 24hr rep2

status: Public on Feb 28 2024

type: SRA

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

library_source: transcriptomic

data_processing:
Illumina NovaSeq 6000 using v3 chemistry. NovaSeq Software: Control v1.6.0, RTA 3.4.4. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
Gene expression was quantified using RSEM version 1.3.1 and STAR version 2.7.1a alignment to a transcriptome derived from the human hg38 primary assembly and ensembl version 98 annotation.
Assembly: hg38 with the ensembl 98 annotation
Supplementary files format and content: 190712Bha_set1_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: 190712Bha_set1_l2tpm.txt.gz is a tab delimited text file of log2 tpm data including a +1 offset

molecule: total RNA

organism:
Homo sapiens
Mus musculus

source_name: Primary human hepatocytes, mouse embryonic fibroblasts

growth_protocol: Hepatocytes were maintained in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM with L-glutamine, Corning) with 10% (v/v) fetal bovine serum (FBS, Gemini), 1% (v/v) ITS+ (insulin/ human transferrin/selenous acid and linoleic acid) premix (BD Biosciences), 7 ng/ml glucagon (Sigma), 40 ng/ml dexamethasone (Sigma), 15 mM HEPES (Gibco), and 1% (v/v) penicillin-streptomycin (Corning). J2-3T3 male murine embryonic fibroblasts  were cultured at <18 passages in fibroblast medium comprising of DMEM with high glucose, 10% (v/v) bovine serum (Thermo Fisher), and 1% (v/v) penicillin-streptomycin (Corning). Primary human hepatocytes were seeded on collagen-coated micropatterned plates as detailed previously (March et al., 2015).

extract_protocol:
Total RNA was extracted using TRIzol (Thermo Fisher) and purified using RNeasy Mini Kit (Qiagen)
RNA integrity was determined using an Agilent Fragment Analyzer and purity and quantity determined using a Thermo Scientific Nanodrop1000 Spectrophotometer. High throughput RNAseq libraries were prepared as previously described (M using 100ng of total RNA input and sequenced on a NovaSeq6000 using 50nt paired-end sequencing

treatment_protocol: To perform circadian synchronization, the cultures were placed in Non-HEPES-buffered CO2 Independent Medium (COI, Thermofisher) with 10% (v/v) fetal bovine serum (FBS, Gemini), 1% (v/v) ITS+ (insulin/ human transferrin/selenous acid and linoleic acid) premix (BD Biosciences) and 7 ng/ml glucagon (Sigma)

tag: tissue

tag: cell line

value: Primary Human Hepatocytes [BioIVT donor:UBV] and J2-3T3 male mouse embryonic fibroblasts [gift of Howard Green, Harvard Medical School]

tag: cell type

value: primary human hepatocyte, mouse embryonic fibroblast

tag: genotype

value: WT

tag: treatment

value: circadian synchronization and RNA extraction

tag: time

value: 24 hours post-synchronization


title: actin-1

city: Salt Lake City

first: Adrian

last: Rothenfluh

state: UT

institute: University of Utah

description: flies_vs_neurons_annotated_differential.csv

library_source: genomic

data_processing:
Fastq files were quality-checked with FastQC v0.11.9
Adapter sequences were trimmed with CutAdapt v3.4
Reads were aligned to the dm6.26 genome assembly using Bowtie2 v2.4.2
Aligned reads were sorted with samtools v1.12 and deduplicated with the markDuplicates function in Picard v2.23.
Differential chromatin accessibility was performed using DiffBind v2.10.0 and DESeq2 v1.32.0
Peaks were annotated using ChIPseekR v1.30.3
Coverage files were generated using Deeptools v3.3.2
Assembly: dm6.26
Supplementary files format and content: Differential chromatin accessibility and peak annotation in .tsv files

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Whole fly

extract_protocol:
Nuclei were isolated as described in Merrill CB,Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. (2022)  Optimized assay for transposon-accessible chromatin by sequencing (ATAC-seq) preparation from adult Drosophila melanogaster neurons. Scientific Reports 12: 6043.
ATAC-seq libraries were constructed by incubating isolated nuclei with Illumina Tn5 enzyme for 23 min at 37 °C. Tagged DNA was purified using a Qiagen MinElute PCR purification kit. Purified fragments were amplified by PCR using Illumina index primers. Amplified libraries were purified and size-selected using AMPure XP beads.

value: Whole fly


title: L834P/+ NPC-2 RNA-seq replicate 3

city: Fukuoka

first: Taichi

last: Shiraishi

address: 1-1-3 Maidashi Higashiku Fukuoka

department: Medical institute of bioregulation

country: Japan

institute: Kyushu university

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.2.0.
Read counting was performed with the use of featureCounts.
Assembly: mm10
Supplementary files format and content: Counts per transcript
Sequenced reads were trimmed for adaptor sequence with Trimmomatic, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Bowtie2 v2.4.5
PCR duprication was removed with Picard and bigwig files were generated with bamCoverage (deeptools v3.5.1)
S3norm was used for data normalization and peakcall was conducted using MACS2 bdgpeakcall with parameters -c 4 -l 400.
Assembly: mm10
Supplementary files format and content: BigWig files for Genome Browser

organism: Mus musculus

source_name: Neural progenitor cell

growth_protocol: ES cells were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in ES culture medium with 15% fetal bovine serum (Life Technologies) and antibiotics. ES cell–derived neural progenitor cells were generated by re-plating d 8 and d 14 neural differentiation cultures on low attachment dish in Neural differential medium.

extract_protocol:
ES and Neural progenitor cells were lysed with ISOGEN (Nippon gene, 311-02501). RNA were purified with the use of  PureLink RNA Mini Kit (Invitrogen). NEBNext Library Quant Kit for Illumina (NEB, E7630L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: timepoint

value: Day14 NPC


title: UBV PHH at 24hr rep1

value: Primary human hepatocytes, mouse embryonic fibroblasts


title: L834P/+ NPC-2 RNA-seq replicate 2


title: Fgfr1 Mutant 3

city: Los Angeles

first: Fei

last: Pei

state: CA

address: 2250 Alcazar St

institute: USC

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using TopHat (Version 2.0.8) with the mm10 genome
RPKM was used to normalize the data and differential expression was calculated by selecting transcripts that changed with p < 0.05
Assembly: mm10
Supplementary files format and content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

source_name: molar

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol: cDNA library preparation and sequencing were performed at the Technology Center for Genomics & Bioinformatics at the University of California, Los Angeles (UCLA).

treatment_protocol: molar samples from Fgfr1fl/fl (control) and Gli1-CreER;Fgfr1fl/fl (mutant) mice were collected at PN7.5 after TMX for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol

value: molar

value: TMX induction


title: Fgfr1 Mutant 2


title: UT_3

city: Charleston

first: Christina

last: Voelkel-Johnson

state: SC

address: 173 Ashley Ave, MSC 250504 room 201

institute: Medical University of South Carolina

data_processing:
base calling: CASAVA software
alignment: STAR software
quantification: HTSeq
differential analysis on readcounts: DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with readcounts for every gene and every sample provided as a tab delimited text file

organism: Homo sapiens

source_name: prostate cancer cell line PPC1

growth_protocol: 7 X 10^5 cells plated in 100 mm plate on day 1 in RPMI 1640  growth media.

extract_protocol:
Qiagen RNAEasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Fgfr1 Mutant 1


title: Fgfr1 WT Control 3

value: wild type


title: CHD8+/- NPC-2 RNA-seq replicate 2


title: UT_1


title: ATAC, Constant zfh1 + ph-KD, rep1

city: Montpellier

first: Vincent

last: Loubiere

state: FRANCE

address: 141 rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: UMR9002; CNRS-UM

description:
ATAC_Constant_zfh1_ph_KD_merge.bw
ATAC_Constant_zfh1_ph_KD_merge.narrowPeak
ATAC_Seq_rescue_normalized_counts.txt
ATAC_zfh1_ph_vs_gfp_white_KD_DESeq2_FC.txt

data_processing:
ATAC-Seq peaks/domains were called for each replicate separately and on merged reads using macs2 (v2.2.7.1) with the following parameters: --keep-dup 1 -g dm -f BAMPE -B --SPMR. Only peaks detected in both replicates (enrichment>0 AND qvalue<0.05) and using merged replicates (enrichment>2 AND qvalue<0.01) were retained for further analyses, after being merged with a minimum gap size of 250 bp.
bw tracks were generated from the .bedGraph output of MACS2.
For the differential analysis of ATAC-Seq, peakswere merged across all conditions (maximum gap of 250 bp) and overlapping reads were counted using the featureCounts function from the Rsubread R package (v2.0.1, isPairedEnd = TRUE).
Differential analysis was then performed using the DESeq2 R package (v1.26.0, size factors= total number of aligned reads, design= ~replicate+condition).
Assembly: dm6
Supplementary files format and content: The .bw binary files can be used to visualize genomic trackes using IGV (https://igv.org/doc/desktop/#QuickStart/).
Supplementary files format and content: The .narrowPeak file format is described at https://genome.ucsc.edu/FAQ/FAQformat.html#format12.
Supplementary files format and content: Normalized counts .txt files contain for each gene (rows), the normalized counts for each sample (one per column).
Supplementary files format and content: FC.txt files contain the differential analysis performed using DESeq2 (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi:10.1186/s13059-014-0550-8.).

source_name: ED

extract_protocol:
ATAC-seq experiments were performed using the ATAC-seq kit from Diagenode (C01080002). 10 eye discs were used as starting material for each replicate and condition.
Tagmentated DNA was amplified by PCR using 13 cycles and the purified DNA libraries were sequenced (paired-end sequencing 150bp, approximately 2Gb/sample) by Novogene (https://en.novogene.com/).

value: ED

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-zfh1RNAi v103205;UAS-PhRNAi v50028/UAS-GFP

value: Constant RNAi (29°C)

value: Day 4 AEL


title: ATAC, Constant gfp + ph-KD, rep2

description:
ATAC_Constant_gfp_ph_KD_merge.bw
ATAC_Constant_gfp_ph_KD_merge.narrowPeak
ATAC_Seq_rescue_normalized_counts.txt
ATAC_gfp_ph_vs_gfp_white_KD_DESeq2_FC.txt

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-gfpRNAi BL9331;UAS-PhRNAi v50028/UAS-GFP


title: ATAC, Constant gfp + ph-KD, rep1


title: Gi_1

value: prostate cancer cell line PPC1

value: radiation induced PGCC

value: 8 Gy radiation + 2 days


title: CHD8+/- NPC-2 RNA-seq replicate 1


title: ATAC, Control gfp + white-KD, rep2

description:
ATAC_Control_gfp_white_KD_merge.bw
ATAC_Control_gfp_white_KD_merge.narrowPeak
ATAC_Seq_rescue_normalized_counts.txt

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-gfpRNAi BL9331;UAS-wRNAi BL33623/UAS-GFP


title: Fgfr1 WT Control 2


title: ATDC5_6h_5uM_Yoda1_Rep3

type: RNA

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on mouse Clariom D Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using  default analysis settings (version 1) and Gene + Exon - SST-RMA as summarization and normalization method.

label: biotin

source_name: ATDC5 cells, 6h treatment

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom D kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific

growth_protocol: ATDC5 cells were cultured in DMEM:F12 medium with 5% FCS at 37°C, 5% CO2, 95% rH.

extract_protocol: RNA was extraced using the Macherey-Nagel NucleoSpin RNA kit according to the manufacturer's instructions.

treatment_protocol: Cells were seeded at a density of 4.3x10^4 per cm^2. The next day, cells were serum starved over night, followed by stimulation with 5µM Yoda1 or the equivalent volume of DMSO for 6 hours in serum-free growth medium.


title: UT_5

value: parental/mitotic


title: ATDC5_6h_5uM_Yoda1_Rep2


title: Fgfr1 WT Control 1


title: ATAC, Control gfp + white-KD, rep1


title: UT_4


title: WT NPC-2 RNA-seq replicate 3

value: WT


title: L834P/+ NPC-2 RNA-seq replicate 1


title: WT NPC-2 RNA-seq replicate 2


title: WT NPC-2 RNA-seq replicate 1


title: ATAC, Transient ph-KD D11 AEL, rep2

description:
ATAC_Transient_ph-KD_D11_merge.bw
ATAC_Transient_ph-KD_D11_merge.narrowPeak
ATAC_Seq_normalized_counts.txt
ATAC_Transient_ph-KD_D11_vs_Control_no_ph-KD_DESeq2_FC.txt

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: Transient RNAi (24h 29°C L1)

value: D11 AEL


title: H9c2 cells, ISO+2-APQC-3

city: Chengdu

first: Wei

last: Liu

state: 四川省

address: 林荫街8号

country: China

institute: Sichuan University

data_processing:
The raw data was handled by Perland data quality was checked by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Theread length was 2×150 bp. Clean reads were aligned to thechicken genome (release:Gallus gallus4.0) from NCBIusing Bowtie, with one mismatch allowed.
Assembly: mm10
Supplementary files format and content: table-delimited text file incledes raw counts for each Sample
Supplementary files format and content: table-delimited text file incledes RPKM values for each Sample

organism: Rattus norvegicus

source_name: H9c2 cell

extract_protocol:
Cells were harvested and total RNA was extracted by using TRIzol reagent. Enrichment of mRNA, fragmentation, reverse transcription, library construction, HiSeq X Ten and data analysis were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China).
Strand-specific librarieswere constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencingwas carried out using the Illumina HiSeq X Ten instrumentby the commercial service of Genergy Biotechnology Co.Ltd. (Shanghai, China).

value: H9c2 cell

value: cardiomyocyte


title: ATAC, Constant zfh1 + ph-KD, rep2


title: UT_2


title: CHD8+/- NPC-2 RNA-seq replicate 3

value: Day14 NPC


title: H9c2 cells, ISO+2-APQC-2


title: ATDC5_6h_DMSO_Rep3

value: DMSO


title: R1242Q/+ NPC RNA-seq replicate 3

value: Day8 NPC


title: ATAC, Transient ph-KD D11 AEL, rep1

value: ED


title: ATDC5_6h_DMSO_Rep2


title: H9c2 cells, ISO-3

value: ISO


title: ATAC, Transient ph-KD D9 AEL, rep2

description:
ATAC_Transient_ph-KD_D9_merge.bw
ATAC_Transient_ph-KD_D9_merge.narrowPeak
ATAC_Seq_normalized_counts.txt

value: D9 AEL


title: R1242Q/+ NPC RNA-seq replicate 2


title: ATDC5_6h_DMSO


title: ATAC, Transient ph-KD D9 AEL, rep1


title: ATDC5_6h_5uM_Yoda1


title: L1072F/+ NPC RNA-seq replicate 3


title: H9c2 cells, ISO-2


title: 126_ZT22_IN

city: Waltham

first: Albert

middle: Dayuan

last: Yu

address: 415 South St.

institute: Brandeis University

data_processing:
Fastq files were trimmed using fastp in single end mode
Reads were aligned to dm6 using bowtie2 with the --very-sensitive-local flag
Aligned reads were converted to bam files, sorted and indexed using samtools
BAM files were deduplicated using picardtools
BW files were generated using deeptools bamcompare against corresponding inputs with the following flags: -bs 5 --smoothLength 60 -bl dm6-blacklist.v2.bed --operation ratio --scaleFactorsMethod SES
Assembly: dm6
Supplementary files format and content: bigwig files with input-normalized visualization of each sample.

source_name: Heads

growth_protocol: ChIP-seq was performed on yw;; WT dCLK-V5(wt) andyw; tim_up126; dCLK-V5. 3-5 day old flies were entrained in LD condition for at least 3 days, then collected every 4 hours throughout the day.

extract_protocol:
Fly heads were homogenizedin homogenization buffer (10mM HEPES-KOH at pH 7.5, 10mM KCl, 1.5mM MgCl2, 0.8M sucrose, 0.5mM EDTA, 1mM DTT, 1× protease inhibitor, 1× phosphatase inhibitor cocktail) at 4°C. Homogenates were loaded on equal volumes of sucrose cushion buffer (with 1.0M sucrose and 10% glycerol in the homogenization buffer) and centrifuged in a HB-6 rotor (Sorvall) at 11,000rpm for 10min at 4°C.Nuclear pellets were suspended in 1ml 1X PBS with 1% formaldehyde and fixed for 15 min at room temperature and quenched by 0.125 M glycine. Chromatin was extensively washed by 1X PBS and sheared using a biorupter (Diagenode) in 500 ul sonication buffer (20mM Tris-HCl at pH 7.5, 150mM NaCl, 10% glycerol, 1% SDS). For each IP, 25 ul of sheared chromatin was reserved as input sample. The remaining chromatin sample were diluted by 10 times of IP buffer (20 mM Tris-HCl at pH 7.5, 150 mM NaCl, 10% glycerol, 1% NP40 and protease inhibitor tablet) and incubated with 30 ul anti-V5 agarose beads (Sigma) overnight at 4°C.Beads were washed and eluted and decrosslinked as described previously (Yu et al. 2006). The DNA was purified using Minelute columns (Qiagen).
30μl of DNA from each IP or 50ng of Input DNA were used to generate ChIP-seq libraries accroding to illumina ChIP-seq protocol. After adaptor ligation, DNA samples were separated by 2% agarose TAE gel and gel slices corresponding to 250-450bps were recovered and purified using QIAGEN gel purification kit.
ChIP-seq libraries were sequenced on a Nextseq 550 (Illumina) and the resulting datasets were mapped to the Drosophila genome (dm6) using Bowtie2 and analyzed using MACS2

value: Heads

tag: time point

tag: antibody

value: input


title: H9c2 cells, ISO-1


title: ATAC, Constant ph-KD, rep2

description:
ATAC_Constant_ph-KD_merge.bw
ATAC_Constant_ph-KD_merge.narrowPeak
ATAC_Seq_normalized_counts.txt
ATAC_Constant_ph-KD_vs_Control_no_ph-KD_DESeq2_FC.txt

value: Constant RNAi (29°C)

value: Day 4 AEL


title: L1072F/+ NPC RNA-seq replicate 2


title: 126_ZT18_IN


title: ATAC, Constant ph-KD, rep1


title: H9c2 cells, control-3


title: H9c2 cells, control-2


title: ATAC, Control no ph-KD, rep2

description:
ATAC_Control_no_ph-KD_merge.bw
ATAC_Control_no_ph-KD_merge.narrowPeak
ATAC_Seq_normalized_counts.txt

value: No RNAi (control 18°C)

value: Day 10 AEL


title: H9c2 cells, control-1

value: WT


title: ATAC, Control no ph-KD, rep1

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP


title: L1072F/+ NPC RNA-seq replicate 1


title: 126_ZT14_IN


title: H9c2 cells, ISO+2-APQC-1


title: 126_ZT10_IN


title: 126_ZT6_IN


title: R910Q/+ NPC RNA-seq replicate 3


title: R910Q/+ NPC RNA-seq replicate 2


title: gDNA, early L3 ph-KD, 144h recovery, rep2

description:
gDNA_raw_variants.snp.vcf.gz
gDNA_raw_variants.indel.vcf.gz

data_processing:
gDNA variants calling was performed by Novogene (https://en.novogene.com/). Briefly, base calling was performed using Illumina pipeline CASAVA v1.8.2, and subjected to quality control using fastp with the following parameters: -g -q 5 -u 50 -n 15 -l 150 --min_trim_length 10 --overlap_diff_limit 1--overlap_diff_percent_limit 10. Then, sequencing reads were aligned to the dm6 version of the Drosophila genome using Burrows-Wheeler Aligner (BWA) with default parameters and duplicate reads were removed using samtools and PICARD (http://picard.sourceforge.net). Raw SNP/InDel sets were called using GATK with the following parameters: --gcpHMM 10 -stand_emit_conf 10 -stand_call_conf 30. Then, SNPs were filtered using the following criteria: SNP: QD<2, FS>60, MQ<30, HaplotypeScore>13, MappingQualityRankSum<-12.5, ReadPosRankSum<-8; For INDEL variants, following criteria were used: QD<2, FS>200, ReadPosRankSum<-20. UCSC known genes were used for gene and region annotations. Finally, variants were compared to the first batch of control, no ph-KD ED in the search for bona fide de novo mutations using the MuTect2 module of the GATK package. Only SNP and INDEL variants that passed Mutect2 filtering (FILTER= â€œPASSâ€) were considered for downstream analyses.
Assembly: dm6
Supplementary files format and content: A description of the Variant Call Format (.vcf) can be found at https://samtools.github.io/hts-specs/VCFv4.2.pdf.

extract_protocol:
Genomic DNA was isolated using QIAamp DNA Micro Kit (Qiagen) following manufacturer's instructions. For each biological replicate around 70 eye discs from female wandering larvae were dissected.
Library preparation was performed by Novogene (https://en.novogene.com/). Briefly, genomic DNA was fragmented to an average size of ~350bp and then processed for DNA library preparation by following manufacturer (Illumina) paired-end protocols. Sequencing was performed using on an Illumina Novaseq 6000 (platform to generate 150bp paired-ends reads) with a coverage of at least 10x for 99% of the genome.

value: Transient RNAi (24h 29°C early L3)

value: 144h recovery


title: 126_ZT2_IN


title: gDNA, early L3 ph-KD, 144h recovery, rep1


title: R910Q/+ NPC RNA-seq replicate 1


title: p60-athymic-female-24

first: Kabir

last: Ahluwalia

address: University of Southern California Accounts Payable

institute: University of Southern California

data_processing:
Data Analysis After investigating the quality of the raw data, sequence reads were trimmed to remove adapter sequences. The trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted. After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis. Using DESeq2, a comparison of gene expression between the groups of samples was performed. The Wald test was used to generate p-values and Log2 fold changes. Genes with adjusted p-values < 0.05 and absolute log2 fold changes > 1 were called as differentially expressed genes for each comparison. A gene ontology analysis was performed on the statistically significant set of genes by implementing the software GeneSCF. The mgi GO list was used to cluster the set of genes based on their biological process and determine their statistical significance. A PCA analysis was performed using the "plotPCA" function within the DESeq2 R package. The plot shows the samples in a 2D plane spanned by their first two principal components. The top 500 genes, selected by highest row variance, were used to generate the plot.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: whole retina

extract_protocol:
Isolated Retinas were homogenized in RNAzol® RT (Sigma-Aldrich, St. Louis, MO) using a TissueLyser II (Qiagen LLC, Germantown, MD). Total RNA was extracted following manufacturer’s instructions and concentration was determine via the NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Waltham, MA).
Library Preparation with PolyA selection and Illumina Sequencing RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA). RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA). The sequencing libraries were clustered onto a flowcell. After clustering, the flowcell was loaded on the Illumina instrument (4000 or equivalent) according to manufacturer’s instructions. The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the Control  software. Raw sequence data (.bcl files) generated the sequencer were converted into fastq files and de- multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence  identification.

value: whole retina

value: Day 60


title: p60-athymic-female-23


title: R1242Q/+ NPC RNA-seq replicate 1


title: 126_V5Clk_ZT22_REP2


title: gDNA, early L3 ph-KD, 96h recovery, rep2

value: 96h recovery


title: L834P/+ NPC RNA-seq replicate 3

value: Day8 NPC


title: p60-athymic-female-22


title: 126_V5Clk_ZT18_REP2


title: L834P/+ NPC RNA-seq replicate 2


title: gDNA, early L3 ph-KD, 24h recovery, rep2

value: ED

value: 24h recovery


title: 126_V5Clk_ZT14_REP2


title: L834P/+ NPC RNA-seq replicate 1


title: p60-WT-male-20

value: RCS-p+


title: gDNA, early L3 ph-KD, 24h recovery, rep1


title: CHD8+/- NPC RNA-seq replicate 3


title: 126_V5Clk_ZT10_REP2

value: Heads


title: gDNA, Control no ph-KD, rep6


title: p60-WT-male-19


title: 126_V5Clk_ZT6_REP2


title: gDNA, Control no ph-KD, rep5


title: CHD8+/- NPC RNA-seq replicate 1


title: p21-athymic-female-6

value: Day 21


title: CHD8+/- NPC RNA-seq replicate 2


title: p21-athymic-female-5


title: 126_V5Clk_ZT22_REP1


title: 126_V5Clk_ZT2_REP2


title: RNA, Constant zfh1 + ph-KD, rep3

description:
RNA_Seq_rescue_normalized_counts.txt
RNA_Constant_zfh1_ph_KD_DESeq2_FC.txt

data_processing:
After initial quality checks of newly generated data using fastqc, paired-end reads were aligned to a custom index consisting of the dm6 version of the Drosophila genome together with GFP, EGFP and mRFP1 sequences, using the align function from the Rsubread R package (v2.0.1) with the following parameters: maxMismatches = 6, unique = TRUE.
Aligned reads were counted for each D. melanogaster transcript (dmel_r6.36 annotation) using the featureCounts function from the Rsubread R package (v2.0.1, isPairedEnd = TRUE)
Differential expression analysis was performed using the DESeq2 R package (v1.26.0, design = ~replicate+condition). For each condition, ph-RNAi were compared to temperature-matched w-RNAi controls.
Assembly: dm6
Supplementary files format and content: Normalized counts .txt files contain for each gene (rows), the normalized counts for each sample (one per column).
Supplementary files format and content: FC.txt files contain the differential analysis performed using DESeq2 (Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi:10.1186/s13059-014-0550-8.).

extract_protocol:
Third instar female larvae were dissected in Schneider medium on ice. Total RNA was extracted using TRIzol reagent. RNA purification was performed using RNA Clean & Concentrator kit (Zymo Research, #R1015).
Poly-A RNAs selection, library preparation and illumina sequencing (20M paired-end reads, 150nt) were performed by Novogene  (https://en.novogene.com/). All experiments were performed in triplicate.

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-zfh1RNAi v103205;UAS-PhRNAi v50028/UAS-GFP

value: Constant RNAi (29°C)

value: Day 5 AEL


title: WT NPC RNA-seq replicate 3


title: RNA, Constant zfh1 + ph-KD, rep2


title: p21-athymic-female-4


title: WT NPC RNA-seq replicate 2


title: 126_V5Clk_ZT14_REP1


title: p21-WT-male-3


title: RNA, Constant zfh1 + ph-KD, rep1


title: p60-WT-male-21


title: gDNA, early L3 ph-KD, 96h recovery, rep1


title: p21-WT-male-2


title: RNA, Constant zfh1 + white-KD, rep3

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-zfh1RNAi v103205;UAS-wRNAi BL33623/UAS-GFP


title: 126_V5Clk_ZT10_REP1


title: R1242Q/+ ES RNA-seq replicate 3

source_name: Embryonic stem cell

value: Day0 ESC


title: p21-WT-male-1


title: 126_V5Clk_ZT6_REP1


title: R1242Q/+ ES RNA-seq replicate 2


title: RNA, Constant zfh1 + white-KD, rep2


title: R1242Q/+ ES RNA-seq replicate 1


title: 25850, LUSC, mRNA

city: Zagreb

first: Maja

last: Šutić

address: Bijenicka street 54

department: Division of Molecular Medicine

country: Croatia

institute: Ruder Boskovic Institute

data_processing:
Quality of sequenced raw reads was checked with FASTQC application on BaseSpace Sequence Hub cloud (Illumina). Reads were aligned to the human genome (NCBI GRCh38 Decoy) with the RNA-Seq Alignment Application (Illumina, BaseSpace Sequence Hub).
Gene counts were generated with Salmon (within RNA-Seq Alignement application, BaseSpace, Illumina)
Assembly: NCBI GRCh38 Decoy
Supplementary files format and content: .quant.genes.sf files include TPM values for each Sample

source_name: FFPE tissue

extract_protocol:
Total RNA was extracted from 2 x 10 µm FFPE tissue slices (23 LUSC and 3 healthy FFPE samples) with RNEasy FFPE kit (Qiagen), according to manufacturer’s instructions.RNA integrity and quality were assessed using RNA Nano 6000 BioAnalyzer chips (Agilent), with DV200 measurement setup. Samples with DV200 values >30% were included in the study. Input of total RNA used for libraries preparation varied from 20-100 ng, depending on DV200 values, according to library manufacturers instruction.
RNA libraries for RNA-seq were prepared using TruSeq RNA Exome kit (Illumina), according to manufacturer’s protocol. Fragmentation step was omitted due to samples type (FFPE).

value: FFPE tissue

tag: Sex

value: male

tag: disease

value: LUSC


title: RNA, Constant zfh1 + white-KD, rep1


title: L1072F/+ ES RNA-seq replicate 3


title: 126_V5Clk_ZT2_REP1


title: Yw_ZT18_IN_REP2

value: yw

value: input


title: L1072F/+ ES RNA-seq replicate 2


title: RNA, Constant Stat92E + ph-KD, rep2

description:
RNA_Seq_rescue_normalized_counts.txt
RNA_Constant_Stat92E_ph_KD_DESeq2_FC.txt

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-Stat92eRNAi BL43866;UAS-PhRNAi v50028/UAS-GFP


title: RNA, Constant Stat92E + ph-KD, rep3


title: Yw_ZT22_IN_REP2


title: 21671, LUSC, mRNA


title: 25609, LUSC, mRNA


title: 126_V5Clk_ZT18_REP1


title: Yw_ZT14_IN_REP2


title: WT NPC RNA-seq replicate 1

value: WT

value: Day8 NPC


title: L1072F/+ ES RNA-seq replicate 1


title: RNA, Constant Stat92E + white-KD, rep2

value: ED

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-Stat92eRNAi BL43866;UAS-wRNAi BL33623/UAS-GFP


title: Yw_ZT10_IN_REP2

value: Heads


title: Yw_ZT6_IN_REP2


title: RNA, Constant Stat92E + white-KD, rep3


title: 20432, LUSC, mRNA


title: R910Q/+ ES RNA-seq replicate 1


title: RNA, Constant Stat92E + white-KD, rep1


title: 20109, LUSC, mRNA


title: 19694, LUSC, mRNA


title: R910Q/+ ES RNA-seq replicate 2


title: RNA, Constant gfp + ph-KD, rep3

description:
RNA_Seq_rescue_normalized_counts.txt
RNA_Constant_gfp_ph_KD_DESeq2_FC.txt

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-gfpRNAi BL9331;UAS-PhRNAi v50028/UAS-GFP


title: R910Q/+ ES RNA-seq replicate 3


title: L834P/+ ES RNA-seq replicate 3


title: 18356, LUSC, mRNA


title: Yw_ZT22_IN_REP1


title: 17444, LUSC, mRNA


title: Yw_ZT14_IN_REP1


title: 17664, LUSC, mRNA


title: RNA, Constant gfp + ph-KD, rep1


title: 17428, LUSC, mRNA


title: Yw_ZT18_IN_REP1


title: L834P/+ ES RNA-seq replicate 1


title: 25486, LUSC, mRNA


title: Yw_ZT10_IN_REP1


title: RNA, Control gfp + white-KD, rep3

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/UAS-gfpRNAi BL9331;UAS-wRNAi BL33623/UAS-GFP


title: RNA, Constant Stat92E + ph-KD, rep1

value: Constant RNAi (29°C)


title: Yw_ZT2_IN_REP2


title: RNA, Control gfp + white-KD, rep1

value: Day 5 AEL


title: Yw_ZT6_IN_REP1


title: Yw_ZT2_IN_REP1


title: RNA, Control gfp + white-KD, rep2


title: CHD8+/- ES RNA-seq replicate 2


title: CHD8+/- ES RNA-seq replicate 3


title: 12698, LUSC, mRNA


title: 16734, LUSC, mRNA

value: female


title: Yw_V5Clk_ZT18_REP2


title: 12364, LUSC, mRNA


title: L834P/+ ES RNA-seq replicate 2

value: Day0 ESC


title: 12545, LUSC, mRNA

value: FFPE tissue


title: RNA, Constant gfp + ph-KD, rep2


title: WT ES RNA-seq replicate 3


title: 12210, LUSC, mRNA

value: male


title: WT ES RNA-seq replicate 2


title: 2L722-2

description: 579_vs_neurons_annotated_differential.csv

source_name: 2L722 neurons

value: 2L722 neurons


title: WT ES RNA-seq replicate 1


title: 8323, LUSC, mRNA

value: LUSC


title: 3R579-1

description: 722_vs_neurons_annotated_differential.csv

source_name: 3R579 neurons

value: 3R579 neurons


title: 7202, LUSC, mRNA


title: 2L722-1


title: Yw_V5Clk_ZT14_REP2

value: yw


title: Yw_V5Clk_ZT10_REP2


title: Yw_V5Clk_ZT6_REP2


title: CHD8+/- ES RNA-seq replicate 1


title: Yw_V5Clk_ZT22_REP2


title: gDNA, Transient ph-KD D11 AEL, batch2

description:
raw_variants_GEO_samples.snp.vcf.gz
raw_variants_GEO_samples.indel.vcf.gz

data_processing:
gDNA variants calling was performed by Novogene (https://en.novogene.com/). Briefly, base calling was performed using Illumina pipeline CASAVA v1.8.2, and subjected to quality control uqing fastp with the following parameters: -g -q 5 -u 50 -n 15 -l 150 --min_trim_length 10 --overlap_diff_limit 1--overlap_diff_percent_limit 10. Then, sequencing reads were aligned to the dm6 version of the Drosophila genome using Burrows-Wheeler Aligner (BWA) with default parameters and duplicate reads were removed using samtools and PICARD (http://picard.sourceforge.net). Raw SNP/InDel sets were called using GATK with the following parameters: --gcpHMM 10 -stand_emit_conf 10 -stand_call_conf 30. Then, SNPs were filtered using the following criteria: SNP: QD<2, FS>60, MQ<30, HaplotypeScore>13, MappingQualityRankSum<-12.5, ReadPosRankSum<-8; For INDEL variants, following criteria were used: QD<2, FS>200, ReadPosRankSum<-20. UCSC known genes were used for gene and region annotations. Finally, variants were compared to the first batch of control, no ph-KD ED in the search for bona fide de novo mutations using the MuTect2 module of the GATK package. Only SNP and INDEL variants that passed Mutect2 filtering (FILTER= â€œPASSâ€) were considered for downstream analyses.
Assembly: dm6

extract_protocol:
Genomic DNA was isolated using QIAamp DNA Micro Kit (Qiagen) following manufacturerâ€™s instructions. For each biological replicate around 70 eye discs from female wandering larvae were dissected.
Library preparation was performed by Novogene (https://en.novogene.com/). Briefly, genomic DNA was fragmented to an average size of ~350bp and then processed for DNA library preparation by following manufacturer (Illumina) paired-end protocols. Sequencing was performed using on an Illumina Novaseq 6000 (platform to generate 150bp paired-ends reads) with a coverage of at least 10x for 99% of the genome.

value: eyFLP, UbiP63E(FRT.STOP)Stinger/+; tub80ts/+; Act(FRT.CD2)Gal4, UAS-RFP/UAS-PhRNAi

value: Transient RNAi (24h 29°C L1)

value: D11 AEL

tag: chip antibody


title: 3R579-2


title: TGFb_H1.0_siRNA_Rep2 [RNA-seq]

first: Thomas

middle: Martin

last: Vondriska

address: 650 Charles Young Dr

department: Anesthesiology

institute: UCLA

data_processing:
Raw fastq.gz files were downloaded and processed as in (PMID:34273410), with the following modifications. Salmon (PMID: 28263959) was used to pseudoalign reads to an mm10 index built from Ensembl build 102.
DESeq2 (PMID: 25516281) was used to perform differential expression testing, specifically on genes that had at least 10 reads measured between the total samples, and significantly differentially expressed genes were defined as those with adjusted pvalue (padj) less than 0.01.
Assembly: mm10
Supplementary files format and content: Entire output directory from Salmon, including sample specific quant.sf quantification file.

source_name: Heart

growth_protocol: Adult female and male C57BL/6J mice cardiac fibroblasts were isolated using enzymatic digestion (7mg/ml collagenase type II; Worthington Biochemical Corporation) followed by centrifugation and cell plating. Cells were maintained in DMEM/F12 media supplemented with 10% FBS, 1% antibiotics (Penicillin and Streptomycin), and 1% insulin-transferrin-selenium (ITS) for two hours after seeding. Media and floating cells were then removed, and fibroblasts were grown in DMEM/F12 media supplemented with 10% FBS, 1% antibiotics and 1% insulin-transferrin-selenium (ITS), and human basic fibroblast growth factor (HBFGF) until reaching 70-80% confluency. Cells with a 70-80% confluency were cultured in serum-free media (0.1% FBS) for 24h prior to TGF-β treatment (10ng/mL; Novoprotein, CA59).

extract_protocol:
Pellets from isolated cardiac fibroblasts transfected with H1.0 or scrambled siRNAs and treated with TGF-β or vehicle were sent to the UCLA Technology Center for Genomics & Bioinformatics core for RNA isolation, library preparation and sequencing. Ribosomal RNA was removed using KAPA RNA HyperPrep kit (Cat.kk8561, Roche). Approximately 40 million paired-end reads per sample (2x150bp) were generated during sequencing.
Paired-end library construction

value: Heart

value: Adult cardiac fibroblasts

value: Wild type

value: TGFbeta + H1.0 siRNA

tag: molecule

value: rRNA depleted mRNA


title: 6452, LUSC, mRNA


title: Yw_V5Clk_ZT2_REP2

value: Heads


title: TGFb_H1.0_siRNA_Rep1 [RNA-seq]


title: 4737, healthy control, mRNA


title: TGFb_H1.0_siRNA_Rep3 [RNA-seq]


title: gDNA, Transient ph-KD D11 AEL, batch1

value: ED


title: Yw_V5Clk_ZT22_REP1


title: Yw_V5Clk_ZT18_REP1


title: Veh_H1.0_siRNA_Rep2 [RNA-seq]

value: Vehicle + H1.0 siRNA


title: 3260, healthy control, mRNA

value: FFPE tissue


title: Veh_H1.0_siRNA_Rep3 [RNA-seq]


title: 4613, healthy control, mRNA

value: male


title: Yw_V5Clk_ZT14_REP1


title: gDNA, Transient ph-KD D9 AEL, batch1

value: D9 AEL


title: gDNA, Transient ph-KD D9 AEL, batch2


title: Yw_V5Clk_ZT10_REP1


title: 2304, LUSC, mRNA

value: female

value: LUSC


title: TGFb_siScramble_Rep3 [RNA-seq]

value: TGFbeta + siScramble


title: Yw_V5Clk_ZT6_REP1

value: yw


title: gDNA, Constant ph-KD, batch1

value: eyFLP, UbiP63E(FRT.STOP)Stinger/+; tub80ts/+; Act(FRT.CD2)Gal4, UAS-RFP/UAS-PhRNAi

value: Constant RNAi (29°C)

value: Day 4 AEL


title: gDNA, Constant ph-KD, batch2


title: Veh_H1.0_siRNA_Rep1 [RNA-seq]

value: Heart

value: Adult cardiac fibroblasts


title: gDNA, Control no ph-KD, batch2

value: No RNAi (control 18°C)

value: Day 10 AEL


title: 55, LUSC, mRNA

value: healthy control


title: Yw_V5Clk_ZT2_REP1

value: Heads


title: 244, LUSC, mRNA


title: gDNA, Control no ph-KD, batch1

value: ED


title: TGFb_siScramble_Rep2 [RNA-seq]

value: Wild type

value: rRNA depleted mRNA


title: TGFb_siScramble_Rep1 [RNA-seq]


title: 44, LUSC, mRNA

value: FFPE tissue

value: male


title: ChIP input, Transient ph-KD D11 AEL, rep1

data_processing:
After initial quality checks of newly generated data using fastqc, paired-end reads were aligned to the dm6 version of the Drosophila genome using bowtie 2 (v2.3.5.1) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700, and low mapping quality were discarded using samtools (-q 30, v1.10, using htslib 1.10.2-3). PH, H3K27me3, H3K27Ac and H2AK118Ub peaks/domains were called for each replicate separately and on merged reads â€“ using IgG as input control â€“ using macs2 (v2.2.7.1) with the following parameters: --keep-dup 1 -g dm -f BAMPE -B --SPMR. Only the peaks that were detected in both replicates (enrichment>0 AND qvalue<0.05) and using merged reads (enrichment>2 AND qvalue<0.01) were retained for further analyses, after being merged with a minimum gap size of 250 bp for narrow peaks (PH and H3K27Ac) and 2.5kb for broad marks (H3K27me3 and H2AK118Ub). macs2 bedgraph files were used for visualization purposes.
Assembly: dm6

extract_protocol:
ChIP-Seq on 3rd instar imaginal eye discs were essentially performed as described in Loubiere, Delest et al., Nature Genetics (2016), with minor modifications. 400 eye discs were used per replicate. When necessary, several batches of dissection/collection were snap frozen in liquid nitrogen and stored at âˆ’80Â°C to collect enough material. Chromatin was sonicated using a Bioruptor Pico (Diagenode) for 10 min (30sec in, 30sec off). PH antibodies were diluted 1:100 for IP. After decrosslinking, DNA was purified using MicroChIP DiaPure columns from Diagenode.
DNA libraries for sequencing were prepared using the NEBNextÂ® Ultraâ„¢ II DNA Library Prep Kit for Illumina. Sequencing (paired-end sequencing 150bp, approx. 4Gb/sample) was performed by Novogene (https://en.novogene.com/).

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: Transient RNAi (24h 29°C L1)

value: D11 AEL

value: Cell Signaling Technology; Cat. N. 2729S


title: ChIP input, Transient ph-KD D11 AEL, rep2


title: Veh_siScramble_Rep3 [RNA-seq]

value: Vehicle + siScramble


title: In24_ZT22_1

data_processing:
Fastq files were trimmed using Fastp in SE mode.
Reads were aligned against dm6 using STAR.
Aligned reads were sorted and indexed using samtools.
A count matrix was produced using featurecounts.
A normalized counts table was produced using DESeq2.
Assembly: dm6
Supplementary files format and content: tab-delimited text file with raw counts for each sample and a csv file with normalized counts for each sample

growth_protocol: Male and female flies were entrained in 12:12 LD conditions for 4 days at 25°C, then collected at ZT2, ZT6, ZT10, ZT14, ZT18 and ZT22.

extract_protocol:
Trizol
TruSeq RNA


title: In24_ZT14_1


title: Veh_siScramble_Rep2 [RNA-seq]


title: Veh_siScramble_Rep1 [RNA-seq]


title: ChIP input, Constant ph-KD, rep2

value: Constant RNAi (29°C)

value: Day 4 AEL


title: In24_ZT10_1


title: In24_ZT18_1


title: ChIP input, Constant ph-KD, rep1


title: ChIP input, Control no ph-KD, rep2


title: H1-0_siRNA_TGFB_Input

data_processing:
H1.0 and FLAG ChIP-seq: Alignment of paired-end reads to the mm10 genome was performed as described (Chapski et al., 2021). Individual sample bigWigs were generated using the bamCoverage function of deepTools (Ramirez et al., 2016) with the following parameters: --normalizeUsing RPGC --effectiveGenomeSize 2652783500.
H3K27ac ChIP-seq: Alignment was performed against the mm10 genome using bowtie2 (Langmead and Salzberg, 2012) followed by SAM-to-BAM conversion and sorting using samtools v1.7 (Li et al., 2009). Peak calling for each sample was performed using MACS v2.2.7.1 (Zhang et al., 2008), using the callpeak function with the following layout and parameters: --treatment ChIP_replicate.sorted.bam --control Input_sorted.bam -f BAMPE -g mm. Differential occupancy of H3K27ac was determined using the DiffBind package (Ross-Innes et al., 2012) v3.6.1 in R, specifically on a set of consensus peaks measured in at least 2 samples across our experiment. We defined significantly differentially occupied regions as those with FDR < 0.05. Individual sample bigWigs were also generated using the bamCoverage function of deepTools v3.0.2 with the following parameters: --normalizeUsing RPGC --effectiveGenomeSize 2652783500.
Assembly: mm10
Supplementary files format and content: bigWigs showing read coverage

extract_protocol:
H1.0 and FLAG ChIP-seq: Primary isolated murine cardiac fibroblasts were transfected with Adv-GFP-H1.0-FLAG for 48 hours.  FLAG and H1.0 chromatin immunoprecipitation was performed using anti-FLAG (Sigma, cat. no. F1804) and anti-H1.0 (Proteintech, cat. no. 17510-1-AP) antibodies. Chromatin shearing was performed using the truChIP Chromatin Shearing kit (Covaris, cat. no. 520154) according to the manufacturer's instructions. DNA fragment size was assessed using a TapeStation 4200 (Agilent). Samples in the 300-500bp range were used for immunoprecipitation using the ChIP-IT High Sensitivity kit (Active Motif, cat. no. 53040). DNA was purified using a Zymo DNA Clean & Concentrator-5 kit (Zymo, cat. no. D4014). Library preparation and DNA sequencing were performed by the UCLA Technology Center for Genomics & Bioinformatics Core. Approximately 35 million paired-end reads per sample (2x150bp) were generated and used for bioinformatic analyses.
H3K27ac ChIP-seq: Three biological replicates of isolated cardiac fibroblasts from passage 1 were transfected with H1.0 or scrambled siRNAs for 48 hours and treated with TGF-β (10 ng/mL) for 24 hours. H3K27ac immunoprecipitation was performed using the same experimental strategy as the H1.0 ChIP-seq experiment, but using an anti-H3K27ac antibody (Abcam, cat. no. ab4729). For each biological condition, a combined input sample of sonicated genomic DNA was obtained from all three biological replicates. Library preparation and paired-end sequencing were performed at the UCLA Technology Center for Genomics and Bioinformatics Core, resulting in ~50-70 million read pairs (2x150bp) per sample.

value: Heart

value: Adult cardiac fibroblasts

value: H1.0 siRNA plus TGFbeta, isolated input DNA


title: H1-0_siRNA_TGFB_anti-H3K27ac_Rep3

value: H1.0 siRNA plus TGFbeta, ChIP using anti-H3K27ac antibody


title: In24_ZT6_1

value: Heads


title: In24_ZT2_1


title: ChIP input, Control no ph-KD, rep1

value: ED

value: No RNAi (control 18°C)

value: Day 10 AEL


title: H1-0_siRNA_TGFB_anti-H3K27ac_Rep2

value: Wild type


title: Up10_ZT22_1


title: H1-0_siRNA_TGFB_anti-H3K27ac_Rep1


title: ChIP PH, Transient ph-KD D11 AEL, rep2

description:
ChIP_PH_Transient_ph-KD_D11_AEL_merge.bw
ChIP_PH_Transient_ph-KD_D11_AEL__confident_peaks.narrowPeak

value: V. Loubiere et al., Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nature genetics 48, 1436-1442 (2016).


title: A. nidulans DgfdB NaCl + sorbitol 3

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A nidulans FGSC A4 or A. wentii CBS141173 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/fasta/data/FungiDB-65_AnidulansFGSCA4_Genome.fasta; https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/gff/data/FungiDB-65_AnidulansFGSCA4.gff; https://fungidb.org/common/downloads/release-65/AwentiiDTO134E9/fasta/data/FungiDB-65_AwentiiDTO134E9_Genome.fasta; https://fungidb.org/common/downloads/release-65/AwentiiDTO134E9/gff/data/FungiDB-65_AwentiiDTO134E9.gff
Supplementary files format and content: excell file includes count and RPKM values for each Sample

organism: Aspergillus nidulans

source_name: mycelium

growth_protocol: Barratt’s minimal broth (100 mL in 500 mL Erlenmeyer flask) inoculated with 1x108 conidia was incubated in a rotary shaker at 25 °C, 220 rpm (approx. 3.7 Hz). A. nidulans mycelia were harvested after 36 h (THS30) or 38 h (ΔgfdB), meanwhile A. wentii mycelia were harvested after 65 h (both CBS141173 and 'c gfdB) cultivation. Different incubation times were used in order we collect exponentially phase mycelia with similar physiological conditions in the case of each strain

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Mycelia were collected, washed and then transferred into 100 mL fresh Barratt’s minimal broth or Barratt’s minimal broth supplemented with 2 M sorbitol, 1 M NaCl, or 1 M NaCl + 2 M sorbitol. Cultures were further incubated at 25 °C and 220 rpm and samples were taken after 0.5 h for RNA isolation.

value: mycelium

value: DsodB mutant

value: NaCl+sorbitol treated


title: Up10_ZT18_1


title: LP 0227 microoxic 3_Götz_mannitol

city: Granada

first: Socorro

last: Mesa

address: C/Profesor Albareda 1

department: Soil and Plant Microbiology

country: Spain

institute: CSIC

description: B. diazoefficiens phaR mutant grown microoxically in minimal medium

hyb_protocol: Hybridisation, washing, staining, and scanning were done according to the Affymetrix manual using a gene chip fluidics station 450 (Affymetrix) and a gene chip scanner 3000 (Affymetrix). For hybridization of individual gene chips, 1.8 µg of labeled cDNA  were used.

scan_protocol: Standard Affymetrix procedures

data_processing: Signal intensities were detected and analyzed with MAS5 statistical algorithm (http://www.affymetrix.com)

organism: Bradyrhizobium diazoefficiens

source_name: phaR mutant grown in minimal medium under microoxic conditions

label_protocol: The fragmented cDNA was end-labeled with biotin-ddUTP using terminal dexoynucleotidyl transferase (Promega) in combination with the gene chip labeling reagent (Affymetrix). The reaction was incubated for 75 min at 37°C and stopped by the addition of 2 µl of 0.5 M EDTA

growth_protocol: B. diazoefficiens cells were grown in Götz minimal medium supplemented with mannitol (Quelas et al., 2006) to mid-exponential phase (OD600 of 0.25-0.45) under microoxic conditions (0.5% O2). Cells were first grown oxically in PSY medium, washed and employed to inoculate the cultures for expression analyses at an OD600 of about 0.02

extract_protocol: RNA was extracted as described by Hauser et al. (2007) and Pessi et al. (2007)

treatment_protocol: No treatment was applied

tag: growth condition

value: microoxic

tag: medium

value: Götz mannitol


title: H1-0_siRNA_Input

value: H1.0 siRNA, isolated input DNA


title: LP 3004 microoxic 1_Götz_mannitol

description: B. diazoefficiens wild type grown microoxically in minimal medium

source_name: wild type grown in minimal medium under microoxic conditions


title: LP 3004 microoxic 2_Götz_mannitol


title: H1-0_siRNA_anti-H3K27ac_Rep3

value: H1.0 siRNA, ChIP using anti-H3K27ac antibody


title: Up10_ZT14_1


title: A. nidulans DgfdB NaCl + sorbitol 2


title: LP 0227 microoxic 2_Götz_mannitol


title: A. nidulans DgfdB NaCl + sorbitol 1


title: ChIP PH, Constant ph-KD, rep2

description:
ChIP_PH_Constant_ph-KD_merge.bw
ChIP_PH_Constant_ph-KD__confident_peaks.narrowPeak

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: Constant RNAi (29°C)

value: Day 4 AEL


title: ChIP PH, Constant ph-KD, rep1


title: A. nidulans DgfdB NaCl 3

value: NaCl treated


title: H1-0_siRNA_anti-H3K27ac_Rep2

value: Heart

value: Adult cardiac fibroblasts


title: ChIP PH, Control no ph-KD, rep2

description:
ChIP_PH_Control_no_ph-KD_merge.bw
ChIP_PH_Control_no_ph-KD__confident_peaks.narrowPeak

value: ED

value: No RNAi (control 18°C)


title: Up10_ZT10_1

value: Heads


title: H1-0_siRNA_anti-H3K27ac_Rep1

value: Wild type


title: LP 0227 microoxic 1_Götz_mannitol


title: A. nidulans DgfdB NaCl 2

value: mycelium


title: Up10_ZT6_1


title: ChIP PH, Control no ph-KD, rep1

value: Day 10 AEL

value: V. Loubiere et al., Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nature genetics 48, 1436-1442 (2016).


title: A. nidulans DgfdB NaCl 1

value: DsodB mutant


title: LP 3004 microoxic 3_Götz_mannitol

value: microoxic

value: Götz mannitol


title: Scramble_TGFB_Input

value: Scrambled siRNA plus TGFbeta, isolated input DNA


title: Up10_ZT2_1


title: Up122_ZT22_2


title: ChIP PH, Transient ph-KD D11 AEL, rep1

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: Transient RNAi (24h 29°C L1)

value: D11 AEL


title: CUT&RUN IgG, Transient ph-KD D11 AEL, rep2

data_processing:
After initial quality checks of newly generated data using fastqc, paired-end reads were aligned to the dm6 version of the Drosophila genome using bowtie 2 (v2.3.5.1) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700, and low mapping quality were discarded using samtools (-q 30, v1.10, using htslib 1.10.2-3). PH, H3K27me3, H3K27Ac and H2AK118Ub peaks/domains were called for each replicate separately and on merged reads â€“ using IgG as input control â€“ using macs2 (v2.2.7.1) with the following parameters: --keep-dup 1 -g dm -f BAMPE -B --SPMR. Only the peaks that were detected in both replicates (enrichment>0 AND qvalue<0.05) and using merged reads (enrichment>2 AND qvalue<0.01) were retained for further analyses, after being merged with a minimum gap size of 250 bp for narrow peaks (PH and H3K27Ac) and 2.5kb for broad marks (H3K27me3 and H2AK118Ub). macs2 bedgraph files were used for visualization purposes.
Assembly: dm6
Library strategy: CUT&RUN

extract_protocol:
Cut&Run experiments were performed as described by Kami Ahmad in protocols.io (https://dx.doi.org/10.17504/protocols.io.umfeu3n) with minor modifications. 50 eye discs were dissected in Schneider medium, centrifuged for 3 min at 700g and washed twice with wash+ buffer before addition of Concanavalin A-coated beads. MNase digestion (pAG-MNase Enzyme from Cell Signaling) was performed for 30 min on ice. After ProteinaseK digestion, DNA was recovered using SPRIselect beads and eluted in 50ul TE.
DNA libraries for sequencing were prepared using the NEBNextÂ® Ultraâ„¢ II DNA Library Prep Kit for Illumina. Sequencing (paired-end sequencing 150bp, approx. 2Gb/sample) was performed by Novogene (https://en.novogene.com/).

value: Cell Signaling Technology; Cat. N. 2729S


title: A. nidulans DgfdB sorbitol 3

value: sorbitol treated


title: Up122_ZT22_1


title: Scramble_TGFB_anti-H3K27ac_Rep3

value: Heart

value: Adult cardiac fibroblasts

value: Scrambled siRNA plus TGFbeta, ChIP using anti-H3K27ac antibody


title: CUT&RUN IgG, Transient ph-KD D11 AEL, rep1

value: ED


title: Scramble_TGFB_anti-H3K27ac_Rep2

value: Wild type


title: Up122_ZT18_2

value: Heads


title: A. nidulans DgfdB sorbitol 2

value: mycelium


title: CUT&RUN IgG, Constant ph-KD, rep2

value: Constant RNAi (29°C)

value: Day 4 AEL


title: Up122_ZT18_1


title: A. nidulans DgfdB sorbitol 1

value: DsodB mutant


title: CUT&RUN IgG, Constant ph-KD, rep1


title: Scramble_Input

value: Scrambled siRNA, isolated input DNA


title: Scramble_TGFB_anti-H3K27ac_Rep1


title: Up122_ZT14_2


title: A. nidulans DgfdB untreated 2

value: untreated


title: Scramble_anti-H3K27ac_Rep2

value: Scrambled siRNA, ChIP using anti-H3K27ac antibody


title: CUT&RUN IgG, Control no ph-KD, rep1

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: No RNAi (control 18°C)

value: Day 10 AEL


title: Up122_ZT14_1


title: A. nidulans DgfdB untreated 3


title: Up122_ZT10_2


title: Scramble_anti-H3K27ac_Rep3


title: H1.0_overexpression_anti-FLAG_Rep2

value: H1.0_overexpression, ChIP using anti-H1.0 antibody


title: Scramble_anti-H3K27ac_Rep1

value: Heart


title: Up122_ZT10_1


title: A. nidulans THS30 NaCl + sorbitol 2

value: THS30 reference strain

value: NaCl+sorbitol treated


title: CUT&RUN H3K27me3, Transient ph-KD D11 AEL, rep1

description:
CUTandRUN_H3K27me3_Transient_ph-KD_D11_AEL_merge.bw
CUTandRUN_H3K27me3_Transient_ph-KD_D11_AEL_confident_peaks.broadPeak

value: ED

value: Transient RNAi (24h 29°C L1)

value: D11 AEL

value: Active motif (39155)


title: H1.0_overexpression_anti-FLAG_Rep1

value: Adult cardiac fibroblasts

value: Wild type


title: CUT&RUN H3K27me3, Constant ph-KD, rep2

description:
CUTandRUN_H3K27me3_Constant_ph-KD_merge.bw
CUTandRUN_H3K27me3_Constant_ph-KD_confident_peaks.broadPeak

value: Constant RNAi (29°C)

value: Day 4 AEL


title: A. nidulans THS30 NaCl + sorbitol 3

value: mycelium


title: A. nidulans THS30 NaCl + sorbitol 1


title: Up122_ZT6_1

value: Heads


title: Up122_ZT6_2


title: CUT&RUN H3K27me3, Constant ph-KD, rep1

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP


title: CUT&RUN H3K27me3, Control no ph-KD, rep2

description:
CUTandRUN_H3K27me3_Control_no_ph-KD_merge.bw
CUTandRUN_H3K27me3_Control_no_ph-KD_confident_peaks.broadPeak

value: No RNAi (control 18°C)


title: CUT&RUN IgG, Control no ph-KD, rep2

value: Day 10 AEL

value: Cell Signaling Technology; Cat. N. 2729S


title: H1.0_overexpression_anti-H1.0_Rep2

value: Heart

value: H1.0_overexpression, ChIP using anti-H1.0 antibody


title: Up122_ZT2_2


title: A. nidulans THS30 NaCl 3

value: THS30 reference strain

value: NaCl treated


title: A. nidulans DgfdB untreated 1

value: DgfdB mutant

value: untreated


title: A. nidulans THS30 NaCl 2


title: H1.0_overexpression_anti-H1.0_Rep1


title: CUT&RUN H3K27me3, Control no ph-KD, rep1

value: ED

value: Active motif (39155)


title: Control_anti-H1.0_Rep2

value: Adult cardiac fibroblasts

value: Wild type

value: Control cells, ChIP using anti-H1.0 antibody


title: CUT&RUN H3K27me3, Transient ph-KD D11 AEL, rep2

value: Transient RNAi (24h 29°C L1)

value: D11 AEL


title: Up122_ZT2_1

value: Heads


title: A. nidulans THS30 NaCl 1

value: mycelium


title: Control_anti-H1.0_Rep1


title: Up_126_ZT22_1


title: CUT&RUN H3K27Ac, Transient ph-KD D11 AEL, rep1

description:
CUTandRUN_H3K27Ac_Transient_ph-KD_D11_AEL_merge.bw
CUTandRUN_H3K27Ac_Transient_ph-KD_D11_AEL__confident_peaks.narrowPeak

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: Active motif (39133)


title: A. nidulans THS30 sorbitol 2

value: sorbitol treated


title: A. nidulans THS30 sorbitol 3


title: Up_126_ZT18_2


title: CUT&RUN H3K27Ac, Constant ph-KD, rep2

description:
CUTandRUN_H3K27Ac_Constant_ph-KD_merge.bw
CUTandRUN_H3K27Ac_Constant_ph-KD__confident_peaks.narrowPeak

value: Constant RNAi (29°C)

value: Day 4 AEL


title: Input1

value: Heart

value: Input DNA from isolated cells


title: Up_126_ZT18_1


title: A. nidulans THS30 sorbitol 1

value: THS30 reference strain


title: Psv NCPPB 3335 gacA SSM medium sample 2

city: Malaga

first: Carla

middle: Ariadna

last: Lavado Benito

address: Boulevar Louis Pasteur

institute: University of Malaga

data_processing:
Raw reads were preprocessed by NextSeq System Suite v.2.2.0. using specific NGS technology configuration parameters. This preprocessing removes low-quality, ambiguous and low-complexity stretches, linkers, adapters, vector fragments and contaminated sequences, and preserves the longest informative parts of the reads. SeqTrimNext also discarded sequences shorter than 25 bp.
Clean reads of the BAM files were aligned and annotated by Bowtie2
Transcript abundance, measured in fragments per kilobase per million mapped reads (FPKM), and differential gene expression were calculated using Tuxedo together with the Cufflinks suit of tools (Ghosh and Chan, 2016; Trapnell et al., 2010). CuffDiff was used to identify differentially expressed genes (DEGs). Only those genes with an adjusted P-value (q-value) < 0.05 and a log2 fold change ≤ -0.5 or ≥ 0.5 were considered significant. Graphical representation of the differential expression results was carried out using the CummeRbund package in R (Goff et al., 2012).
Assembly: sequences were aligned to the reference whole chromosome genome (accession no. CP008742.1) and the three native plasmids of Psv NCPPB 3335 (pPsv48A, FR820585.2; pPsv48B, FR820586.1; pPsv48C, FR820587.2)
Supplementary files format and content: Processed data files show differential gene expression were calculated using Tuxedo together with the Cufflinks suit of tools for each sample

organism: Pseudomonas savastanoi pv. savastanoi

source_name: gacA mutant

growth_protocol: To purify RNA, pre-inocula of 20 mL of NCPPB 3335 and Psv-ΔgacA were grown overnight in both KB and SSM media at 28 ºC. Bacterial cells from each medium were diluted in fresh KB or SSM to a final optical density at 600 nm (OD600) of 0.1, to prepare three biological replicates of 110 mL for each medium and grown at 28 °C with gentle shaking to a final OD600 of 0.5 (approximately 5x107 CFUs/mL). Next, bacterial cells from these SSM cultures were collected, each biological replicate resuspended in 12 mL of fresh SSM and divided in twelve 1 mL samples that were frozen in liquid nitrogen and stored at -80 ºC. Liquid cultures from each biological replicate grown on KB were pelleted, washed twice with one volume of sterile 10 mM MgCl2, and each resuspended in 110 mL of HIM and incubated at 28 °C for 6 hours. After this, bacterial cells were collected, and each biological replicate resuspended in 12 mL of HIM and divided in twelve 1 mL samples. After a centrifugation step, the pellets were flash-frozen in liquid nitrogen and stored at -80 °C.

extract_protocol:
RNA extractions were performed with the RNAeasy Mini Kit (Qiagen; Hilden, Germany) and following the manufacturer's instructions. Subsequently, the RNA was cleaned up from traces of genomic DNA using the TURBO DNA-free kit (Invitrogen Corp, CA, USA) following the manufacturer's instructions. For ribosomal RNA degradation, the Illumina Ribo-Zero Plus rRNA Depletion kit Bacteria (Illumina; CA, USA) was used.
For RNA sequencing analysis, 200-500 bp single-end read libraries were prepared using a TruSeq stranded total RNA kit (Illumina). The libraries were sequenced using a NextSeq550 instrument (Illumina).

value: gacA mutant

value: SSM medium


title: CUT&RUN H3K27Ac, Constant ph-KD, rep1

value: ED


title: A. nidulans THS30 untreated 3

value: untreated


title: Up_126_ZT14_2


title: A. nidulans THS30 untreated 2


title: Psv NCPPB 3335 SSM medium sample 2

source_name: WT

value: WT


title: Up_126_ZT22_2


title: Up_126_ZT14_1


title: CUT&RUN H3K27Ac, Control no ph-KD, rep1

description:
CUTandRUN_H3K27Ac_Control_no_ph-KD_merge.bw
CUTandRUN_H3K27Ac_Control_no_ph-KD__confident_peaks.narrowPeak

value: No RNAi (control 18°C)

value: Day 10 AEL


title: CUT&RUN H3K27Ac, Transient ph-KD D11 AEL, rep2

value: Transient RNAi (24h 29°C L1)

value: D11 AEL


title: Psv NCPPB 3335 SSM medium sample 1


title: CUT&RUN H2AK118Ub, Transient ph-KD D11 AEL, rep2

description:
CUTandRUN_H2AK118Ub_Transient_ph-KD_D11_AEL_merge.bw
CUTandRUN_H2AK118Ub_Transient_ph-KD_D11_AEL_confident_peaks.broadPeak

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: Cell Signaling Technology; Cat. N. 8240S (D27C4)


title: Up_126_ZT10_1

value: Heads


title: hyphae_PYY, rep3

city: Chicago

first: Eugene

last: Chang

state: IL

address: 900 E 57th St

department: Medicine

institute: University of Chicago

data_processing:
Raw Fastq reads were processed using FastQC for quality control, STAR with splice-variant sensitivity for alignment (C. albicans strain SC5314), and featureCounts for assigning reads to genomic features.
Assembly: GCA_000182965.3ASM18296v3
Supplementary files format and content: ECAK_featurecounts.csv

organism: Candida albicans

source_name: hyphae

extract_protocol:
Candida albicans cultures were extracted for RNA using the YeaStar RNA Kit (Zymo Research)
Olido-dt mRNA directional - Ilumina TruSeq stranded mRNA Library Prep

tag: strain

value: hyphae


title: hyphae_PYY, rep2


title: CUT&RUN H2AK118Ub, Constant ph-KD, rep2

description:
CUTandRUN_H2AK118Ub_Constant_ph-KD_merge.bw
CUTandRUN_H2AK118Ub_Constant_ph-KD_confident_peaks.broadPeak

value: Constant RNAi (29°C)

value: Day 4 AEL


title: Up_126_ZT6_2


title: Psv NCPPB 3335 gacA HIM medium sample 1

value: HIM medium


title: Psv NCPPB 3335 HIM medium sample 2


title: hyphae_PYY, rep1


title: Psv NCPPB 3335 HIM medium sample 1


title: CUT&RUN H2AK118Ub, Constant ph-KD, rep1


title: hyphae_ctrl, rep3

value: control


title: Up_126_ZT2_2


title: Up_126_ZT6_1


title: Psv NCPPB 3335 gacA SSM medium sample 1

value: gacA mutant


title: CUT&RUN H2AK118Ub, Control no ph-KD, rep2

description:
CUTandRUN_H2AK118Ub_Control_no_ph-KD_merge.bw
CUTandRUN_H2AK118Ub_Control_no_ph-KD_confident_peaks.broadPeak


title: CUT&RUN H3K27Ac, Control no ph-KD, rep2

value: Active motif (39133)


title: Solvent, rep5

city: Ste-Anne-de-Bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

data_processing:
Processed using the Seq2Fun Module on EcoOmicsAnalyst.ca and manually formatted for ExpressAnalyst.ca
Assembly: Seq2Fun database (protein ortholog database) for birds
Supplementary files format and content: Count table in a tab-delimited text file format with Seq2Fun IDs in rows and samples in columns

organism: Phalacrocorax auritus

source_name: Left-lobe liver

growth_protocol: Incubation at 37.5°C and 60% humidity

extract_protocol:
Liver tissue was homogenized in buffer RLT using a TissueLyser II (Qiagen, Toronto, ON, CA), and RNA was extracted using the RNeasy® Mini QIAcube Kit (Qiagen) following the manufacturer’s protocol. An extra DNase I digestion step was included to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aircell injection of 50 µl dosing solution prior to incubation

value: Left-lobe liver

tag: developmental stage

value: embryonic day 14

value: DMSO (solvent)


title: Up_126_ZT2_1

tag: tissue


title: Up_126_ZT10_2


title: CUT&RUN H2AK118Ub, Control no ph-KD, rep1

source_name: ED

value: ED

value: No RNAi (control 18°C)


title: Solvent, rep4


title: Yw_ZT22_2

value: yw


title: RNA, Transient white-KD, rep3

description:
RNA_Transient_white-KD_merge.bw
RNA_Seq_normalized_counts.txt

data_processing:
After initial quality checks of newly generated data using fastqc, paired-end reads were aligned to a custom index consisting of the dm6 version of the Drosophila genome together with GFP, EGFP and mRFP1 sequences, using the align function from the Rsubread R package (v2.0.1) with the following parameters: maxMismatches = 6, unique = TRUE. Then, aligned reads were counted for each D. melanogaster transcript (dmel_r6.36 annotation) using the featureCounts function from the Rsubread R package (v2.0.1, isPairedEnd = TRUE) and differential expression analysis was performed using the DESeq2 R package (v1.26.0, design = ~replicate+condition). For each condition, ph-RNAi were compared to temperature-matched w-RNAi controls.
Assembly: dm6

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-wRNAi BL33623/UAS-GFP

value: Transient RNAi (24h 29°C L1)

value: D9 AEL


title: A. nidulans THS30 untreated 1

value: mycelium

value: THS30 reference strain

value: untreated


title: yeast_PYY, rep3

source_name: yeast

value: yeast


title: Solvent, rep3


title: hyphae_ctrl, rep1

value: hyphae


title: Yw_ZT22_1

value: Heads


title: Psv NCPPB 3335 gacA HIM medium sample 2

tag: cell line

value: gacA mutant

value: HIM medium


title: RNA, Transient white-KD, rep2


title: CUT&RUN H2AK118Ub, Transient ph-KD D11 AEL, rep1

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: D11 AEL

value: Cell Signaling Technology; Cat. N. 8240S (D27C4)


title: RNA, Transient white-KD, rep1

value: ED


title: Solvent, rep2

value: Left-lobe liver

value: embryonic day 14

value: DMSO (solvent)


title: yeast_PYY, rep1


title: yeast_PYY, rep2


title: Yw_ZT18_1

value: yw


title: 3.33 µg EE2/g, rep5

value: 3.33 ug EE2/g egg weight (actual:2.3 ug EE2/g egg weight)


title: RNA, Constant white-KD, rep3

description:
RNA_Constant_white-KD_merge.bw
RNA_Seq_normalized_counts.txt

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-wRNAi BL33623/UAS-GFP

value: Constant RNAi (29°C)

value: Day 4 AEL


title: yeast_ctrl, rep3

value: yeast

value: control


title: Yw_ZT14_1

value: Heads


title: hyphae_ctrl, rep2

value: hyphae


title: RNA, Constant white-KD, rep2


title: yeast_ctrl, rep2


title: Yw_ZT10_2


title: 3.33 µg EE2/g, rep3


title: yeast_ctrl, rep1


title: RNA, Constant white-KD, rep1


title: RNA, Control no white-KD, rep3

description:
RNA_Control_no_white-KD_merge.bw
RNA_Seq_normalized_counts.txt

value: No RNAi (control 18°C)

value: Day 10 AEL


title: Yw_ZT10_1


title: Esc8-3 EtOH

city: Boston

first: Andrew

last: Day

address: 136 Harrison Ave

department: Molecular Microbiology

institute: Tufts University

data_processing:
Raw counts determined using DESeq2
Assembly: Candida albicans SC5314 (assembly ASM18296v3)
Supplementary files format and content: Each file contains raw counts from the comparisons within strains between water and ethanol conditions. Each column represents a different biological replicate

organism: Candida albicans SC5314

source_name: yeast cells

extract_protocol:
RNA extracted from yeast cells using bead beating and Invitrogen PureLink RNEasy Kit
mRNA chemically fragmented, cDNA synthesis, and adaptor hybridization

value: yeast cells

tag: cell type

value: DMEM w/ 10% EtOH


title: RNA, Control no white-KD, rep2

value: ED

tag: genotype


title: 3.33 µg EE2/g, rep2

value: Left-lobe liver

tag: treatment


title: 3.33 µg EE2/g, rep1

value: embryonic day 14


title: Esc8-2 EtOH


title: Yw_ZT6_2

source_name: Heads


title: RNA, Control no white-KD, rep1

tag: time


title: Yw_ZT14_2


title: Yw_ZT6_1


title: Esc8-1 EtOH


title: Solvent, rep1

value: DMSO (solvent)


title: 33.3 µg EE2/g, rep4

value: 33.3 ug EE2/g egg weight (actual:31.9 ug EE2/g egg weight)


title: 3.33 µg EE2/g, rep4

value: 3.33 ug EE2/g egg weight (actual:2.3 ug EE2/g egg weight)


title: Yw_ZT2_2

value: yw


title: RNA, Transient ph-KD D9 AEL, rep3

description:
RNA_Transient_ph-KD_D9_AEL_merge.bw
RNA_Seq_normalized_counts.txt
Transient ph-KD D9 AEL vs Transient w-KD Deseq2_FC.txt

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP

value: Transient RNAi (24h 29°C L1)

value: D9 AEL


title: Esc8-3 H2O

value: DMEM w/ 10% H2O


title: Esc8-2 H2O


title: RNA, Transient ph-KD D9 AEL, rep2


title: 33.3 µg EE2/g, rep3


title: 33.3 µg EE2/g, rep5


title: Esc8-1 H2O


title: RNA, Transient ph-KD D9 AEL, rep1


title: Yw_ZT2_1

value: Heads


title: CS_ZT14

data_processing:
ATAC-Seq files were adaptor-trimmed using fastp. Bowtie2 was used to aligned trimmed files using the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no- discordant --phred33 -I 10 -X 700. Samtools was used to remove PCR duplicates and Sambamba was used to remove multimapping reads. Tn5 insertion bias was corrected using a custom python script and peaks were called using MACS2.
Peaks called from MACS2 were intersected between replicates using bedtools, and peaks across conditions were merged and converted into a reference annotation in SAF format (62). Featurecounts was used to count reads in each sample within each region in the reference file, and input into DESeq2 in R. DESeq2 was used to perform differential peak quantification, and normalization factors were produced as well. Normalization factors were used to produce normalize bigwig files for visualization using Deeptools bamcoverage
Assembly: dm6
Supplementary files format and content: peak-signal normalized bigwig files

source_name: heads

growth_protocol: Two weeks old flies were collected at ZT02 and ZT14.

extract_protocol:
ATAC-Seq was performed on FACS-sorted clock neurons and glia using Clk856-Gal4 and Repo-Gal4, crossed to UAS-unc84-GFP, respectively. Brains were dissected in Schneider’s media and incubated with 0.75mg/ml Collagenase and 0.4mg/ml Dispase at room temperature for 30 minutes. Brains were then triturated 50-80 times to obtain a single-cell suspension for FACS sorting.
Sorted cells and nuclei were centrifuged at 1000 rpm for 10mins at 4°C and the pellet was resuspended in 50uL of Transposition mix (25uL 2xTD buffer, 16.5uL PBS, 0.05 μl 10% v/v Tween, 0.05 μL 1% v/v Digitonin, and 2.5uL TDE1 Enzyme (Illumina, San Diego, CA, USA Catalog #20034198) and incubated at 37 °C for 30 mins. Tagmented DNA was purified using Zymo DNA clean and concentrator kit. Purified DNA fragments were amplified using single-indexed Nextera primers (Integrated DNA Technologies) for 12 PCR cycles. Amplified libraries were purified using AMPure XP beads (Beckman Coulter, Brea, CA, USA Catalog #A63880), and size distribution was accessed using TapeStation High-Sensitivity D1000 Screentape. Final libraries were sequenced on a Nextseq 550 (Illumina).

value: heads

value: CantonS


title: CS_ZT02


title: Esc7-3 EtOH


title: Repo_CLK_OE_ZT14

source_name: Glia

value: Glia


title: 33.3 µg EE2/g, rep1


title: RNA, Transient ph-KD D11 AEL, rep3

description:
RNA_Transient_ph-KD_D11_AEL_merge.bw
RNA_Seq_normalized_counts.txt
Transient ph-KD D11 AEL vs Transient w-KD Deseq2_FC.txt

value: D11 AEL


title: RNA, Transient ph-KD D11 AEL, rep2


title: 33.3 µg EE2/g, rep2


title: WT_GX_4h_2

city: Tianjin

first: Jingen

last: Li

address: Xiqi Dao 32, Tianjin Airport Economic Area

institute: Tianjin institute of industrial biotechnology,Chinses Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with NGSQCToolkit (v2.3).
Clear reads were mapped to Myceliophthora thermophila ATCC 42464 genome using Tophat (version 2.0.8b) with parameters -i 10 -g 1 --segment-length 24 --b2-very-sensitive --no-convert-bam --library-type fr-unstranded.
The counts of reads uniquely mapped to only one gene for each gene were calculated by HTseq-count(version 0.13.5).
Assembly: Myceliophthora thermophila ATCC 42464(https://genome.jgi.doe.gov/Spoth2/Spoth2.home.html)
Supplementary files format and content: tab-delimited text files including Reads count for each sample.

organism: Thermothelomyces thermophilus

growth_protocol: Precultured mycelium from M. thermophila WT strain (ATCC42464) were shifted into 5 mL 1×Vogel’s salt with 2% G2 (cellobiose), 2% X2 (xylobiose), G2X2 (2% cellobiose and 2% xylobiose), GX (1% glucose and 1% xylose), or no carbon in in round-bottomed 24-well plates. for the induciton of additional 4 h.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mycelium


title: Repo_CLK_OE_ZT02


title: Esc7-2 EtOH

value: yeast cells

value: DMEM w/ 10% EtOH


title: Esc7-1 EtOH


title: WT_GX_4h_1


title: Esc7-3 H2O


title: nSyb_CLK_OE_ZT14

source_name: all neurons

value: all neurons


title: RNA, Constant ph-KD, rep3

description:
RNA_Constant_ph-KD_merge.bw
RNA_Seq_normalized_counts.txt
Constant ph-KD vs Constant w-KD Deseq2_FC.txt

value: ED

value: Constant RNAi (29°C)

value: Day 4 AEL


title: Esc7-2 H2O


title: RNA, Constant ph-KD, rep2


title: nSyb_CLK_OE_ZT02


title: WT_X2_4h_2


title: RNA, Constant ph-KD, rep1


title: Esc7-1 H2O


title: WT_X2_4h_1


title: RNA, Control no ph-KD, rep3

description:
RNA_Control_no_ph-KD_merge.bw
RNA_Seq_normalized_counts.txt
Control no ph-KD vs Control no w-KD Deseq2_FC.txt

value: No RNAi (control 18°C)

value: Day 10 AEL


title: Esc6-3 EtOH


title: nSyb_ZT014_1


title: nSyb_ZT02_2


title: RNA, Control no ph-KD, rep2

value: eyFLP, Act5C (FRT.CD2) Gal4 /+; tubGAL80ts/+;UAS-PhRNAi v50028/UAS-GFP


title: Esc6-2 EtOH


title: nSyb_ZT02_1


title: Esc6-1 EtOH


title: WT_G2_4h_1


title: RNA, Control no ph-KD, rep1


title: WT_G2_4h_2


title: Repo_ZT14_1


title: WT_NoCarbon2_4h_2


title: WT_G2X2_4h_2


title: Esc6-3 H2O


title: RNA, Transient ph-KD D11 AEL, rep1

value: Transient RNAi (24h 29°C L1)


title: nSyb_CLK_OE_ZT02_2


title: RNA, Transient white-KD constGFP, rep3

value: eyFLP, UbiP63E(FRT.STOP)Stinger/+; tub80ts/+; Act(FRT.CD2)Gal4, UAS-RFP/UAS-wRNAi BL33623

value: D9 AEL


title: RNA, Transient white-KD constGFP, rep2


title: WT_G2X2_4h_1


title: Repo_ZT02_1


title: Esc6-2 H2O

value: DMEM w/ 10% H2O


title: WT_NoCarbon2_4h_1


title: WT_XA_4h_2

growth_protocol: Precultured mycelium from M. thermophila WT strain (ATCC42464) were shifted into 100 mL 1×Vogel’s salt with 2% Xylan or 2% AX (1% Avicel and 1% Xylan) in 250-mL Erlenmeyer flask for the induciton of additional 4 h.


title: RNA, Transient white-KD constGFP, rep1


title: Esc6-1 H2O


title: Clk856_ZT02_2

source_name: clock neurons

value: clock neurons


title: WT_XA_4h_1


title: RNA, Constant white-KD constGFP, rep2


title: Clk856_ZT02_1


title: WT_Xylan_4h_2


title: SC5314-2 EtOH

value: Parental SC5314


title: SC5314-1 EtOH


title: RNA, Constant white-KD constGFP, rep1


title: WT_Xylan_4h_1


title: SC5314-3 H2O


title: S93S

city: Philadelphia

first: Stephanie

last: Daws

state: PA

address: 3500 N Broad St

institute: Temple University

data_processing:
Basecalling was performed with BGI proprietary software
Raw sequencing reads were filtered to remove reads with low quality tags, 5’ primer contaminants, tags without a 3’ primer, tags with poly A and those shorter than 18nt and the remaining reads were stored in FASTQ format.
Bowtie2 was used to align clean reads to the reference genome (rn6).
miRDeep2 was used to predict novel miRNA based on harpin structure of miRNA precursors.
miRNAs expression level was calculated as Transcripts Per Kilobase Million (TPM) to directly compare differences in gene expression between samples.
Assembly: rn6
Supplementary files format and content: Excel spreadsheet

source_name: orbitofrontal cortex

extract_protocol:
Total RNA was isolated using the miRvana PARIS kit (AM1556) from Invitrogen according to the manufacturer's protocol.
Small-RNA sequencing was performed on four biological replicates per group by BGI Genomics (BGI Americas Corp, Cambridge, MA, USA). Total RNA was assessed for quality before library preparation and RNA Integrity Numbers (RIN) were ≥ 7.5 with 28S/18S ≥ 1.3. Small RNAs (18-30 nt) were separated from total RNA by PAGE gel. Selected small RNAs were ligated with 3’ and 5’ adapters. The formed strands were reverse transcribed in cDNA and PCR amplified with high-ping polymerase. The PCR products (100-120bp) were separated by PAGE gel to eliminate primer-dimers and other byproducts and purified. The PCR yield was quantified followed by single strand DNA cyclization (ssDNA circle) for final library construction. DNA nanoballs (DNBs) were generated by ssDNA circle by rolling circle replication. The DNBs were then loaded onto the BGISEQ-500 platform sequencing for 100bp paired end reads.

treatment_protocol: Adult male Sprague Dawley rats were aged 8 weeks on arrival. For heroin exposure, animals were acclimited to the animal facility for 1 week then underwent jugular vein catheterization. Following 1 week of recovery, animals self-administered  heroin at dose of 0.03mg/kg/infusion for 6 hours per day in 10 daily sessions. Sucrose animals self-administered 45mg sucrose pellets for 2 hours per day. Naive animals were briefly handled each day. Following the last self-administration session, animals remained in their homecage for 48 hours. After 2 days, animals were euthanized and their brains were frozen in ice cold isopentane. Orbitofrontal cortex tissue was dissected from each animal on dry ice then RNA extraction proceeded.

value: orbitofrontal cortex

value: Sprague Dawley

value: male

value: 10 days of sucrose self-administration

tag: age

value: adult


title: RNA, Control no white-KD constGFP, rep2

extract_protocol:
Third instar female larvae were dissected in Schneider medium on ice. Total RNA was extracted using TRIzol reagent. RNA purification was performed using RNA Clean & Concentrator kit (Zymo Research, #R1015).
Poly-A RNAs selection, library preparation and illumina sequencing (20M paired-end reads, 150nt) were performed by Novogene  (https://en.novogene.com/). All experiments were performed in triplicate.

value: ED


title: Clk856_ZT14_1

tag: time point


title: S91S


title: SC5314-1 H2O

value: yeast cells


title: S84S


title: SC5314-2 H2O


title: RNA, Control no white-KD constGFP, rep1


title: RNA, Transient ph-KD D11 AEL constGFP, rep3

description:
RNA_Seq_constGFP_normalized_counts.txt
Transient ph-KD D11 AEL constGFP vs Transient w-KD constGFP Deseq2_FC.txt

value: eyFLP, UbiP63E(FRT.STOP)Stinger/+; tub80ts/+; Act(FRT.CD2)Gal4, UAS-RFP/UAS-PhRNAi v50028

value: D11 AEL


title: S79H

value: 10 days of heroin self-administration (0.03mg/kg)


title: SC5314-3 EtOH

value: DMEM w/ 10% EtOH


title: RNA, Constant white-KD constGFP, rep3

value: Constant RNAi (29°C)

value: Day 4 AEL


title: D39_AMXT1501_Treated_Rep4

city: Starkville

first: Bindu

last: Nanduri

state: MS

address: 240 Wise Center Dr.

institute: Mississippi State University

data_processing:
CLC Genomic Workbench 23.0.3
Sequence reads were trimmed for adaptor sequence and low quality.
The mapping process utilized CLC's proprietary read mapper, with specific parameters including a mismatch cost of 2, an insertion or deletion cost of 3, and a similarity/length fraction of 0.8.
Read counting was achieved with the EM estimation algorithm, and differentially expressed genes were pinpointed based on fold changes generated by a Generalized Linear Model.
Assembly: GCF_000014365.2_ASM1436v2
Supplementary files format and content: D39_DFMO vs D39_Untreated RNASeq.csv: differentially expressed genes with DFMO treatement
Supplementary files format and content: D39_AMXT vs D39_Untreated RNASeq.csv: differentially expressed genes with AMXT 1501 treatement

organism: Streptococcus pneumoniae D39

source_name: Bacteria cells

growth_protocol: Streptococcus pneumoniae D39 (n = 4)  cultured in THY medium between optical density 0.4–0.5 (at 600 nm )

extract_protocol:
RNA extracted and purified using the Rneasy Midi Kit (Qiagen). 5 µg of total RNA was used for construction of sequencing libraries
RNA libraries prepared using KAPA RNA Hyper Kit with RiboErase (Kapa) following manufacturer's protocols

treatment_protocol: Four replicates each of (1) Untreated (2) ⅛ MIC DFMO (34 mM) treatment and (3) ½ MIC AMXT 1501 (7.4 µM) treatment

value: Bacteria cells

value: AMXT 1501 Treated Cells


title: D39_AMXT1501_Treated_Rep3


title: S77H


title: RNA, Control no white-KD constGFP, rep3

value: eyFLP, UbiP63E(FRT.STOP)Stinger/+; tub80ts/+; Act(FRT.CD2)Gal4, UAS-RFP/UAS-wRNAi BL33623

value: No RNAi (control 18°C)

value: Day 10 AEL


title: S76H

value: orbitofrontal cortex

value: Sprague Dawley


title: RNA, Transient ph-KD D11 AEL constGFP, rep1

value: Transient RNAi (24h 29°C L1)


title: RNA, Transient ph-KD D9 AEL constGFP, rep3

description:
RNA_Seq_constGFP_normalized_counts.txt
Transient ph-KD D9 AEL constGFP vs Transient w-KD constGFP Deseq2_FC.txt

value: D9 AEL


title: S66H

value: male

value: adult


title: S36_LiZL_NS

city: Beijing

first: Jing

last: Dong

address: Beiguan Street

institute: Beijing Chest Hospital, Capital Medical University

hyb_protocol: In Hybridization Oven, according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes with Gene Expression Wash Buffer Kit, followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7. Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 8

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color, following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit.

extract_protocol: PBMCs were collected from Peripheral blood (3 ml) isolated by density gradient. Total RNA was extracted from PBMCs for microarray

value: Peripheral Blood Mononuclear Cell

value: tuberculosis patient


title: D39_AMXT1501_Treated_Rep2


title: S28_NS

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 6


title: S29_146112_NS

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 7


title: D39_AMXT1501_Treated_Rep1


title: S23_142324_NS

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 5


title: S20_NS

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 3


title: S21_142336_NS

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 4


title: RNA, Transient ph-KD D9 AEL constGFP, rep2

first: Vincent

last: Loubiere

address: 141 rue de la Cardonille

institute: UMR9002; CNRS-UM

value: ED

value: eyFLP, UbiP63E(FRT.STOP)Stinger/+; tub80ts/+; Act(FRT.CD2)Gal4, UAS-RFP/UAS-PhRNAi v50028


title: S4N

value: naïve, handled


title: RNA, Transient ph-KD D9 AEL constGFP, rep1


title: RNA, Transient ph-KD D11 AEL constGFP, rep2

value: D11 AEL


title: D39_DFMO_Treated_Rep3

value: Bacteria cells

value: DFMO Treated Cells


title: RNA, Constant ph-KD constGFP, rep3

description:
RNA_Seq_constGFP_normalized_counts.txt
Constant ph-KD constGFP vs Constant w-KD constGFP Deseq2_FC.txt

value: Constant RNAi (29°C)

value: Day 4 AEL


title: S3N


title: S2N


title: RNA, Constant ph-KD constGFP, rep2


title: D39_DFMO_Treated_Rep2


title: S1N


title: D39_DFMO_Treated_Rep4


title: D39_DFMO_Treated_Rep1


title: RNA, Constant ph-KD constGFP, rep1


title: RNA, Control no ph-KD constGFP, rep3

description:
RNA_Seq_constGFP_normalized_counts.txt
Control no ph-KD constGFP vs Control no w-KD constGFP Deseq2_FC.txt

value: No RNAi (control 18°C)

value: Day 10 AEL


title: D39_Untreated_Rep3

value: Control Cells


title: VNO scRNA-seq female replicate 1

city: Hyderabad

first: Adish

last: Dani

state: Telangana

address: 36/P, Gopanpally

country: India

institute: Tata Institute of Fundamental Research, Hyderabad

library_source: transcriptomic single cell

data_processing:
Raw reads for each sample were trimmed as per requirements specified by 10X genomics (read 1 - 28 bps and read 2 - 91 bps) using trim galore (ver. 0.6.6). Trimmed reads were aligned separately to reference genome mm10 (Mus_musculus.GRCm38.dna.primary_assembly.fa) and the count matrix was generated using cellranger-5.0.1 for each sample. To avoid alignment errors, read-through transcripts were removed from the reference. Male (2) and female (2) replicates were integrated by using the cellranger’s ‘aggr’ option. Ambient RNA contamination was removed using soupX software (ver. 1.6.2) with default parameters in auto mode. The adjusted count matrix from soupX consisting of 10615 cells was used as an input to Seurat (ver. 4.3.0) for further analysis.
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files

source_name: Vomeronasal neuroepithelium

extract_protocol:
C57BL/6J animals: 6 male, 10 female were euthanized, VNOs were dissected and processed separately. The sensory epithelium was separated using forceps and immediately placed in EBSS equilibrated with 95% CO2, 5% O2. Neuroepithelial tissue from multiple animals of same sex was transferred to the papain dissociation buffer(20U/mL Papain,1mM L-cysteine, 0.5mM EDTA, 12 U/mL RNase-free DNase). The tissue was cut into small pieces and the suspension was transferred to 14 mL tube. The suspension was incubated with gentle shaking at 37°C for 30 minutes on a thermomixer (Eppendorf) by passing 95% CO2 ,5% O2 on top of the liquid headspace. During this incubation, the solution was triturated with fire-polished Pasteur pipette every 10 minutes and at the end the incubation. After incubation, the suspension was passed sequentially through 70µm, 35µm filters to remove tissue debris. The filtered suspension was further layered over a mix of ovomucoid inhibitor (2.5 mg/mL) and albumin (2.5 mg/mL) in EBSS and centrifuged at 400 x g for 5 minutes at room temperature to remove subcellular debris or membrane fragments. The supernatant was discarded, and the resuspended cell pellet was used for library preparation after Hank's balanced Salt solution (HBSS) wash.
Dissociated neurons resuspended in HBSS were used for library preparation. Using hemocytometer and trypan blue staining, cell density was estimated at 1200 cells/ul and 1100 cell/ul for male and female samples, respectively with greater than 80% cell viability. Single-cell capture, library preparation was done using a Chromium Next GEM Single Cell 3’ GEM, Library and Gel Bead Kit v3.1 on a 10X Chromium controller (10X Genomics). Single cell suspension from male and female samples was loaded onto two separate wells of different chips giving a total of four libraries (2 male and 2 female samples).

value: Vomeronasal neuroepithelium

value: 7-8 weeks old

value: Female

value: Wildtype


title: VNO scRNA-seq female replicate 2


title: D39_Untreated_Rep4


title: S16_MuZY_NS

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 2

value: Peripheral Blood Mononuclear Cell


title: S511_NS

source_name: Peripheral Blood Mononuclear Cell from health control 7

value: health control


title: S547_NS

source_name: Peripheral Blood Mononuclear Cell from health control 9


title: RNA, Control no ph-KD constGFP, rep2

source_name: ED

value: ED


title: S542_NS

source_name: Peripheral Blood Mononuclear Cell from health control 8


title: S470_NS

source_name: Peripheral Blood Mononuclear Cell from health control 6


title: S456_NS

source_name: Peripheral Blood Mononuclear Cell from health control 5


title: VNO scRNA-seq male replicate 2

value: Male


title: S13_HanJY_NS

source_name: Peripheral Blood Mononuclear Cell from tuberculosis patient 1

value: tuberculosis patient


title: RNA, Control no ph-KD constGFP, rep1

value: eyFLP, UbiP63E(FRT.STOP)Stinger/+; tub80ts/+; Act(FRT.CD2)Gal4, UAS-RFP/UAS-PhRNAi v50028


title: D39_Untreated_Rep2

value: Bacteria cells


title: D39_Untreated_Rep1


title: VNO scRNA-seq male replicate 1


title: S452_NS

source_name: Peripheral Blood Mononuclear Cell from health control 4


title: No template control; rep2 [protein expression level]

status: Public on Feb 27 2024

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

library_source: other

data_processing:
library strategy: GeoMx NGS readout
Raw FASTQ files were processed via Nanostring's NGS pipeline (v1.0) with default parameters. According to the manufacturer, reads are first processed for quality before trimming adapters and merging paired-end reads. The resulting high quality reads are then aligned to the proprietary Readout Tag Sequence-ID (RTS-ID) barcode. PCR duplicates are removed by matching on the Unique Molecular Index (UMI) and output DCC files are then generated for each region of interest (ROI) or area of illumination (AOI).
Processed DCC files were then mapped to protein targets and collapsed into a single count table using the R package GeoMxTools (v 3.3.0) and themanufactor's reference for each of the target panels ( .pkc files).
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes)
Supplementary files format and content: GeoMx pipeline readable digital counts (DCC) - contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: Values represented in the collapsed target count table are the raw counts of the probes for a given protein target - or in the case that multiple probes were used, the averaged raw counts.

molecule: protein

organism: blank sample

source_name: No template control

extract_protocol:
Samples were incubated with the following target panels for the Nanostring GeoMx DSP: (v1.0) Mouse NGS Protein Core, (v1.0) Mouse NGS Alzheimer's Pathology Extended Protein, (v1.0) Mouse NGS Alzheimer's Pathology Protein, (v1.0) Mouse NGS Autophagy Protein, (v1.0) Mouse NGS Cell Death Protein, (v1.0) Mouse NGS Glial Cell Subtyping Protein, (v1.0) Mouse NGS MAPK Signaling Protein, (v1.0) Mouse NGS Neural Cell Typing Protein, (v1.0) Mouse NGS PI3K/AKT Signaling Protein, (v1.0) Mouse NGS Parkinson's Pathology Protein. For extraction, regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).
Manufactor's protocol for Nanostring GeoMx DSP with NGS readout; Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed ROIs were pooled and purified prior to sequencing.

value: No template control

tag: region

tag: slide

tag: roi


title: No template control; rep1 [protein expression level]

value: No Template Control


title: S385_NS

source_name: Peripheral Blood Mononuclear Cell from health control 1

tag: disease


title: S411_NS

source_name: Peripheral Blood Mononuclear Cell from health control 2


title: 20 s Irradiation vs Unirradiated Replicate 2

city: Braunschweig

first: Mattes

last: Hintmann

address: Rebenring 56

department: Institut für Mikrobiologie

institute: TU Braunschweig

description: Biological replicate 2 of 3

hyb_protocol: using the Gene Assay Hybridization Kit (Agilent) according to the manufacturers instructions and samples were applied to microarrays. After hybridization, slides were washed sequential

scan_protocol: the Agilent C Scanner (Agilent; Scan Control 8.4.1; Feature Extraction 10.7.3.1)

data_processing:
Agilent Scan Control 8.4.1 and Feature Extraction 10.7.3.1
normalized log10 ratio (Cy5/Cy3) representing test/reference

organism: Escherichia coli

source_name: Unirradiated cells (reference)

label_protocol: “ULS Fluorescent Labeling Kit for Agilent Arrays with Cy3 and Cy5” (Kreatech Biotechnology, Amsterdam, Netherlands) was used following the manufacturer´s instruction for two-colour microarray-based gene expression analysis

growth_protocol: E. coli cells were grown in LB-medium in baffled flasks until the exponential phase (180 rpm, 37 °C), sedimented (4000 xg, 10 min), washed three times and suspended in isotonic NaCl (9 g(L)

extract_protocol: Total RNA was extracted using RNeasyminiKit (Qiagen) and Dnase treated using TurboDNase (Thermo fisher) according to the manufacturers instructions

treatment_protocol: 2.5 mL of cells (OD578 nm) were transfered to a 10x20 mm quartz cuvette, the cells were the irradiated (448 nm, blue laser) for  5 s (310 J/cm2) or 20 s (1240 J/cm2) both with an intensity of 62 W/cm2, the cells were then transfered to a 15 mL tube and incubated at room temperature under slight agitation for 60 min, the cells were then pelleted (5 min, 4000 xg) and stored at -80 °C

value: Unirradiated

source_name: irradiated cells 20 s

value: Irradiated 20 s


title: 20 s Irradiation vs Unirradiated Replicate 1

description: Biological replicate 1 of 3


title: 20 s Irradiation vs Unirradiated Replicate 3

description: Biological replicate 3 of 3


title: S446_NS

source_name: Peripheral Blood Mononuclear Cell from health control 3


title: 5 s Irradiation vs Unirradiated Replicate 2

description: Biological replicate 2 of 3

source_name: irradiated cells 5 s

value: Irradiated 5 s


title: 5 s Irradiation vs Unirradiated Replicate 3

description: Biological replicate 3 of 3


title: No Template Control; rep2

molecule: other

source_name: brain

extract_protocol:
Samples were incubated with the following target panels for the Nanostring GeoMx DSP: (v1.0) Mouse NGS Whole Transcriptome Atlas RNA (Lot# MWTA12001). For extraction, regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).
Manufactor's protocol for Nanostring GeoMx DSP with NGS readout; Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR. After PCR, indexed ROIs were pooled and purified prior to sequencing.

value: brain

value: NA;NA

tag: molecule type

value: targeted RNA


title: No Template Control; rep1