title: gaf chip neg rep1 [GAF IP]

description: GAF IP

tag: factors added


title: CD4_none_12_F_TC35_rep1

status: Public on Jun 10 2021

type: RNA

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw signals, detection p-values, bead numbers, and bead-level standard errors were exported for regular and control probes from GenomeStudio. Data were imported into R using the Bioconductor beadarray and illuminaHumanv4.db packages. Data were background-corrected, quantile-normalised and log2-transformed using the limma implementation of the neqc method (Shi et al. Nucl Acids Res 2010).

molecule: total RNA

organism: Homo sapiens

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC35, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C6)

label_protocol: Illumina® TotalPrep™ RNA Amplification Kit (Ambion); protocol according to manufacturer instructions (from 100-500 ng RNA).

growth_protocol: Primary CD4+ T cells and memory CD4+ T cells were isolated from PBMCs of healthy donors using the total CD4 T cell isolation kit II and the memory CD4+ T cell isolation kit by Miltenyi Biotec, respectively.

extract_protocol: 2E5 to 2E6 primary CD4+ T cells were harvested at the indicated time post-infection. RNA was isolated using the miRNeasy kit with on-column DNase treatment (Qiagen).

treatment_protocol: Infections were initiated by spin infection of the cells with HIV-1 particles (0,5 to 1 g/mL p24Gag) for 2 h at 2000 g and at 30 degrees Celsius. The cells were then incubated at 37 degrees for 1 h prior to extensive washes in PBS1X. Fresh and pre-warmed media (containing anti-CD3 and -CD28 antibodies) was added and the cells placed back at 37 degrees for the indicated incubation times, prior to RNA extraction.

tag: celltype

tag: virus

tag: vprsuppl

value: no

tag: timepoint

tag: donor

value: F

tag: age

tag: Sex

value: M

tag: arraybatch

tag: plateposition

tag: experiment

tag: replicate


title: L09_ROI05_TME

type: SRA

city: Seattle

first: Patrick

last: Danaher

state: WA

address: 530 Fairview Ave N

country: USA

institute: NanoString Technologies, Inc.

description:
photocleaved oligonucleotide barcodes
Samples were pooled during library preparation and split across lanes. Individual FASTQ files were generated for each lane, forward & reverse primers. The Fastq files contain the same identifier as the sample name for aggregation

library_source: transcriptomic

data_processing:
Library strategy: GeoMx-Seq
Adapter trimming with trim galore,  trimGaloreOpts = " --hardtrim5 26 --dont_gzip"
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts = " -m 26 -e 26 -f 26 -s 1 -r 27"
Extract UMIs in bowtie2, umiExtractOpts = " --bc-pattern=NNNNNNNNNNNNNN"
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts = " --end-to-end -L 4 --trim5 0 --trim3 0 --norc"
Deduplication using UMI-tools, umiDedupOpts = " --edit-distance-threshold=1"
Genome_build: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform
Supplementary_files_format_and_content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, 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 counts tab are the geometric mean of the probes for a given, removing any targets flagged as outliers. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments.

source_name: NSCLC tumor

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. 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)
Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

tag: tissue

value: TME

tag: roi


title: CD4_none_4.5_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, mock-infected as part of experiment TC36, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position F7)

value: B


title: CD4_IIIB_8_B_TC36_rep1

source_name: bulk CD4 T cells from donor B, infected with HIV-1 strain IIIB as part of experiment TC36, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position G2)

value: IIIB


title: p1x2x3  Night time replicate2

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

institute: Wellcome - MRC Cambridge Stem Cell Institute

data_processing:
The original image data is transformed into raw sequence data via base calling.
Sequenced reads were demultiplexed, pre-filtered and with the adaptor sequences trimmed off and then aligned against Arabidopis thaliana TAIR10 transcriptome models using bowtie2 with the “-very-sensitive” preset.
Transcript quantification was performed by the eXpress software v1.5.1 using default parameters.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited files include quantification metrics for each sample

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Surface sterilised Arabidopsis thaliana seeds were sown directly onto half strength Murashige and Skoog (MS) (Duchefa Biochemie, Netherlands) 0.8 % bactoagar (BD, USA). Stratification at 4° C in the dark was for two days, before transfer to Sanyo (UK) growth cabinets (19 – 22° C, 100 µmol m-2 s-2; 12 hours light/12 hours dark).   40 mg fresh weight of two-week-old seedlings were collected for RNA extraction.

extract_protocol:
RNA was extracted from 40 mg fresh weight of two-week-old seedlings using a Qiagen (Manchester, UK) RNeasy plant mini kit with on-column DNase treatment as per manufacturer’s instructions.
RNA libraries were prepared using the Illumina TruSeq RNA Prep Kit v2

treatment_protocol: Arabidopsis two-week-old seedlings were collected at ZT6 and ZT18 representing the day and night samples.

tag: genotype

value: parp1-2 x parp2-1 x parp3


title: CD4_IIIB.DEnv_24_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DEnv as part of experiment TC35, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D7)


title: CD4_IIIB_48_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC35, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D2)


title: CD4_none_48_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC35, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C8)


title: CD4_none_24_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC35, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C7)


title: CD4_BK132_12_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain BK132 as part of experiment TC35, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D9)


title: CD4_none_8_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC35, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C4)


title: CD4_IIIB_8_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC35, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C10)


title: CD4_IIIB_24_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC35, 24h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D1)


title: CD4_IIIB.DEnv_12_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DEnv as part of experiment TC35, 12h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D6)


title: L09_ROI05_Tumor

value: Tumor


title: L09_ROI04_TME


title: parp3-1 Night time replicate3


title: nurf chip +C rep1 [NURF IP]

city: Munich

first: Nikolas

last: Eggers

address: Grosshaderner Strasse 9

department: Molecular Biology

country: Germany

institute: LMU Munich

description:
NURF IP
merged.nurf_chip_cm.bw

library_source: genomic

data_processing:
RTA software von Illumina, version ist 1.18.66.3
sequenced reads were demultiplexed and trimmed using JE Demultiplexer
Demultiplexed reads were aligned to the dm6 genome using bowtie 2 version 2.2.9. with settings: -p 24 --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant -I 10 -X 220
filtering and sorting was done using samtools 1.9 with -q 10.
genomic tracks were made by Homer 4.9 and normalized to the negative control or the input.
replicates were summarized by subsampling them to the same read counts and adding them und samtools 1.9
peaks were called using findPeaks form Homer 4.9  with settings: -style factor -size 150 -F 8 -L 2
Genome_build: dm6
Supplementary_files_format_and_content: .bw files

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: BG-3 cells

growth_protocol: purified genomic DNA from bg-3 cells was assembled to chromatin for 5h.

extract_protocol:
DNA was purified using Phenol-Chloroform Extraction.
libraries were made using the NEB library Kit for Illumina

treatment_protocol: Respective Proteins were added to the chromatin and bound for 30 min. samples were crosslinked and partially digested by Mnase.

tag: ip target

value: NURF

value: 25nM CLAMP


title: nurf chip cntrl rep 2 [NURF IP]

description:
NURF IP
merged.nurf_chip_neg.bw


title: HSAEC-Never3

city: Chuo-ku

first: Yusuke

last: Yamamoto

state: Tokyo

address: 5-1-1, Tsukiji, Chuo-ku

country: Japan

institute: National cancer center research institute

data_processing:
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Genome_build: hg19

source_name: Primary Human small airway epithelial cells

growth_protocol: Freshly isolated HSAECs were plated onto rat tail collagen type I-coated dishes in Small Airway Epithelial Growth Medium (SAGM, Lonza) with a 1% antibiotic–antimycotic solution (AA, Invitrogen) at 37 °C in 5% CO2. HSAECs were used until passage 2.

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
cDNA libraries for RNA sequencing were established from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for selecting poly-A mRNA followed by strand-specific library preparation using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech). The resulting double-stranded library fragments were further processed into single-stranded circular DNA (sscDNA), which is the final form of MGI library. The sscDNA libraries were quantified by Qubit ssDNA Assay Kit and used for generating DNA nanoballs (DNBs) by rolling circle replication reaction. DNBs were then loaded into a flow cell for sequencing on DNBSEQ-G400 platform (MGI tech), according to the manufacturer’s instructions.

tag: sample type

value: never smoked


title: parp3-1 Night time replicate2


title: nurf chip input rep 2 [NURF IP]

description: NURF IP

tag: factors added


title: CD4_IIIB.DEnv_8_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DEnv as part of experiment TC35, 8h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D4)

tag: celltype


title: L09_ROI14_TME


title: L09_ROI03_TME


title: L09_ROI04_Tumor


title: L09_ROI03_Tumor


title: HSAEC-Never2


title: p1x2x3  Night time replicate1


title: nurf chip input rep1 [NURF IP]

description: NURF IP


title: parp3-1 Night time replicate1


title: clamp chip +C +M rep 2 [CLAMP IP]

description:
CLAMP IP
merged.clamp_chip_cm.bw

value: CLAMP

value: CLAMP and MSL2


title: L09_ROI02_TME


title: nurf chip cntrl rep1 [NURF IP]

description:
NURF IP
merged.nurf_chip_neg.bw


title: parp2-1 Night time replicate3


title: clamp chip +C +M rep1 [CLAMP IP]

description:
CLAMP IP
merged.clamp_chip_cm.bw


title: HSAEC-COPD3

value: COPD


title: HSAEC-Never1


title: HSAEC-COPD2


title: CD4_IIIB.DEnv_4.5_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DEnv as part of experiment TC35, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D3)

tag: virus


title: L09_ROI02_Tumor

source_name: NSCLC tumor


title: clamp chip +C rep 2 [CLAMP IP]

description:
CLAMP IP
merged.clamp_chip_alone.bw


title: parp2-1 Night time replicate1


title: parp2-1 Night time replicate2


title: L09_ROI01_TME


title: parp1-2 Night time replicate3


title: HSAEC-COPD1


title: CD4_IIIB.DEnv_48_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB.DEnv as part of experiment TC35, 48h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position D8)

tag: vprsuppl


title: CD4_IIIB_4.5_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, infected with HIV-1 strain IIIB as part of experiment TC35, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C9)

tag: timepoint


title: L09_ROI01_Tumor


title: CD4_none_4.5_F_TC35_rep1

source_name: bulk CD4 T cells from donor F, mock-infected as part of experiment TC35, 4.5h post infection, intra-experimental technical replicate 1, hybridised Nov-12 (from sample well position C3)

tag: donor


title: parp1-2 Night time replicate2

source_name: seedlings


title: parp1-2 Night time replicate1


title: ATAC-seq acetabulum E67

first: Terence

middle: D

last: Capellini

state: MA

address: 11 Divinity Avenue

department: Human Evolutionary Biology

institute: Harvard Univserity

data_processing:
alignment to hg19: Bowtie2 version 2.3.2 default parameters for hg19 alignment
filter for duplicates: MACS2 version 2.1.1.2 macs2 filterdup -i file -g hs --keep-dup 1 -o outfile
peak calling: MACS2 version 2.1.1.2 macs2 callpeak -B -t rep1file -n name --nomodel --shift -100 --extsize 200
peak filtering : IDR https://github.com/nboley/idr idr --samples rep1file rep2file --peak-list pooled_peaks --input-file-type narrowPeak --output-file IDR_output --rank p.value --soft-idr-threshold 0.05 –plot
MACS2 .narrowPeak output was cut using the number of peaks below the IDR threshold, sorting by MACS2 reported p-value
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain the coordinates of the peaks called and filtered for each ATAC-seq experiment

source_name: Acetabulum E67

growth_protocol: in vivo collected E67 growth plate chondrocytes

extract_protocol:
Upon arrival the sample was dissected under a light dissection microscope in identical fashion to all mouse samples reported. ll forelimb and hindlimb long bone elements were complete but then manually separated from one another, and each proximal or distal cartilaginous end was then micro-dissected from the bony diaphysis. Proximal and distal bone end samples for each long bone (i.e., femur, tibia, humerus, radius) were then sent out for sequencing running a pooled library for 3 rounds of sequencing on the Illumina NextSeq 500 in order to obtain approximately 50 million reads per sample.
Samples were subjected to PCR amplification and barcoding following Buenrostro et al., 2015. 10 ul of transposed DNA was then placed in a reaction containing NEBNext High-Fidelity PCR Master Mix, ddH20, and primers. After amplification, samples were transferred to micro-centrifuge tubes and subjected to the OMEGA Bead Purification Protocol following manufacturers protocol. The samples were eluted in 30 ul of TE, run on a nanodrop, diluted to 5 ng/ul and run on a bioanalyzer. Prior to sequencing sample concentrations were determined using the KAPA Library Quantification Complete Kit (KK4824). Samples were then sent out to the Harvard University Bauer Core Facility for sequencing on one lane of the Illumina NextSeq 500, for three rounds, after which raw reads for each sample were pooled.

treatment_protocol: Human products of conception were collected from late first-trimester and early second-trimester terminations through the Laboratory of Developmental Biology in full compliance with the ethical guidelines of the National Institutes of Health and with the approval of the University of Washington Institutional Review Boards for the collection and distribution of human tissues for research, and Harvard University for the receipt and use of such materials. The Laboratory of Developmental Biology obtained written consent from all tissue donors.

tag: cell type

value: chondrocytes

tag: reagent

value: tn5 transposase


title: clamp chip neg rep1 [CLAMP IP]

description: CLAMP IP


title: ATAC-seq distal tibia E67

source_name: Distal tibial growth plates E67


title: Kim

city: Giheung-gu, Yongin-si, Gyeonggi-do 16995

first: Yong Woo

last: Ji

address: 363, Dongbaekjukjeon-daero

country: South Korea

institute: Department of Ophthalmology, Yonsei University College of Medicine, Yongin Severance Hospital

data_processing:
We preprocessed the raw reads obtained from the sequencer to remove low-quality reads and adapter sequences before analysis. High-quality reads were then aligned to the Homo sapiens (GRCh38) reference genome using HISAT2 v2.1.0. The reference genome sequence of Homo sapiens (GRCh38) and annotation data were downloaded from National Center for Biotechnology Information. Transcript assembly of known transcripts was processed by StringTie v1.3.4d. Based on the results, expression abundance of transcripts was calculated as read count or fragments per kilobase of exon per million fragments mapped (FPKM) value per sample. The relative abundance of transcripts was measured in read count using StringTie. For the DEG set, hierarchical clustering analysis was performed using complete linkage and Euclidean distance as measures of similarity.
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: cell from cornea

extract_protocol:
Endothelial cell were isolated from cornea, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) and Illumina protocols

treatment_protocol: Normal CECs were obtained from age/sex-matched donors, and normal AH was obtained from age/sex-matched patients with cataract during surgery. All samples were stored at -80˚C until measurement.

value: cornea


title: Yoon


title: ATAC-seq proximal tibia E67

source_name: Proximal tibial growth plates E67


title: Lee


title: Heo


title: msl2 chip +M +G rep 2 [MSL2 GAF titration]

description:
MSL2 GAF titration
MSL2_CHIP_GAF_TIT_.GM_all.bw

value: MSL2 and 25nM GAF


title: msl2 chip +M +G rep1 [MSL2 GAF titration]


title: ATAC-seq distal femur E67

source_name: Distal femoral growth plates E67


title: clamp chip +C rep1 [CLAMP IP]

description:
CLAMP IP
merged.clamp_chip_alone.bw


title: Col-0 Night time replicate2


title: Col-0 Night time replicate1


title: Input-3

city: Beijing

first: Ting

last: Li

address: Taiping Road 27

country: China

institute: NCBA

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 version 2.3.4 with default parameters
Data were filtered using the following specification: aligned bam files were first sorted with samtools and then duplicated reads  were removed with PICARD.
peaks were called using macs2 version 2.2.5 with the following setting: macs2 callpeak -g hs.
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

growth_protocol: HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's standard protocol.

treatment_protocol: non-treatment

tag: cell line

value: HeLa

value: stable cell lines

tag: treatment

value: untreated


title: clamp chip neg rep 2 [CLAMP IP]

description: CLAMP IP


title: ATAC-seq proximal femur E67

source_name: Proximal femoral growth plates E67


title: msl2 chip +GCM3 rep 2 [MSL2 GAF titration]

description:
MSL2 GAF titration
MSL2_CHIP_GAF_TIT_.GCM3_all.bw

value: CLAMP and MSL2 and 75nM GAF


title: IgG-3

tag: chip antibody

value: IgG (Cell Signaling, 2729)


title: srt1x2 Day time replicate3

value: srt2-1 x heterozygous srt1-4


title: srt1x2 Day time replicate2


title: msl2 chip +GCM3 rep1 [MSL2 GAF titration]


title: esant12_rep2

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
More than 21 M of clean reads of each sample were mapped to the Arabidopsis genome (TAIR10) with the sensitive alignment program HISAT2 (2.1.0) with the default parameters.
The reads mapped on the exon were counted using featureCounts.
The significant (|log2 (fold change) |> 1 and P-value < 0.01) differentially expressed genes (DEGs) and TEs were identified by the edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a long-day (LD) photoperiod (23℃, 16 h light/ 22℃, 8 h darkness).

extract_protocol:
Total RNA was isolated from 14-day-old seedlings in LD using Trizol reagent.
Sequencing libraries were built for RNA-seq (the single-end 50-bp strategy).

tag: growth conditions

value: long day (16 h light, 8 h dark)


title: Col-0 Night time replicate3


title: msl2chip +GCM2 rep 2 [MSL2 GAF titration]

description:
MSL2 GAF titration
MSL2_CHIP_GAF_TIT_.GCM2_all.bw

value: CLAMP and MSL2 and 25nM GAF


title: Input-2


title: msl2chip +GCM2 rep1 [MSL2 GAF titration]


title: srt2-1  Day time replicate3


title: srt2-1  Day time replicate2


title: IgG-2


title: srt1x2 Day time replicate1


title: msl2 chip +GCM1 rep 2 [MSL2 GAF titration]

description:
MSL2 GAF titration
MSL2_CHIP_GAF_TIT_.GCM1_all.bw

value: CLAMP and MSL2 and 8nM GAF


title: KANSL1-2

value: KANSL1 (Abnova, PAB20355; lot  A114005)


title: srt2-1  Day time replicate1


title: KANSL1-3


title: msl2 chip +GCM1 rep1 [MSL2 GAF titration]


title: msl2 chip +M +C rep 2 [MSL2 GAF titration]

description:
MSL2 GAF titration
MSL2_CHIP_GAF_TIT_.CM_all.bw


title: IgG-1


title: srt1-4   Day time replicate3

value: srt1-4 (At5g55760, SAIL_552_E02; heterozygous)


title: KANSL1-1


title: msl2 chip +M +C rep1 [MSL2 GAF titration]

value: CLAMP and MSL2


title: msl2 chip neg rep 2 [MSL2 GAF titration]

description: MSL2 GAF titration


title: srt1-4   Day time replicate2


title: Blood, Female, Old-Irradiated-rep5

city: New York

first: Constantinos

last: Broustas

state: NY

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia 24 h post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: gender

value: female

tag: strain

tag: age

value: Old

value: Irradiated

tag: tissue

value: blood


title: srt1-4   Day time replicate1

tag: genotype


title: msl2 chip neg rep1 [MSL2 GAF titration]

description: MSL2 GAF titration

source_name: BG-3 cells

tag: ip target

tag: factors added


title: TYMP3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

institute: Hokkaido University

data_processing:
Illumina NovaSeq 6000
An average of 33 million reads (paired-end reads of 100 bp) per sample was mapped by alignment to the human genome (GRCh38) using STAR, gene expression level was quantified using RSEM, and differentially expressed genes (DEGs) were analyzed using DESeq2 Wald test (R software packages).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited test files include count, TPM and FPKM values for each Sample

source_name: macrophage stimulated by TYMP

growth_protocol: Human monocytes obtained from the blood of healthy donors (Asian, 3 males with ages of 30-45 years) were isolated by density gradient centrifugation (Ficoll-PaqueTM PLUS: GE Healthcare, Waukesha, WI, USA) followed by MACS Pan monocyte isolation kit (Miltenyi Biotec, Auburn, CA, USA) 36. Cells were suspended in growth medium containing minimum essential medium Eagle (MEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), a 5% penicillin/streptomycin solution, and 5% L-glutamine and cultured in a 37°C-humidified atmosphere containing 5% CO2 in a 75 cm2 flask for 3 h. Thereafter, the medium was discarded and adherent monocytes (CD14+) were cultured in growth medium supplemented with 25 ng/ml human recombinant macrophage colony-stimulating factor (MCSF; Peprotech, Japan). After 3 days of cultivation, the adherent cells were washed 3 times with ice-cold phosphate-buffered saline (PBS; Nacalai Tesque, Kyoto, Japan) and detached by treatment with a 1% trypsin-EDTA solution (GE Healthcare). Cells were washed with PBS (Nacalai), seeded on a 96-well plate (1 x 104) and cultured in growth medium supplemented with 25 ng/ml MCSF (Peprotech, Japan) with or without 50 ng/ml of one growth factors for 8 days.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions, and the integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
High-quality libraries assayed by Bioanalyzer High sensitivity DNA kit (Agilent) were subjected to Illumina NovaSeq 6000 System (Illumina).

treatment_protocol: Growth factors included human recombinant proteins of Receptor activator of nuclear factor kappa-Β ligand (RANKL),  TYMP (Aviva systems biology). The growth medium for the cultures was regularly replenished with fresh growth medium supplemented with each recombinant protein at 3-day intervals.

value: macrophage

value: stimulated by TYMP


title: Blood, Female, Old-Irradiated-rep1


title: p1x2x3  Day time replicate3

value: parp1-2 x parp2-1 x parp3


title: Input-1

value: HeLa

value: stable cell lines

value: untreated


title: msl2 chip +M +C +Hexokinase [MSL2 ATP]

description:
MSL2 ATP
merged.both_hk_all.bw

value: MSL2 and CLAMP and Hexokinase


title: msl2 chip +M +Hexokinase [MSL2 ATP]

description:
MSL2 ATP
merged.msl_hk_all.bw

value: MSL2 and Hexokinase


title: Blood, Female, Old-Irradiated-rep4


title: TYMP1


title: p1x2x3  Day time replicate2


title: Blood, Female, Old-Irradiated-rep2


title: Blood, Female, Old-Irradiated-rep3


title: RANKL3

source_name: macrophage stimulated by RANKL

value: stimulated by RANKL


title: p1x2x3  Day time replicate1


title: msl2 chip H1 tiration 0nM H1 +C +M  rep 2 [MSL2 and H1]

description:
MSL2 and H1
merged.chip_msl2_cm_0his_all.bw


title: Blood, Female, Old-UnIrradiated-rep3

value: UnIrradiated


title: msl2 chip H1 tiration 0nM H1 +C +M  rep1 [MSL2 and H1]


title: RANKL2


title: TYMP2


title: parp3-1 Day time replicate3


title: Blood, Female, Old-UnIrradiated-rep5


title: parp3-1 Day time replicate2


title: msl2 chip H1 tiration 100nM H1 +C +M  rep 2 [MSL2 and H1]

description:
MSL2 and H1
merged.chip_msl2_cm_2his_all.bw

value: CLAMP and MSL2 and 100nM H2


title: Blood, Female, Old-UnIrradiated-rep4


title: MCSF4

source_name: control macrophage

value: control


title: parp3-1 Day time replicate1


title: RANKL1


title: Blood, Female, Old-UnIrradiated-rep2


title: Blood, Female, Old-UnIrradiated-rep1


title: MCSF2


title: parp2-1 Day time replicate3


title: MCSF1


title: msl2 chip H1 tiration neg rep2 [MSL2 and H1]

description: MSL2 and H1


title: parp2-1 Day time replicate2


title: RNA-seq of HBL1 KO (line #150) hiPSCs (cardiac differentiation for 5 days)

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W. Walnut St.

department: Department of Pediatrics

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 10 in more than one of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts

source_name: hiPSCs-derived cells (cardiac differentiation for 5 days)

growth_protocol: For the undifferentiated samples, hiPSCs were routinely cultured in mTesR medium in a matrigel-coated 6-well plate. For cardiac differentiation, hiPSCs were routinely cultured in mTesR medium (a matrigel-coated 6-well plate), when cells density were 100%, medium were changed to cardiac differentiation medium (please see the detailed protocol in manuscript).

extract_protocol: Total RNAs were purified by QIAGEN miRNeasy kit.

tag: tag

value: human


title: msl2 chip H1 tiration 100nM H1 +C +M  rep1 [MSL2 and H1]

value: CLAMP and MSL2 and 100nM H1


title: Blood, Female, Young-Irradiated-rep4

value: female

value: Young


title: parp2-1 Day time replicate1


title: Blood, Female, Young-Irradiated-rep5

value: Irradiated

value: blood


title: parp1-2 Day time replicate3


title: msl2 chip +M +C  rep 3 [MSL2 and CLAMP]

description:
MSL2 and CLAMP
merged.msl2_chip_cm.bw

value: CLAMP and MSL2


title: RNA-seq of HBL1 KO (line #22) hiPSCs (cardiac differentiation for 5 days)

value: hiPSCs-derived cells (cardiac differentiation for 5 days)


title: parp1-2 Day time replicate1


title: msl2 chip +M +C  rep1 [MSL2 and CLAMP]

description:
MSL2 and CLAMP
merged.msl2_chip_cm.bw


title: parp1-2 Day time replicate2


title: RNA-seq of HBL1 KO (line #150) hiPSCs (cardiac differentiation for 3 days)

source_name: hiPSCs-derived cells (cardiac differentiation for 3 days)


title: RNA-seq of WT hiPSCs (cardiac differentiation for 5 days)


title: Blood, Female, Young-Irradiated-rep2


title: HUVEC in the presence of neutralizing antibody against PDGFB_3

city: nanjing

first: zhi

last: yang

state: jiangsu

address: 101 Longmian Avenue

institute: nanjing medical university

description:
Sequenced twice due to inadequate sequecing depth
Treated-CS3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: HUVEC

extract_protocol:
Extraction of total RNA was performed using TRIzol reagent (Thermo Fisher, MA, USA) according to the manufacturer’s protocols. Briefly, RNA samples were quantified using fluorimetric RiboGreen assay and quality was assessed using an Agilent 2100 Bioanalyzer. Total RNA (500 ng and RIN of 8) was Illumina sequenced using Illumina TruSeq mRNA Library Preparation kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using Illumina TruSeq mRNA Library Preparation kit according to the manufacturer’s instructions.

value: HUVEC

value: treated by conditioned media obtained from gastric cancer anoikis resistant cells in the presence of neutralizing antibody against PDGFB


title: Blood, Female, Young-UnIrradiated-rep5


title: msl2 chip H1 tiration neg rep1 [MSL2 and H1]

description: MSL2 and H1


title: RNA-seq of WT hiPSCs (cardiac differentiation for 3 days)

value: hiPSCs-derived cells (cardiac differentiation for 3 days)


title: RNA-seq of HBL1 KO (line #22) hiPSCs (cardiac differentiation for 3 days)


title: msl2 chip +M rep 2 [MSL2 and CLAMP]

description:
MSL2 and CLAMP
merged.msl2_chip_alone.bw


title: Col-0 Day time replicate3


title: Blood, Female, Young-Irradiated-rep1


title: msl2 chip +M rep1 [MSL2 and CLAMP]


title: Col-0 Day time replicate2


title: Blood, Female, Young-UnIrradiated-rep4


title: Blood, Female, Young-UnIrradiated-rep3


title: HUVEC in the presence of neutralizing antibody against PDGFB_1


title: Col-0 Day time replicate1


title: RNA-seq of HBL1 KO (line #150) hiPSCs (undifferentiation)

source_name: hiPSCs

value: hiPSCs


title: msl2 chip +M +C  rep 2 [MSL2 and CLAMP]

description:
MSL2 and CLAMP
merged.msl2_chip_cm.bw


title: HUVEC in the absence of neutralizing antibody against PDGFB_3

value: treated by conditioned media obtained from gastric cancer anoikis resistant cells in the absence of neutralizing antibody against PDGFB


title: Blood, Female, Young-UnIrradiated-rep2


title: RNA-seq of HBL1 KO (line #22) hiPSCs (undifferentiation)


title: msl2 chip +M rep 3 [MSL2 and CLAMP]


title: HUVEC in the absence of neutralizing antibody against PDGFB_2


title: HUVEC in the presence of neutralizing antibody against PDGFB_2


title: msl2 chip neg rep 2 [MSL2 and CLAMP]

description: MSL2 and CLAMP


title: Rice Ilpum GRH

city: Miryang

first: ROLLY

middle: NKULU

last: KABANGE

state: Gyeongsangnamdo

address: Jompiljaero 20, Naei-dong

department: Department of Southern Area Crop Science

institute: Rural Development Administration

description:
IO_1
Oryza sativa L.

data_processing:
Illumina HCS 3.3.52 software used for basecalling.
The total number of bases, reads, GC (%), Q20 (%), Q30 (%) were calculated for 4 samples. Trimmomatic program (Bolger et al., 2014) was used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
For assembled genes, longest contigs of the assembled contigs were filtered and clustered into the non-redundant transcripts using CD-HIT-EST (Li et al., 2006; Li et al., 2001) . We defined these transcripts as ‘unigenes’ which are used for predicting the ORFs (Open Reading Frames), annotating against several known sequence databases, and analyzing differentially expressed genes (DEGs). ORF prediction for unigenes was performed using TransDecoder program to identify candidate coding regions within transcript sequence. After extracting ORFs that are at least 100 amino acids long, TransDecoder predicted the likely coding regions.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
For functional annotation of the unigenes, the Gene Ontology (GO) database was applied to classify the annotated unigenes using BLASTX of DIAMOND with an E-value cut-off of 1.0E-5. Classification of GO terms was subsequently performed using in-house script. The GO terms belonging to biological process (BP), cellular component (CC) and molecular function (MF) were listed (Figure S2). The Oryza sativa japonica (Japanese rice) (RAPDB) was used for alignment.
To identify the proteins distributed in eukaryotic orthologous groups (KOG), clusters of orthologous groups (COGs), and non-supervised orthologous groups (NOGs), we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on EggNOG (Evolutionary genealogy of genes) database. The annotated unigenes were mapped to the annotation of the corresponding orthologous groups in EggNOG database.
For functional annotation of the unigenes, we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Bi-directional best hit (BBH), which is a widely used method to infer orthology was used to search against the KEGG database to obtain the KO (reference pathway) number of the KEGG annotation. The KO number of the transcriptome was also obtained according to KEGG annotation. For functional annotation of the unigenes, we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on UniProt (Universal Protein Resource) database. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible were added. For functional annotation of the unigenes, we carried out BLASTX of DIAMOND with an E-value cut-off of 1.0E-5 on Pfam database. The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Proteins are generally composed of one or more functional regions, commonly termed domains. The identification of domains that occur within proteins can therefore provide insights into their function.
Genome_build: Oryza sativa japonica (Japanese rice) (RAPDB)
Supplementary_files_format_and_content: *.gene_abund.anno.tab: Tab-delimited text files include FPKM and TPM values for each Sample.
Supplementary_files_format_and_content: *.gtf
Supplementary_files_format_and_content: Expression_Profile.IRGSP-1.0_transcript_exon_2018-11-26.gene.txt
Supplementary_files_format_and_content: Expression_Profile.IRGSP-1.0_transcript_exon_2018-11-26.transcript.txt
Supplementary_files_format_and_content: MapMan_NIL.xls
Supplementary_files_format_and_content: MapMan_Ilpum.xls

organism: Oryza sativa Japonica Group

source_name: Leaf

growth_protocol: Two rice lines, Ilpum (the GRH susceptible cultivar) and a near isogenic line (NIL) carrying the Grh1 (a gene conferring resistance towards GRH) derived from a cross between Shingwang (indica, P1) and Ilpum (japonica, P2) (Park et al., 2013) were use as genetic materials to perform the experiments. Prior to germination, rice seeds were surfaced sterilized using nitric acid (HNO3, 0.7%) (CAS: 7697-37-2, Junsei Chemical Co. Ltd, Tokyo, Japan) overnight to break the dormancy (Kabange et al., 2021), followed by incubation for 48 h at 27 °C to induced germination. Then, germinated rice seeds were grown in 50-well trays containing an enriched soil (company name) until 3 leaf-stage.

extract_protocol:
Total RNA was isolated from leaf samples, and DNA contamination were eliminated using DNase. mRNA purification kit was used to prepare the library. RNA fragments were randomly purified for short read sequencing, followed by reverse transcription of fragmented RNA into cDNA. The adapters were ligated onto both ends of the cDNA fragments. After amplifying fragments using PCR, fragments with insert sizes between 200–400 bp were selected, and both ends of the cDNA were sequenced by the read length (paired-end sequencing).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Seedlings with a uniform height were placed in test tubes after washing the loose soil from the roots. Seedlings were infested with second instar nymphs green rice leafhoppers for 48 h at room temperature as described earlier (Park et al., 2013). Leaf samples for RNA-Seq analysis were collected and sent for sequencing (Macrogen, Daejeon, Korea).

tag: line

value: Ilpum

value: wild type

value: Leaf

value: 21 days after germination

value: Green rice leafhopper (GRH)


title: Rice Ilpum control

description:
IX_1
Oryza sativa L.

value: Control


title: RNA-seq of WT hiPSCs (undifferentiation)

value: human


title: msl2 chip neg rep 3 [MSL2 and CLAMP]

description: MSL2 and CLAMP


title: Blood, Female, Young-UnIrradiated-rep1

value: female

value: Young

value: UnIrradiated


title: HUVEC in the absence of neutralizing antibody against PDGFB_1


title: msl2 chip neg rep1 [MSL2 and CLAMP]

description: MSL2 and CLAMP


title: Wt_Lm_3

status: Public on Jun 09 2021

city: Vienna

first: Thomas

last: Decker

state: Vienna

address: Dr Bohr Gasse 9

department: Microbiology, Immunobiology and Genetics

country: Austria

institute: University of Vienna, Max Perutz  Labs

description: Infected Wt replicate 3

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes based on Picard tools 2.18.7 and 2.19.2 (https://github.com/DanieleBarreca/picard)
The transcriptome analysis was performed using the Tuxedo suite. TopHat2 (v2.1.1, http://genomebiology.com/2013/14/4/R36/abstract) was supplied with reads passing vendor quality filtering (PF reads) and the Ensembl transcript set (Homo sapiens, e87, December 2016) as reference. TopHat2 analyses were run independently for each replicate.
Cufflinks (v2.2.1, http://www.nature.com/nbt/journal/v31/n1/full/nbt.2450.html) was then used to assemble transcripts from spliced read alignments, again using the Ensembl e87 transcriptome as the reference, allowing also de novo assembly of transcript models.
Transcriptome sets of all replicates for each sample group were combined with Cuffmerge.
Differential expression was assessed with Cuffdiff v2.2.1 (http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html).
cummeRbund (http://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html) and biomaRt (http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html) were used in combination with custom R scripts to perform quality assessment and further refine analysis results.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Cufflinks FPKM estimates per gene (tsv)

source_name: Liver

extract_protocol:
The livers were harvested from the uninfected and infected animals and RNA was isolated using the Qiagen AllPrep DNA/RNA Mini Kit according to the manufacturer's guidelines.
RNA-seq libraries were prepared with TruSeq Stranded mRNA LT sample preparation kit (Illumina) using Sciclone and Zephyr liquid handling robotics (PerkinElmer). Library amounts were quantified using Qubit 2.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using Experion Automated Electrophoresis System (Bio-Rad). For sequencing, libraries were pooled, diluted and sequenced on an Illumina HiSeq 3000 instrument using 50 bp single-read chemistry.

value: Whole liver

value: Wt

value: one-day-Lm-infected

tag: sex of the mice

value: Male

tag: age of the mice

value: 9.1 weeks


title: Irf9-/-_unt_2

description: Uninfected Irf9-/- replicate 2

tag: cell type

value: uninfected

value: 10.6 weeks


title: Ifnar-/-_Lm_2

description: Infected Ifnar1-/- replicate 2

value: Ifnar 1-/-

value: 9.6 weeks


title: Irf9-/-_unt_3

description: Uninfected Irf9-/- replicate 3


title: Irf9-/-_Lm_2

description: Infected Irf9-/- replicate 2

value: Female

value: 9.4 weeks


title: Ifnar-/-_unt_3

description: Uninfected Ifnar1-/- replicate 3

value: 9.7 weeks


title: Irf9-/-_Lm_1

description: Infected Irf9-/- replicate 1


title: Ifnar-/-_unt_1

description: Uninfected Ifnar1-/- replicate 1


title: Ifnar-/-_Lm_1

description: Infected Ifnar1-/- replicate 1


title: Irf9-/-_unt_1

description: Uninfected Irf9-/- replicate 1


title: Ifnar-/-_Lm_3

description: Infected Ifnar1-/- replicate 3


title: Ifnar-/-_unt_2

description: Uninfected Ifnar1-/- replicate 2


title: Wt_unt_1

description: Uninfected Wt replicate 1


title: Wt_Lm_1

description: Infected Wt replicate 1


title: Wt_unt_2

description: Uninfected Wt replicate 2


title: Irf9-/-_Lm_3

description: Infected Irf9-/- replicate 3


title: Wt_Lm_2

description: Infected Wt replicate 2


title: Wt_unt_3

description: Uninfected Wt replicate 3


title: Input_0h

city: Aachen

first: Antje

last: Ostareck-Lederer

address: Pauwelsstr. 30

department: Dept. of Intensive Care Medicine

institute: University Hospital RWTH Aachen

description: Input total cytoplasmic RNA untreated RAW 264.7 cells

data_processing:
Trimming of low quality reads and adapters was performed using Trimmomatic v.0.33 (Bolger, et al., 2014) with the following settings: ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Data quality was evaluated using the FastQC software v0.11.2 before and after trimming.
Mapping was performed using Tophat v.2.0.14 (Kim, et al., 2013) with standard parameters and the additional annotation file.
Quantification of unique read counts per gene was performed using HTSeq-0.6.1 (Anders, et al., 2015) with default parameters except for stranded=no. Differential expression analysis was performed in R using edgeR (Robinson, et al., 2010).
Initial assessment of replicates by pairwise distance and principal component analysis (PCA) led to removal of one replicate (LUC 2 h replicate III) as apparent outlier.
Comparison of the remaining data yielded 52 RNAs that were specifically enriched in the P23 IP compared to LUC IP at the 0 hrs time point (adjusted p-value ≤ 0.05, Benjamini Hochberg correction, log2-transformed fold change > 0) (Benjamini and Hochberg, 1995). In order to assess changes in P23 binding to the 52 RNAs after LPS treatment, means of TPM values from the replicates were used to calculate ratios for P23/LUC at 0 hrs and 2 hrs LPS treatment.
Genome_build: Mouse reference genome (version GRCm38/mm10) and gene annotation (Ensembl release 83) downloaded from Ensembl were used.
Supplementary_files_format_and_content: selection_compilation_table.xlsx; replicates-read-counts, replicate-counts_vst, counts-ratio_logFC, counts-ratio_p, counts-ratio_FDR, mgi-description, GO-ID

source_name: macrophages

growth_protocol: RAW 264.7 cells (ATCC, Wesel, Germany, TIB-71) were cultured in DMEM (Thermo Fisher Scientific, 12430054) supplemented with 10% heat inactivated FBS (Biochrom, Berlin, Germany, S0613), 1x penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol:
Immunoprecipitation from 1mg cytoplasmic extract of crosslinked naïve or 2hrs LPS treated RAW 264.7 cells was performed with antibodies against P23 or LUC (Liepelt, et al., 2016) in independent biological replicates. RNA was extracted using Trizol. (Thermo Fisher Scientific).
Barcoded RNA-seq libraries were prepared from either from pulled-down or high quality total RNA samples (25 ng/sample) using the Illumina TruSeq total RNA Sample Preparation v2 Kit.
Libraries that passed the QC step were combined in equimolar amounts into pools of 7 libraries; 8 pM solution of each pool was loaded per lane of the Illumina sequencer HiSeq 2000 flowcell and sequenced bi-directionally (each read 50 bases long, altogether 100 bases) with the Illumina v3 SBS chemistry. Sequencing generated >60 million of paired sequence reads/library (~450 million of paired sequence reads/lane).

treatment_protocol: For LPS treatment, E.coli LPS (serotype 0111:B4, Sigma-Aldrich, St. Louis, MO, USA,) 10ng/ml was added to the medium for 2hrs

value: untreated

tag: ip antibody


title: Input_2h

description: Input total cytoplasmic RNA, RAW 264.7 cells treated with LPS for 2hrs

tag: cell line

value: treated with 10ng/ml LPS for 2hrs


title: LUC_IP_0h_rep2

description: LUC control IP, untreated RAW 264.7 cells, replicate 2

tag: treatment

value: LUC (Santa Cruz sc-57604, luci17)


title: LUC_IP_0h_rep3

description: LUC control IP, untreated RAW 264.7 cells, replicate 3


title: LUC_IP_2h_rep2

description: LUC control IP, RAW 264.7 cells terated with LPS for 2hrs, replicate 2


title: LUC_IP_0h_rep1

description: LUC control IP, untreated RAW 264.7 cells, replicate 1


title: P23_IP_2h_rep3

description: P23 IP, RAW 264.7 cells terated with LPS for 2hrs, replicate 3

value: P23 (Abcam AB2814)


title: P23_IP_2h_rep1

description: P23 IP, RAW 264.7 cells terated with LPS for 2hrs, replicate 1


title: P23_IP_2h_rep2

description: P23 IP, RAW 264.7 cells terated with LPS for 2hrs, replicate 2


title: LUC_IP_2h_rep1

description: LUC control IP, RAW 264.7 cells terated with LPS for 2hrs, replicate 1


title: Blood, Female, Young-Irradiated-rep3

value: female

value: Young

value: Irradiated

value: blood


title: P23_IP_0h_rep3

description: P23 IP, untreated RAW 264.7 cells, replicate 3


title: P23_IP_0h_rep2

description: P23 IP, untreated RAW 264.7 cells, replicate 2


title: P23_IP_0h_rep1

description: P23 IP, untreated RAW 264.7 cells, replicate 1


title: H3K9me3_nmt1hht2G13D01uM_REIID

type: genomic

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: ChIP was performed using anti-H3K9me3 antibody (ab8898) followed by microarray analysis

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: log. growing cells

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to grow cultures at 32˚C, described in detail in methods

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with H3K9me3 antibody (Abcam, ab8898), H3K9me2 antibody (Abcam, ab115159) or myc antibody (Santa Cruz, 9E10). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at room temperature. For myc ChIPs, cultures were incubated for 2 h at 18°C prior to fixation (at 18°C) and were subjected to additional crosslinking with 10 mM DMA for 45 min at room temperature.

tag: sample type

value: H3K9me3 immunoprecipitated DNA

value: Whole-cell extract DNA


title: H3K9me2_clr4CD_REIID

description: ChIP was performed using anti-H3K9me2 antibody (ab115159) followed by microarray analysis

value: H3K9me2 immunoprecipitated DNA


title: H3K9me2_WT_REIID_2

value: WT


title: H3K9me3_nmt1hht2G13D05uM_REIID


title: H3K9me2_hht2G13D_REIID_2


title: H3K9me3_hht2G13D_REIID_1


title: H3K9me3_nmt1hht2G13D20uM_REIID


title: Raf2myc_WT_REIID

description: ChIP was performed using anti-myc antibody (9E10) followed by microarray analysis

value: Raf2-myc immunoprecipitated DNA


title: H3K9me3_nmt1hht220uM_REIID


title: H3K9me3_clr4CD_REIID


title: H3K9me2_WT_KD


title: H3K9me2_hht2G13D_REIID


title: Raf2myc_hht2G13Dclr4CD_REIID

value: G13D clr4CD


title: Raf2myc_clr4CD_REIID


title: H3K9me3_nmt1hht20uM_REIID


title: H3K9me2_WT_REIID


title: H3K9me3_nmt1hht201uM_REIID


title: H3K9me3_WT_REIID_1


title: H3K9me3_nmt1hht2G13D0uM_REIID


title: H3K9me2_hht2G13Dclr4CD_REIID


title: H3K9me3_hht2G13D_REIID_2


title: H3K9me3_nmt1hht205uM_REIID


title: H3K9me3_EMS32_KD


title: Sham day14 S4

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

data_processing:
alignment with bwa mem v0.7.14 to custom filter reference to remove rRNA, tRNA etc.
alignment to rnor6 genome using STAR v2.4.0.i
determination of raw counts using subread (v1.5.1) featureCounts and Ensembl gene annotation v79
differential expression analysis using DESeq2 with timepoints as covariate
Genome_build: rnor5, Ensembl v79
Supplementary_files_format_and_content: tab-separated text file containing rlog normalized counts

organism: Rattus norvegicus

source_name: kidney

growth_protocol: Pregnant female Wistar rats were allowed an ad libitum access to standard diet (#1320, Altromin, Lage, Germany) and tap water in a room maintained at 22±2°C with a 12h dark/light cycle.

extract_protocol:
Kidneys were weighed and prepared for further analyses. Tissue samples were fixed and embedded in paraffin for histology and immunohistochemistry or frozen on liquid nitrogen for RNA isolation. RNA was isolated from tissue samples UNXd1 30-60mg and UNXd14 60-100mg after homogenization with a disperser (T10 basic Ultra-Turrax; IKA, Staufen, Germany) using the RNeasy Standard Tissue Midi Kit (Qiagen, Hilden, Germany). In this procedure DNase was used to remove genomic DNA.
Libraries were prepared with the Ovation Universal RNA-Seq Kit (NUGEN) according to the manufacturer's instructions. Depletion of unwanted sequences was performed with custom rat-specific oligonucleotides.

treatment_protocol: After spontaneous delivery, male pups were divided into two groups: Neonatal left sided uninephrectomy (UNX) was performed on day 1 (UNXd1) and day 14 (UNXd14) of life under isoflurane anesthesia. Three days after UNX, auxologic data was assessed and animals were killed.

value: Wistar, male

value: Sham operation at day 14 of life

tag: timepoint

value: 3 days after surgery


title: Raf2myc_hht2G13D_REIID


title: Sham day14 S3


title: H3K9me3_WT_KD


title: H3K9me2_EMS32_KD


title: H3K9me3_hht2G13Dclr4CD_REIID


title: UNX day14 S4

value: left-sided uninephrectomy at day 14 of life


title: Sham day14 S1


title: Sham day1 S4

value: Sham operation at day 1 of life


title: UNX day14 S1


title: UNX day14 S3


title: Sham day1 S2


title: UNX day14 S2


title: UNX day1 S2

value: left-sided uninephrectomy at day 1 of life


title: UNX day1 S1


title: Sham day1 S3


title: Sham day1 S1


title: Sham day14 S2


title: UNX day1 S3


title: si_Control_06

city: LYON

first: Jean-Marc

last: Vanacker

address: 32-34 avenue Tony Garnier

country: France

institute: IGFL, ENS de Lyon, CNRS UMR 5242

data_processing:
Libraries were sequenced on SOLiD 5500W (Life Technologies) giving primary output as XSQ files (1 file per lane).
Data were filtered before mapping to remove ribosomal sequences rRNA and tRNA using the filter file human_filter_reference.fasta
The Lifescope analysis pipeline (LifeScope Command Shell v2.5, LifeTechnologies) dedicated to Solid data was used for alignment based on the analysis protocol whole.transcriptome.frag.
Mapping was performed by the LifeScope pipeline: it was based on the UCSC_genes_hg19.gtf file and lead to bam files creation.
Raw counts were calculated with HT-seq using options -mode=union and -s reverse
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include raw count values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB231 cells were grown in DMEM, supplemented with 10% FCS

extract_protocol:
RNA were extracted using RNeasy Qiage kit
RNA libraries were prepared using Lexogen technology and prepared for SOLiD sequencer acording to the protocole Wildfire Template Amplification protocol for ICS 2.1

treatment_protocol: siRNA were transfected using interferin under conditions recommended by the supplier (Ozyme)

value: cancer cells

value: breast cancer

tag: sirna

value: siCtrl


title: si_SET7-A_02


title: si_SET7-B_04


title: si_SET7-B_03


title: si_SET7-B_09


title: si_Control_01


title: si_SET7-A_07


title: si_Control_05


title: si_SET7-A_08


title: nath-10(icb99) loss of function rep2

city: London

first: Michalis

last: Barkoulas

address: Sir Alexander Fleming Building, Imperial College RD

department: Faculty of Natural Sciences

institute: Imperial College London

data_processing:
Fastq.gz files were aligned to the most recent C.elegans transcriptome using Kallisto in a Linux terminal
Kalisto abundance files were converted and analysed using DEseq2 in a R pipeline, with a filter  > than 5 reads per million in >0.47% of the samples
Standard DEseq2 protocols were used to calculate differential expression
The mean and standard deviation of each transcript was then used to calculate the co-efficient of variation for all aligned transcripts which passed the above filter.
Genome_build: WBcel235
Supplementary_files_format_and_content: Kalisto abundance files; matrix for normalised DEseq2 counts for all samples

organism: Caenorhabditis elegans

source_name: whole animal C. elegans at Larval stage 2

growth_protocol: Populations of wild-type and nath-10 loss of function animals were synchronised by bleaching and grown for 27 hours, harvested and processed for RNA extraction

extract_protocol:
animals were washed using M9 buffer and total RNA was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA) and freeze fracturing. Illumina sequencing was performed by BGI (China).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: nath-10 loss of function


title: nath-10(icb102) loss of function rep3

tag: age


title: nath-10(icb99) loss of function rep1


title: nath-10(icb102) loss of function rep2


title: nath-10(icb99) loss of function rep3


title: UNX day1 S4


title: N2 wild-type rep2

value: wild-type


title: N2 wild-type rep1


title: WT_RNAseq_B

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

institute: Oklahoma Medical Research Foundation

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
Signal per gene was normalized by the number of all S. pombe reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: acCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary_files_format_and_content: Processed CSV files contain normalized signal for all analyzed features (5797 mRNA genes).

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: 30 degrees in rich medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins. Newly synthesized RNA molecules were labeled for 5 minute with 4-thioU.

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3


title: WT_RNAseq_A


title: Toa1_RNAseq_IAA_C

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, TOA1-3xV5 IAA7


title: Ssl2_RNAseq_IAA_C

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, ssl2delta-::KanMX/pSH1947 (LEU2 SSL2-3xV5 IAA7)


title: nath-10(icb102) loss of function rep1


title: Toa1_RNAseq_DMSO_A


title: Toa1_RNAseq_IAA_A


title: Toa1_RNAseq_DMSO_C


title: Toa1_RNAseq_DMSO_B


title: Toa1_RNAseq_IAA_B


title: Ssl2_RNAseq_IAA_B


title: Htz1_RNAseq_DMSO_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, HTZ1-3xV5 IAA7::KanMX


title: Ssl2_RNAseq_IAA_A


title: Ssl2_RNAseq_DMSO_A


title: Htz1_RNAseq_IAA_A


title: Ssl2_RNAseq_DMSO_B


title: N2 wild-type rep3


title: Htz1_RNAseq_DMSO_A


title: Ssl2_RNAseq_DMSO_C


title: Esa1_RNAseq_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, esa1delta-::KanMX/pRD8 (LEU2 ESA1-3xV5 IAA7)


title: Esa1_RNAseq_DMSO_A


title: Esa1_RNAseq_DMSO_B


title: Esa1_RNAseq_IAA_A


title: Bdf2_RNAseq_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX


title: Bdf2_RNAseq_DMSO_B


title: Bdf2_RNAseq_DMSO_A


title: bdf2del_RNAseq_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HPH


title: Bdf1_RNAseq_IAA_A

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, BDF1-3xV5 IAA7::KanMX


title: bdf2del_RNAseq_A


title: Bdf1_RNAseq_DMSO_B


title: Bdf1_RNAseq_DMSO_A


title: Bdf1dbdf2_RNAseq_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HPH, BDF1-3xV5 IAA7::KanMX


title: Bdf1dbdf2_RNAseq_IAA_A


title: Bdf12_RNAseq_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3


title: Htz1_RNAseq_IAA_B


title: Bdf2_RNAseq_IAA_A


title: Bdf12_RNAseq_IAA_A


title: Bdf12_RNAseq_DMSO_C


title: Bdf12_RNAseq_DMSO_A


title: Bdf12_RNAseq_DMSO_B


title: TFIIB_Taf13deg_IAA_AI

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all S. pombe reads mapped for the sample, multiplied by 10000 (arbitrarily chosen number) and multiplied by the ratio of S. pombe to S. cerevisiae reads in the corresponding input sample.
Genome_build: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

extract_protocol:
ChIP-seq was performed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.

treatment_protocol: After reaching appropriate OD selected samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins.

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, TAF13-3xV5 IAA7::KanMX, SUA7-13xMyc::HPH

value: input


title: TFIIB_Taf13deg_IAA_B

value: IP


title: TFIIB_Taf13deg_IAA_BI


title: TFIIB_Taf13deg_DMSO_B


title: H3K9me3_WT_REIID_2

value: WT

value: H3K9me3 immunoprecipitated DNA

value: Whole-cell extract DNA


title: TFIIB_Bdf12deg_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, SUA7-3xFlag::NatMX


title: TFIIB_Taf13deg_DMSO_BI


title: TFIIB_Bdf12deg_IAA_BI


title: Bdf1_RNAseq_IAA_B


title: TFIIB_Taf13deg_DMSO_AI


title: TFIIB_Taf13deg_DMSO_A


title: TFIIB_Bdf12deg_IAA_A


title: TFIIB_Bdf12deg_IAA_AI


title: Bdf12_RNAseq_IAA_C


title: Bdf1dbdf2_RNAseq_DMSO_B


title: Bdf1dbdf2_RNAseq_DMSO_A


title: TFIIB_Bdf12deg_DMSO_BI


title: TFIIB_Bdf12deg_DMSO_A


title: TFIIB_Bdf12deg_DMSO_AI


title: Taf1_ChIPseq_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, TAF1-3xFlag::NatMX


title: Taf1_ChIPseq_IAA_A


title: Taf1_ChIPseq_IAA_BI


title: Taf1_ChIPseq_IAA_AI


title: TFIIB_Taf13deg_IAA_A


title: Taf1_ChIPseq_DMSO_B


title: Taf1_ChIPseq_DMSO_AI


title: Taf1_ChIPseq_DMSO_BI


title: Spt5_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, SPT5-3xFlag::NatMX


title: Spt5_IAA_A


title: Taf1_ChIPseq_DMSO_A


title: Spt5_DMSO_AI


title: Rpb1_Taf1deg_IAA_total_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, TAF1-3xV5 IAA7::KanMX


title: Rpb1_Taf1deg_IAA_S5P_A


title: Rpb1_Taf1deg_IAA_total_A


title: Spt5_IAA_AI


title: Spt5_IAA_BI


title: TFIIB_Bdf12deg_DMSO_B


title: Rpb1_Taf1deg_IAA_BI


title: Rpb1_Taf1deg_IAA_S5P_B


title: Rpb1_Taf1deg_IAA_S2P_B


title: Rpb1_Taf1deg_IAA_AI


title: Spt5_DMSO_A


title: Rpb1_Taf1deg_DMSO_S2P_B


title: Rpb1_Taf1deg_DMSO_S5P_A


title: Rpb1_Taf1deg_DMSO_total_B


title: Rpb1_Taf1deg_DMSO_BI


title: Rpb1_Taf1deg_DMSO_total_A


title: Rpb1_Bdf12deg_IAA_total_B


title: Rpb1_Taf1deg_DMSO_AI


title: Rpb1_Bdf12deg_IAA_total_A


title: Spt5_DMSO_BI


title: Rpb1_Bdf12deg_IAA_S5P_B


title: Spt5_DMSO_B


title: Rpb1_Bdf12deg_IAA_S5P_A


title: Rpb1_Bdf12deg_IAA_S2P_B


title: Rpb1_Taf1deg_IAA_S2P_A


title: Rpb1_Bdf12deg_IAA_BI


title: Rpb1_Bdf12deg_IAA_AI


title: Rpb1_Bdf12deg_DMSO_S5P_B


title: Rpb1_Bdf12deg_DMSO_S5P_A


title: Rpb1_Bdf12deg_IAA_S2P_A


title: Rpb1_Bdf12deg_DMSO_total_B


title: Rpb1_Bdf12deg_DMSO_S2P_B


title: Rpb1_Bdf12deg_DMSO_S2P_A


title: H4K12ac_IAA_BI

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, esa1delta-::KanMX, BDF1-MNase::TRP1/pRD8 (LEU2 ESA1-3xV5 IAA7)


title: Rpb1_Bdf12deg_DMSO_BI


title: H4K12ac_IAA_B


title: Rpb1_Bdf12deg_DMSO_AI


title: H4K12ac_IAA_A


title: Rpb1_Taf1deg_DMSO_S2P_A


title: H4K12ac_IAA_AI


title: Boar frozen-thawed sperm-IP, rep3

city: Chengdu

first: Ziyue

last: Qin

address: Huimin Road 211

institute: Sichuan Agricultural University

data_processing:
Firstly, the quality control was performed by Q30, which was followed by trimming of the 3’ adaptors and removal of low-quality reads using cutadapt software (v1.9.3).
Secondly, the clean reads of all samples were matched to the reference genome (UCSCsusScr11,http://hgdownload.soe.ucsc.edu/goldenPath/susScr11/bigZips/susScr11.fa.gz) by using the Hisat2 software.
Thirdly, the Model-based Analysis of ChIP-Seq (MACS) softwarewas used to identify the methylated genes in each sample. Differentially methylated sites with a |fold change| ≥ 2 and P < 0.00001 were identiﬁed with the diffReps software, and a proprietary program was used to screen the peaks on the mRNA for corresponding annotation.
Genome_build: AilMel_1.0, Sscrofa11.1
Supplementary_files_format_and_content: peak calling and differential methylated genes identification

organism: Sus scrofa

source_name: Boar frozen-thawed sperm-IP

growth_protocol: All ejaculates boar were equally divided into two groups (Fresh sperm and cryopreserved sperm), respectively. The fresh sperm was directly used for RNA extraction.

extract_protocol:
The total RNA of fresh and frozen-thawed sperm was extracted using the TRIzol LS Reagent kit (Invitrogen, Carlsbad, CA, USA).
The Ribo-Zero rRNA Removal Kit (Illumina, Inc., San Diego, CA, USA) was used to reduce the ribosomal RNA content of total RNA. Then, the RNA was chemically fragmented into about 100 nucleotides in length using fragmentation buffer (Illumina, Inc., CA, USA). RNA fragments were incubated with anti-m6A polyclonal antibody (Synaptic Systems, Göttingen, Germany) in immunoprecipitation (IP) buffer for 2 h at 4 °C. The mixture was then immunoprecipitated by incubation with protein-A beads (Thermo Fisher Scientiﬁc, Waltham, MA, USA) for 2 h at 4 °C. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, Ann Arbor, MI, USA) in IP buffer and then extracted with Trizol Reagent. The NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA, USA) was used to construct RNA sequencing libraries for the non-immunoprecipitated input RNA samples (mRNA-seq) and immunoprecipitated IP RNA samples (MeRIP-seq). Libraries quality control was performed by BioAnalyzer 2100 analyzer (Agilent, Santa Clara, CA, USA) and high-throughput sequencing was subjected to 150-bp double-ended mode sequencing on Illumina HiSeq 4000 sequencer (Illumina, Inc., San Diego, CA, USA). The image analysis, base recognition, quality control and original reads (Raw Data) were generated after Illumina HiSeq 4000 sequencer sequencing.

treatment_protocol: The other part (Fts) was cryopreserved according to our previously described procedure (PMID: 24974820). Briefly, at initial step the diluted sperms were slowly cooled to 17 °C, then centrifuged at 240 g for 5 min and supernatant was to discarded. The sperm pellets were re-diluted by using lactose-egg yolk extender (LEY: 11 g β-lactose and 20 mL hen’s egg yolk were added to 80 mL ddH2O). After 4 h of cooling at 4 °C, sperms were further diluted with second extender (lactose-egg yolk extender supplemented with glycerol having 6% concentration). Finally, the mixtures were packed in 0.2 mL straw (FHK, Tokyo, Japan) and equilibrated at approximately -130 °C above liquid nitrogen vapor for 15 min, then the straws were plunged in liquid nitrogen for till use.

tag: breed

value: Duroc

value: Boar spermatozoa

value: treated by frozen protocol

tag: rip antibody


title: H4K12ac_DMSO_B

tag: genotype


title: H4K12ac_DMSO_BI


title: Boar frozen-thawed sperm-IP, rep2


title: H4K12ac_DMSO_A


title: H4K12ac_DMSO_AI

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0  RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, esa1delta-::KanMX, BDF1-MNase::TRP1/pRD8 (LEU2 ESA1-3xV5 IAA7)


title: Boar frozen-thawed sperm-Input, rep2

source_name: Boar frozen-thawed sperm-Input


title: Ctk1_IAA_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, CTK1-3xFlag::NatMX


title: Rpb1_Bdf12deg_DMSO_total_A

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3


title: Boar frozen-thawed sperm-Input, rep1


title: Boar fresh sperm-IP, rep3

source_name: Boar fresh sperm-IP


title: Ctk1_IAA_A


title: Ctk1_IAA_BI


title: Boar fresh sperm-IP, rep2


title: Ctk1_IAA_AI


title: Boar fresh sperm-Input, rep3

source_name: Boar fresh sperm-Input


title: Boar fresh sperm-IP, rep1


title: Ctk1_DMSO_B


title: Boar fresh sperm-Input, rep2


title: Boar frozen-thawed sperm-IP, rep1


title: Ctk1_DMSO_BI


title: HNS_LB3

city: Fullerton

first: M. S.

last: Ramirez

state: CA

address: 800 N. State College Blvd

institute: California State University Fullerton

data_processing:
Low-quality reads were removed using Trimmomatic v0.36
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
RNA-seq counts were deetermined using FeatureCounts
RNA-seq differential expression analysis was performed using DESeq2
Genome_build: RNA-seq reads were aligned to sequences of the whole genome of strain Acinetobacter baumannii AB5075
Supplementary_files_format_and_content: tsv file generated by DESeq2 provides gene ID, base mean reads, log2 fold-change, log2 fold-change standard error, Wald statistic, Wald test p-value, and Bonferroni Hochberg corrected p-value for the expression of each gene.

organism: Acinetobacter baumannii

source_name: bacteria

growth_protocol: Bacteria were grown in a rotary shaker with agitation at 37oC.

extract_protocol: Total RNA was extracted using the TRI REAGENT® Kit

treatment_protocol: Bacteria were cultured in Luria-Bertani broth (LB) with or without  4 % HPF or 0.2 % HSA for 18 h. Overnight cultures were then diluted 1:10 in fresh LB broth and incubated for additional 7 h.

value: AB5075 Dhns

tag: condition

value: LB

tag: biological replicate


title: Boar fresh sperm-Input, rep1


title: Ctk1_DMSO_A

value: IP


title: HNS_LB1


title: Bur1_IAA_C

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xV5 IAA7::KanMX, BDF1-3xV5 IAA7::URA3, BUR1-3xFlag::NatMX


title: Ctk1_DMSO_AI

value: input


title: Rpb1_Taf1deg_DMSO_S5P_B


title: HNS_LB2


title: wild-type/het clutch 4 at 30 hpf

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description:
MR-11
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt

data_processing:
Step 1: Quality control of RNA-Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions.
Step 2: The high-quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without novel splicing form calls.
Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1.
Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05.
Genome_build: Ensembl GRCz11
Supplementary_files_format_and_content: 30-426592019.htseq-count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) files contain gene names and FPKM values.

organism: Danio rerio

source_name: Whole zebrafish embryos at 30 hpf

growth_protocol: Zebrafish embryos were grown in embryo medium (E3) at 28.5°C water temperature as per standard protocols.

extract_protocol:
After thawing the samples, each with 30 embryos per phenotype and time point (in triplicate) homogenized in 500 µl TRIzol (Invitrogen/Thermo Fisher Scientific, 15596026), samples were transferred into a pre-spun (16,000 x g, 30 s, room temperature) 2-ml 5PRIME Phase Lock Gel Heavy tube (Quantabio, 2302830). After addition of 100 µl chloroform (Sigma-Aldrich, C2432), the tube was vigorously inverted for 15 sec, incubated at room temperature for 3 min and spun at 12,000 x g for 15 min at 4°C. The supernatant was transferred into a RNase-free 1.7-ml tube. 150 µl buffer-saturated phenol (Invitrogen/Thermo Fisher Scientific, 15513039) and 150 µl chloroform were added, the samples vortexed for 15 sec, and incubated and spun as before. The supernatant was transferred into a fresh RNase-free 1.7-ml tube, 300 µl chloroform added, the samples were vortexed, incubated and spun as before. The supernatant was transferred into a fresh RNase-free 1.7-ml tube, 250 µl 2-propanol (VWR, BDH1133) added, the samples were inverted 10 times, samples were spun at 17,000 x g for 10 min at 4°C, and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 µl 75% ethanol in nuclease-free water (Invitrogen/Thermo Fisher Scientific, AM9937) followed by spinning at 17,000 x g for 5 min at 4°C. After the final wash, samples were air-dried and resuspended in 50 µl nuclease-free water. 5 µg of RNA was DNase-treated with the TURBO DNA-free Kit (Ambion, AM1907) as per the manufacturer’s protocol, in a volume of 50 µl for 30 min at 37°C. Instead of adding the DNase Inactivation Reagent, the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads (Beckman Coulter, A63987) following the manufacturer’s instructions. The final elution volume was 28 µl.
1 µg DNase-treated RNA samples were spiked with ERCC ExFold RNA Spike-In Mixes (Thermo Fisher Scientific, 4456739) as per the manufacturer’s protocol. Ribosomal RNAs were removed with the NEBNext rRNA Depletion Kit v2 (NEB, E7400), followed by a clean-up with RNAClean XP SPRI paramagnetic beads (Beckman Coulter, A63987). Strand-specific libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760) and NEBNext Multiplex Oligos for Illumina (NEB, E7335), all according to the manufacturer’s protocols. For quality control and pooling purposes, the final libraries were run on a HS D1000 ScreenTape in the Agilent 2200 TapeStation System. The average library size was 278 bp. Libraries were sequenced on the Illumina HiSeq 4000.

treatment_protocol: No treatment.

tag: tissue

value: Whole body

tag: genotype/variation

value: wild-type/het

tag: developmental stage

value: 30 hpf

tag: clutch


title: Bur1_IAA_B


title: wild-type/het clutch 9 at 30 hpf

description:
MR-12
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: Bur1_IAA_BI


title: wild-type/het clutch 3 at 30 hpf

description:
MR-10
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: Boar frozen-thawed sperm-Input, rep3

tag: cell type


title: Bur1_IAA_A


title: Bur1_IAA_CI


title: wild-type/het clutch 13 at 22 hpf

description:
MR-9
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt

source_name: Whole zebrafish embryos at 22 hpf

value: 22 hpf


title: Bur1_DMSO_C


title: Bur1_DMSO_CI


title: wild-type/het clutch 9 at 22 hpf

description:
MR-7
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: wild-type/het clutch 11 at 22 hpf

description:
MR-8
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: Bur1_IAA_AI


title: Bur1_DMSO_BI


title: Bur1_DMSO_B


title: mon clutch 3 at 30 hpf

description:
MR-4
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt

value: mon


title: mon clutch 4 at 30 hpf

description:
MR-5
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: Bdf2_ChIPseq_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF2-3xFlag::NatMX


title: mon clutch 13 at 22 hpf

description:
MR-3
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: Bur1_DMSO_AI


title: mon clutch 11 at 22 hpf

description:
MR-2
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: TU + tif1γ KD + Leflunomide, tailbud stage, replicate #3

description:
MR-12
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt

data_processing:
Step 1: Quality control of RNA-Seq datasets was performed by FastQC and Cutadapt to remove adaptor sequences and low quality regions.
Step 2: The high-quality reads were aligned to Ensembl genome assembly GRCz11 using Tophat 2.0.11 without novel splicing form calls.
Step 3: Transcript abundance and differential expression were calculated with Cufflinks 2.2.1.
Step 4: FPKM values were used to normalize and quantify each transcripts; the resulting list of differential expressed genes are filtered by log2 fold change > 2 and q value < 0.05.
Genome_build: Ensembl GRCz11
Supplementary_files_format_and_content: 170104_7001405_0663_AH722FBCXY.htseq-count.out.txt: Fragments Per Kilobase of transcript per Million mapped reads (FPKM) files contain gene names and FPKM values.

source_name: Whole zebrafish embryos at 10 hpf (= tailbud stage)

extract_protocol:
109 snap-frozen embryos of each genotype and treatment group (in triplicate) were homogenized in 700 µl TRIzol (Invitrogen/Thermo Fisher Scientific, 15596026) using a tissue homogenizer with hard tissue Omni tip plastic homogenizing probes (Omni International, 30750H). 300 µl TRIzol was added and the samples transferred into a pre-spun (16,000 x g, 30 s, room temperature) 2-ml 5PRIME Phase Lock Gel Heavy tube (Quantabio, 2302830). After addition of 200 µl chloroform (Sigma-Aldrich, C2432), the tube was vigorously inverted for 15 sec, incubated at room temperature for 3 min and spun at 12,000 x g for 15 min at 4°C. The supernatant was transferred into a RNase-free 1.7-ml tube. 300 µl buffer-saturated phenol (Invitrogen/Thermo Fisher Scientific, 15513039) and 300 µl chloroform were added, the samples vortexed for 15 sec, and incubated and spun as before. The supernatant was transferred into a fresh RNase-free 1.7-ml tube, 600 µl chloroform added, the samples were vortexed, incubated and spun as before. The supernatant was transferred into a fresh RNase-free 1.7-ml tube, 600 µl 2-propanol (VWR, BDH1133) was added, the samples were inverted 10 times and stored at -80°C overnight. Samples were spun at 17,000 x g for 30 min at 4°C, and the supernatant was pipetted off. Samples were handled on ice from now on. Samples were washed three times with 1000 µl 75% ethanol in nuclease-free water (Invitrogen/Thermo Fisher Scientific, AM9937) followed by spinning at 17,000 x g for 5 min at 4°C. After the final wash, samples were air-dried and resuspended in 50 µl nuclease-free water. 5 µg of RNA was DNase-treated with the TURBO DNA-free Kit (Ambion, AM1907) as per the manufacturer’s protocol, in a volume of 50 µl for 30 min at 37°C. Instead of adding the DNase Inactivation Reagent, the reaction was cleaned up using RNAClean XP SPRI paramagnetic beads (Beckman Coulter, A63987) following the manufacturer’s instructions. The final elution volume was 48 µl.
1.5 µg DNase-treated RNA samples were spiked with ERCC ExFold RNA Spike-In Mixes (Thermo Fisher Scientific, 4456739) as per the manufacturer’s protocol. Ribosomal RNAs were removed with the Ribo-Zero Magnetic Gold Kit (Illumina, MRZG12324), and strand-specific libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420) and NEBNext Multiplex Oligos for Illumina (NEB, E7335) all according to the manufacturer’s protocols. For quality control and pooling purposes, the final libraries were run on a high sensitivity DNA chip (Agilent, 5067-46426) on the Agilent 2100 Bioanalyzer. The average library size was 265 bp. Libraries were sequenced on the Illumina HiSeq 4000.

treatment_protocol: tif1γ KD and Ctrl KD embryos were treated with 7 µM leflunomide or the equivalent amount of DMSO from 5.3 hpf until 10 hpf when embryos were harvested by snap-freezing them.

value: TU + tif1<gamma> KD

value: Leflunomide

value: 10 hpf (= tailbud stage)


title: Bdf2_ChIPseq_BI


title: mon clutch 9 at 22 hpf

description:
MR-1
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: Bdf2_ChIPseq_A


title: TU + tif1γ KD + DMSO, tailbud stage, replicate #3

description:
MR-11
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt

value: DMSO


title: Bdf2_ChIPseq_AI


title: Bdf1_ChIPseq_B

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, BDF1-3xFlag::NatMX


title: TU + control morpholino + Leflunomide, tailbud stage, replicate #3

description:
MR-10
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt

value: TU + control morpholino


title: Bdf1_ChIPseq_BI


title: mon clutch 9 at 30 hpf

description:
MR-6
Zebrafish
rRNA depleted RNA
Directional RNA-seq
30-426592019.htseq-count.out.txt


title: TU + control morpholino + Leflunomide, tailbud stage, replicate #2

description:
MR-6
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: TU + tif1γ KD + Leflunomide, tailbud stage, replicate #2

description:
MR-8
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: Bdf1_ChIPseq_AI


title: TU + tif1γ KD + DMSO, tailbud stage, replicate #2

description:
MR-7
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: Bdf1_ChIPseq_A


title: Taf7_IAA_F

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

extract_protocol:
ChEC-seq was performed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
Sequencing libraries were constructed as previously described (Donczew et al., 2020; PMID: 31913117). Detailed protocol is available in publication accompaning this submission.
OTHER: ChEC-seq

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of selected proteins.

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 RPB3-3x Flag::NatMX, pGPD1-OSTIR::HIS3, bdf2delta-::HygMX, BDF1-3xV5 IAA7::KanMX, TAF7-MNase::TRP1


title: Taf7_IAA_D


title: TU + tif1γ KD + DMSO, tailbud stage, replicate #1

description:
MR-3
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: Taf7_IAA_E


title: TU + control morpholino + DMSO, tailbud stage, replicate #2

description:
MR-5
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: Taf7_IAA_C


title: Bur1_DMSO_A


title: TU + tif1γ KD + Leflunomide, tailbud stage, replicate #1

description:
MR-4
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: TU + control morpholino + Leflunomide, tailbud stage, replicate #1

description:
MR-2
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: Taf7_IAA_B


title: TU + control morpholino + DMSO, tailbud stage, replicate #1

description:
MR-1
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: Taf7_IAA_A


title: Taf7_DMSO_E


title: Taf7_DMSO_D


title: 6m-ko3

city: shanghai

first: qian

last: yu

address: Dongchuan road 800#

institute: SJTU

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Genome_build: mm9
Supplementary_files_format_and_content: raw counts and differential expression. In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.

source_name: Cornea epithelium

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

value: Cornea

value: Rela-/-


title: 6m-ko1


title: 6m-ko2


title: TU + control morpholino + DMSO, tailbud stage, replicate #3

description:
MR-9
Zebrafish
rRNA depleted RNA
Directional RNA-seq
170104_7001405_0663_AH722FBCXY.htseq-count.out.txt


title: Taf7_DMSO_C


title: 6m-wt2

value: WT


title: 6m-wt3


title: Taf7_DMSO_B


title: 6m-wt1


title: mature tomato fruit, WT, pool 2

city: Hurlingham

first: Pia

middle: Guadalupe

last: Dominguez

state: Buenos Aires

address: N. REPETTO Y LOS RESEROS S/N

department: IABIMO

country: Argentina

institute: INTA (National Institute of Agriculture Technology)

description: Gene expression data from mature fruits of line WT

hyb_protocol: The hybridization step was done following the Expression Analysis Technical Manual, with Specific protocols for Use with the Hybridization, Wash, and Stain Kit (Affymetrix®). 15 Ug of cRNA were hibridised during 16 hs in a GeneChip Tomato Genome Array® .

scan_protocol: The scan was done using the Affymetrix® GeneChip® Scanner 3000 according to the manufacturer´s specifications (Affymetrix®).

data_processing: The data was sujected to RMA normalization and Rank Product statistical analysis using the default settings of Robin software (Lohse et al., 2010).

label: biotin

organism: Solanum lycopersicum

source_name: Tomato mature fruit

label_protocol: Biotin-labeled cRNA was prepared from 100 ng of total mRNA employing the MessageAmp Premier Amplification Kit (Ambion) following the manufacturer´s specifications.

growth_protocol: Plants were grown in controlled greenhouse conditions (80% relative humidity; 200 mmol PAR s-1m-2; 16 hours of light and 8 hours of darkness).

extract_protocol: RNA was extracted with phenol (TRIzol Reagent®; Gibco). RNA quantification and contamination assessment were done by spectrophotometry (NanoDrop 2000c UV-Vis Spectrophotometer). RNA integrity was analyzed with the Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: Asr1-silenced lines (AS5 and AS17) and control plants (WT).

tag: cultivar

value: cv Money Maker

tag: lines

value: WT, pool 2


title: Taf7_DMSO_A


title: mature tomato fruit, WT, pool 1

value: WT, pool 1


title: Taf7_DMSO_F


title: Taf1_Med14deg_IAA_C

value: mat-alpha delta-ade2::hisG his3delta-200 leu2delta-0 lys2delta-0 met15delta-0 trp1delta-63 ura3delta-0 pGPD1-OSTIR::HIS3, MED14-3xV5 IAA7::KanMX, TAF1-MNase::TRP1


title: mature tomato fruit, WT, pool 3

value: WT, pool 3


title: 2m_ko1

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
We used SOAPnuke (v1.5.2) to filter reads and generate FASTQ format
Then aligned clean reads to the reference mouse genome using the Bowtie2 (v2.2.5) with default parameters
calculated gene expression level with RSEM (v1.2.12)
Genome_build: mm9
Supplementary_files_format_and_content: raw counts and differential expression


title: 2m_ko3


title: Taf1_Med14deg_IAA_A


title: 2m_ko2


title: 2m_wt3


title: Taf1_Med14deg_DMSO_C


title: Taf1_Med14deg_IAA_B


title: 2m_wt2


title: Taf1_Med14deg_DMSO_B


title: 2m_wt1


title: Taf1_Med14deg_DMSO_A


title: mature tomato fruit, line AS5, pool 2

description: Gene expression data from mature fruits of line AS5

value: line AS5, pool 2


title: mature tomato fruit, line AS17, pool 2

description: Gene expression data from mature fruits of line AS17

value: line AS17, pool 2


title: mature tomato fruit, line AS17, pool1

value: line AS17, pool 1


title: mature tomato fruit, line AS5, pool 1

value: line AS5, pool 1