title: embryos_14_16_R4_elavpos_flagpos_wt.neurons_females

description:
deltaelav.neuron_versus_wild-type.neuron.female.DESeq2.tsv
wild-type.neuron.female_versus_non.neuronal.DESeq2.tsv
all_rawcounts.tsv.gz

data_processing:
RNA-seq data wereanalyzed usingthe RNA-seq module fromsnakePipes(Bhardwaj et al., 2019) with default parameters for --trim , -m “alignment-free,alignment”.
Normalized abundance measures were obtained with DESeq2 for each relevant pairwise comparison (default settings)
Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: all_rawcounts.tsv.gz: files containing raw counts as created by featureCounts within the snakePipes pipeline
Supplementary files format and content: tsv files: DESeq2 standard results output for all relevant comparisons
Supplementary files format and content: bw files: BigWig files containing normalized counts in RPKM

source_name: embryo

growth_protocol: Flies were grown at 25C, following standard fly husbandry protocols.

extract_protocol:
Treated cells were pipetted vigorously in 3:1 Trizol LS (Ambion) and RNA was extracted according to the manufacturer’s protocol.
The libraries were constructed using Illumina TruSeq Stranded Total RNA (Gold): removal of rRNA using biotinylated, target-specific oligos combined with magnetic Ribo-Zero rRNA removal beads. Gold: depletion of both cytoplasmic and mitochondrial rRNA, cDNA prep (random priming, dUTP incorporation for strand specificity), indexed.

treatment_protocol: Drosophila embryos were collected after 16 to 16 hours. All further steps were carried on in the cold until cell sorting, and all washes were done in cold, RNAse-free PBS (Alfa Aesar) with RNase inhibitor (1:250) (Ribolock, ThermoFischer) at 1000g for 2 minutes, to preserve RNAs from degradation. Embryos were dounced in RNAse-free PBS with RNase inhibitor (1:250), and cell debris were filtered out by filtration through a 40m strainer at 400g. Cells were washed twice, and stained with Zombie Aqua (BioLegend) for live/dead separation, for 15min in the dark, in PBS with 1:100 RNase inhibitor.Cells were washed twice and then fixed with 4% formaldehyde in PBS for 15min, in the dark. Fixation was stopped with incubation for 3min with a quenching buffer (750 mM TrisHCl pH 7.5 in DEPC-PBS, 1:100 RNase inhibitor) and cells were washed again twice. Cells were incubated with primary antibodies: polyclonal anti-Elav 1:500 (rabbit, generated in Carrasco et al, 2020) and mouse-anti-FLAG M2 at 1:500 (Sigma) for 45 minutes in the dark, with agitation, at 4 °C in staining buffer (1% BSA (w/v), 0.1% saponin, 1:200 RiboLock). They were washed twice in 0.2% BSA, 0.1% saponin in PBS, 1:100 RiboLock and incubated with fluorescently conjugated antibodies at1:500, for 45 minutes in the dark, with agitation, at 4 °C in staining buffer with 488 anti-rabbit (Life Technologies) and 555 anti-mouse (Abcam). Cells were then washed twice and resuspended in sorting buffer (0.5% BSA, 2mM EDTA, 1:500 RiboLock). They were filtered through a 40µm nylon mesh, sorted using a FACSymphony (Becton Dickinson), and collected in cold sorting buffer. Cells were pelleted and RNA-protein complexes were reverse cross-linked with proteinase K (Ambion AM2546) in 10mM Tris, pH8, 10mM NaCl, 1mM EDTA, 1:100 proteinase K 1:100 RiboLock), for 20 minutes at 50° C.

value: embryo

value: delta_elav;fneFLAG/FM7 flies

tag: developmental stage

value: Embryo - 14-16 h AEL

value: wild-type neuron

tag: Sex

value: female


title: [DDB_PD_022]_[HMP3427_crash_30L]_[Batch]_[0h]_[R1]

status: Public on Jun 01 2025

type: SRA

city: Kgs. Lyngby

first: Felix

last: Beulig

address: Kemitorvet 220

country: Denmark

institute: Novo Nordisk Center for Biosustainability

library_source: transcriptomic

data_processing:
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM).
Assembly: Reference genome E. coli MG1655 (NC_000913.3)
Supplementary files format and content: Raw data files and comma-delimited text file reporting logtpm values for each sample

molecule: total RNA

organism: Escherichia coli

source_name: Escherichia coli cells

growth_protocol: Batch-to-fed-batch fermentation experiments were performed in 0.25 L Ambr® fermenters (Sartorius) with 2 different media compositions (“High Metal” and “Low Metal” medium)

extract_protocol:
All transcriptome samples were collected and prepared in biological duplicates, whereby either 2 ml of culture (low cell density culture, batch phase) or 0.5 ml of culture (high cell density culture, fed batch phase) was added to 6 ml of Qiagen RNA-protect Bacteria Reagent immediately after sample collection. This solution was then vortexed for 30 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80° C. The RNeasy Mini Kit (Qiagen) was used to extract and purify RNA from the cell pellets per vendor protocol, including on-columns DNase treatment for 30 minutes at room temperature. RNA was quantified using qubit fluorometer (Thermofisher) and integrity was assessed using fragment analyzer (Agilent Technologies).
Ribosomal RNA was removed using QIAseq FastSelect –5S/16S/23S kit (Qiagen). Sequencing libraries were prepared with the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) and assessed using fragment analyzer (Agilent Technologies). The libraries were then subjected to paired end sequencing on Illumina Nextseq using Nextseq Mid Output kit (Illumina) with a read length of 150 bp.

treatment_protocol: The “Low Metal” batch media contained base medium (22 g L-1 D-(+)-glucose monohydrate, 7.6 g L-1 (NH4)2SO4, 15.7 g L-1 KH2PO4, 0.241 g L-1 MgSO4, 100 mg L-1 thiamine hydrochloride, 0.5 mL L-1 Antifoam 204), and 1 mL L-1 of trace metal solution (0.48 g L-1 CuSO4·5H2O, 0.54 mg L-1 CoCl·7H2O, 0.54 g L-1 ZnSO4·7H2O, 2 g L-1 CaCl2·2H2O, 41.8 g L-1 FeCl3·6H2O, 0.3 g L-1 MnSO4·H2O, 33.4 g L-1 Na2EDTA, 0.5 g L-1 Na2MoO4·2H2O). The “High Metal” batch media contained the same base medium, 3.5 mL L-1 trace metal solution and was additionally supplemented with 1.86 g L-1 citric acid monohydrate and 41.8 mg L-1 FeCl3·6H2O, 21.6 mg L-1 ZnSO4·5H2O). Initial batch fermentations were performed with base medium until complete glucose consumption, marked by a 50% decline in the rate of CO2 formation, triggering an automatic switch to fed-batch operation with continuous supply of the feed medium (550 g L-1 D-(+)-glucose monohydrate, 13.7 g L-1 MgSO4·7H2O)

tag: cell type

value: Escherichia coli cells

tag: strain


title: Pediatric day 14 with vector library

city: Houston

first: JP

last: McGinnis

state: TX

address: 5306 Creekbend Dr

department: Neurosurgery

country: USA

institute: Baylor College of Medicine

description:
Library name: 3v4-5-6-d14-BC_S1
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using the Cell Ranger software.
Assembly: GrCH38
Supplementary files format and content: HDF5

molecule: nuclear RNA

organism: Homo sapiens

source_name: Brain with AAVs

extract_protocol:
For the tissue sections that received barcoded viral libraries (total titer 2.1E9 in 4 µL PBS per tissue slice), 14 days after virus application the tissue was gently removed from its well, flash frozen in liquid nitrogen, and stored at -80 oC. On the day of processing, frozen tissue was dissociated using GentleMACS nuclei isolation protocol (nuclei isolation buffer [Miltenyi Biotec, cat# 130-128-024], Protector RNAse Inhibitor [Millipore Sigma, cat# 3335402001], GentleMACS C tubes [Miltenyi Biotec, cat# 130-093-237], GentleMACS Octo Dissociator [Miltenyi Biotec, cat# 130-096-427], MACS SmartStrainers 70um [Miltenyi Biotec, cat# 130-098-462], MACS SmartStrainers 30um [Miltenyi Biotec, cat# 130-098-458]). In brief, samples were placed in 2 mL of Miltenyi Nuclei Isolation Buffer and Protector RNAse Inhibitor in GentleMACS C tubes. Samples then underwent the preprogrammed “nuclei isolation” program on a GentleMACS Octo Dissociator. Immediately after dissociation, samples were strained through a 70um MACS SmartStrainer and collected in a 15 ml tube, centrifuged at 300xg for 5 minutes at 4°C. The supernatant was extracted and discarded, and the resulting pellet resuspended in 1mL of ice-cold PBS. Resuspended samples were then run through a 30um MACS SmartStrainer, centrifuged, and resuspended in ~250-500 µL. Nuclei were then FACS sorted using DAPI on a Sony MA900 in the Baylor Cytometry and Cell Sorting Core.
The single-cell gene expression libraries were prepared according to the Chromium Single Cell Gene Expression 3’v3.1 instruction (PN-1000121, PN-1000120, PN-1000213, 10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions) where full-length cDNA was synthesized and barcoded for each molecule of mRNA (UMI) and each single cell (cell barcode). Subsequently, the GEMS were broken and cDNA from each single cell was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product was fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification.

tag: tissue

value: Brain with AAVs

tag: treatment

value: 14 AAV library, then cultured 14 days


title: [DDB_PD_019]_[HMP3427_crash_1L]_[Fed-batch]_[20h]_[R1]


title: Adult day 0

description:
Library name: 3v4-620-STL-d0-GEX_S1
10X Genomics

source_name: Brain

value: Brain

value: Frozen just after resection


title: embryos_14_16_R4_elavpos_flagneg_wt.neurons_mixed

city: Freiburg

first: Valérie

last: Hilgers

address: Stübeweg 51

country: Germany

institute: MPI of Immunobiology and Epigenetics

description:
wild-type.neuron.mixed_versus_non.neuronal.DESeq2.tsv
all_rawcounts.tsv.gz

organism: Drosophila melanogaster

tag: genotype

value: pooled male and female


title: Pediatric day 0

description:
Library name: 3v4-5-6-d0_S1
10X Genomics


title: Embryo_CRY2CBP_BlueLight_R3

city: Madison

first: Melissa

last: Harrison

state: Wisconsin

address: 6204B Biochemical Sciences Building, 440 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin- Madison

library_source: genomic

data_processing:
Adapter sequences were trimmed from reads using NGmerge v0.377.
Bowtie2 v2.4.478 was used to align trimmed reads to the dm6 reference genome with a mapping quality threshold of ≥ 30. Reads with a poor mapping quality or aligned to mitochondrial or scaffold DNA were thrown out. For analysis, only fragment sizes smaller than 100bp were used.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized

molecule: genomic DNA

source_name: Embryo (15min into NC14)

growth_protocol: Drosophila embryos were maintained at 25˚C on molasses plates for 90mins after egg laying in which they were mounted for live imaging on a fluorescent scope and precisely staged by nuclear density at nuclear cycle 10 for catalytic inactivation experiments or 15min into nuclear cycle 14 for CBP knockdown experiments. S2 cells were cultured in Schneider’s medium with supplemented antibiotic/antimycotic and 10% FBS at 27 ˚C.

extract_protocol:
Embryos were collected and washed prior to mounting in halocarbon oil on a glass bottom dish. Real time staging of embryos was possible through the His2av-RFP marker used to measure nuclear density (nuclei/2500µm2). Live imaging was performed on a Nikon Eclipse Ti2 inverted fluorescent microscope. Embryos were processed for ATACseq exactly 15 min into NC14. For optogenetic experiments, His2Av-RFP and CBPCRY2;His2Av-RFP embryos were treated with a repeating sequence of 60s exposure to 470nm filtered light followed immediately by a 10 ms exposure to 555nm. This sequence was initiated upon entry into NC10 and ended 15 min into nuclear-cycle 14. Staged single embryos were picked and homogenized in 10µL of pre-chilled lysis buffer (10mM Tris pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1%NP-40). Embryo homogenate was resuspended by adding an additional 40µL of lysis buffer and spun down at 500g for 10 min at 4˚C. The supernatant was removed under a dissecting scope to ensure the small pellet was not disturbed. 2.5µL of water, 2.5µL of Tn5 enzyme, and 5µL of TD buffer (Illumina Tagment DNA Enzyme and Buffer Kit) were added to resuspend the pellet, followed by a 37˚C incubation for 30 min. ATAC-seq in S2 cells was carried out similarly, in which 200,000 cells were spun down for 3min at 600g at 4˚C, washed with 1X PBS, and resuspended in 100μL lysis buffer. Lysed cell material was pelleted after centrifuging for 10min at 600g at 4˚C. The supernatant was replaced with 47.5UL TD buffer and 2.5 Tn5 enzyme (Illumina) and incubated at 37˚C for exactly 30min.
Libraries were prepared using IDT for Illumina Nextera DNA Unique Dual indices, and PCR amplified with NEBNext Hi-Fi 2x PCR Master Mix (72˚C for 5min, 98˚C for 30s, followed by 12 cycles of 98˚C for 10s, 63˚C for 30s, and 72˚C for 1min). Libraries were DNA purified using magnetic axygen beads and washed with ethanol (Thermo Fisher Scientific).

treatment_protocol: S2 cells were induced to express Zld using CuSO4, and were treated either with control DMSO drug or a CBP catalytic inhibitor A485.

value: Embryo (15min into NC14)

value: CRY2nej;his2avRFP III

value: Blue light

tag: condition


title: [DDB_PD_019]_[HMP3427_crash_1L]_[Fed-batch]_[17h]_[R1]


title: 15286X049_blastomere_546A_type_IVF_cell_number_2

city: dallas

first: Edward

last: Grow

state: TEXAS

address: 7053 beltau lane

institute: UTSW

description: cellnumber 2

library_source: genomic single cell

data_processing:
RNA-seq reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned to bostau7 with Bowtie2 (v2.2.6) with the following parameters: (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant).
PCR duplicates were removed using bedtools
mitochondrial reads were removed using sed '/chrM/d'
counts for each ATACseq union region were generated using ‘Get datasets’ (https://metacpan.org/pod/distribution/Bio-ToolBox/scripts/get_datasets.pl).
Assembly: bostau7
Supplementary files format and content: 20230629-scATAC-seq-cell-ID-conversion.xls excel file containing sample ID and information
Supplementary files format and content: 20180822-scATAC-819-cells-vs-302830-regions.tabular count file for n=819 retained high quality scATACseq libraries in ATAC-seq peaks regions created as a union dataset, tabular format

organism: Bos indicus x Bos taurus

source_name: IVF

growth_protocol: Oocyte collection and in vitro maturation: Bovine ovaries were collected from a local abattoir (JBS, Hyrum, Utah) and transported in a cooler containing 0.9% saline solution to the laboratory. Because this research used discarded tissues to generate embryos that were then disposed of without implantation, approval of this work via the Institutional Animal Care and Use Committee was not required. The cumulus-oocyte complexes (COCs) were aspirated from 3-8 mm follicles using an 18-gauge needle and vacuum system. Only compact COCs with homogenous ooplasm and intact layers of cumulus cells were used for somatic cell nuclear transfer (SCNT) or in vitro fertilization (IVF). Following aspiration, COCs were cultured at 38.5°C with 5% CO2 for 22–24 h. The oocytes were cultured in TCM199 maturation medium containing Earles salts, L-glutamine, and sodium bicarbonate (Sigma M4530) supplemented with 10% (v/v) fetal bovine serum (FBS) (Hyclone, SH30070.03), 0.05 mg/ml of bovine follicle stimulating hormone (Sioux Biochemicals, Sioux city, IA), 5 mg/ml of bovine luteinizing hormone (Sioux Biochemicals, Sioux Center, Iowa), 100 U/ml of penicillin, and 100 mg/ml of streptomycin (Gibco 15070-063).  In vitro fertilization: Following 22–24 h of maturation, MII oocytes were fertilized by using the laboratory’s standard in vitro fertilization protocol [Reproduction, 2006, 131:45-51]. Briefly, one straw of cryopreserved bovine semen (Hoffman AI, Logan, Utah) was removed from the liquid nitrogen tank and placed into a 35°C water bath to thaw. Live sperm were isolated by centrifugation through a 45%/90% percoll gradient (MP Biomedical, Irvine, California), suspended (final concentration 1x106/ml) in Tyrodes albumin lactate pyruvate containing 10 μg/ml porcine heparin and used to fertilize the oocytes. Twenty to 22 h post-IVF, cumulus cells were removed by vortexing, and fertilized zygotes were washed in phosphate buffered saline with 0.32 mM sodium pyruvate, 5.55 mM glucose, and 3 mg/ml bovine serum albumin (PB1+). After washing, zygotes were cultured in 40 μl of synthetic oviductal fluid (SOFaa) [Human Reproduction 2000; 15:395-401] with 3% FBS (Hyclone, SH30070.03, Logan, Utah) overlaid with mineral oil. The embryos were cultured at 38.5°C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture. Historically, production of IVF embryos via these methods followed by blastocyst embryo transfers to cattle recipients has generated successful pregnancies at an approximate rate of 50% (number live births/number of embryo transfer procedures) by our research group (unpublished observations). The timing of embryo collection post-fertilization was approximately 24–36 h for 2-cell stage, 48–60 h for 8-cell stage, 156–168 h for morula stage, and 192–204 h for blastocyst stage. Embryos that were obviously dead or arrested by microscopic examination were removed from culture.  Somatic cell nuclear transfer (SCNT): Primary bovine fibroblast cultures were established from ear biopsy tissues from multiple donor Brahma Spanish bull crosses by using well-established procedures [PNAS USA; 2000; 97:990-995]. These cell lines have been previously employed on multiple projects to evaluate their efficiency to generate live calves via SCNT (unpublished observations). Frozen/thawed cells were grown to 80-100% confluence then passaged, with cells from passages 4-5 used as nuclear donors. Three days prior to a cloning session, donor fibroblast cells were thawed and propagated, and incubated in DMEM medium (Hyclone, Logan, Utah) supplemented with 15% (v/v) FBS at 39°C with 5% CO2. Bovine fibroblasts at 80-90% confluence were serum-starved by replacing culture medium with DMEM containing 0.5% (v/v) FBS 24 h prior to SCNT. Oocytes were matured for 18–20 h, then denuded by using 100 μl of 1% (v/v) hyaluronidase (Sigma H3506), incubated for 5 min at 38.5°C with 5% CO2, followed by gentle pipetting. The denuded oocytes were then rinsed with PB1+, and oocytes with polar bodies were selected and separated. SCNT was performed according to established protocols [Reproduction 2006; 131:45-51; Anim Reprod Sci 2006; 95:234-243; Mol Reprod Dev 2004; 68189-197]. Briefly, oocytes with polar bodies were incubated in 0.6 μg/ml demecolcine for 30–40 min and a metaphase plate and a polar body were removed by using a beveled pipette. Fibroblast cells were covered in 0.25% trypsin (Gibco, Carlsbad, CA) for 1 min, and then the trypsin was removed, and fibroblasts were incubated for another 6 min at 39°C with 5% CO2. Once fibroblast cells were detached, they were rinsed in warm medium and centrifuged at 150 × g for 6 min. The supernatant was removed, and the cellular pellet was resuspended in 100 μl of Hepes SOF medium [Hum Reprod 2000; 15:395-401]. One fibroblast cell was injected into the perivitelline space of the recipient oocyte and fused by using one direct pulse of 1.2 kV/cm for 22 μs by an Electro Cell Manipulator 2001 (BTX, San Diego, CA) in 0.28 M sorbitol, 0.05% (w/v) BSA, 0.1 mM CaCl2, 0.5 mM MgCl2, and 0.5 mM Hepes. Following fusion, embryos were washed through Hepes SOF, and incubated in embryo culture medium for 1 h. Activation was then performed, with successfully fused embryos cultured in 5 μM ionomycin for 5 min, followed by 4 h of incubation in activation medium composed of SOFaa medium with 10 μg/ml cyclohexamide and 1 mM 6-dimethylaminopyridine at 38.5°C with 5% CO2. Following activation, embryos were cultured in 40 μl drops of SOFaa with 3% (v/v) FBS overlaid with mineral oil. The embryos were cultured at 38.5°C in a humidified atmosphere with 5% CO2. Half of the SOFaa medium was removed and replaced with fresh, equilibrated medium every other day starting the day after in vitro culture. The timing of embryo collection was the same as for IVF embryos as described above. The rates of development for IVF and SCNT embryos were similar at each developmental stage.

extract_protocol:
ATAC-seq was performed using 2x Tris-DMF-tagmentation buffer (10mM Tris-pH=8.0, 5mM MgCl, 20% DMF). Add (batch-determined actitivty) 2 to 2.5 uL of Nextera Tn5 transposase (Cat# FC-121-1030, Illumina. Samples were incubated at 37C for 30 minutes in a PCR machine. The reactions were stopped with 0.5uL of 10% SDS, pipetted up and down, and placed on ice 5 min. 5x volume of PB buffer was added to the ATAC-seq reaction and purified using a ampure beads and eluted in 10mM Tris-pH=8.0 + 1mM EDTA.
Libraries were PCR amplified in 25uL reaction volumes using custom Nextera PCR primers from Buenrostro, et al. Nature 2015. PCR reaction conditions: ~10uL tagmented DNA, 12.5 uL of 2xphusion PCR mastermix (Phusion High-Fidelity PCR Master Mix with HF Buffer - 100 rxns, NEB, cat #M0531S), 0.625uL of 100uM F primer, 0.625uL of 100uM R primer. QS to 50uL total with H20. Do 5 cycles of “pre-amp” PCR. PCR cycling conditions: 72C incubation for 5 min. 5 cycles of the following: 95C for 30 sec, 72C for 90 sec. Remove 5uL of the “pre-PCR” reaction for qPCR. qPCR reaction conditions: 20uL qPCR reaction: 5uL of pre-amp PCR product, 10 ul of 2x syber (SsoAdvanced SYBR Green Supermix, Biorad catalog #1725275), 0.25uL of 100uM F primer, 0.25uL of 100uM R primer. Run 30-40 cycles of qPCR with the same cycling conditions as above. Select the additional number of PCR cycles to perform as per Buenrostro, et al. Nature Methods 2013. Ampure bead purification (Beckman Coulter, catalog # A63881) as per manufacturer’s instructions.
Nextera tagmentation

treatment_protocol: Each embryo was dissociated into single blastomeres in a single drop of Ca+2/Mg+2 free PBS+0.1% PVP-40 with gentle pipetting. Each individual blastomere of the embryo was pipetted into a PCR strip tube for lysis and ATAC-seq, retaining the embryo identity of each single-cell ATACseq library.

value: IVF


title: 15286X048_blastomere_545B_type_IVF_cell_number_2

description: cellnumber 2


title: embryos_14_16_R4_elavneg_flagneg_nonneurons

description:
wild-type.neuron.mixed_versus_non.neuronal.DESeq2.tsv
wild-type.neuron.female_versus_non.neuronal.DESeq2.tsv
all_rawcounts.tsv.gz

value: non-neuronal


title: [DDB_PD_019]_[HMP3427_crash_1L]_[Fed-batch]_[15h]_[R1]


title: 15286X047_blastomere_545A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X046_blastomere_544B_type_IVF_cell_number_2

description: cellnumber 2


title: E15

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

description:
Library name: E15
Column name in gene_count.txt: E15

data_processing:
Novogene
Assembly: P. miniata v3.0 genome assembly
Supplementary files format and content: tab delimited excel file include feature count for each sample

molecule: polyA RNA

organism: Patiria miniata

source_name: Day4 embryos

growth_protocol: Pm sea star embryos were cultured in sea water in presence or absence of BAPN

extract_protocol:
RNA was extracted with trizol
Novogene polyA library from total RNA

treatment_protocol: Embryos were treated with the indicated concentration of BAPN at the indicated time of development

value: Day4 embryos

value: wild type

value: BAPN 0.8 mM from hatched blastula to day 2 followed by recovery from day2 to day4


title: E14

description:
Library name: E14
Column name in gene_count.txt: E14

value: Control for E9


title: [DDB_PD_019]_[HMP3427_crash_1L]_[Fed-batch]_[11h]_[R1]


title: 15286X045_blastomere_544A_type_IVF_cell_number_2

description: cellnumber 2


title: E13

description:
Library name: E13
Column name in gene_count.txt: E13

value: Control for E10


title: 15286X044_blastomere_543B_type_IVF_cell_number_2

description: cellnumber 2


title: embryos_14_16_R2_elavpos_flagneg_wt.neurons_mixed

value: embryo

value: delta_elav;fneFLAG/FM7 flies

value: Embryo - 14-16 h AEL

value: wild-type neuron


title: E16

description:
Library name: E16
Column name in gene_count.txt: E16

value: BAPN 1.2 mM from hatched blastula to day 2 followed by recovery from day2 to day4


title: embryos_14_16_R2_elavpos_flagpos_wt.neurons_females

value: female


title: E12

description:
Library name: E12
Column name in gene_count.txt: E12

value: BAPN 0.8 mM from mid gastrula to day 4


title: E11

description:
Library name: E11
Column name in gene_count.txt: E11

value: BAPN 1.2 mM from mid gastrula to day 4


title: [DDB_PD_009]_[DDB30_del_tnaA]_[Fed-batch]_[15h]_[R2]

value: Escherichia coli cells


title: 15286X043_blastomere_543A_type_IVF_cell_number_2

description: cellnumber 2


title: embryos_14_16_R4_elavneg_flagpos_mutant.neurons_males

description:
deltaelav.neuron_versus_wild-type.neuron.female.DESeq2.tsv
all_rawcounts.tsv.gz

value: delta_elav neuron

value: male


title: [DDB_PD_009]_[DDB30_del_tnaA]_[Fed-batch]_[15h]_[R1]


title: [DDB_PD_019]_[HMP3427_crash_1L]_[Fed-batch]_[13h]_[R1]


title: [DDB_PD_019]_[HMP3427_crash_1L]_[Fed-batch]_[9h]_[R1]


title: Embryo_ctrl_BlueLight_R2

value: Embryo (15min into NC14)

value: his2avRFP III

value: Blue light


title: embryos_14_16_R2_elavneg_flagneg_nonneurons

value: non-neuronal

value: pooled male and female


title: 15286X042_blastomere_542B_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: [DDB_PD_009]_[DDB30_del_tnaA]_[Fed-batch]_[6h]_[R2]


title: embryos_14_16_R1_elavpos_flagpos_wt.neurons_females

value: embryo


title: E10

description:
Library name: E10
Column name in gene_count.txt: E10

value: Day4 embryos

value: wild type

value: BAPN 0.8 mM from hatched blastula to day 4


title: 15286X041_blastomere_542A_type_IVF_cell_number_2

description: cellnumber 2


title: embryos_14_16_R1_elavpos_flagneg_wt.neurons_mixed

value: delta_elav;fneFLAG/FM7 flies

value: Embryo - 14-16 h AEL

value: wild-type neuron


title: E9

description:
Library name: E9
Column name in gene_count.txt: E9

value: BAPN 1.2 mM from hatched blastula to day 4


title: [DDB_PD_009]_[DDB26_del_luxS]_[Fed-batch]_[15h]_[R2]

value: Escherichia coli cells


title: [DDB_PD_009]_[DDB30_del_tnaA]_[Batch]_[0h]_[R2]


title: E8

description:
Library name: E8
Column name in gene_count.txt: E8

source_name: Day3 embryos

value: Day3 embryos

value: Control for E7


title: embryos_14_16_R1_elavneg_flagpos_mutant.neurons_males

value: delta_elav neuron

value: male


title: embryos_14_16_R2_elavneg_flagpos_mutant.neurons_males


title: E7

description:
Library name: E7
Column name in gene_count.txt: E7

value: BAPN 0.8 mM from mid gastrula to day 3


title: 15286X039_blastomere_541A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_009]_[DDB26_del_luxS]_[Fed-batch]_[15h]_[R1]


title: embryos_14_16_R1_elavneg_flagneg_nonneurons

value: non-neuronal


title: E5

description:
Library name: E5
Column name in gene_count.txt: E5

value: BAPN 1.2 mM from mid gastrula to day 3


title: embryos_18_20_B2_R4_elavpos_flagpos

description:
deltaelav,deltafne.neuron_versus_wild-type.neuron.DESeq2.tsv
all_rawcounts.tsv.gz

growth_protocol: Flies were grown at 25C, following standard fly husbandry protocols. Ebryos were collected on apple juice plate from cages.

extract_protocol:
cells were pipetted vigorously in 3:1 Trizol LS (Ambion) and RNA was extracted according to the manufacturer’s protocol.
The libraries were constructed using Illumina Stranded Total RNA w/ Ribo-Zero Plus, acoording to the manufacturer's protocol

value: Embryo - 18-20 h AEL

value: delta_elav,delta_fne neuron


title: 15286X038_blastomere_540B_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: [DDB_PD_009]_[DDB26_del_luxS]_[Fed-batch]_[6h]_[R2]


title: 15286X035_blastomere_539A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X037_blastomere_540A_type_IVF_cell_number_2

description: cellnumber 2


title: E3

description:
Library name: E3
Column name in gene_count.txt: E3

source_name: Day2 embryos

value: Day2 embryos

value: wild type

value: BAPN 0.8 mM from hatched blastula to day 2


title: embryos_18_20_B2_R3_elavpos_flagpos

value: embryo


title: embryos_18_20_B2_R4_elavneg_flagneg

description:
wild-type.neurons_versus_non-neuronal.DESeq2.tsv
all_rawcounts.tsv.gz

value: pooled male and female


title: 15286X034_blastomere_538B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_009]_[DDB26_del_luxS]_[Fed-batch]_[6h]_[R1]


title: embryos_18_20_B2_R4_elavpos_flagneg

description:
deltaelav,deltafne.neuron_versus_wild-type.neuron.DESeq2.tsv
wild-type.neurons_versus_non-neuronal.DESeq2.tsv
all_rawcounts.tsv.gz

value: wild-type neuron


title: embryos_18_20_B2_R3_elavpos_flagneg


title: E1

description:
Library name: E1
Column name in gene_count.txt: E1

value: BAPN 1.2 mM from hatched blastula to day 2


title: E4

description:
Library name: E4
Column name in gene_count.txt: E4

value: Control for E3


title: 15286X040_blastomere_541B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X036_blastomere_539B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_009]_[DDB26_del_luxS]_[Batch]_[0h]_[R1]

value: Escherichia coli cells


title: embryos_18_20_B2_R3_elavneg_flagneg


title: E2

description:
Library name: E2
Column name in gene_count.txt: E2

value: Control for E1


title: [DDB_PD_009]_[DDB26_del_luxS]_[Batch]_[0h]_[R2]


title: E6

description:
Library name: E6
Column name in gene_count.txt: E6

value: Day3 embryos

value: Control for E5


title: 15286X033_blastomere_538A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_009]_[DDB27_del_lsrK]_[Fed-batch]_[15h]_[R2]_reseq


title: [DDB_PD_009]_[DDB27_del_lsrK]_[Fed-batch]_[15h]_[R1]


title: embryos_18_20_B1_R2_elavpos_flagpos

value: male


title: 15286X032_blastomere_537B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_009]_[DDB27_del_lsrK]_[Fed-batch]_[15h]_[R2]


title: PHGDH-2

city: La Jolla

first: Sheng

last: Zhong

state: California

address: 9500 Gilman Drive, MC 0412

department: Department of Bioengineering

institute: University of California, San Diego

library_source: other

data_processing:
STAR_2.5.4b used for mapping
featureCounts used for gene quantification
Assembly: hg38

molecule: other

growth_protocol: About 2x107 HEK293T (ATCC, CRL3216) Cells were collected and lysed in 500 µL of the lysis buffer (50 mM Tris-HCl, pH 7.5 (Invitrogen™, 15567027), 100 mM NaCl (Thermo Fisher Scientific, AM9759), 1% Triton X-100 (Sigma-Aldrich, T8787-50ML), 0.1% SDS (Invitrogen™, AM9820), 0.5% Sodium Deoxycholate (Sigma-Aldrich, 30970-25G), and a protease inhibitor cocktail (Roche, 4693159001)) together with 200 U of RNasin® Plus Ribonuclease Inhibitor (40 U/µL, Promega, N2618) on ice for 30 minutes with occasional mixing and were then centrifuged at 15k rpm for 15 minutes.

extract_protocol:
RNA was precipitated by the addition of 3 µL of glycogen (5 mg/mL, Invitrogen™, AM9510), 50% of 2-propanol (Sigma-Aldrich, I9516-500ML), and 10% of 3 M sodium acetate, pH 5.5 (Invitrogen™, AM9740) with an incubation at -80℃ overnight. The RNA was then pelleted by centrifugation at 14k rpm for 30 minutes at 4℃, washed with 1 mL of 75% ethanol (Sigma-Aldrich, 493546), and air-dried. The RNA was then suspended in 20 µL of UltraPure™ DNase/RNase-Free distilled water (Invitrogen™, 10977015).
A library was prepared by cDNA synthesis, amplification, fragmentation, and adaptor ligation using NEBNext® Low Input RNA Library Prep Kit (NEB, E6420) and sequenced 150 base pairs from each end on an Illumina MiniSeq.

treatment_protocol: Immunoprecipitation was conducted by incubating 500 µL of the cell lysate from each sample with the pre-equilibrated bead slurry as below at 4°C on a rocking platform overnight.Beads were sequentially washed twice with 1 mL of high salt buffer (50 mM Tris-HCl, pH 7.5 (Invitrogen™, 15567027), 1 M NaCl (Thermo Fisher Scientific, AM9759), 1 mM EDTA pH 8.0 (Invitrogen™, AM9260G), 1% Triton X-100 (Sigma-Aldrich, T8787-50ML), 0.1% SDS (Invitrogen™, AM9820), and 0.5% Sodium Deoxycholate (Sigma-Aldrich, 30970-25G)) and 1 mL of wash buffer (20 mM Tris-HCl, pH 7.5 (Invitrogen™, 15567027), 10 mM MgCl2 (Invitrogen™, AM9530G), and 0.2% Tween-20 (Sigma-Aldrich, P9416-100ML)).Complex in each tube was released from beads by incubation with a mixing of 20 µL of Proteinase K (800 U/mL, NEB, P8107S) and 180 µL of PK buffer (50 mM Tris-HCl, pH 7.5 (Invitrogen™, 15567027)) and 10 mM MgCl2 (Invitrogen™, AM9530G)) at 50℃ for 40 minutes. The supernatant was collected, and RNA was extracted by 1 mL of TRIzol Reagent (Invitrogen™, 15596026) for each sample. 200 µL of chloroform (Acros Organics, A0425256) was added into the supernatant to remove other impurities. After being centrifuged at 14k rpm for 15 minutes at 4℃, the upper layer was collected.

tag: cell line

value: anti-PHGDH antibody


title: IgG-2

value: anti-IgG antibody


title: [DDB_PD_009]_[DDB27_del_lsrK]_[Fed-batch]_[6h]_[R1]


title: embryos_18_20_B1_R2_elavneg_flagneg

value: Embryo - 18-20 h AEL

value: non-neuronal


title: [DDB_PD_009]_[DDB27_del_lsrK]_[Fed-batch]_[6h]_[R2]


title: embryos_18_20_B1_R2_elavpos_flagneg


title: [DDB_PD_009]_[DDB27_del_lsrK]_[Batch]_[0h]_[R2]


title: 15286X029_blastomere_536A_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: 15286X028_blastomere_535B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X030_blastomere_536B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X027_blastomere_535A_type_IVF_cell_number_2

description: cellnumber 2


title: PHGDH-1


title: [DDB_PD_009]_[DDB27_del_lsrK]_[Batch]_[0h]_[R1]


title: embryos_18_20_B1_R1_elavpos_flagneg


title: IgG-1


title: PBMCs_healthy control_sample 9

type: RNA

city: Beijing

first: Siyu

last: Yao

address: Tongzhou District, No.9 Beiguan Street, Yard 1

country: China

institute: Beijing Chest Hospital Affiliated toCapital Medical University

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: PBMCs_healthy control_sample 9

label_protocol: Total RNA was labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from PBMCs using the miRNeasy® Mini kit (QIAGEN, Germany) according to the protocols recommended by the manufacturer.

tag: cell

value: peripheral blood mononuclear cells

tag: gender

value: Female


title: 15286X031_blastomere_537A_type_IVF_cell_number_2

description: cellnumber 2


title: PBMCs_healthy control_sample 7

source_name: PBMCs_healthy control_sample 7

value: Male


title: [DDB_PD_009]_[DDB32_del_baeR]_[Fed-batch]_[16h]_[R2]


title: [DDB_PD_009]_[DDB32_del_baeR]_[Fed-batch]_[8h]_[R2]


title: 15286X026_blastomere_534B_type_IVF_cell_number_2

description: cellnumber 2


title: PBMCs_healthy control_sample 8

source_name: PBMCs_healthy control_sample 8


title: embryos_18_20_B1_R1_elavneg_flagneg

value: embryo

value: pooled male and female


title: PBMCs_healthy control_sample 6

source_name: PBMCs_healthy control_sample 6


title: S2cells_empty_vector_PJCS25_72h_recovery_Rep4

source_name: s2 cells

growth_protocol: S2R+ cells were maintained at 25℃ in standard Schneider insect medium supplemented with 10% FBS

treatment_protocol: S2 cells underwent transfection in six-well plates utilizing the Effectene transfection reagent (Qiagen; Cat. No. 301425). 300 ng of lN lamba (empty plasmid) and ELAV CDS plasmid were used for transfection per replicate (total no. of replicates = 3). 24 hours after transfection, the cells were provided with fresh medium. 48 hours after transfection, the cells were harvested

value: empty vector

value: s2 cells

value: not determined


title: PBMCs_healthy control_sample 5

source_name: PBMCs_healthy control_sample 5


title: [DDB_PD_009]_[DDB32_del_baeR]_[Fed-batch]_[8h]_[R1]

value: Escherichia coli cells


title: 15286X024_blastomere_533B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X025_blastomere_534A_type_IVF_cell_number_2

description: cellnumber 2


title: embryos_18_20_B1_R1_elavpos_flagpos

value: delta_elav,delta_fne neuron


title: S2cells_empty_vector_PJCS25_72h_recovery_Rep2


title: 15286X023_blastomere_533A_type_IVF_cell_number_2

description: cellnumber 2


title: PBMCs_healthy control_sample 4

source_name: PBMCs_healthy control_sample 4


title: [DDB_PD_009]_[DDB32_del_baeR]_[Batch]_[0h]_[R2]


title: PBMCs_healthy control_sample 3

source_name: PBMCs_healthy control_sample 3


title: 15286X021_blastomere_532A_type_IVF_cell_number_2

description: cellnumber 2


title: PBMCs_healthy control_sample 2

source_name: PBMCs_healthy control_sample 2


title: [DDB_PD_009]_[DDB31_del_arcA]_[Fed-batch]_[15h]_[R2]

source_name: Escherichia coli cells


title: S2cells_ELAV_vector_pVH95_72h_recovery_Rep4

value: ELAV vector


title: 15286X019_blastomere_509A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_009]_[DDB31_del_arcA]_[Fed-batch]_[6h]_[R2]


title: S2cells_empty_vector_PJCS25_72h_recovery_Rep1


title: S2cells_ELAV_vector_pVH95_72h_recovery_Rep2


title: 15286X022_blastomere_532B_type_IVF_cell_number_2

description: cellnumber 2


title: PBMCs_MTB patient_sample 10

source_name: peripheral blood mononuclear cells, MTB patient, sample 10


title: [DDB_PD_009]_[DDB32_del_baeR]_[Batch]_[0h]_[R1]


title: 15286X018_blastomere_508B_type_IVF_cell_number_2

description: cellnumber 2


title: w1118_heads_R2_RR

source_name: head

extract_protocol:
RNA was extracted with Trizol LS (Ambion 10296028) and glycogen (Invitrogen AM9515), according to the manufacturer's protocol.
The libraries were constructed using Illumina TruSeq Stranded Total RNA (Gold): removal of rRNA using biotinylated, target-specific oligos combined with magnetic Ribo-Zero rRNA removal beads. Gold: depletion of both cytoplasmic and mitochondrial rRNA, cDNA prep (random priming, dUTP incorporation for strand specificity), indexed.

treatment_protocol: 2µg RNA per sample were treated with 10 U RNAse R (Applied Biological Materials, E049) - or not, for non-treated controls, in 20 µL, for 20 minutes at 37° C.

value: head

value: adult

value: RNaseR treated


title: PBMCs_MTB patient_sample 8

source_name: peripheral blood mononuclear cells, MTB patient, sample 8


title: [DDB_PD_009]_[DDB31_del_arcA]_[Fed-batch]_[6h]_[R1]


title: PBMCs_MTB patient_sample 7

source_name: peripheral blood mononuclear cells, MTB patient, sample 7


title: [DDB_PD_009]_[DDB31_del_arcA]_[Batch]_[0h]_[R2]


title: 15286X017_blastomere_508A_type_IVF_cell_number_2

description: cellnumber 2

source_name: IVF


title: PBMCs_MTB patient_sample 9

source_name: peripheral blood mononuclear cells, MTB patient, sample 9


title: w1118_heads_R2_NT

value: untreated


title: w1118_heads_R1_RR


title: 15286X016_blastomere_507B_type_IVF_cell_number_2

description: cellnumber 2


title: S2cells_ELAV_vector_pVH95_72h_recovery_Rep3


title: 15286X020_blastomere_509B_type_IVF_cell_number_2

description: cellnumber 2


title: S2cells_empty_vector_PJCS25_72h_recovery_Rep3


title: [DDB_PD_009]_[DDB31_del_arcA]_[Batch]_[0h]_[R1]


title: 15286X015_blastomere_507A_type_IVF_cell_number_2

description: cellnumber 2


title: PBMCs_MTB patient_sample 5

source_name: peripheral blood mononuclear cells, MTB patient, sample 5


title: [DDB_PD_009]_[DDB31_del_arcA]_[Fed-batch]_[15h]_[R1]


title: PBMCs_MTB patient_sample 6

source_name: peripheral blood mononuclear cells, MTB patient, sample 6


title: 15286X014_blastomere_506B_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_006]_[DDB29_del_rpoS]_[Fed-batch]_[15h]_[R1]


title: PBMCs_healthy control_sample 1

source_name: PBMCs_healthy control_sample 1


title: w1118_embryos_14_16_R3_RR

source_name: embryo

value: Embryo - 14-16 h AEL


title: w1118_embryos_14_16_R2_RR


title: 15286X012_blastomere_505B_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: w1118_embryos_14_16_R1_RR


title: 15286X013_blastomere_506A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_006]_[DDB29_del_rpoS]_[Batch]_[0h]_[R2]


title: [DDB_PD_006]_[DDB29_del_rpoS]_[Fed-batch]_[6h]_[R2]_reseq


title: w1118_heads_R1_NT


title: 15286X010_blastomere_504B_type_IVF_cell_number_2

description: cellnumber 2


title: flyhead, wild-type, FLAG IP, R3

data_processing:
RNA-seq data wereanalyzed usingthe RNA-seq module fromsnakePipes(Bhardwaj et al., 2019) with default parameters for --trim , -m “alignment-free,alignment”.
Normalized abundance measures were obtained with DESeq2 for each relevant pairwise comparison (default settings)
Assembly: dm6_ensembl ; D. melanogaster Annotation: ensembl release 96
Supplementary files format and content: rawcounts.tsv.gz: files containing raw counts as created by featureCounts within the snakePipes pipeline
Supplementary files format and content: tsv files: DESeq2 standard results output for all relevant comparisons
Supplementary files format and content: bw files: BigWig files containing normalized counts in RPKM

extract_protocol:
RNA was purified using TRIzol LS Reagent following the manufacturer's protocol. Equal volumes of total RNA from both input and IP samples were utilized to prepare libraries for total RNA-seq.
using TruSeq Stranded Total RNA (Gold): removal of rRNA using biotinylated, target-specific oligos combined with magnetic Ribo-Zero rRNA removal beads, depletion of both cytoplasmic and mitochondrial rRNA, cDNA prep (random priming, dUTP incorporation for strand specificity), indexing

treatment_protocol: Drosophila head powder underwent UV cross-linking, nuclei were isolated, and FLAG-tagged protein-RNA complexes were purified using anti-FLAG M2 magnetic beads.

tag: rip antibody

value: FLAG


title: PBMCs_STB patient_sample 6

source_name: peripheral blood mononuclear cells, STB patient, sample 6

value: peripheral blood mononuclear cells


title: PBMCs_MTB patient_sample 2

source_name: peripheral blood mononuclear cells, MTB patient, sample 2

value: Female


title: PBMCs_MTB patient_sample 4

source_name: peripheral blood mononuclear cells, MTB patient, sample 4

value: Male


title: w1118_embryos_14_16_R1_NT

value: embryo


title: PBMCs_MTB patient_sample 1

source_name: peripheral blood mononuclear cells, MTB patient, sample 1


title: [DDB_PD_006]_[DDB25_del_lsrR]_[Fed-batch]_[15h]_[R2]


title: 15286X009_blastomere_504A_type_IVF_cell_number_2

description: cellnumber 2


title: w1118_embryos_14_16_R2_NT


title: [DDB_PD_006]_[DDB25_del_lsrR]_[Fed-batch]_[15h]_[R2]_reseq


title: [DDB_PD_006]_[DDB25_del_lsrR]_[Fed-batch]_[15h]_[R1]


title: 15286X011_blastomere_505A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_006]_[DDB29_del_rpoS]_[Fed-batch]_[15h]_[R2]


title: flyhead, wild-type, FLAG Input, R3


title: flyhead, wild-type, FLAG IP, R2


title: PBMCs_MTB patient_sample 3

source_name: peripheral blood mononuclear cells, MTB patient, sample 3


title: [DDB_PD_006]_[DDB29_del_rpoS]_[Fed-batch]_[6h]_[R1]


title: 15286X005_blastomere_502A_type_IVF_cell_number_2

description: cellnumber 2


title: [DDB_PD_006]_[DDB29_del_rpoS]_[Fed-batch]_[6h]_[R2]


title: PBMCs_STB patient_sample 5

source_name: peripheral blood mononuclear cells, STB patient, sample 5


title: flyhead, wild-type, FLAG Input, R1


title: PBMCs_STB patient_sample 2

source_name: peripheral blood mononuclear cells, STB patient, sample 2


title: [DDB_PD_006]_[DDB25_del_lsrR]_[Fed-batch]_[6h]_[R1]

source_name: Escherichia coli cells


title: PBMCs_STB patient_sample 1

source_name: peripheral blood mononuclear cells, STB patient, sample 1


title: 15286X007_blastomere_503A_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X008_blastomere_503B_type_IVF_cell_number_2

description: cellnumber 2


title: 15286X004_blastomere_501B_type_IVF_cell_number_2

description: cellnumber 2


title: PBMCs_STB patient_sample 4


title: flyhead, wild-type, FLAG IP, R1

source_name: head


title: PBMCs_STB patient_sample 3

source_name: peripheral blood mononuclear cells, STB patient, sample 3


title: [DDB_PD_006]_[DDB28_del_lsrB]_[Fed-batch]_[15h]_[R2]


title: flyhead, wild-type, ELAV IP, R2

value: ELAV


title: Embryo_GFPCBP_Rpb3_R2

description: Library name: CUT_Tag_87

data_processing:
Sequencing data were uploaded to the Galaxy public server usegalaxy.org. CUT&Tag reads with trimmed adapters (Cutadapt Version 4.9; Nextera transposon sequence CTGTCTCTTATACAC) were mapped to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 (v.2.4.5) in the very sensitive local alignment mode.
Assembly: dm6
Supplementary files format and content: The unstranded BedGraph spike-in normalized files from individual replicates were generated using the BedTools (v.2.30.0) tool “Genome Coverage” using the default parameters. A spike-in scaling factor was calculated as 10^8/[mapped D. virilis reads]. BedGraph files were converted to bigWig format.
Library strategy: CUT&Tag

source_name: Embryo (2-3 hour AEL)

growth_protocol: Drosophila embryos were collected at 25˚C for 1 hour on apple juice agar plates and aged for 2 hours afterwords.

extract_protocol:
Embryos were  dechorionated, rinsed in embryo wash buffer (PBS, 0.1% Triton X-100), and crude nuclear extracts prepared using a glass douncer in Nuclear Extraction buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.5 mM spermidine, 0.1% Triton X-100, 20% glycerol with protease inhibitor cocktail (Roche))90 and centrifuged at 700g for 10 min at 4°C. The nuclear pellets were resuspended in a Nuclear Extraction buffer and mixed with Drosophila virilis nuclei extracted from 3rd instar larvae (approximately 10% of the total number of nuclei). Nuclei corresponding to at least 100 embryos per reaction were incubated with 25 μl of BioMag®Plus Concanavalin A beads (Polysciences) (prepared in Binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1mM CaCl2, and 1 mM MnCl2)) on a nutator for 10 min at 4°C. CUT&Tag was performed according to a published protocol Kaya-Okur, H.S., Janssens, D.H., Henikoff, J.G., Ahmad, K., and Henikoff, S. (2020). Efficient low-cost chromatin profiling with CUT&Tag. Nat Protoc 15, 3264–3283. https://doi.org/10.1038/s41596-020-0373-x. We used the following antibodies: 1 μl rabbit H3K27ac (Abcam, ab4729), 1 μl rabbit H3K18ac (Abcam, ab1191), 1 μl rabbit H3K9ac (Abcam, ab4441), 1.2 μl rabbit CBP, 1 μl TBP (a kind gift from Jim Kadonaga, UCSD), 1.2 μl rabbit anti-BRD4/fs(1)h (a gift of Renato Paro, kindly provided by Nicola Iovino), 1.2 μl rabbit anti-CycT (a kind gift of Kazuko Hanyu-Nakamura), rabbit anti-RNA Polymerase II CTD repeat YSPTSPS (phospho-serine 5) (5SerP) (Abcam, ab5131), rabbit anti-RNA Polymerase II CTD repeat YSPTSPS (phospho-serine 2) (2SerP) (Abcam, ab5095). Following overnight incubation, the experimental procedure was followed using guinea pig α-rabbit antibody (Antibodies online cat. no. ABIN101961) secondary antibodies and purified pA-Tn5 (Protein Science Facility, KI, Stockholm).
Tagmented DNA was PCR amplified using custom i5 and i7 PCR primers and Phusion® High-Fidelity PCR Master Mix with GC Buffer (NEB). PCR conditions were as follows: 72°C for 5 min, 98°C for 30 s, followed by thermocycling (98°C for 10 s and 63°C for 10 s) for 14 cycles and final extension at 72°C for 1 min.  Amplified libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) (1.1:1 bead to sample volume ratio).

treatment_protocol: CRY2CBP embryos were exposed to blue light for 2 hours after 1 hour collection on 25˚C

value: Embryo (2-3 hour AEL)

tag: cut&tag antibody

value: Rpb3 (from Karin Adelman)


title: [DDB_PD_006]_[DDB28_del_lsrB]_[Fed-batch]_[15h]_[R1]

value: Escherichia coli cells


title: [DDB_PD_006]_[DDB28_del_lsrB]_[Fed-batch]_[6h]_[R2]_reseq


title: flyhead, wild-type, FLAG Input, R2


title: Embryo_DeGradCBP_Rpb3_R2

description: Library name: CUT_Tag_85


title: [DDB_PD_006]_[DDB25_del_lsrR]_[Fed-batch]_[6h]_[R2]


title: 15286X001_blastomere_500A_type_IVF_cell_number_2

description: cellnumber 2

source_name: IVF


title: [DDB_PD_006]_[DDB28_del_lsrB]_[Fed-batch]_[6h]_[R2]


title: 15286X002_blastomere_500B_type_IVF_cell_number_2

description: cellnumber 2


title: flyhead, wild-type, ELAV IP, R1


title: Embryo_GFPCBP_Rpb3_R1

description: Library name: CUT_Tag_86


title: Pure culture

city: College Park

first: Sultana

last: Solaiman

state: MD

address: 5001 Campus Drive

institute: US Food and Drug Administration

description:
Library name: Sample 19
pure culture in liquid

data_processing:
Salmon and SAMSA
Assembly: Salmon
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Salmonella enterica subsp. enterica serovar Agona

source_name: bacterial cell

growth_protocol: S. Agona grown in Tryptic Soy Agar and Tryptic Soy Broth

extract_protocol:
RNA was extracted from the freeze-dried cell pellet with Quick-RNA Fungal/Bacterial Miniprep Kit.
RNA libraries were prepared using Zymo Zymo-Seq RiboFree Total RNA Library Kit.

treatment_protocol: Desiccation stress maintaining relative humidity less than 25% in the desiccation chamber

value: bacterial cell

value: WT

value: Pure Culture


title: flyhead, wild-type, ELAV Input, R2

value: head


title: Embryo_DeGradCBP_Rpb3_R1

description: Library name: CUT_Tag_84


title: HiC_L854F

city: Bronx

first: Matanel

last: Yheskel

state: NY

address: 1300 Morris Park

department: Genetics

institute: Albert Einstein College of Medicine

description:
Library name: HiC_L854F
HiC for L854F

data_processing:
Juicer Tools
HiC Explorer
Assembly: dm6
Supplementary files format and content: mcool files

source_name: Brain

extract_protocol:
Arima HiC Kit
Arima Library Prep Kit

value: Brain


title: flyhead, wild-type, ELAV IP, R3


title: flyhead, wild-type, ELAV Input, R1


title: [DDB_PD_006]_[DDB28_del_lsrB]_[Batch]_[0h]_[R2]


title: 24h Post inoculation, biol rep2

description:
Library name: Sample 17
post drying, inoculated, 24h

value: 24 hours post drying


title: flyhead, elav-flag, IP, R4

value: elavFLAG


title: 15286X003_blastomere_501A_type_IVF_cell_number_2

description: cellnumber 2

value: IVF


title: [DDB_PD_006]_[DDB28_del_lsrB]_[Fed-batch]_[6h]_[R1]


title: HiC_JmjC

description:
Library name: HiC_JmjC
HiC for JmjC

value: JmjC


title: HiC_WT

description:
Library name: HiC_WT
HiC for WT


title: flyhead, elav-flag, IP, R3

value: FLAG


title: [DDB_PD_006]_[DDB28_del_lsrB]_[Batch]_[0h]_[R1]


title: 15286X006_blastomere_502B_type_IVF_cell_number_2

description: cellnumber 2


title: flyhead, elav-flag, IP, R2


title: 4h Post inoculation, biol rep2

description:
Library name: Sample 14
post drying, inoculated, 4h

value: 4 hours post drying


title: Embryo_w1118_CBP_R2

value: CBP (rb, Holmqvist et al., 2012)


title: [DDB_PD_006]_[DDB32_del_baeR]_[Fed-batch]_[6h]_[R1]_reseq


title: flyhead, elav-flag, IP, R1


title: [DDB_PD_006]_[DDB32_del_baeR]_[Batch]_[0h]_[R2]


title: Embryo_w1118_CBP_R3


title: 4h Post inoculation, biol rep1

description:
Library name: Sample 13
post drying, inoculated, 4h


title: flyhead, elav-flag, input, R4


title: flyhead, wild-type, ELAV Input, R3


title: 2h Post inoculation, biol rep3

description:
Library name: Sample 12
post drying, inoculated, 2h

value: 2 hours post drying


title: [DDB_PD_006]_[DDB32_del_baeR]_[Fed-batch]_[6h]_[R1]


title: 24h Post inoculation, biol rep3

description:
Library name: Sample 18
post drying, inoculated, 24h


title: Embryo_w1118_H3K9ac_R2

value: H3K9ac (Abcam, ab4441)


title: [DDB_PD_006]_[DDB32_del_baeR]_[Batch]_[0h]_[R1]


title: Embryo_w1118_H3K9ac_R1

value: Embryo (2-3 hour AEL)


title: flyhead, elav-flag, input, R3


title: 24h Post inoculation, biol rep1

description:
Library name: Sample 16
post drying, inoculated, 24h


title: 4h Post inoculation, biol rep3

description:
Library name: Sample 15
post drying, inoculated, 4h


title: 2h Post inoculation, biol rep1

description:
Library name: Sample 10
post drying, inoculated, 2h


title: Embryo_w1118_CBP_R1


title: [DDB_PD_005]_[DDB12_del_qseB]_[Fed-batch]_[15h]_[R1]


title: flyhead, elav-flag, input, R1


title: flyhead, elav-flag, input, R2


title: Embryo_w1118_H3K18ac_R3

value: H3K18ac (Abcam, ab1191)


title: [DDB_PD_005]_[DDB12_del_qseB]_[Fed-batch]_[15h]_[R2]

value: Escherichia coli cells


title: Embryo_w1118_H3K18ac_R2


title: transplantation_spatial_2

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseg coding genes were quantified using Space Ranger's default settings
Assembly: mm10 and EGFP
Supplementary files format and content: filtered_feature_bc_matrix.h5
Library strategy: Spatial Transcriptomics

organism:
Homo sapiens
Mus musculus

source_name: Mus musculus and Homo sapiens chimerism

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to  manufacturer's construction

value: kidney

value: urine-derived SOX9+ epithelial cells


title: [DDB_PD_005]_[DDB12_del_qseB]_[Fed-batch]_[6h]_[R1]_reseq


title: [DDB_PD_005]_[DDB12_del_qseB]_[Fed-batch]_[6h]_[R1]


title: [DDB_PD_005]_[DDB12_del_qseB]_[Fed-batch]_[6h]_[R2]


title: 1h Post inoculation, biol rep3

description:
Library name: Sample 9
post drying, inoculated, 1h

value: bacterial cell

value: WT

value: 1 hour post drying


title: 1h Post inoculation, biol rep1

description:
Library name: Sample 7
post drying, inoculated, 1h


title: Embryo_w1118_H3K18ac_R1


title: [DDB_PD_005]_[DDB12_del_qseB]_[Batch]_[0h]_[R1]


title: Embryo_w1118_H3K27ac_R3

value: H3K27ac (Abcam, ab4729)


title: 2h Post inoculation, biol rep2

description:
Library name: Sample 11
post drying, inoculated, 2h


title: 30mins Post inoculation, biol rep2

description:
Library name: Sample 5
post drying, inoculated, 30 mins

value: 30 mins post drying


title: 6110_HM_CON

city: West Lafayette

first: Jacquelyn

last: Boerman

state: Indiana

address: 270 S. Russell Street

department: Animal Sciences

institute: Purdue University

data_processing:
Trimmomatic v.0.36 (Bolger et al., 2014) was used to remove adapter sequences and nucleotides with poor quality.
The trimmed reads were mapped to theBos taurusreference genome (ARS-UCD1.2) available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: ARS-UCD1.2
Supplementary files format and content: raw counts data for each sample is supplied in an individual text file
Supplementary files format and content: normalized counts data is supplied in a single csv file with each sample labeled.

organism: Bos taurus

source_name: longissimus dorsi muscle

extract_protocol:
The RNeasy Plus Universal Mini Kit (QIAGEN, Germantown, MD)
RNA-sequencing library prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB No. E7775; NEB, Ipswich, MA)
RNAseq, following ribosome depletion with QIAseq FastSelect –rRNA HMR kits (Cat. No./ID: 335376; QIAGEN)

value: longissimus dorsi muscle

tag: group

value: HM

value: CON


title: Embryo_w1118_H3K27ac_R2


title: 6105_LM_BCVFA

value: LM

value: BCVFA


title: [DDB_PD_005]_[DDB15_del_phoB]_[Fed-batch]_[15h]_[R2]


title: [DDB_PD_005]_[DDB12_del_qseB]_[Batch]_[0h]_[R2]


title: Embryo_w1118_H3K27ac_R1


title: Embryo_CBPHAT_CBP_R3

value: CBPHAT FRT19A

value: CBP (rb, Holmqvist et al., 2012)


title: 30mins Post inoculation, biol rep3

description:
Library name: Sample 6
post drying, inoculated, 30 mins


title: 0h Post inoculation, biol rep3

description:
Library name: Sample 3
post drying, inoculated, 0h

value: 0 hour post drying


title: Embryo_CBPHAT_CBP_R2

value: Embryo (2-3 hour AEL)


title: 6087_LM_CON


title: 30mins Post inoculation, biol rep1

description:
Library name: Sample 4
post drying, inoculated, 30 mins


title: 6091_HM_CON


title: 6083_HM_CON


title: 1h Post inoculation, biol rep2

description:
Library name: Sample 8
post drying, inoculated, 1h


title: 6090_LM_BCVFA


title: [DDB_PD_005]_[DDB15_del_phoB]_[Batch]_[0h]_[R2]

value: Escherichia coli cells


title: 0h Post inoculation, biol rep1

description:
Library name: Sample 1
post drying, inoculated, 0h


title: 6085_HM_CON


title: [DDB_PD_005]_[DDB15_del_phoB]_[Fed-batch]_[6h]_[R2]


title: replum-ovule, mutant, rep3

city: Raleigh

first: Albert

last: Tucci

email: atucci@alumni.unc.edu, atucci@ncsu.edu

state: North Carolina

address: 100 Pillsbury Circle

department: Plant and Microbial Biology

institute: North Carolina State University

description: Library name: Mn_RO_6_S12

data_processing:
Trimmomatic, v0.39, ILLUMINACLIP:TruSeq.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36
STAR, v2.7.11b, --readFilesCommand zcat --outSAMattributes NH HI AS nM jM jI --outFilterMismatchNoverReadLmax 0.04 --sjdbGTFfile MguttatusTOL_551_v5.0.gtf --outFilterIntronMotifs RemoveNoncanonical --chimSegmentMin 40 --outSAMmapqUnique 60 --twopassMode Basic --outSAMunmapped Within KeepPairs
picard, v2.25.6, MarkDuplicates
samtools, v1.12, index
featureCounts, v1.22.2
Assembly: Mimulus guttatus TOL v5.0
Supplementary files format and content: CSV containing read counts with rows corresponding to genes in the TOL v5.0 reference genome assembly, and columns corresponding to sample

organism: Erythranthe nudata

source_name: replum and ovule

growth_protocol: An inbreed line (form from ≥ 6 generations of self-fertilization) of Mimulus nudatus (GMR2) was grown in a chamber at 18-hour days, 21°C, 30% relative humidity.

extract_protocol:
Three biological replicates of homozygous Wt and mutant plants were selected for harvesting 6 gynoeciums/plant from opened flowers, and then the valves were removed to collect the ovules attached to the septum. Ovules/septum were immediately collected in cold TRIzol LS (Ambion) for further total RNA isolation. We used the RNeasy Micro Kit (Qiagen) with the following modifications: ovules/septum in cold TRIzol were ground gently with a pellet pestle in a 1.7 mL microcentrifuge tube for 2 min then mixed with 220 uL of chloroform. The solution was then shaken vigorously by hand for 15 s, then incubated for 2 min at room temperature followed by a centrifugation at 12,000g for 15 min at 4 °C to separate phases. Total RNA was isolated according to the manufacturer’s instructions, which includes in column Dnase-I treatment for removal of contaminated DNA.
We generated and sequenced a total of 6 RNA sequencing libraries. The RNA integrity number for all samples >7.3, as determined by an Agilent 2100 Bioanalyzer. Six strand-specific complementary DNA (cDNA) libraries were prepared from approximately 100 ng of total RNA by the North Carolina State University Genomic Science Laboratory (GSL) using a NEB Ultra Directional Library Prep Kit for Illumina then sequenced on an Illumina NovaSeq 6000.

treatment_protocol: Mutant plants showing carpeloid ovules were serendipitously discovered among the population and were selected as pollen donors for further genetic crosses with wild-type (Wt) plants for the generation of F1, and F2 plants. Since the carpeloid ovule phenotype is recessive, and it is only manifested in the F2 generation, 150 F2 plants were screened phenotypic- and genotypically to identify heterozygous/homozygous Wt and mutant lines.

value: replum and ovule

value: mutant


title: [DDB_PD_005]_[DDB15_del_phoB]_[Fed-batch]_[15h]_[R1]


title: Embryo_CBPHAT_H3K9ac_R2

value: H3K9ac (Abcam, ab4441)


title: [DDB_PD_005]_[DDB15_del_phoB]_[Batch]_[0h]_[R1]_reseq


title: Embryo_CBPHAT_H3K9ac_R1


title: [DDB_PD_005]_[DDB15_del_phoB]_[Batch]_[0h]_[R1]


title: Embryo_CBPHAT_H3K18ac_R3

value: H3K18ac (Abcam, ab1191)


title: 6069_LM_BCVFA


title: 6034_HM_BCVFA


title: replum-ovule, mutant, rep2

description: Library name: Mn_RO_5_S11


title: [DDB_PD_005]_[DDB15_del_phoB]_[Fed-batch]_[6h]_[R1]


title: replum-ovule, wildtype, rep3

description: Library name: Mn_RO_3_S9

value: wildtype


title: 0h Post inoculation, biol rep2

description:
Library name: Sample 2
post drying, inoculated, 0h

value: bacterial cell

value: WT


title: 5995_LM_BCVFA

value: longissimus dorsi muscle


title: replum-ovule, mutant, rep1

description: Library name: Mn_RO_4_S10


title: [DDB_PD_005]_[DDB7_WT]_[Fed-batch]_[15h]_[R1]


title: Embryo_CBPHAT_CBP_R1


title: Embryo_CBPHAT_H3K18ac_R2


title: [DDB_PD_005]_[DDB7_WT]_[Fed-batch]_[15h]_[R2]


title: [DDB_PD_005]_[DDB7_WT]_[Fed-batch]_[6h]_[R1]


title: Embryo_CBPHAT_H3K27ac_R3

value: H3K27ac (Abcam, ab4729)


title: Embryo_CBPHAT_H3K18ac_R1


title: 5955_LM_CON

value: CON


title: Embryo_CBPHAT_H3K27ac_R2


title: 6095_LM_BCVFA

value: LM


title: [DDB_PD_005]_[DDB7_WT]_[Fed-batch]_[6h]_[R2]_reseq


title: HNSCC_69_TME

type: protein

city: Brisbane

first: Arutha

last: Kulasinghe

state: QLD

address: 37 kent st

country: Australia

institute: University of Queensland

scan_protocol: The slides were incubated overnight with primary antibodies, which included module antibodies and morphology markers, excluding the nuclei stain. Following the incubation, post-fixation and nuclei staining were conducted to complete the staining process.

data_processing:
Quality control of the data was conducted based on previously established pipeline for spatial data (standR, Liu et al, Nucleic Acids Research. 2023) using the probe normalised protein (probeQC) counts. Low expressing proteins with less than 5 counts per sample in more than 90% of the samples were removed. Sample QC filters out low expression FOVs based on protein expression depth (> 100,000 per FOW) and nuclei count (> 100 cells per FOV). The filtered data is normalised using the "relative log expression” (RLE) scaling factor method. The normalised/scaled log2-transformed counts per million (logCPM) of the data is provided as inputs.
The "relative log expression” (RLE) normalised log2-transformed counts per million (logCPM) of the the QC filtered data is provided

molecule: protein

source_name: biopsy

label_protocol: FFPE tissue sections were prepared for GeoMX DSP profiling. Briefly, tissue sections were mounted on VWR Superfrost Plus Micro slides (cat# 48311-703) were baked overnight at 60°C.After baking, the slides underwent deparaffinization, rehydration, and antigen retrieval to prepare the tissue for staining.

extract_protocol: total protein

treatment_protocol: Samples were fixed in formalin and paraffin embedded (FFPE) for GeoMx processing

tag: age

value: M

tag: tissue location

value: Tongue

tag: case

value: 1 OC

tag: tumor stage

tag: deceased

value: UK

tag: tumor stage (general)

value: early


title: Embryo_CBPHAT_H3K27ac_R1

value: Embryo (2-3 hour AEL)

value: CBPHAT FRT19A


title: replum-ovule, wildtype, rep1

description: Library name: Mn_RO_1_S7

value: replum and ovule


title: 5954_HM_CON

value: HM


title: [DDB_PD_005]_[DDB7_WT]_[Fed-batch]_[6h]_[R2]

extract_protocol:
All transcriptome samples were collected and prepared in biological duplicates, whereby either 2 ml of culture (low cell density culture, batch phase) or 0.5 ml of culture (high cell density culture, fed batch phase) was added to 6 ml of Qiagen RNA-protect Bacteria Reagent immediately after sample collection. This solution was then vortexed for 30 seconds, incubated at room temperature for 5 minutes, and then centrifuged. The supernatant was then removed and the cell pellet was stored at -80° C. The RNeasy Mini Kit (Qiagen) was used to extract and purify RNA from the cell pellets per vendor protocol, including on-columns DNase treatment for 30 minutes at room temperature. RNA was quantified using qubit fluorometer (Thermofisher) and integrity was assessed using fragment analyzer (Agilent Technologies).
Ribosomal RNA was removed using QIAseq FastSelect –5S/16S/23S kit (Qiagen). Sequencing libraries were prepared with the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa Biosystems) and assessed using fragment analyzer (Agilent Technologies). The libraries were then subjected to paired end sequencing on Illumina Nextseq using Nextseq Mid Output kit (Illumina) with a read length of 150 bp.

tag: cell type

value: Escherichia coli cells

tag: strain


title: HNSCC_69_TUMOUR

tag: Sex


title: HNSCC_68_TME

value: F

value: 2 OC

value: Y

value: Advanced


title: 5977_LM_CON

tag: tissue

value: longissimus dorsi muscle

tag: treatment


title: replum-ovule, wildtype, rep2

description: Library name: Mn_RO_2_S8

tag: genotype

value: wildtype


title: Embryo_GFPCBP_TBP_R1

value: TBP (rb, from Jim Kadonaga)


title: [DDB_PD_005]_[DDB7_WT]_[Batch]_[0h]_[R1]


title: [DDB_PD_005]_[DDB7_WT]_[Batch]_[0h]_[R2]


title: 5940_HM_CON

value: CON


title: 5924_LM_CON

value: LM


title: 5935_LM_CON


title: Embryo_GFPCBP_TBP_R2


title: Embryo_GFPCBP_pSer5_R3

value: 5SerP (Abcam, ab5131)


title: HNSCC_67_TUMOUR

value: M

value: Tongue

value: 3 OC

value: N


title: HNSCC_67_TME

value: early


title: [DDB_PD_005]_[DDB16_WT]_[Fed-batch]_[15h]_[R2]


title: Embryo_GFPCBP_pSer5_R1

value: Embryo (2-3 hour AEL)


title: Embryo_GFPCBP_pSer5_R2


title: 5915_HM_BCVFA

value: HM

value: BCVFA


title: HNSCC_66_TME

value: 4 OC


title: [DDB_PD_006]_[DDB29_del_rpoS]_[Batch]_[0h]_[R1]

value: Escherichia coli cells


title: [DDB_PD_005]_[DDB16_WT]_[Fed-batch]_[15h]_[R1]


title: [DDB_PD_005]_[DDB16_WT]_[Fed-batch]_[6h]_[R1]


title: 5960_HM_BCVFA


title: HNSCC_68_TUMOUR

value: F

value: 2 OC

value: Y

value: Advanced


title: Embryo_GFPCBP_CBP_R2

value: CBP (rb, Holmqvist et al., 2012)


title: [DDB_PD_005]_[DDB16_WT]_[Fed-batch]_[6h]_[R2]


title: Embryo_GFPCBP_CBP_R1


title: 5884_HM_CON

value: longissimus dorsi muscle

value: CON


title: 5910_HM_CON


title: HNSCC_66_TUMOUR

value: M


title: [DDB_PD_005]_[DDB16_WT]_[Batch]_[0h]_[R2]


title: 5919_HM_CON


title: HNSCC_65_TME

value: Tongue

value: 5 OC


title: 5747_HM_BCVFA


title: [DDB_PD_005]_[DDB16_WT]_[Batch]_[0h]_[R1]_reseq


title: 5777_LM_CON

value: LM


title: HNSCC_65_TUMOUR


title: Embryo_GFPCBP_H3K18ac_R1

value: H3K18ac (Abcam, ab1191)


title: Embryo_GFPCBP_H3K18ac_R2

value: Embryo (2-3 hour AEL)


title: HNSCC_64_TME

value: 6 OC

value: UK


title: 5709_HM_BCVFA

value: HM

value: BCVFA


title: Embryo_GFPCBP_H3K27ac_R2

value: H3K27ac (Abcam, ab4729)


title: HNSCC_64_TUMOUR


title: 5676_HM_BCVFA


title: [DDB_PD_005]_[DDB25_del_lsrR]_[Batch]_[0h]_[R2]

value: Escherichia coli cells


title: [DDB_PD_005]_[DDB25_del_lsrR]_[Batch]_[0h]_[R1]


title: HNSCC_63_TME

value: 7 OC


title: Embryo_DeGradCBP_TBP_R2

value: TBP (rb, from Jim Kadonaga)


title: HNSCC_63_TUMOUR

value: Advanced


title: [DDB_PD_004]_[DDB11_del_qseC]_[Fed-batch]_[15h]_[R1]


title: Embryo_DeGradCBP_TBP_R1


title: 5609_LM_BCVFA

value: longissimus dorsi muscle


title: Embryo_GFPCBP_H3K27ac_R1


title: 5610_HM_CON

value: CON


title: HNSCC_62_TME

value: M

value: 8 OC

value: Y


title: [DDB_PD_005]_[DDB16_WT]_[Batch]_[0h]_[R1]


title: Embryo_DeGradCBP_pSer5_R2

value: 5SerP (Abcam, ab5131)


title: HNSCC_62_TUMOUR

value: Tongue


title: [DDB_PD_004]_[DDB11_del_qseC]_[Fed-batch]_[6h]_[R1]


title: Embryo_DeGradCBP_pSer5_R1

value: Embryo (2-3 hour AEL)


title: 2237_HM_CON


title: HNSCC_61_TME

value: F

value: 9 OC

value: N

value: early


title: [DDB_PD_004]_[DDB11_del_qseC]_[Fed-batch]_[6h]_[R2]


title: Embryo_DeGradCBP_CBP_R2

value: CBP (rb, Holmqvist et al., 2012)


title: 2236_HM_CON

value: HM


title: HNSCC_61_TUMOUR


title: [DDB_PD_004]_[DDB11_del_qseC]_[Batch]_[0h]_[R2]

value: Escherichia coli cells


title: HNSCC_60_TME

value: 10 OC


title: [DDB_PD_004]_[DDB11_del_qseC]_[Batch]_[0h]_[R1]


title: Embryo_DeGradCBP_CBP_R1


title: 2231_HM_CON


title: Embryo_DeGradCBP_H3K18ac_R1

value: H3K18ac (Abcam, ab1191)


title: Embryo_DeGradCBP_H3K18ac_R2


title: HNSCC_59_TME

value: 11 OC

value: Advanced


title: 2230_LM_CON

value: longissimus dorsi muscle

value: LM

value: CON


title: Embryo_DeGradCBP_H3K27ac_R2

value: H3K27ac (Abcam, ab4729)


title: 2240_LM_CON


title: HNSCC_60_TUMOUR

value: M

value: Tongue

value: Y


title: [DDB_PD_004]_[DDB10_del_qseB]_[Fed-batch]_[15h]_[R1]


title: 2223_HM_BCVFA

value: BCVFA


title: [DDB_PD_004]_[DDB10_del_qseB]_[Fed-batch]_[15h]_[R2]


title: HNSCC_59_TUMOUR


title: [DDB_PD_004]_[DDB10_del_qseB]_[Fed-batch]_[6h]_[R1]


title: [DDB_PD_004]_[DDB11_del_qseC]_[Fed-batch]_[15h]_[R2]


title: 2210_LM_CON


title: Embryo_DeGradCBP_H3K27ac_R1

value: Embryo (2-3 hour AEL)


title: 2218_LM_BCVFA


title: 2204_LM_BCVFA


title: HNSCC_57_TME

value: 13 OC


title: [DDB_PD_004]_[DDB10_del_qseB]_[Fed-batch]_[6h]_[R2]


title: [DDB_PD_004]_[DDB10_del_qseB]_[Batch]_[0h]_[R2]


title: 2201_HM_BCVFA


title: HNSCC_58_TME

value: F

value: 12 OC

value: N


title: HNSCC_58_TUMOUR


title: HNSCC_56_TME

value: 14 OC


title: [DDB_PD_004]_[DDB13_del_kdpE]_[Fed-batch]_[6h]_[R2]

value: Escherichia coli cells


title: Embryo_CRY2CBP_Dark_CycT_R2

value: CRY2nej;his2avRFP III

value: Dark

value: CycT (rb, Hanyu-Nakamura et al. 2008)


title: 2203_LM_BCVFA

value: longissimus dorsi muscle

value: LM


title: [DDB_PD_004]_[DDB13_del_kdpE]_[Fed-batch]_[15h]_[R2]


title: Embryo_CRY2CBP_Dark_BRD4_R2

value: BRD4 (rb, Kockmann et al., 2013)


title: Embryo_CRY2CBP_Dark_pSer5_PolII_R3

value: 5SerP (Abcam, ab5131)


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep7

data_processing:
RNA-seq reads were trimmed and filtered for quality using BBDuk and FastQC (version 0.10.1).
Processed reads were aligned using TopHat2 version 2.1.0 (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant),
and counts for each transcript were generated using ‘Get datasets’ (https://metacpan.org/pod/distribution/Bio-ToolBox/scripts/get_datasets.pl).
Assembly: Bostau7
Supplementary files format and content: FPKM table stringtie de novo assembly of transcriptome

source_name: embryo

growth_protocol: IVF or SCNT embryos were grown in SOF media and cultered under oil at 38.5C

extract_protocol:
SMART-seq lysis buffer
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio, catalong #634890). cDNA was tagmented using Nextera XT DNA Library Preparation Kit (Illumina catalog #FC-131-1024) and libraries were amplified by PCR

value: embryo

tag: cell line

value: 8-cell stage

value: embryo culture


title: [DDB_PD_004]_[DDB13_del_kdpE]_[Batch]_[0h]_[R1]


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep5


title: Embryo_CRY2CBP_Dark_BRD4_R1

value: Embryo (2-3 hour AEL)


title: HNSCC_56_TUMOUR

value: M

value: Tongue

value: Y

value: Advanced


title: [DDB_PD_004]_[DDB14_del_basS]_[Fed-batch]_[15h]_[R1]


title: Embryo_CRY2CBP_Dark_pSer2_PolII_R1

value: pSer2 (Abcam, ab5095)


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep4


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep8


title: HNSCC_57_TUMOUR

value: 13 OC


title: HNSCC_55_TUMOUR

value: F

value: 15 OC


title: HNSCC_55_TME


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep6


title: [DDB_PD_004]_[DDB13_del_kdpE]_[Batch]_[0h]_[R2]

value: Escherichia coli cells


title: [DDB_PD_004]_[DDB14_del_basS]_[Fed-batch]_[15h]_[R2]


title: [DDB_PD_004]_[DDB14_del_basS]_[Fed-batch]_[6h]_[R1]


title: HNSCC_53_TME

value: Oral cavity

value: 17 OC


title: Embryo_CRY2CBP_Dark_pSer5_PolII_R1

value: CRY2nej;his2avRFP III

value: Dark


title: [DDB_PD_004]_[DDB13_del_kdpE]_[Fed-batch]_[15h]_[R1]


title: Embryo_CRY2CBP_Dark_pSer2_PolII_R2


title: HNSCC_54_TME

value: 16 OC


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep2

value: embryo

value: 8-cell stage


title: Embryo_CRY2CBP_Dark_CBP_R2

value: Embryo (2-3 hour AEL)

value: CBP (rb, Holmqvist et al., 2012)


title: Embryo_CRY2CBP_Dark_CBP_R1


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep1

value: embryo culture


title: BosTaurus_parthenotes_8cell_rep11


title: HNSCC_54_TUMOUR

value: Y


title: HNSCC_53_TUMOUR

value: M

value: Advanced


title: [DDB_PD_004]_[DDB14_del_basS]_[Batch]_[0h]_[R1]


title: Embryo_CRY2CBP_Dark_pSer5_PolII_R2

value: 5SerP (Abcam, ab5131)


title: HNSCC_52_TUMOUR

value: 19 OC

value: early


title: HNSCC_52_TME


title: Embryo_CRY2CBP_Dark_H3K9ac_R1

value: H3K9ac (Abcam, ab4441)


title: BosTaurus_parthenotes_8cell_rep10


title: BosTaurus_parthenotes_8cell_rep9


title: Embryo_CRY2CBP_Dark_H3K18ac_R2

value: H3K18ac (Abcam, ab1191)


title: HNSCC_51_TME

value: Oral cavity

value: 20 OC

value: UK


title: Embryo_CRY2CBP_Dark_H3K18ac_R3

value: CRY2nej;his2avRFP III

value: Dark


title: [DDB_PD_003]_[DDB12_del_qseF]_[Fed-batch]_[21h]_[R1]

value: Escherichia coli cells


title: Embryo_CRY2CBP_Dark_H3K18ac_R1

value: Embryo (2-3 hour AEL)


title: [DDB_PD_003]_[DDB12_del_qseF]_[Fed-batch]_[21h]_[R2]


title: [DDB_PD_004]_[DDB14_del_basS]_[Fed-batch]_[6h]_[R2]


title: Embryo_CRY2CBP_Dark_H3K9ac_R2


title: [DDB_PD_003]_[DDB12_del_qseF]_[Fed-batch]_[6h]_[R1]


title: HNSCC_50_TME

value: 21 OC

value: N


title: Embryo_CRY2CBP_Dark_H3K27ac_R3

value: H3K27ac (Abcam, ab4729)


title: BosTaurus_parthenotes_8cell_rep6

value: embryo

value: 8-cell stage

value: embryo culture


title: [DDB_PD_003]_[DDB12_del_qseF]_[Fed-batch]_[6h]_[R2]


title: HNSCC_50_TUMOUR

value: M

value: Advanced


title: [DDB_PD_004]_[DDB14_del_basS]_[Batch]_[0h]_[R2]


title: BosTaurus_parthenotes_8cell_rep5


title: Embryo_CRY2CBP_Dark_H3K27ac_R2


title: [DDB_PD_003]_[DDB12_del_qseF]_[Batch]_[0h]_[R2]


title: BosTaurus_parthenotes_8cell_rep4


title: HNSCC_49_TME

value: 22 OC


title: [DDB_PD_004]_[DDB13_del_kdpE]_[Fed-batch]_[6h]_[R1]


title: [DDB_PD_003]_[DDB12_del_qseF]_[Batch]_[0h]_[R1]


title: Embryo_CRY2CBP_BlueLight_CycT_R2

value: Blue light

value: CycT (rb, Hanyu-Nakamura et al. 2008)


title: HNSCC_51_TUMOUR

value: Oral cavity

value: 20 OC

value: early


title: BosTaurus_parthenotes_8cell_rep3


title: [DDB_PD_003]_[DDB15_del_phoB]_[Fed-batch]_[21h]_[R1]


title: BosTaurus_parthenotes_8cell_rep7


title: Embryo_CRY2CBP_BlueLight_CycT_R1

value: CRY2nej;his2avRFP III


title: BosTaurus_parthenotes_8cell_rep2


title: BosTaurus_parthenotes_8cell_rep8


title: Embryo_CRY2CBP_BlueLight_BRD4_R2

value: BRD4 (rb, Kockmann et al., 2013)


title: [DDB_PD_003]_[DDB15_del_phoB]_[Fed-batch]_[21h]_[R2]

value: Escherichia coli cells


title: HNSCC_48_TUMOUR

value: F

value: 23 OC

value: UK


title: [DDB_PD_003]_[DDB15_del_phoB]_[Fed-batch]_[6h]_[R1]


title: HNSCC_47_TME

value: 24 OC

value: Y


title: HNSCC_47_TUMOUR


title: BosTaurus_parthenotes_8cell_rep1

value: embryo

value: 8-cell stage

value: embryo culture


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep8


title: Embryo_CRY2CBP_BlueLight_BRD4_R1

value: Embryo (2-3 hour AEL)


title: [DDB_PD_003]_[DDB15_del_phoB]_[Fed-batch]_[6h]_[R2]


title: Embryo_CRY2CBP_BlueLight_pSer2_PolII_R2

value: Blue light

value: pSer2 (Abcam, ab5095)


title: HNSCC_49_TUMOUR

value: M

value: Oral cavity

value: 22 OC

value: N

value: Advanced


title: HNSCC_46_TME

value: 25 OC

value: early


title: [DDB_PD_003]_[DDB15_del_phoB]_[Batch]_[0h]_[R2]

value: Escherichia coli cells


title: Embryo_CRY2CBP_BlueLight_pSer2_PolII_R1

value: CRY2nej;his2avRFP III


title: HNSCC_46_TUMOUR


title: Embryo_CRY2CBP_BlueLight_pSer5_PolII_R3

value: 5SerP (Abcam, ab5131)


title: HNSCC_48_TME

value: F

value: 23 OC

value: UK


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep6

value: embryo

value: 8-cell stage

value: embryo culture


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[21h]_[R2]_reseq


title: HNSCC_45_TUMOUR

value: 26 OC


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep4


title: HNSCC_43_TME

value: 29 OC


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep7


title: HNSCC_45_TME

value: M

value: Oral cavity


title: Embryo_CRY2CBP_BlueLight_pSer5_PolII_R2

value: Embryo (2-3 hour AEL)

value: Blue light


title: Embryo_CRY2CBP_BlueLight_CBP_R3

value: CBP (rb, Holmqvist et al., 2012)


title: HNSCC_43_TUMOUR

value: N

value: early


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep2


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[21h]_[R1]

value: Escherichia coli cells


title: Embryo_CRY2CBP_BlueLight_pSer5_PolII_R1

value: CRY2nej;his2avRFP III

value: 5SerP (Abcam, ab5131)


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[21h]_[R1]_reseq


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[21h]_[R2]


title: Embryo_CRY2CBP_BlueLight_CBP_R2


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep3


title: [DDB_PD_003]_[DDB15_del_phoB]_[Batch]_[0h]_[R1]


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep1


title: IP-shNC-2

first: liu

last: cihang

address: Xueyuan Road

institute: Peking University Health Science Center

data_processing:
Raw reads in fastq format were first processed using cutadapt (v1.12).Clean reads were obtained by trimming adapters, removing sequences containing unknown bases more than 5% , low quality bases and less than 18nt. All the downstream analyses were based on the clean reads.
The reference genome and gene model annotation files were downloaded directly from the genome website. The reference genome index was built using BWA(v0.7.13), and paired-end clean reads were aligned to the reference genome(version hg38) using BWA(v0.7.13).
Peak calling was performed using MACS (v1.4.2) with default parameters. The p-value could be adjusted based on the total clean reads. The location and length of peaks could be obtained, which would be used in the downstream analyses.
MAnorm was used to identify unique peaks and common peaks between different samples .
Peak-associated genes were calculated by in-house perl script with the criterion that the gene body and its 2000bp upstream or downstream had overlap with peaks.
Assembly: hg38
Supplementary files format and content: Supplementary Table 1 Differentially enriched common target genes simultaneously regulated by DNMT1 and NSun2 obtained from MeRIP-seq analysis
Supplementary files format and content: Supplementary Table 2 Statistics for FPKM of input genes in group NC
Supplementary files format and content: Supplementary Table 3 Statistics for FPKM of input genes in group SiDNMT1.
Supplementary files format and content: Supplementary Table 4 Increasingly enriched candidate genes used for GO analysis by DAVID.

growth_protocol: U2OS cells were cultured in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1% antibiotics, at 37 °C in 5% CO2.

extract_protocol:
lnput and co-IP RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: NSun2 mutant plasmid was transfected into U6 and shDNMT1 U2OS cells.

value: Osteosarcoma

value: WT

value: co-immunoprecipitated RNA by NSun2 mutant


title: BosTarus_x_BosIndicus_F1-8cell-IVF-SMARTseq-rep5

value: embryo

value: 8-cell stage


title: HNSCC_42_TUMOUR

value: 30 OC

value: UK


title: [DDB_PD_003]_[DDB7_RiboRid]_[Fed-batch]_[21h]_[R2]

data_processing:
First, raw read trimming was performed using Trim Galore with default options, followed by FastQC on the trimmed reads. Next, reads were aligned to the E. coli K-12 MG1655 reference genome (NC_000913.3) using Bowtie. The read direction was inferred using RSeQC. Read counts were generated using featureCounts. All quality control metrics were compiled using MultiQC. Finally, the expression dataset was reported in units of log-transformed transcripts per million (log(TPM).
Assembly: Reference genome E. coli MG1655 (NC_000913.3)
Supplementary files format and content: Raw data files and comma-delimited text file reporting logtpm values for each sample


title: Embryo_CRY2CBP_BlueLight_H3K9ac_R2

value: H3K9ac (Abcam, ab4441)


title: Embryo_CRY2CBP_BlueLight_CBP_R1


title: IP-shNC-1


title: HNSCC_41_TME

value: M

value: Pharynx

value: Y

value: Advanced


title: [DDB_PD_003]_[DDB7_RiboRid]_[Fed-batch]_[21h]_[R1]


title: Embryo_CRY2CBP_BlueLight_H3K9ac_R1

value: Embryo (2-3 hour AEL)

value: Blue light


title: Embryo_CRY2CBP_BlueLight_H3K18ac_R3

value: H3K18ac (Abcam, ab1191)


title: IP-shDNMT1-1

value: DNMT1 knockdown


title: HNSCC_40_TME

value: early


title: [DDB_PD_003]_[DDB7_NEB]_[Fed-batch]_[21h]_[R1]

value: Escherichia coli cells


title: HNSCC_40_TUMOUR


title: IP-shDNMT1-2

value: Osteosarcoma


title: [DDB_PD_003]_[DDB7_NEB]_[Fed-batch]_[21h]_[R2]


title: [DDB_PD_003]_[DDB7_WT]_[Fed-batch]_[21h]_[R2]


title: HNSCC_42_TME

value: Oral cavity

value: N


title: [DDB_PD_003]_[DDB7_WT]_[Fed-batch]_[21h]_[R1]


title: Embryo_CRY2CBP_BlueLight_H3K18ac_R2

value: CRY2nej;his2avRFP III


title: HNSCC_41_TUMOUR


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[6h]_[R2]_reseq


title: Embryo_CRY2CBP_BlueLight_H3K18ac_R1


title: input shDNMT1

value: no


title: Embryo_CRY2CBP_BlueLight_H3K27ac_R2

value: H3K27ac (Abcam, ab4729)


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[6h]_[R2]


title: HNSCC_39_TUMOUR


title: Embryo_CRY2CBP_BlueLight_H3K27ac_R3


title: input shNC

value: WT


title: Embryo_CRY2CBP_BlueLight_H3K27ac_R1


title: HNSCC_38_TME

value: M


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[6h]_[R1]_reseq


title: HNSCC_38_TUMOUR

value: Pharynx


title: Embryo_GFPCBP_PROseq_R2

data_processing:
Sequencing data were uploaded to the Galaxy public server usegalaxy.org. qPRO-seq reads were mapped after trimming adapters to the Drosophila melanogaster (dm6) genome assembly using Bowtie2 (v.2.4.5) with the very sensitive end-to-end analysis mode. Then the bam files were deduplicated using UMI.
Assembly: dm6
Supplementary files format and content: Aligned reads were annotated to genes using FeatureCounts 2.0 in a stranded mode and normalizied by spike-in and gene length.
Supplementary files format and content: Strand-separated spike-in normalized BedGraph coverage files from individual replicates were generated using the BedTools (v.2.30.0) tool “Genome Coverage” using the default parameters. A spike-in scaling factor was calculated as 10^8/[mapped D. virilis reads]. Strand-separated BedGraph were converted to bigWig format.
Library strategy: PRO-seq

source_name: Embryo 2-3h (nc14)

extract_protocol:
A variant of PRO-seq, qPRO-seq was performed on CBPdeGrad and CBPCRY2 embryos collected for one hour and aged for a further two hours (2–3 h AEL). Collected embryos were dechorionated in dilute bleach and rinsed thoroughly in embryo wash buffer (PBS, 0.1% Triton X-100) before being flash-frozen in liquid nitrogen and stored at −80°C. qPRO-seq was performed as previously described Judd, J., et al., 2020, bioRxiv, https://doi.org/10.1101/2020.05.18.102277. Briefly, embryos were resuspended in cold nuclear extraction buffer A (10 mM Tris-HCl pH 7.5, 300 mM sucrose, 10 mM NaCl, 3 mM CaCl2, 2 mM MgCl2, 0.1% Triton X, 0.5 mM DTT, protease inhibitor cocktail (Roche) and 4 µ/ml RNase inhibitor (SUPERaseIN, Ambion)), transferred to a dounce homogenizer and dounced with the loose pestle for 20 strokes. To remove large debris, the suspension was passed through Miracloth tissue (Merck, 475855-1R) followed by douncing with a tight pestle for 10 strokes. Nuclei were pelleted at 700g for 10 min at 4°C and washed twice in buffer A and once in buffer D (10 mM Tris-HCl pH 8, 25% glycerol, 5mM MgAc2, 0.1 mM EDTA, 0.5 mM DTT). For qPRO-seq, we used 2 million nuclei resuspended in buffer D and stored at −80°C. For further spike-in normalization, they were mixed with Drosophila virilis embryo nuclei (2% of the total number of nuclei). Nuclear run-on assays were performed in biological duplicatesusing all four biotinylated dNTPs  exactly as previously described  in Judd, J., et al., 2020, bioRxiv, https://doi.org/10.1101/2020.05.18.102277.
Libraries were produced as descibed in Judd, J., et al., 2020, bioRxiv, https://doi.org/10.1101/2020.05.18.102277. We have skipped preCR step and performed amplification with 15 cycles based on test amplification. Libraries were PAGE purified before sequencing.

value: Embryo 2-3h (nc14)


title: HNSCC_39_TME


title: HNSCC_37_TME

value: UK


title: [DDB_PD_003]_[DDB7_RiboRid]_[Fed-batch]_[6h]_[R1]


title: HNSCC_36_TME


title: Embryo_DeGradCBP_PROseq_R2


title: B-cells from young, Rps15 wildtype mouse, biological replicate 2

city: Boston

first: Catherine

middle: J.

last: Wu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
Library name: ATGTCA_Wt2
Mice aged 3-6 months

data_processing:
Adapters were removed using fastx_clipper from FASTX-Toolkit (Ribo-seq)
UMIs were removed using umi_tools (Ribo-seq)
Ribosomal RNA and tRNA were removed using Bowtie version 1.0.05 (Ribo-seq)
Transcriptomic alignment with STAR (v2.7.0a) (--alignIntronMin 20 --alignIntronMax 100000 --outFilterMismatchNmax 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --twopassMode Basic)
Ribo-seq reads were further aligned to padded (± 20 nucleotides) canonical protein-coding ORFs using STAR (v2.7.0a) (-alignIntronMin 2 --alignIntronMax 1 --outFilterMismatchNmax ---scoreDelOpen -10000 --scoreInsOpen -10000 1 --outFilterType BySJout --outFilterMismatchNoverLmax 0.04 --twopassMode Basic)
RSEM (v1.2.31) was used for transcript and ORF expression quantitation.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited quantitation files show raw RPF or RNA transcript counts

organism: Mus musculus

source_name: B-cells

extract_protocol:
Spleens or femurs of mice were mechanically dissociated into a single cell suspension. B-cells were negatively selected using the MACS Mouse B cell Isolation Kit (Miltenyi Biotec, #130-090-862). Total RNA was extracted with Qiagen RNAeasy kits.
200 ng per sample was used as input into an automated variant of the Illumina TruSeq Stranded mRNA Sample Preparation Kit (which preserves strand orientation of the RNA transcript). Oligo dT beads were used to enrich mRNA from the total RNA sample, followed by heat fragmentation and cDNA synthesis. The resultant 400 bp cDNA underwent dual-indexed library preparation, including ‘A’ base addition, adapter ligation using P7 adapters, and PCR enrichment using P5 adapters.

value: B-cells


title: B-cells from young, Rps15 wildtype mouse, biological replicate 3

description:
Library name: CCGTCC_Wt3
Mice aged 3-6 months


title: Embryo_CRY2CBP_Dark_CycT_R1

value: Embryo (2-3 hour AEL)

value: Dark

value: CycT (rb, Hanyu-Nakamura et al. 2008)


title: B-cells from young, Rps15 wildtype mouse, biological replicate 1

description:
Library name: AGTCAA_Wt1
Mice aged 3-6 months


title: [DDB_PD_003]_[DDB7_Qiagen]_[Fed-batch]_[6h]_[R1]


title: [DDB_PD_003]_[DDB7_Qiagen]_[Fed-batch]_[6h]_[R2]


title: Embryo_DeGradCBP_PROseq_R1


title: BosTarus_x_BosIndicus_F1_late8cell-IVF-SMARTseq-rep3

value: embryo

value: 8-cell stage

value: embryo culture


title: IE-F-H-x20 3

city: Maebashi

first: Izuki

last: Amano

state: Gunma

address: 3-9-22 Showa-machi

department: Department of Integrative Physiology, Graduate School of Medicine

country: Japan

institute: Gunma University

description:
Gene expression from 20-fold iodine excess group
IE-F-06

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

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

source_name: hippocamupus, 20-fold iodine

label_protocol: For cRNA amplification and labeling, Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) were used following the manufacter’s instructions.

extract_protocol: Total RNA was extracted from dorsal hippocampus after behavioral test battery using the RNeasy Lipid Tissue Mini kit (QIAGEN, Hilden, Germany) followed by manufacturer’s protocol.

value: hippocampus

tag: gender

value: female

value: 20-fold iodine


title: HNSCC_36_TUMOUR

value: early


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 4

description:
Library name: ATTCCT_Hom4
Mice aged 3-6 months


title: Embryo_CRY2CBP_Dark_PROseq_R2

value: CRY2nej;his2avRFP III


title: IE-F-H-x20 2

description:
Gene expression from 20-fold iodine excess group
IE-F-05


title: HNSCC_35_TME

value: N


title: [DDB_PD_003]_[DDB7_RiboRid]_[Fed-batch]_[6h]_[R2]

first: Felix

last: Beulig

address: Kemitorvet 220

institute: Novo Nordisk Center for Biosustainability

value: Escherichia coli cells


title: [DDB_PD_003]_[DDB7_NEB]_[Fed-batch]_[6h]_[R2]


title: [DDB_PD_003]_[DDB7_RiboZero]_[Fed-batch]_[6h]_[R1]


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 3

description:
Library name: ACTGAT_Hom3
Mice aged 3-6 months


title: IE-F-H-C 3

description:
Gene expression from control group
IE-F-03

source_name: hippocamupus, control

value: control


title: Embryo_CRY2CBP_Dark_PROseq_R1

value: Embryo 2-3h (nc14)


title: Embryo_GFPCBP_PROseq_R1


title: HNSCC_37_TUMOUR

value: M

value: Pharynx

value: UK


title: HNSCC_34_TME

value: Y


title: Embryo_CRY2CBP_BlueLight_PROseq_R2

value: Blue light


title: B-cells from young, Rps15-S138F homozygous mutant mouse, biological replicate 1

description:
Library name: CGTACG_Hom1
Mice aged 3-6 months

value: B-cells


title: HNSCC_35_TUMOUR


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 3

description:
Library name: GTTTCG_Het3
Mice aged 3-6 months


title: Embryo_CRY2CBP_BlueLight_PROseq_R1


title: [DDB_PD_003]_[DDB7_WT]_[Fed-batch]_[6h]_[R2]

source_name: Escherichia coli cells


title: HNSCC_33_TME

value: F

value: Advanced


title: [DDB_PD_003]_[DDB7_WT]_[Batch]_[0h]_[R2]


title: Myometrium from fibroid patient (MyoF), patient NW63

type: genomic

city: Grand Rapids

first: Jose

middle: M

last: Teixeira

state: MI

address: 400 Monroe Ave NW

department: Ob/Gyn

institute: Michigan State University

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw idat files were processed into beta values in R  using the openSesame pipeline from Sesame (version  1.23.6). Beta values were then batch corrected using ChAMP (version 2.36.0)
Batch corrected beta values using ChAMP, following initial openSesame pipeline using Sesame.

label: Cy3 and Cy5

source_name: myometrium

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using colums from the Qiagen DNEasy Blood and Tissue kit

value: myometrium

tag: race/ethnicity

value: AA

value: Not Available

tag: batch


title: Myometrium from fibroid patient (MyoF), patient NW206


title: IE-F-H-C 2

description:
Gene expression from control group
IE-F-02

value: hippocampus

value: female


title: HNSCC_34_TUMOUR

value: early


title: HNSCC_33_TUMOUR


title: Myometrium from fibroid patient (MyoF), patient NW1


title: [DDB_PD_003]_[DDB7_NEB]_[Fed-batch]_[6h]_[R1]

city: Kgs. Lyngby

value: Escherichia coli cells


title: B-cells from leukemic, Rps15 wildtype, Trp53 +/- double mutant mouse, biological replicate 3, technical replicate 2

description:
Library name: WT3_TTAGGC_20210208
Mice aged 3-6 months


title: [DDB_PD_003]_[DDB7_RiboZero]_[Batch]_[0h]_[R2]_reseq


title: B-cells from young, Rps15-S138F heterozygous mutant mouse, biological replicate 1

description:
Library name: GTCCGC_Het1
Mice aged 3-6 months


title: [DDB_PD_003]_[DDB7_WT]_[Fed-batch]_[6h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient NW166


title: Myometrium from fibroid patient (MyoF), patient MP423


title: [DDB_PD_003]_[DDB7_RiboZero]_[Batch]_[0h]_[R2]


title: HNSCC_32_TUMOUR


title: B-cells from leukemic, Rps15 wildtype, Trp53 +/- double mutant mouse, biological replicate 3, technical replicate 1

description:
Library name: WT3_CTTGTA_20210208
Mice aged 3-6 months


title: [DDB_PD_003]_[DDB7_RiboZero]_[Batch]_[0h]_[R1]_reseq


title: B-cells from leukemic, Rps15 wildtype, Trp53 +/- double mutant mouse, biological replicate 2,  technical replicate 2

description:
Library name: WT2_GGCTAC_20210208
Mice aged 3-6 months


title: Embryo_CRY2CBP_Dark_H3K27ac_R1

value: Embryo (2-3 hour AEL)

value: CRY2nej;his2avRFP III

value: Dark

tag: cut&tag antibody

value: H3K27ac (Abcam, ab4729)


title: [DDB_PD_003]_[DDB7_RiboZero]_[Batch]_[0h]_[R1]


title: B-cells from leukemic, Rps15 wildtype, Trp53 +/- double mutant mouse, biological replicate 2,  technical replicate 1

description:
Library name: WT2_CGATGT_20210208
Mice aged 3-6 months


title: Myometrium from fibroid patient (MyoF), patient MP419

tag: age


title: HNSCC_31_TUMOUR

value: M

tag: tissue location

value: Pharynx

value: UK


title: HNSCC_30_TME

tag: case

value: N


title: Myometrium from fibroid patient (MyoF), patient MP416


title: B-cells from leukemic, Rps15 wildtype, Trp53 +/- double mutant mouse, biological replicate 1,  technical replicate  1

description:
Library name: WT1_ATCACG_20210208
Mice aged 3-6 months

value: B-cells


title: HNSCC_29_TME

tag: tumor stage


title: [DDB_PD_003]_[DDB7_Qiagen]_[Batch]_[0h]_[R1]


title: Myometrium from fibroid patient (MyoF), patient MP396

value: C


title: B-cells from leukemic, Rps15-S138F, Trp53 +/- double mutant mouse, biological replicate 3

description:
Library name: HOM3_GATCAG_20210208
Mice aged 3-6 months


title: Myometrium from fibroid patient (MyoF), patient MP380

value: myometrium


title: Myometrium from fibroid patient (MyoF), patient MP381

value: AA


title: [DDB_PD_003]_[DDB7_Qiagen]_[Batch]_[0h]_[R2]


title: HNSCC_31_TME

tag: deceased


title: HNSCC_29_TUMOUR

tag: tumor stage (general)


title: [DDB_PD_003]_[DDB7_NEB]_[Batch]_[0h]_[R2]

tag: cell type


title: HNSCC_32_TME

value: Y


title: HNSCC_28_TME

value: F

value: Advanced


title: Myometrium from fibroid patient (MyoF), patient MP369


title: Myometrium from fibroid patient (MyoF), patient MP364


title: [DDB_PD_003]_[DDB7_RiboRid]_[Batch]_[0h]_[R2]

tag: strain


title: Myometrium from fibroid patient (MyoF), patient MP366


title: HNSCC_28_TUMOUR

tag: Sex


title: B-cells from leukemic, Rps15-S138F, Trp53 +/- double mutant mouse, biological replicate 1

description:
Library name: HOM1_CAGATC_20210208
Mice aged 3-6 months


title: B-cells from leukemic, Rps15-S138F/+, Trp53 +/- double mutant mouse, biological replicate 3

description:
Library name: HET3_GCCAAT_20210208
Mice aged 3-6 months


title: [DDB_PD_003]_[DDB7_RiboRid]_[Batch]_[0h]_[R1]


title: B-cells from leukemic, Rps15 wildtype, Trp53 +/- double mutant mouse, biological replicate 1, technical replicate 2

description:
Library name: WT1_TAGCTT_20210208
Mice aged 3-6 months


title: HNSCC_30_TUMOUR

value: early


title: [DDB_PD_002]_[HMP3397_slow_feed]_[Fed-batch]_[86h]_[R2]

value: Escherichia coli cells


title: [DDB_PD_003]_[DDB7_NEB]_[Batch]_[0h]_[R1]


title: HNSCC_27_TME


title: B-cells from leukemic, Rps15-S138F, Trp53 +/- double mutant mouse, biological replicate 2

description:
Library name: HOM2_ACTTGA_20210208
Mice aged 3-6 months


title: B-cells from leukemic, Rps15-S138F/+, Trp53 +/- double mutant mouse, biological replicate 1

description:
Library name: HET1_TGACCA_20210208
Mice aged 3-6 months


title: [DDB_PD_002]_[HMP3397_slow_feed]_[Fed-batch]_[86h]_[R1]


title: [DDB_PD_002]_[HMP3397_slow_feed]_[Fed-batch]_[53h]_[R1]


title: HNSCC_27_TUMOUR


title: B-cells from leukemic, Rps15-S138F/+, Trp53 +/- double mutant mouse, biological replicate 2

description:
Library name: HET2_ACAGTG_20210208
Mice aged 3-6 months


title: B-cells from young, Rps15 wildtype mouse, biological replicate 3 (paired RNA-seq)

description:
Library name: WT4_CATACGGA_TACGACGT
Mice aged 3-6 months


title: HNSCC_26_TME


title: B-cells from young, Rps15 wildtype mouse, biological replicate 2 (paired RNA-seq)

description:
Library name: WT3_TCACCTAG_ACCTAGAC
Mice aged 3-6 months


title: Myometrium from fibroid patient (MyoF), patient MP353

tag: tissue


title: Myometrium from fibroid patient (MyoF), patient MP351


title: [DDB_PD_002]_[HMP3397_fast_feed]_[Fed-batch]_[27h]_[R1]


title: HNSCC_26_TUMOUR


title: [DDB_PD_002]_[HMP3397_fast_feed]_[Fed-batch]_[27h]_[R2]