title: oxidative stress reaction, 3h in 1mM H2O2; control is LoKoLiquide; replica 1

description:
Library name: H2O2_1
QuantSeq 3′ mRNA-Seq library


title: HDAC1fl/fl Cd4 Cre pTh2 cells, after 24h in culture, sample 1

status: Public on Jan 30 2025

type: SRA

city: Vienna

first: Nicole

last: Boucheron

address: Lazarettgasse 19

country: Austria

institute: Institute of Immunology

library_source: genomic

data_processing:
Illumina NovaSeq Control Software (NCS) 1.8.1 was used for the data acquisition on the sequencing instrument and on-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 3.4.4.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/epigen/picard/) was based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
NGS reads in unaligned BAM files were converted into FASTQ format with samtools, NGS adapter sequences were removed via fastp (0.23.2, GTCTCGTGGGCTCGG) and the reads were aligned to the GRCm38 (UCSC Genome Browser mm10) assembly with Bowtie2 (2.4.5, --very-sensitive, --no-discordant, --maxins 2000), before deduplicating with samblaster (0.1.24).
Alignment statistics and mitochondrial read fractions were collected with samtools. Peaks were called with MACS2 (2.2.7.1, --no-model, --keep-dup auto, –extsize 147) and both, peak annotation and motifs discovery was performed with Homer (4.11). UCSC Track hubs allowed for visual inspection of results. A consensus peak set was compiled and all peaks in mm10 assembly regions blacklisted by the ENCODE project were removed.
Assembly: GRCm38 (UCSC Genome Browser mm10)
Supplementary files format and content: MACS2 peak calls in tav-spearated value (TSV) format (_peaks.xls)
Supplementary files format and content: Consensus regions in UCSC BED format (consensus_regions.bed.gz)
Supplementary files format and content: Consensus counts in comma-separated value (CSV) format (consensus_counts.csv.gz)

molecule: genomic DNA

organism: Mus musculus

source_name: Cell culture from Spleen/Lymph nodes

extract_protocol:
Cells were harvested, counted and 50000 cells centrifuged at 500 g for 5 min at 4°C. Cell pellets were resuspended in a tagmentation-mix containing Tagment DNA buffer, Tagment DNA Enzyme (Illumina), Digitonin (Promega) and Proteinase K (Roche). The lysate was incubated for 30min at 37°C with shaking (300rpm). The reaction was stopped by incubating the samples on ice. DNA was isolated using the MinElute PCR Purification Kit (Qiagen) according to the manufacturer’s instructions and eluted into 12 μl of elution buffer.
1 µl eluate was used in a quantitative PCR (qPCR) reaction to estimate the optimal number of cycles for library amplification. The remaining 10 µl of each tagmented sample was then amplified corresponding to the Cqvalue (i.e., the cycle number at which fluorescence has increased above background levels) in the presence of custom Nextera primers. PCR amplification was followed by SPRI (Beckman Coulter, Brea, CA, USA) size selection to exclude fragments larger than 1,200 bp. The DNA concentration of each library was assessed with a Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA), before pooling in equimolar amounts.

tag: tissue

value: Cell culture from Spleen/Lymph nodes

tag: cell line

value: primary cell culture material

tag: cell type

tag: genotype

value: KO

tag: treatment

value: anti-CD3/anti-CD28 activation with IL-4, anti-GITR agonist, TSLP. anti-IFNg, anti-TGFb1

tag: Sex

value: male

tag: age

value: 6-12 weeks


title: B2_WT_3MBiP_FLG22_1H-2

city: Boston

first: Jen

last: Sheen

state: MA

address: 185 Cambridge st. CPZN7620

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
Total RNA (500 ng) was used for making the library. The library was prepared using Illumina TruSeq RNA sample Prep Kit v2 according to the manufacture's  guidelines. The libraries were sequenced for 50 cycles on an Illumina HiSeq 2500 rapid mode using two lanes of a flow cell.
51 nucleotide reads from single-end sequncing in fastq files were aligned to the Arabidopsis genome, TAIR10, with the Tophat aligner.
htseq-count from the HTSeq python library was used to determine numbers of reads per gene
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files contain the counts table output of HTseq analysis

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Plants were grown in a chamber with 12 h light /12 h dark (75 µmol m-2 s-1) at 23°C/20°C light/dark temperature, and 65 % relative humidity.  For experimental design 1) and 2), seedlings were grown in 0.5 X MS liquid media, 0.5 % Sucrose, pH5.8 in 6-well tissue culture plate (Falcon, USA) (8 seedlings per ml per well). For experimental design 3), plants  were grown in Jiffy Quick Soil Mix (QSM) pellets (Jiffy) (one plant per jiffy pellet).

extract_protocol:
Eight seedlings were pooled and total RNA was isolated using Trizol (Invitrogen).
The library was prepared for sequencing using standrad protocols of Illumina TruSeq RNA sample Prep Kit v2.

treatment_protocol: For experimental design 1) 7-d-old wild type seedlings grown in liquid medium were treated with 100nM flg22 and harvested at various time points. For experimental design 2) 7-d-old seedlings of wild type, impk36, and impk4 grown in liquid medium was pretreated with 0.1 % DMSO (Mock treatment) or 10 uM 3MBiP for 15 min. Then various stimuli signals (2 nM flg22 peptide, 100 nM pep3 peptide, 20 uM ABA, 50 uM MeJA, mechanical wounding by forceps, 40W UVB, 10 mM H2O2) were applied and incubated for 1 h before harvest. For experimental design 3) 4-week-old plants were sprayed with 1 % DMSO or 100 uM 3MBiP and harvested at various time points.

value: Seedlings

value: Wild type

value: 10 uM 3MBiP/ 2nM Flg22


title: B2_WT_3MBiP_FLG22_1H-1


title: Control for the liquids, replica 3

city: Szeged

first: Botond

last: Hegedüs

state: Csongrád-Csanád

address: Temesvári krt. 62

department: Institute of Biochemistry

country: Hungary

institute: Biological Research Center

description:
Library name: LoKoLiquide_3
QuantSeq 3′ mRNA-Seq library

data_processing:
The raw reads were trimmed using the BBduk.sh script from BBtools 38.92 and then mapped to the reference genome using STAR version 2.6.1a_08-27. The trimming and mapping parameters were set according to the manufacturer’s recommendations (https://www.lexogen.com/quantseq-data-analysis/).
The number of reads overlapping the transcript annotations was determined using the featureCounts function of the Rsubread package version 2.6.4
Assembly: CopciAB_V2_genome.fasta
Supplementary files format and content: Genome sequence of the Corinopsis cinerea AmutBmut V2 strain used for read alignment (CopciAB_V2_genome.fasta).
Supplementary files format and content: GTF-formatted annotation file of the Coprinopsis cinerea AmutBmut V2 strain, which was used to determine the read count values (CopciAB_V2_annotation.gtf).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample (CopciAB_V2_rawCounts.tsv)
Supplementary files format and content: Text file includes detailed description of the growth conditions (growth_protocol.pdf).

molecule: polyA RNA

organism: Coprinopsis cinerea AmutBmut pab1-1

source_name: Vegetative mycelium

growth_protocol: A detailed description of the growth conditions can be found in the document growth_protocol.pdf

extract_protocol:
RNA was extracted using Quick-RNA Miniprep kit (Zymo Research, USA, catalog number: R1054), following the manufacturer’s instructions.
The libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna). To begin, 100 ng of total RNA was used as input for first strand cDNA generation with an oligo-dT primer, followed by RNA removal. Next, second strand synthesis was initiated with random priming and the resulting products were purified with magnetic beads. Finally, the libraries were amplified and barcoded using PCR. The Agilent 4200 TapeStation (Agilent) was used to assess all libraries for the formation of adapter dimers during PCR. The QuantSeq libraries were sequenced on the Illumina NextSeq550 platform, producing 75 bp single-end reads.

value: Vegetative mycelium


title: PrS-MOK20012C-G07-hyp

city: Hinxton

first: MorPhiC

last: Consortium

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

description:
Library name: CE_G07__Hypoxia_GT23-11307_GCACGGAC-TGCGAGAC_S17
KOLF2.2J derived knockout cell line, EPAS1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

data_processing:
Reads are aligned to the reference genome using STAR aligner, count matrices are built with Salmon
Assembly: GRCh38 gencode.v44.primary_assembly
Supplementary files format and content: study1_featureCounts.csv study1_genesCounts.csv study1_genesRawCounts.csv study1_genesTPM.csv study1_stats.csv study1_txCounts.csv study1_txRawCounts.csv study1_txTPM.csv

organism: Homo sapiens

extract_protocol:
Arcturus PicoPure RNA isolation Kit Applied biosystems
KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina NovaSeq X

value: iPSC

tag: editing strategy

value: Critical exon

tag: altered gene_symbol

tag: altered locus

tag: time

value: day 6

tag: model system

value: primitive syncytium

tag: condition

value: hypoxia

tag: parental cell_line


title: PrS-MOK20012C-E06-hyp

description:
Library name: CE_E06__Hypoxia_GT23-11306_ATGTAAGT-CATAGAGT_S38
KOLF2.2J derived knockout cell line, EPAS1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: HDAC1fl/fl Cd4 Cre Th2 cells, after 24h in culture, sample 1

value: anti-CD3/anti-CD28 activation with IL-4, anti-IFNg, anti-TGFb1


title: Control for the liquids, replica 1

description:
Library name: LoKoLiquide_1
QuantSeq 3′ mRNA-Seq library


title: Control for the liquids, replica 2

description:
Library name: LoKoLiquide_2
QuantSeq 3′ mRNA-Seq library


title: HDAC1fl/fl Th2 cells, after 24h in culture, sample 1

value: WT


title: HDAC1fl/fl pTh2 cells, after 24h in culture, sample 1

value: Cell culture from Spleen/Lymph nodes


title: B2_WT_3MBiP_FLG22_30M-3


title: PrS-MOK20012W-B02-hyp

description:
Library name: KO_B02__Hypoxia_GT23-11305_CGGCGTGA-ACAGGCGC_S18
KOLF2.2J derived knockout cell line, EPAS1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen

value: Full coding length


title: PrS-MOK20012W-B01-hyp

description:
Library name: KO_B01__Hypoxia_GT23-11304_TAATACAG-GTGAATAT_S26
KOLF2.2J derived knockout cell line, EPAS1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: HDAC1fl/fl pTh2 cells, after 48h in culture, sample 1

value: primary cell culture material


title: Drought stress. control is DM_84h; replica 3

description:
Library name: DR_3
QuantSeq 3′ mRNA-Seq library


title: B2_WT_3MBiP_FLG22_30M-1


title: fxvehE

city: Barcelona

first: Andrés

last: Ozaita

address: Dr Aiguader, 88

department: Department of Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

data_processing:
Pseudogenes were removed from Ensembl GRCm39 annotation to further obtain transcripts abundance in transcripts per million (TPM) using Salmon 1.3
Low counts reads were filtered out based on mean expression greater than 0
Gene were quantified using tximport (1.18) and differential expression were analyzed with DESeq2 (1.30)
Assembly: GRCm39/mm10
Supplementary files format and content: Tab-delimited text file including raw gene counts for each sample

source_name: Brain

extract_protocol:
Synaptoneurosomes enriched fractions and hippocampal homogenate preparations were obtained from frozen hippocampus, and RNA was isolated using RNAeasy miniKit (74104, QIAGEN). Then, RNA concentration and  integrity was evaluated with Agilent 2100 Bioanalyzer.
RNA libraries were obtained using SMARTer Ultra Low Input kit and samples were sequenced using Illumina NovaSeq 6000 flow cell

value: Brain

value: Fmr1 KO

tag: source

value: Hippocampal synaptoneurosomes

tag: strain

value: Vehicle


title: fxvehD


title: PrS-MOK20012W-A03-hyp

description:
Library name: KO_A03__Hypoxia_GT23-11303_TGACGAAT-GCCTACTG_S33
KOLF2.2J derived knockout cell line, EPAS1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation in 3% oxygen


title: Drought stress. control is DM_84h; replica 2

description:
Library name: DR_2
QuantSeq 3′ mRNA-Seq library


title: B2_WT_3MBiP-3

value: Seedlings

value: Wild type

value: 10 uM 3MBiP


title: PrS-MOK20010-WT

description:
Library name: KOLF2_POU2F3_1_GT23-10491_CCGTGAAG-ATCCACTG_S38
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Not Applicable

value: Not applicable


title: Drought stress. control is DM_84h; replica 1

description:
Library name: DR_1
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: B2_WT_3MBiP-2


title: Carbon dioxide treatment - plates sealed after inoculation 28°C 6 days in the dark; control is DM_132h; replica 3

description:
Library name: CO2_3
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20010P-G09

description:
Library name: POU2F3_PTC_G09_GT23-10511_TCCAACGC-AAGTCCAA_S29
KOLF2.2J derived knockout cell line, POU2F3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon

value: day 6

value: primitive syncytium


title: fxvehB


title: osmotic stress, 2h in 10% sorbitol; control is LoKoLiquide; replica 1

description:
Library name: Sor_1
QuantSeq 3′ mRNA-Seq library


title: B2_WT_3MBiP-1


title: PrS-MOK20010P-A10

description:
Library name: POU2F3_PTC_A10_GT23-10510_CTTGGTAT-GGACTTGG_S42
KOLF2.2J derived knockout cell line, POU2F3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Carbon dioxide treatment - plates sealed after inoculation 28°C 6 days in the dark; control is DM_132h; replica 2

description:
Library name: CO2_2
QuantSeq 3′ mRNA-Seq library


title: B1_impk4_3MBiP_PEP3-3

value: 10 uM 3MBiP/ 100 nM Pep3


title: Carbon dioxide treatment - plates sealed after inoculation 28°C 6 days in the dark; control is DM_132h; replica 1

description:
Library name: CO2_1
QuantSeq 3′ mRNA-Seq library


title: B2_WT_3MBiP_FLG22_30M-2

value: 10 uM 3MBiP/ 2nM Flg22


title: fxamE


title: Heat shock at 47 °C for 2 hours - 6 days old culture; control is DM_132h; replica 3

description:
Library name: HS47_3
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20010C-B06

description:
Library name: POU2F3_CE_B06_GT23-10508_ACTAAGAT-CCGCGGTT_S23
KOLF2.2J derived knockout cell line, POU2F3 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Critical exon


title: B1_impk4_3MBiP_PEP3-2


title: fxamC

value: Brain


title: PrS-MOK20010C-B05

description:
Library name: POU2F3_CE_A06_GT23-10507_ATGAGGCC-CAATTAAC_S24
KOLF2.2J derived knockout cell line, POU2F3 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: Heat shock at 47 °C for 2 hours - 6 days old culture; control is DM_132h; replica 2

description:
Library name: HS47_2
QuantSeq 3′ mRNA-Seq library


title: B1_impk4_3MBiP_JA-3

value: 10 uM 3MBiP/ 50 uM MeJA


title: fxvehC

value: Fmr1 KO

value: Hippocampal synaptoneurosomes


title: fxamB


title: Heat shock at 47 °C for 2 hours - 6 days old culture; control is DM_132h; replica 1

description:
Library name: HS47_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20010W-G03

description:
Library name: POU2F3_KO_G03_GT23-10505_AACGTTCC-AGTACTCC_S37
KOLF2.2J derived knockout cell line, POU2F3 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Full coding length


title: fxamA


title: PrS-MOK20010C-A06

description:
Library name: POU2F3_CE_B05_GT23-10506_GCAGAATT-TGGCCGGT_S17
KOLF2.2J derived knockout cell line, POU2F3 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: B1_impk4_3MBiP_JA-2

value: Seedlings


title: Control for Cocl, replica 3

description:
Library name: CoK_3
QuantSeq 3′ mRNA-Seq library


title: OHT_3

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

country: Germany

institute: TUD Dresden University of Technology

description: biological replicate 3

data_processing:
bcl2fastq2 - 2.20.0
adapter trimming - Adapters (nextera:CTGTCTCTTATA) and polyA/T tails were trimmed with cutadapt (v2.6)[12] and pairs where one or both reads were shorter than 35bp were removed
alignment - Fragments were aligned to the mouse reference genome GRCm39 using the aligner gsnap (v2020-12-16) with Ensembl 104 mouse splice sites as support
data processing step - Quality control of the sequencing data was performed with FastQC (version 0.11.9). Kallisto (version 0.64.1) (Bray et al, 2016) was used to align trimmed reads to mouse GRCm39.
Assembly: genome build/assembly - mus musculus GRCm39
Supplementary files format and content: processed data files format and content - tab separated file where each row represents a gene and each column either gene information (e.g. chromosome, strand) or the TPM values per gene per sample

source_name: C57BL/6J neocortex

growth_protocol: Mouse NSCs were isolated and cultured as previously described (Cubillos et al., 2024; Schütze et al., 2022)

extract_protocol:
RNA was extracted using the Quick-RNA FFPE MiniPrep kit.
RNA-seq was performed as previously described (Cubillos et al., 2024). RNA of differentiating NSCs was isolated using the Quick-RNA MiniPrep kit (Zymo Research, #R1008). Transcriptome libraries were prepared using an adapted version of the SmartSeq2 protocol (Picelli et al, 2013). Isolated total RNA from an equivalent of one 24-well was denatured for 3 minutes at 72°C in 4 μL hypotonic buffer (0.2% Triton-X 100) in the presence of 2.4 mM dNTP, 240 nM dT-primer (Table EV1) and 4 U RNase Inhibitor (NEB, M0314L). Reverse transcription was performed at 42°C for 90 min after filling up to 10 µL with RT buffer mix for a final concentration of 1X Superscript II buffer (Invitrogen), 1 M Betaine, 5 mM DTT, 6 mM MgCl2, 1 µM TSO-primer (Table EV1), 9 U RNase inhibitor and 90 U Superscript II. The reverse transcriptase was inactivated at 70°C for 15 min. For subsequent PCR amplification of the cDNA, the optimal PCR cycle number was determined with an aliquot of 1 μL unpurified cDNA in a 10 μL qPCR containing 1X Kapa HiFi Hotstart Readymix (Roche), 1X SybrGreen and 0.2 μM UP primer (Table EV1). The residual 9 μL cDNA were subsequently amplified using Kapa HiFi HotStart Readymix (Roche) at a 1X concentration together with 250 nM UP-primer (Table EV1) under the following cycling conditions: initial denaturation at 98°C for 3 min, 22 cycles [98°C 20 sec, 67°C 15 sec, 72°C 6 min] and final elongation at 72°C for 5 min. Amplified cDNA was purified using 1X volume of Sera-Mag SpeedBeads (GE Healthcare) resuspended in a buffer consisting of 10 mM Tris, 20 mM EDTA, 18.5% (w/v) PEG 8000 and 2 M sodium chloride solution. The cDNA quality and concentration were determined using a Fragment Analyzer (Agilent).  For library preparation, 2 µL amplified cDNA was tagmented in 1X Tagmentation Buffer using 0.8 µL bead-linked transposome (Illumina DNA Prep, (M) Tagmentation, Illumina) at 55°C for 15 min in a total volume of 4 µL. The reaction was stopped by adding 1 µL of 0.1% SDS (37°C, 15 min). Magnetic beads were bound to a magnet, the supernatant was removed, beads were resuspended in 14 µL indexing PCR Mix containing 1X KAPA Hifi HotStart Ready Mix (Roche) and 700 nM unique dual indexing primers (i5 and i7), and subjected to a PCR (72°C 3 min, 98°C 30 sec, 12 cycles [98°C 10 sec, 63°C 20 sec, 72°C 1 min], 72°C 5 min). Libraries were purified with 0.9X volume Sera-Mag SpeedBeads, followed by a double size selection with 0.6X and 0.9X volume of beads, and a final 0.9X purification to obtain a fragment size distribution of 200–700 bp. Sequencing was performed after quantification using a Fragment Analyzer on an Illumina Novaseq 6000 in 100 bp paired-end XP mode with an average sequencing depth of 40 million fragments per library.

treatment_protocol: NSCs were either treated with Ethanol as control (EtOH) or with 1 μM OH-Tamoxifen (OHT) to induce deletion of Pcgf2/4.

value: C57BL/6J neocortex

value: Pcgf2F/F; Pcgf4F/F; Nes::CreERT2/+

value: NSC (4d of neural diff)

value: Pcgf2/4 deletion

value: OH-Tamoxifen


title: fxvehA

value: Vehicle


title: B1_impk4_3MBiP_JA-1


title: PrS-MOK20010W-F04

description:
Library name: POU2F3_KO_F04_GT23-10504_GGTACCTT-GACGTCTT_S33
KOLF2.2J derived knockout cell line, POU2F3 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: day 6

value: Not applicable


title: OHT_2

description: biological replicate 2


title: Control for Cocl, replica 2

description:
Library name: CoK_2
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: PrS-MOK20010P-A09

description:
Library name: POU2F3_PTC_A09_GT23-10509_GTCGGAGC-TTATAACC_S7
KOLF2.2J derived knockout cell line, POU2F3 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon

value: primitive syncytium


title: Control for Cocl, replica 1

description:
Library name: CoK_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20013-WT

description:
Library name: KOLF2_GRHL1_2_GT23-10492_TTACAGGA-GCTTGTCA_S6
KOLF2.2J differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Not Applicable


title: B1_impk4_3MBiP_ABA-3

value: 10 uM 3MBiP/ 20 uM ABA


title: B1_impk4_3MBiP_ABA-2


title: B1_impk4_3MBiP_ABA-1


title: PrS-MOK20013P-C09

description:
Library name: GRHL1_PTC_C09_GT23-10502_ATGTAAGT-CATAGAGT_S19
KOLF2.2J derived knockout cell line, GRHL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: OHT_1

description: biological replicate 1


title: EtOH_3

description: biological replicate 3

value: Ctrl

value: EtOH


title: 2 mM Cobalt Chloride on 7 days old culture, 2h light induction then 22h in darkness; control is CoK; replica 3

description:
Library name: Cocl_3
QuantSeq 3′ mRNA-Seq library


title: B1_impk4_3MBiP_PEP3-1

value: Seedlings

value: 10 uM 3MBiP/ 100 nM Pep3


title: EtOH_2

description: biological replicate 2

value: C57BL/6J neocortex

value: Pcgf2F/F; Pcgf4F/F; Nes::CreERT2/+


title: EtOH_1

description: biological replicate 1

value: NSC (4d of neural diff)


title: B1_impk4_3MBiP-3

value: 10 uM 3MBiP


title: B1_impk4_3MBiP-2


title: 2 mM Cobalt Chloride on 7 days old culture, 2h light induction then 22h in darkness; control is CoK; replica 1

description:
Library name: Cocl_1
QuantSeq 3′ mRNA-Seq library


title: WT_F_VEH_E

data_processing:
Transcript abundances in Transcripts Per Million (TPM) were quantified with Salmon 1.5.2
Low counts reads were filtered out based on mean expression greater than 0
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for each sample
Supplementary files format and content: Matrix table with raw transcripts counts for each ample

extract_protocol:
Synaptoneurosomes were isolated from hippocampal tissue and total RNA were obtained using RNeasy mini kit (Qiagen)
Libraries were obtained using SMARTer Ultra Low Input kit according to the manufacturer’s instructions

value: Brain

value: female

value: Hippocampal synaptoneurosomes

value: Vehicle


title: PrS-MOK20010W-B04

description:
Library name: POU2F3_KO_B04_GT23-10503_GCACGGAC-TGCGAGAC_S14
KOLF2.2J derived knockout cell line, POU2F3 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: iPSC

value: Full coding length

value: day 6

value: Not applicable


title: PrS-MOK20013P-A09

description:
Library name: GRHL1_PTC_A09_GT23-10500_TAATACAG-GTGAATAT_S2
KOLF2.2J derived knockout cell line, GRHL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Termination codon

value: primitive syncytium


title: PrS-MOK20013C-D07

description:
Library name: GRHL1_CE_D07_GT23-10499_TGACGAAT-GCCTACTG_S31
KOLF2.2J derived knockout cell line, GRHL1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation

value: Critical exon


title: 30 minutes on -20°C - 6 days old mycelium; control is DM_132h; replica 2

description:
Library name: min20_2
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: WT_F_VEH_D


title: 30 minutes on -20°C - 6 days old mycelium; control is DM_132h; replica 1

description:
Library name: min20_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20013C-A08

description:
Library name: GRHL1_CE_A08_GT23-10498_CAGTAGGC-ATTCGTCA_S39
KOLF2.2J derived knockout cell line, GRHL1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: WT_F_VEH_B


title: B1_impk36_3MBiP_PEP3-3

value: Seedlings

value: 10 uM 3MBiP/ 100 nM Pep3


title: B1_impk36_3MBiP_PEP3-2


title: PrS-MOK20013C-A05

description:
Library name: GRHL1_CE_A05_GT23-10497_TTGGACTC-CTGCTTCC_S12
KOLF2.2J derived knockout cell line, GRHL1 CE, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: 2 mM Cobalt Chloride on 7 days old culture, 2h light induction then 22h in darkness; control is CoK; replica 2

description:
Library name: Cocl_2
QuantSeq 3′ mRNA-Seq library


title: WT_F_AM_F


title: B1_impk36_3MBiP_PEP3-1


title: PrS-MOK20013W-H04

description:
Library name: GRHL1_KO_H04_GT23-10496_CCAAGTCT-TCATCCTT_S35
KOLF2.2J derived knockout cell line, GRHL1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: LI samples after the dark growing put into 12-12h light/dark cycle, 24h, replica 3

description:
Library name: L_D_24h_3
QuantSeq 3′ mRNA-Seq library

source_name: Primordium

value: Primordium


title: B1_impk36_3MBiP_JA-3

value: 10 uM 3MBiP/ 50 uM MeJA


title: 30 minutes on -20°C - 6 days old mycelium; control is DM_132h; replica 3

description:
Library name: min20_3
QuantSeq 3′ mRNA-Seq library


title: LI samples after the dark growing put into 12-12h light/dark cycle, 24h, replica 2

description:
Library name: L_D_24h_2
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20013P-A10

description:
Library name: GRHL1_PTC_A10_GT23-10501_CGGCGTGA-ACAGGCGC_S30
KOLF2.2J derived knockout cell line, GRHL1 PTC, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: WT_F_AM_E


title: LI samples after the dark growing put into 12-12h light/dark cycle, 24h, replica 1

description:
Library name: L_D_24h_1
QuantSeq 3′ mRNA-Seq library


title: PrS-MOK20013W-G04

description:
Library name: GRHL1_KO_G04_GT23-10495_CTCTCGTC-AGGTTATA_S15
KOLF2.2J derived knockout cell line, GRHL1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: PrS-MOK20013W-D02

description:
Library name: GRHL1_KO_D02_GT23-10494_TCTCTACT-GAACCGCG_S26
KOLF2.2J derived knockout cell line, GRHL1 KO, differentiated to the trophoblast lineage and favoring primitive syncytium formation


title: WT_F_AM_D


title: B1_impk36_3MBiP_JA-1


title: B1_impk4_3MBiP-1

value: 10 uM 3MBiP


title: B1_impk36_3MBiP_JA-2


title: WT_F_AM_B

value: Brain


title: NMDA+Senolytic 20dpi Rep 3

city: Nashville

first: Gregory

last: Konar

state: TN

address: 1161 21st Ave S

department: Biological Sciences

institute: Vanderbilt University

data_processing:
Adapter sequences and low-quality reads were trimmed and read files underwent paired sequence validation using Trim Galore! v0.6.10, a wrapper for CutAdapt v4.8, using the --paired and --illumina parameters.
Trimmed reads were quantified using Salmon v1.10.3 in quasi-mapping mode with the optional paramaters --validateMappings and --gcBias against the Ensembl release 111 Danio rerio GRCz11.111 transcriptome, with the primary assembly from the same release serving as decoys.
Read counts were imported to R using tximport v1.32.0 and processed using DESeq2 v1.44.0.
Assembly: GRCz11.111
Supplementary files format and content: tab-delimited text file with estimated relative abundance and number of reads as well as all additional output files from Salmon v1.10.3 run in quasi-mapping mode

organism: Danio rerio

source_name: Retina

extract_protocol:
RNA was harvested using Trizol and Phenol-chloroform extraction
Libraries were prepared utilizing the stranded mRNA (polyA-selected) library preparation kit

value: Retina

value: NMDA Damage


title: LI samples after the dark growing put into 12-12h light/dark cycle, 18h, replica 3

description:
Library name: L_D_18h_3
QuantSeq 3′ mRNA-Seq library


title: LI samples after the dark growing put into 12-12h light/dark cycle, 18h, replica 2

description:
Library name: L_D_18h_2
QuantSeq 3′ mRNA-Seq library


title: LI samples after the dark growing put into 12-12h light/dark cycle, 18h, replica 1

description:
Library name: L_D_18h_1
QuantSeq 3′ mRNA-Seq library


title: Young_Male

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode processing and gene counting were made using CellRanger software (v7.2.0)
The pooled libraries were then sequenced using the NovaSeq 6000 S4 system (Illumina), targeting 400 million reads per library. Count matrices generation was conducted using the 10x Genomics Cell Ranger pipeline (version 5.0.0), following the 10x Genomics guidelines. The demultiplexed FASTQ files were aligned to the mm10 reference genome.Data normalization, integration, and clustering were subsequently carried out using the Seurat package (version 4.3.0). Quality control filtering was applied, removing cell barcodes of low complexity. The following parameters were used for filtering: cells with less than 5% of reads mapping to the mitochondrial chromosome, Unique Molecular Identifier (UMI) counts > 500, and a detected gene count > 500.
Assembly: mm10
Supplementary files format and content: h5 file

source_name: Bone marrow stroma

extract_protocol:
Bone marrow cells were harvested from 10 male C57BL/6 mice and 10 female C57BL/6 mice. Stromal cells were sorted by cell surface marker CD45-, Lin-, Ter119-, and 7-AAD-.
Sorted cells were evaluated using acridine orange and ethidium homodimer and all showed viability of 90% or greater. Cell suspension was partitioned in a 10x Genomics Chromium Controller to target the capture of 10,000 cells per sample. cDNA and libraries were prepared using the 10x Genomics Next GEM 3’ Gene Expression Kit (v3.1-Single Index) as recommended by the manufacturer. Constructed libraries were evaluated by bioanalyzer prior to sequencing.

value: Bone marrow stroma

value: Male


title: NMDA+Senolytic 20dpi Rep 2


title: NMDA+Senolytic 20dpi Rep 1


title: Young_Female

description: 10X Genomics

value: Female


title: LI samples after the dark growing put into 12-12h light/dark cycle, 12h, replica 3

description:
Library name: L_D_12h_3
QuantSeq 3′ mRNA-Seq library


title: NMDA Only 20dpi Rep 3

value: Control


title: LI samples after the dark growing put into 12-12h light/dark cycle, 12h, replica 2

description:
Library name: L_D_12h_2
QuantSeq 3′ mRNA-Seq library


title: B1_impk36_3MBiP_ABA-1

value: 10 uM 3MBiP/ 20 uM ABA


title: Colon, WT, snATAC

city: Seodaemun-gu

first: Insuk

last: Lee

state: Seoul

address: 50 Yonsei-ro

department: Biotechnology

country: South Korea

institute: Yonsei University

description: 10x Genomics

data_processing:
Barcode processing, peak detection, fragment processing, and matric generation were made using the Cell Ranger ATAC software v2.0.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac)
Assembly: mm10
Supplementary files format and content: fragments.tsv: CellRanger-atac product. TSV file for peak fragments
Supplementary files format and content: filtered_peak_bc_matrix.h5 : CellRanger-atac product. H5 file for peak by cell matrix
Supplementary files format and content: singlecell.csv : CellRanger-atac product. CSV file for Metadata of each cell (barcode)

source_name: Colon

growth_protocol: Mice were cohoused littermates

extract_protocol:
On the day of nuclei isolation, the snap-frozen colons were put into dounce tissue grinders containing 500 ul ice-cold lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA, prepared in nuclease-free water. Colon tissues were then gently dounced 20 times with pestle on ice and incubated on ice for 5 min. Thereafter, 1 ml of ice-cold wash buffer (10 mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, prepared in nuclease-free water) was added to the samples which were sequentially filtered through 70 um and 20 um cell strainers into pre-chilled 1.5 ml Eppendorf tubes. The homogenates were centrifuged at 450 g, 4 °C for 4 min to pellet the nuclei. After centrifugation, supernatants were carefully removed. The nuclei were resuspended in 1X ice-cold Nuclei Buffer (10x Genomics, PN 2000153/2000207)
Nuclei were counted on the LUNA-FX7 Automated Cell Counter (Logos Biosystems) using fluorescence detection for viability with an acridine orange/propidium iodide stain (Part No. F23011). Samples had viabilities between 1.6%-10.3% with concentration ranges from ~5,325-6,500 nuclei/ul. After counting, all samples were transposed in a bulk solution and then loaded into individual wells of Chip H per the user guide from 10x Genomics, no alterations were made at any step of the protocol (Part No. CG000209 Rev G). GEMs were formed targeting 10,000 nuclei and GEM incubation completed immediately after. Post GEMs were cleaned up and library construction completed using PCR amplification for a total of 9 cycles with each sample receiving a unique single index (Part No. 1000212). Final libraries were diluted and ran using the High Sensitivity D5000 tape and reagents (Part No. 5067-5592 & 5067-5593) on the 4200 TapeStation (Agilent Technologies). Libraries were quantified via Kapa qPCR using the Complete Universal Kit (Part No. 07960140001, Roche Sequencing Solutions) and the CFX96 Touch Real-Time PCR Detection System (Bio-Rad). Libraries were sequenced on an Illumina NovaSeq instrument using the parameters outlined in the user guide (Read1: 50 bp, i7 index: 8 bp, i5 index: 16 bp, Read2: 50 bp).

treatment_protocol: Mice were subjected to 0.5% DSS in drinking water ad libitum for 7 days followed by 7 days of normal drinking water

value: Colon

value: WT


title: B1_impk36_3MBiP-3


title: LI samples after the dark growing put into 12-12h light/dark cycle, 6h, replica 3

description:
Library name: L_D_6h_3
QuantSeq 3′ mRNA-Seq library


title: MEFs, EZR KO, biological rep4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
Transcriptome profile of EZR KO, biological rep4
KO_4

data_processing:
Data analysis was performed using the pipeline already established at the Bioinformatics and Statistics Core Facility at TIGEM. Briefly, the reads were trimmed to remove adapter sequences and low-quality ends and reads mapping to contaminating sequences (e.g. ribosomal RNA, phIX control) were filtered-out. Alignment was performed with STAR 2.6.0a3 on mm10 reference assembly obtained from cellRanger website4 (Ensembl assembly release 93). The expression levels of genes were determined with htseq-count 0.9.15 by using mm10 Ensembl assembly (release 93) downloaded from cellRanger website4. We have filtered out all genes having < 1 cpm in less than n_min samples and Perc MM reads > 20% simultaneously. Differential expression analysis was performed using edgeR6.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: Cells were grown in standard conditions

extract_protocol:
RNA was quantified and mixed at 10ng/µl
libraries were prepared according manufacturer’s instructions (TruSeq RNA Sample Preparation kit, Illumina) starting from 4 μg of total RNA.
Quality control of library templates was performed using a High Sensitivity DNA Assay kit (Agilent Technologies) on a Bioanalyzer (Agilent Technologies). The Qubit quantification platform (Qubit 2.0 Fluorometer, Life Technologies) was used to normalise samples for the library preparation.

treatment_protocol: 4 biologial replicates, for each cell line were plated in standard conditions and total RNA was estracted when the cells become confluent.

value: mouse embryonic fibroblasts (MEFs)

value: EZR knockout

tag: gender

value: not determined


title: LI samples after the dark growing put into 12-12h light/dark cycle, 12h, replica 1

description:
Library name: L_D_12h_1
QuantSeq 3′ mRNA-Seq library

tag: tissue


title: NMDA Only 20dpi Rep 1


title: MEFs, EZR KO, biological rep3

description:
Transcriptome profile of EZR KO, biological rep3
KO_3


title: B1_impk36_3MBiP-2

value: Seedlings


title: B1_impk36_3MBiP-1


title: NMDA+Senolytic 12dpi Rep 3


title: B1_WT_3MBiP_PEP3-3

value: Wild type

value: 10 uM 3MBiP/ 100 nM Pep3


title: B1_impk36_3MBiP_ABA-2


title: NMDA+Senolytic 12dpi Rep 2


title: LI samples after the dark growing put into 12-12h light/dark cycle, 6h, replica 1

description:
Library name: L_D_6h_1
QuantSeq 3′ mRNA-Seq library

value: Primordium


title: MEFs, wt, biological rep4

description:
Transcriptome profile of MEF wt, biological rep4
WT_4

value: wt


title: B1_WT_3MBiP_PEP3-2


title: MEFs, EZR KO, biological rep2

description:
Transcriptome profile of EZR KO, biological rep2
KO_2


title: LI samples after the dark growing put into 12-12h light/dark cycle, 6h, replica 2

description:
Library name: L_D_6h_2
QuantSeq 3′ mRNA-Seq library


title: MEFs, EZR KO, biological rep1

description:
Transcriptome profile of EZR KO, biological rep1
KO_1


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, HK - hyphal knot, 24h, replica 3

description:
Library name: LI_24h_HK_3
QuantSeq 3′ mRNA-Seq library

source_name: Hyphal knot

value: Hyphal knot


title: Colon, IL18bp-/-, snATAC

description: 10x Genomics


title: B1_WT_3MBiP_PEP3-1


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, HK - hyphal knot, 24h, replica 2

description:
Library name: LI_24h_HK_2
QuantSeq 3′ mRNA-Seq library


title: MEFs, wt, biological rep3

description:
Transcriptome profile of MEF wt, biological rep3
WT_3


title: NMDA+Senolytic 12dpi Rep 1

value: Retina

value: NMDA Damage


title: NMDA Only 12dpi Rep 2


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, HK - hyphal knot, 24h, replica 1

description:
Library name: LI_24h_HK_1
QuantSeq 3′ mRNA-Seq library


title: NMDA Only 20dpi Rep 2


title: MEFs, wt, biological rep2

description:
Transcriptome profile of MEF wt, biological rep2
WT_2


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, AM - attached mycelium, 24h, replica 3

description:
Library name: LI_24h_AM_3
QuantSeq 3′ mRNA-Seq library

source_name: Attached mycelium

value: Attached mycelium


title: NMDA Only 12dpi Rep 1


title: B1_WT_3MBiP_JA-2

value: 10 uM 3MBiP/ 50 uM MeJA


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, AM - attached mycelium, 24h, replica 2

description:
Library name: LI_24h_AM_2
QuantSeq 3′ mRNA-Seq library


title: NMDA+Senolytic 3dpi Rep 3


title: B1_WT_3MBiP_JA-1


title: MEFs, wt, biological rep1

description:
Transcriptome profile of MEF wt, biological rep1
WT_1


title: 19511

type: genomic

city: Hyderabad

first: Kommu

middle: Naga

last: Mohan

state: Hyderabad

address: Jawahar nagar

country: India

institute: Birla Institute of Technology and Science

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina HumanMethylation 450K Bead Chip

scan_protocol: Arrays were imaged using BeadArray Reader and standard recommended illumina scanner setting

data_processing: Methylation Module in GenomeStudio

label: Cy3 and Cy5

source_name: Genomic DNA isolated from cerebellum of an autism spectrum disorder individual individual

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from cerebellum samples were extracted using Proteinase K Phenol-chloroform method

value: Cerebellum

value: M

tag: age in years


title: B1_WT_3MBiP_ABA-3

value: 10 uM 3MBiP/ 20 uM ABA


title: 16641


title: NMDA+Senolytic 3dpi Rep 2


title: 14762


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, AE-aerial mycelium, 24h, replica 3

description:
Library name: LI_24h_AE_3
QuantSeq 3′ mRNA-Seq library

source_name: Aerial mycelium

value: Aerial mycelium


title: NMDA Only 12dpi Rep 3

value: Control


title: B1_WT_3MBiP_ABA-2


title: B1_WT_3MBiP_ABA-1


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, AM - attached mycelium, 24h, replica 1

description:
Library name: LI_24h_AM_1
QuantSeq 3′ mRNA-Seq library


title: NMDA Only 3dpi Rep 3


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, AE-aerial mycelium, 24h, replica 1

description:
Library name: LI_24h_AE_1
QuantSeq 3′ mRNA-Seq library


title: DM 156h samples after 2h of light induction and 1h/6h/12h/24h of darkness, AE-aerial mycelium, 24h, replica 2

description:
Library name: LI_24h_AE_2
QuantSeq 3′ mRNA-Seq library


title: 13872

value: F


title: B1_WT_3MBiP_JA-3


title: 8873


title: B1_WT_3MBiP-3

value: 10 uM 3MBiP


title: NMDA Only 3dpi Rep 2


title: Sampled after light induction in the dark phase, AM – attached mycelium, 18h; replica 3

description:
Library name: LI18hAM_3
QuantSeq 3′ mRNA-Seq library


title: B1_WT_3MBiP-2

value: Seedlings


title: 7014


title: NMDA Only 3dpi Rep 1


title: B1_WT_3MBiP-1

value: Wild type


title: 6856


title: IFNg-2_BATF2

city: Cleveland

first: Jessica

middle: L

last: Williams

state: OH

address: 9620 Carnegie Ave N Bldg

department: Neurosciences

institute: Cleveland Clinic

description:
Library name: 4_0EDB_01XLCCF_IFNg-2_BATF2_hs_i57
IFNg Technical Replicate 2, human spinal cord astrocytes BATF2 ChIPseq

data_processing:
Reads were then aligned to the human genome (hg38) using the BWA algorithm. Duplicated reads were removed and uniquely mapped reads (25 mapping quality) that aligned with no more than 2 mismatches were used for downstream analysis.
MACS software (v 2.1.0) was used to call unique peaks relative to the pooled input with cutoffs of 1e-7 for narrow peaks and 1e-1 for broad peaks. Peaks were then filtered by removing false ChIP Seq peaks as defined by the ENCODE blacklist.
Known motifs were identified using the findMotifsGenome program of the HOMER packagea using default parameters and input sequences comprising +/- 100 bp from the center of the top 2500 peaks.
Resulting signal maps were stored in bigWigs files and also analyzed by Active Motif using proprietary analysis software.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Spinal Cord

growth_protocol: ScienCell Astrocyte Medium (Catalog No. 1801), 10% FBS, 1x penicllin/streptomycin. Cells were cultured at 37C in 5% CO2.

extract_protocol:
Cells were fixed for 15 min in 1/10 volume Formaldehyde solution (11% Formaldehyde, 0.1M NaCl, 1mM EDTA pH 8.0, 50mM Hepes pH 7.9 in milliQ H2O) at room temperature. Fixation was stopped by adding 1/20 volume glycine solution (2.5M in milliQ H2O) for 5 min at room temperature. Cells were then scraped, transferred into 50mL conical tubes, and kept on ice. Tubes were centrifuged at 800xg at 4°C for 10 min. Pelleted cells were then resuspended in 10mL of chilled PBS-Igepal solution (0.5% Igepal in 1X PBS). Cells were repelleted as before and washed twice more with PBS-Igepal, adding 100uL of PMSF (1mM in ethanol) after the second wash to each sample. Pellets were then snap frozen on dry ice.Further processing for ChIP sequencing and analysis, including chromatin extraction, fragmentation, antibody precipitation, and library preparation was performed commercially by Active Motif Services using a validated antibody to BATF2 (Proteintech 16592-1-AP).
Sequence libraries were generated using the standardized steps of enzymatic end polishing, dA-addition, and adaptor ligation. Following PCR amplification, the resulting libraries were quantified, sequenced, and quality filtered using Illumina software (75 nucleotide reads, single end).

treatment_protocol: After reaching 75% confluency, cells were treated with 10ng/mL of human (IFN)g or with media as a control for 24 hours.

value: Spinal Cord

tag: cell type

value: Primary Astrocyte

value: IFNg


title: IFNg-1_BATF2

description:
Library name: 3_0EBR_01XLCCF_IFNg-1_BATF2_hs_i56
IFNg Technical Replicate 1, human spinal cord astrocytes BATF2 ChIPseq


title: Sampled after light induction in the dark phase, AM – attached mycelium, 18h; replica 1

description:
Library name: LI18hAM_1
QuantSeq 3′ mRNA-Seq library


title: NMDA+Senolytic 3dpi Rep 1

tag: genotype


title: 6677


title: Media-2_BATF2

description:
Library name: 2_0EDA_01XLCCF_Media-2_BATF2_hs_i50
Media Technical Replicate 2, human spinal cord astrocytes BATF2 ChIPseq

tag: treatment

value: Media


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 18h; replica 3

description:
Library name: LI18hAE_3
QuantSeq 3′ mRNA-Seq library


title: 6640

tag: Sex


title: B1_WT_DMSO-2

tag: age

value: Mock (0.1 % DMSO)


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 18h; replica 2

description:
Library name: LI18hAE_2
QuantSeq 3′ mRNA-Seq library


title: Media-1_BATF2

description:
Library name: 1_0EBP_01XLCCF_Media-1_BATF2_hs_i49
Media Technical Replicate 1, human spinal cord astrocytes BATF2 ChIPseq


title: B1_WT_DMSO-1


title: SCAC-Pooled_Input

description:
Library name: 0_0ECI_01XLCCF_SCAC-Pooled_Input_hs_i59
Pooled Input


title: Sampled after light induction in the dark phase, AM – attached mycelium, 12h; replica 3

description:
Library name: LI12hAM_3
QuantSeq 3′ mRNA-Seq library


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 18h; replica 1

description:
Library name: LI18hAE_1
QuantSeq 3′ mRNA-Seq library


title: CAL27 cells, TNFAIP2_overexpression_3_RNASeq

city: Jinan

first: Teng

last: Xu

state: Shandong Province

address: 247 Beiyuan Street, Jinan, Shandong Province, People’s Republic of China

country: China

institute: Shandong University

description:
Library name: Sample 6
Colume name in counts_allSamples.csv: OV3_Hcount

data_processing:
Raw data were processed through trim_galore (version 0.6.4).
After removing removing reads containing adaptors, low-quality reads and ribosome RNA reads,, the clean reads were aligned to the reference genome (GRCh38.104) using HISAT2 (version 2.2.0).
The Read Counts of transcripts were calculated by htseq-count (version 0.13.5). And the expression of mRNA was normalized to FPKM.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: CAL27 cells were maintained within DMEM containing 10% fetal bovine serum in 5% CO2 atmosphere at 37℃.

extract_protocol:
RNA was harvested using Rneasy Micro kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CAL27 cell line overexpressing TNFAIP2 was constructed by plasmid

tag: cell line

value: Human oral squamous cell carcinoma cells

value: TNFAIP2 overexpression


title: Sampled after light induction in the dark phase, AM – attached mycelium, 18h; replica 2

description:
Library name: LI18hAM_2
QuantSeq 3′ mRNA-Seq library

value: Attached mycelium


title: Sampled after light induction in the dark phase, AM – attached mycelium, 12h; replica 2

description:
Library name: LI12hAM_2
QuantSeq 3′ mRNA-Seq library


title: 6365

value: Cerebellum


title: Flg22_WT_flg22_30m-2

value: 100 nM flg22


title: B1_WT_DMSO-3


title: Flg22_WT_flg22_30m-1


title: 6469


title: Sampled after light induction in the dark phase, AM – attached mycelium, 12h; replica 1

description:
Library name: LI12hAM_1
QuantSeq 3′ mRNA-Seq library


title: CAL27 cells, TNFAIP2_overexpression_1_RNASeq

description:
Library name: Sample 4
Colume name in counts_allSamples.csv: OV1_Hcount


title: CAL27 cells, TNFAIP2_overexpression_2_RNASeq

description:
Library name: Sample 5
Colume name in counts_allSamples.csv: OV2_Hcount


title: Flg22_WT_flg22_15m-2


title: 6337

value: M


title: Flg22_WT_flg22_60m-1


title: CAL27 cells, control_3_RNASeq

description:
Library name: Sample 3
Colume name in counts_allSamples.csv: NC3_Hcount

value: WT

value: vector transfection


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 12h; replica 3

description:
Library name: LI12hAE_3
QuantSeq 3′ mRNA-Seq library

value: Aerial mycelium


title: 6294


title: CAL27 cells, control_2_RNASeq

description:
Library name: Sample 2
Colume name in counts_allSamples.csv: NC2_Hcount


title: Flg22_WT_flg22_60m-2


title: Flg22_WT_flg22_15m-1


title: 6401


title: 6184

value: F


title: Flg22_WT_flg22_10m-2

value: Seedlings


title: 6399


title: CAL27 cells, control_1_RNASeq

description:
Library name: Sample 1
Colume name in counts_allSamples.csv: NC1_Hcount


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 12h; replica 1

description:
Library name: LI12hAE_1
QuantSeq 3′ mRNA-Seq library


title: 5666


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 12h; replica 2

description:
Library name: LI12hAE_2
QuantSeq 3′ mRNA-Seq library


title: Flg22_WT_flg22_10m-1

value: Wild type


title: DU145_TCF3 Myc_input

city: shanghai

first: Huixiang

last: Xiao

state: shanghai

address: pujian road 160

institute: shanghai jiaotong university

description: Library name: sample4

data_processing:
The qualified libraries were pooled and sequenced on Illumina platforms with PE150  strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to  effective library concentration and data amount required
Assembly: hg38
Supplementary files format and content: txt including peaks

source_name: prostate

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris)
the purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit （NEB, USA, Catalog #: E7645L）for ChIP-seq library preparation.

value: prostate

value: Human prostate cancer cell


title: Sampled after light induction in the dark phase, AM – attached mycelium, 6h; replica 3

description:
Library name: LI6hAM_3
QuantSeq 3′ mRNA-Seq library


title: 5569


title: DU145_TCF3 Myc ChIP

description: Library name: sample3


title: Flg22_WT_flg22_5m-2


title: 5342


title: DU145_ATOH8 Flag_input

description: Library name: sample2


title: 5334


title: Sampled after light induction in the dark phase, AM – attached mycelium, 6h; replica 2

description:
Library name: LI6hAM_2
QuantSeq 3′ mRNA-Seq library


title: Flg22_WT_flg22_5m-1


title: Sampled after light induction in the dark phase, AM – attached mycelium, 6h; replica 1

description:
Library name: LI6hAM_1
QuantSeq 3′ mRNA-Seq library


title: DU145 ATOH8 Flag ChIP

description: Library name: sample1


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 6h; replica 3

description:
Library name: LI6hAE_3
QuantSeq 3′ mRNA-Seq library


title: Flg22_WT_flg22_0m-2

value: Mock (water)


title: 5308


title: 5173


title: DU145_oeATOH8 rep3

description: Library name: SAMPLE 12

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to hg38 with orientation mode using HISAT2  software
The mapped reads of each sample were assembled by StringTie  in a reference-based approach
differential expression analysis was performed using the DESeq2
Assembly: GRCh38
Supplementary files format and content: excel sheet includs tpm of each sample
Supplementary files format and content: excel sheet includs count of each sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai BioMarker Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA)

value: OE ATOH8


title: 5144


title: BG4_CnT_U2OS_DMSO_rep5

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

institute: University of Cambridge

data_processing:
fq files were trimed with cutadapt version 1.18 to remove adaptors and bases with quality lower than 20 (-q 20) mapped with bwa-mem 0.7.17-r2188 to hg38 genome and only the reads within the whitelist have been retained.
bw files presented here were created using bamCoverage with counts per milion normalisation (CPM)  after extending the paired-end reads and accepting maximum mapped fragment length of 350nt.
Assembly: hg38
Supplementary files format and content: bigWig, bedgraph, counts

growth_protocol:
Human osteosarcoma U2OS cells (ATCC, HTB-96) were cultured in phenol red free Dulbecco's Modified Eagle Medium (DMEM) (high glucose and L-glutamine plus, Gibco, catalogue no. 21063045) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS) (Gibco, catalogue no. 10082147) and 1 mM sodium pyruvate. Cells were grown at 37 ℃ in a humidified 5% CO2 atmosphere. After thawed, cells were passaged at least twice before being used in experiments. Cells were confirmed mycoplasma-free by periodic tests.
The G4-CUT&Tag was adapted from that described previously41. pA-Tn5-adaptor complex was prepared as described previously41. Concanavalin A-coated beads were prepared with Dynabeads MyOne Streptavidin T1 beads (Invitrogen, catalogue no. 65601) and biotin-conjugated concanavalin A solution (Sigma Aldrich, catalogue no. C2272) as described previously51. Briefly, U2OS cells (~300,000 cells per 100 μl for each sample) were bound to concanavalin A-conjugated beads (10 μl). The bead-bound cells were permeabilized and incubated in 50 μl of ~600 nM BG4 antibody9 solution dliluted in antibody buffer at 4 ℃ overnight, followed by an incubation in 50 μl rabbit anti-FLAG antibody (Cell Signaling Technology, catalogue no. 2368S) solution at a 1:25 dilution in Dig-wash buffer at room temperature for 1 h. After a further incubation with 50 μl Guinea Pig anti-Rabbit IgG secondary antibody solution at 1:100 dilution in Dig-wash buffer at room temperature for 1 h, 50 μl pA-Tn5 adaptor complex dilution at 1:250 dilution in Dig-300 buffer was added to cells for incubation at room temperature for 1 h, followed by the tagmentation reaction at 37 ℃ for 1 h. After proteinase K digestion, the DNA fragments were extracted for the library preparation and Illumina sequencing.

extract_protocol:
Cells were washed twice in 200 μl TAPS wash buffer (10 mM TAPS, 0.2 mM EDTA), and resuspended in 100 μl extraction buffer (10 mM Tris HCl, pH 8.0, 0.5 mg/ml proteinase K (Thermo Scientific, catalogue no. EO0491), 0.5% SDS) with vortexing, and incubated at 55 ℃ for 1.5 h at 800 rpm. DNA extraction was performed using the DNA Clean & Concentrator-5 kit (Zymo Research, catalogue no. D4013). DNA was eluted in 25 μl provided DNA Elution Buffer from the column after incubation at room temperature for 10 min.
To amplify DNA libraries, PCR was performed by mixing 21 μl tagmented DNA with 2 μl uniquely barcoded v2 Ad1.x primer (10 μM) and 2 μl uniquely barcoded v2 Ad2.x primer (10 μM)51, and 25 μl NEBNext Ultra II Q5 2× PCR Master mix (New England Biolabs, catalogue no. M0544) using the following cycle: 72 ℃ for 5 min; 98 ℃ for 30 s; 10 cycles of 98 ℃ for 10 s and 63 ℃ for 10 s; 72 ℃ for 1 min. Libraries were cleaned up by adding 1.3× volume (65 μl) of Ampure XP beads (Beckman Coulter, catalogue no. A63882), incubated at room temperature for 10 min, washed twice gently in 200 μl of 80% ethanol. DNA was eluted in 25 μl of 10 mM Tris HCl, pH 8.0.
The size distribution of libraries was confirmed by TapeStation analysis using High Sensitivity D1000 ScreenTape (Agilent, catalogue no. 5067–5584). The libraries were quantified using the NEBNext Library Quant Kit (New England Biolabs, catalogue no. E7630L). Libraries were balanced and pooled, followed by size selection by adding 0.4× volumn of Ampure XP beads and incubation at room temperature for 10 min. The supernatant was transferred to a new DNA LoBind tube, and 1.3× volumn of Ampure XP beads was then added and incubated at room temperature for 10 min. On-bead libraries were washed twice with 80% ethanol and eluted in 30 μl of 10 mM Tris HCl, pH 8.0. Paired-end sequencing of libraries was performed on an NextSeq 2000 sequencer (Illumina) using the NextSeq 1000/2000 P2 reagent kit (100 cycles) (Illumina, catalogue no. 20046811).
For chem-map competition experiments, U2OS cells were grown to a 70~80% confluence until treatment with PDS (4 μM or 20 μM) or vehicle DMSO at 37 ℃ for 3 h. Cells were washed twice with PBS, followed by performing standard G4switch Chem-map protocol.

value: epithelial osteosarcoma

tag: chip antibody


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 6h; replica 2

description:
Library name: LI6hAE_2
QuantSeq 3′ mRNA-Seq library


title: BG4_CnT_U2OS_DMSO_rep4


title: DU145_oeATOH8 rep2

description: Library name: SAMPLE 11


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 6h; replica 1

description:
Library name: LI6hAE_1
QuantSeq 3′ mRNA-Seq library


title: Sampled after light induction in the dark phase, AM – attached mycelium, 2h; replica 3

description:
Library name: LI2hAM_3
QuantSeq 3′ mRNA-Seq library


title: 5000


title: BG4_CnT_U2OS_DMSO_rep3


title: DU145_oeCTRL rep3

description: Library name: SAMPLE 9

value: OE CTRL


title: Sampled after light induction in the dark phase, AM – attached mycelium, 2h; replica 2

description:
Library name: LI2hAM_2
QuantSeq 3′ mRNA-Seq library


title: DU145_oeATOH8 rep1

description: Library name: SAMPLE 10


title: BG4_CnT_U2OS_DMSO_rep2


title: 4925


title: Sampled after light induction in the dark phase, AM – attached mycelium, 2h; replica 1

description:
Library name: LI2hAM_1
QuantSeq 3′ mRNA-Seq library


title: DU145_oeCTRL rep1

description: Library name: SAMPLE 7


title: DU145_oeCTRL rep2

description: Library name: SAMPLE 8


title: 4498


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 2h; replica 3

description:
Library name: LI2hAE_3
QuantSeq 3′ mRNA-Seq library


title: BG4_CnT_U2OS_DMSO_rep1


title: DU145_RSL3 rep3

description: Library name: SAMPLE 6


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 2h; replica 2

description:
Library name: LI2hAE_2
QuantSeq 3′ mRNA-Seq library


title: Flg22_WT_flg22_0m-1


title: SLAM-seq_U2OS_G4switch_dark_rep3

growth_protocol:
Human osteosarcoma U2OS cells (ATCC, HTB-96) were cultured in phenol red free Dulbecco's Modified Eagle Medium (DMEM) (high glucose and L-glutamine plus, Gibco, catalogue no. 21063045) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS) (Gibco, catalogue no. 10082147) and 1 mM sodium pyruvate. Cells were grown at 37 ℃ in a humidified 5% CO2 atmosphere. After thawed, cells were passaged at least twice before being used in experiments. Cells were confirmed mycoplasma-free by periodic tests.
U2OS cells were seeded at a density of 2.1 × 105 cells per well in a 6-well plate in phenol red free full DMEM media and grown for 24 h. Cells were then treated with G4switch (6 μM) and vehicle DMSO in 1 ml phenol red free full DMEM media, followed by incubation at 37 ℃ for 30 min in a light-proof box, either in the dark (for cis-G4switch and DMSO treatments) or with pulsed LED illuminations [405 nm for 90 s + 75 ms every 15 s (for cis-to-trans photoswitching of G4switch treatment)]; alternating phases of pulsed 405 nm and 525 nm illuminations in the following order: 405 nm (from the top) for 90 s, then 525 nm from the bottom for 120 s, following with immediate 405 nm for 75 ms and 525 nm for 375 ms in every 15 s (for cis-to-trans, then trans-to-cis photoswitching of G4switch treatment); 525 nm for 120 s + 375ms every 15s (green light control)] to pre-establish light-controlled G4 targeting. Newly synthesized RNA was labelled by a final concentration of 250 μM added 4sU (Sigma-Aldrich, catalogue no. T4509) at 37 ℃ for 60 min in dark. Cells were washed twice in 2 ml PBS, followed by RNA extraction using the RNeasy Plus Mini Kit (QIAGEN, catalogue no. 74134). Total RNA was quantified by a Nanodrop One (Thermo Fisher Scientific), and 3 μg RNA was subjected to iodoacetamide (IAA) alkylation using the SLAMseq Kinetics Kit (Lexogen, catalogue no. 061). 500 ng alkylated RNA was then used for preparation of 3’-end mRNA sequencing libraries using the QuantSeq 3' mRNA-Seq Library Prep kit (FWD) (Lexogen, catalogue no. 015) and PCR Add-on kit (Lexogen, catalogue no. 020) for Illumina. Libraries were sequenced on a NextSeq 500 sequencer (Illumina) using the High Output kit (Illumina, catalogue no. FC-404-2005).


title: 3345


title: DU145_RSL3 rep2

description: Library name: SAMPLE 5


title: Sampled after light induction in the dark phase, AE-aerial mycelium, 2h; replica 1

description:
Library name: LI2hAE_1
QuantSeq 3′ mRNA-Seq library


title: SLAM-seq_U2OS_G4switch_dark_rep2


title: DU145_RSL3 rep1

description: Library name: SAMPLE 4


title: Sampled during light induction, 1h (half way) 2h (end of LI), AM - attached mycelium, 2h; replica 3

description:
Library name: ELI2hAM_3
QuantSeq 3′ mRNA-Seq library


title: SLAM-seq_U2OS_G4switch_dark_rep1


title: DU145_DMSO rep3

description: Library name: SAMPLE 3

value: DMSO


title: Sampled during light induction, 1h (half way) 2h (end of LI), AM - attached mycelium, 2h; replica 2

description:
Library name: ELI2hAM_2
QuantSeq 3′ mRNA-Seq library

value: Attached mycelium


title: 10251

source_name: Genomic DNA isolated from cerebellum of a healthy individual

value: Cerebellum


title: 4849


title: Sampled during light induction, 1h (half way) 2h (end of LI), AM - attached mycelium, 2h; replica 1

description:
Library name: ELI2hAM_1
QuantSeq 3′ mRNA-Seq library


title: DU145_DMSO rep2

description: Library name: SAMPLE 2


title: DU145_DMSO rep1

description: Library name: SAMPLE 1


title: SLAM-seq_U2OS_G4switch_525nm_rep3


title: SLAM-seq_U2OS_G4switch_525nm_rep2


title: 4231


title: 5180


title: Sampled during light induction, 1h (half way) 2h (end of LI), AE-aerial mycelium, 2h; replica 2

description:
Library name: ELI2hAE_2
QuantSeq 3′ mRNA-Seq library


title: Kidney Pre-treatment Biopsy, NAXIVA Responder, Patient 19

first: James

middle: O

last: Jones

state: Cambridgeshire

description:
FFPE extracted
sample-19

data_processing:
Reads were mapped using Salmon (v1.10.0) with GRCh38.p44 from Gencode. Samples were only included in analysis if the sequencing duplication rate was < 65%. Genes were included if the maximum count per biopsy was > 10 and if more than 50% of the biopsies had counts > 0.
Assembly: GRCh38.p44
Supplementary files format and content: csv includes raw counts for each sample.

source_name: Kidney

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using the ReliaPrep FFPE Total RNA kit, according to manufacturer’s instructions, and assessed by Qubit and Agilent RNA ScreenTape System and for quantity and quality.
RNA library preparation was done using the Watchmaker Genomics RNA Library Prep Kit with Polaris Depletion, according to manufacturer’s instructions and running 18X PCR cycles for each sample. Indexing was done using the xGen™ Stubby Adaptor and UDI primers from Integrated DNA Technologies™, and sequencing via Illumina sequencing. The samples were run on an S4 flow cell on NovaSeq6000 with a read length of PE50. Manufacturer’s instructions followed for the run, including spike-in of 1% PhiX.

value: Kidney

tag: group

value: NAXIVA responder

value: Neoadjuvant axitinib


title: SLAM-seq_U2OS_G4switch_525nm_rep1


title: SLAM-seq_U2OS_G4switch_dark_rep4


title: SLAM-seq_U2OS_G4switch_525nm_rep4


title: 5282

value: M


title: Kidney Pre-treatment Biopsy, NAXIVA Responder, Patient 18

description:
FFPE extracted
sample-18


title: 1182


title: Sampled during light induction, 1h (half way) 2h (end of LI), AE-aerial mycelium, 2h; replica 1

description:
Library name: ELI2hAE_1
QuantSeq 3′ mRNA-Seq library

value: Aerial mycelium


title: 4337


title: SLAM-seq_U2OS_G4switch_405nm_rep4


title: Kidney Pre-treatment Biopsy, NAXIVA Responder, Patient 17

description:
FFPE extracted
sample-17


title: 4332


title: SLAM-seq_U2OS_G4switch_405nm_rep3


title: 3439

value: F


title: SLAM-seq_U2OS_G4switch_405nm_rep2


title: Kidney Pre-treatment Biopsy, NAXIVA Responder, Patient 15

description:
FFPE extracted
sample-15


title: 2456


title: 2830


title: Kidney Pre-treatment Biopsy, NAXIVA Responder, Patient 13

description:
FFPE extracted
sample-13


title: 4670


title: Kidney Pre-treatment Biopsy, NAXIVA Non responder, Patient 7

description:
FFPE extracted
sample-7

value: NAXIVA Non responder


title: 3428


title: Mycelium grown in the dark - This timepoint shows the state just before the light induction (LI), 156h, AM, replica 3

description:
Library name: DM_156h_AM_3
QuantSeq 3′ mRNA-Seq library


title: Sampled during light induction, 1h (half way) 2h (end of LI), AM - attached mycelium, 1h; replica 1

description:
Library name: ELI1hAM_1
QuantSeq 3′ mRNA-Seq library


title: Sampled during light induction, 1h (half way) 2h (end of LI), AE-aerial mycelium, 2h; replica 3

description:
Library name: ELI2hAE_3
QuantSeq 3′ mRNA-Seq library


title: SLAM-seq_U2OS_G4switch_405nm_rep1


title: 2880


title: Kidney Pre-treatment Biopsy, NAXIVA Non responder, Patient 8

description:
FFPE extracted
sample-8


title: Sampled during light induction, 1h (half way) 2h (end of LI), AE-aerial mycelium, 1h; replica 3

description:
Library name: ELI1hAE_3
QuantSeq 3′ mRNA-Seq library


title: Sampled during light induction, 1h (half way) 2h (end of LI), AE-aerial mycelium, 1h; replica 2

description:
Library name: ELI1hAE_2
QuantSeq 3′ mRNA-Seq library


title: Kidney Pre-treatment Biopsy, NAXIVA Non responder, Patient 5

description:
FFPE extracted
sample-5


title: Kidney Pre-treatment Biopsy, NAXIVA Non responder, Patient 12

description:
FFPE extracted
sample-12


title: SLAM-seq_U2OS_G4switch_405nm+525nm_rep2


title: SLAM-seq_U2OS_G4switch_405nm+525nm_rep4


title: SLAM-seq_U2OS_G4switch_405nm+525nm_rep1


title: 1981


title: SLAM-seq_U2OS_G4switch_405nm+525nm_rep3


title: Mycelium grown in the dark - This timepoint shows the state just before the light induction (LI), 156h, AM, replica 2

description:
Library name: DM_156h_AM_2
QuantSeq 3′ mRNA-Seq library


title: Sampled during light induction, 1h (half way) 2h (end of LI), AM - attached mycelium, 1h; replica 2

description:
Library name: ELI1hAM_2
QuantSeq 3′ mRNA-Seq library


title: 2149


title: Kidney Pre-treatment Biopsy, NAXIVA Responder, Patient 16

description:
FFPE extracted
sample-16


title: Kidney Pre-treatment Biopsy, NAXIVA Non responder, Patient 3

description:
FFPE extracted
sample-3


title: Sampled during light induction, 1h (half way) 2h (end of LI), AM - attached mycelium, 1h; replica 3

description:
Library name: ELI1hAM_3
QuantSeq 3′ mRNA-Seq library


title: SLAM-seq_U2OS_DMSO_rep4


title: Sampled during light induction, 1h (half way) 2h (end of LI), AE-aerial mycelium, 1h; replica 1

description:
Library name: ELI1hAE_1
QuantSeq 3′ mRNA-Seq library


title: Mycelium grown in the dark - This timepoint shows the state just before the light induction (LI), 156h, AM, replica 1

description:
Library name: DM_156h_AM_1
QuantSeq 3′ mRNA-Seq library


title: Kidney Pre-treatment Biopsy, NAXIVA Non responder, Patient 1

description:
FFPE extracted
sample-1


title: 1860


title: Mycelium grown in the dark - This timepoint shows the state just before the light induction (LI), 156h, AE, replica 3

description:
Library name: DM_156h_AE_3
QuantSeq 3′ mRNA-Seq library


title: Mycelium grown in the dark - This timepoint shows the state just before the light induction (LI), 156h, AE, replica 2

description:
Library name: DM_156h_AE_2
QuantSeq 3′ mRNA-Seq library


title: SLAM-seq_U2OS_DMSO_rep3


title: Senescent IMR90 5SA YAP dox+ rep2

city: Seoul

first: Jaejin

last: Kim

address: Gwanak-ro 1

institute: Seoul National University

data_processing:
The sequence reads were trimmed using Trimmomatic version 0.36 and mapped against the human reference genome (hg38) using Hisat2 version 2.1.0.
Read counts per gene were calculated by using featureCounts version 1.6.3.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Lung

growth_protocol: IMR90 cells were maintained in 3% O2 and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS), penicillin/streptomycin, and 0.1 mM nonessential amino acids.

extract_protocol:
Total RNAs were isolated using the acid phenol extraction method.
One microgram of high-quality RNA samples (RIN > 7.0) was used to construct RNA-seq libraries using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina). Total RNA integrity was checked using an Agilent 2200 TapeStation. RNA-seq was performed on an Illumina NovaSeq 6000 sequencer at Macrogen.

treatment_protocol: Senescent cells were assessed at 9 days after exposure to bleomycin (10 ug/ml for 24 h). Doxycycline (1ug/ml) were treated for 11 days to express N-terminally Flag tagged YAP5SA.

value: Lung

value: Fibroblast

value: hTERT pinducer20 N-terminally Flag tagged YAP5SA

value: 9 days after exposure to bleomycin (10 ug/ml for 24 h), Doxycycline for the last 11 days (1ug/ml)


title: Kidney Pre-treatment Biopsy, NAXIVA Non responder, Patient 2

description:
FFPE extracted
sample-2


title: 1713


title: 1906


title: 1712


title: Mycelium grown in the dark - This timepoint shows the state just before the light induction (LI), 156h, AE, replica 1

description:
Library name: DM_156h_AE_1
QuantSeq 3′ mRNA-Seq library

data_processing:
The raw reads were trimmed using the BBduk.sh script from BBtools 38.92 and then mapped to the reference genome using STAR version 2.6.1a_08-27. The trimming and mapping parameters were set according to the manufacturer’s recommendations (https://www.lexogen.com/quantseq-data-analysis/).
The number of reads overlapping the transcript annotations was determined using the featureCounts function of the Rsubread package version 2.6.4
Assembly: CopciAB_V2_genome.fasta
Supplementary files format and content: Genome sequence of the Corinopsis cinerea AmutBmut V2 strain used for read alignment (CopciAB_V2_genome.fasta).
Supplementary files format and content: GTF-formatted annotation file of the Coprinopsis cinerea AmutBmut V2 strain, which was used to determine the read count values (CopciAB_V2_annotation.gtf).
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample (CopciAB_V2_rawCounts.tsv)
Supplementary files format and content: Text file includes detailed description of the growth conditions (growth_protocol.pdf).

extract_protocol:
RNA was extracted using Quick-RNA Miniprep kit (Zymo Research, USA, catalog number: R1054), following the manufacturer’s instructions.
The libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna). To begin, 100 ng of total RNA was used as input for first strand cDNA generation with an oligo-dT primer, followed by RNA removal. Next, second strand synthesis was initiated with random priming and the resulting products were purified with magnetic beads. Finally, the libraries were amplified and barcoded using PCR. The Agilent 4200 TapeStation (Agilent) was used to assess all libraries for the formation of adapter dimers during PCR. The QuantSeq libraries were sequenced on the Illumina NextSeq550 platform, producing 75 bp single-end reads.


title: Mycelium grown in the dark, sampled from the earliest timepoint, 132h, replica 3

description:
Library name: DM_132h_3
QuantSeq 3′ mRNA-Seq library

source_name: Vegetative mycelium

value: Vegetative mycelium


title: Mycelium grown in the dark, sampled from the earliest timepoint, 132h, replica 2

description:
Library name: DM_132h_2
QuantSeq 3′ mRNA-Seq library


title: 1547


title: SN7_SN_Park. dis. with dementia

city: Jerusalem

first: Nimrod

last: Madrer

address: The Edmond J. Safra Campus, Guvat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: Short RNA seq of post-mortem sample

data_processing:
FASTQ files were checked for quality using FastQC
Adaptors were removed using FLEXBAR according to the pipeline manual
Adaptor-less output FASTQ files were then aligned to tRFs using MINTmap
Assembly: Human NCBI genome build 37 (GRCh37)
Supplementary files format and content: Raw tRF counts (of SN or Blood), tRF names comply with MINTmap naming system

source_name: Substantia nigra

extract_protocol:
Brain and blood samples were obtained from the Netherlands Brain. Brain RNA was extracted using the miRNeasy Mini Kit (Qiagen, 217004), and blood RNA was extracted using the NucleoSpin RNA Blood Mini kit for RNA from blood (Machery-Nagel, 740200), both according to the manufacturer's protocol. This was followed by RNA concentration determination (NanoDrop 2000, Thermo Scientific), standard gel electrophoresis for quality assessment, and RIN determination (Bioanalyzer 6000, Agilent).
Libraries were generated (NEBNext Multiplex Small RNA library prep set for Illumina, New England Biolabs, NEB E7560S) and the small RNA fraction was sequenced

value: Substantia nigra

tag: brainid

value: Male

value: PD

tag: diagnosis

value: Park. dis. with dementia

tag: rin

tag: braak

tag: amyloid

value: B

tag: braaklb

tag: apoe

tag: pmd

tag: pd length

tag: sepsis


title: SN6_SN_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

tag: tissue

value: O


title: SN8_SN_Park. dis. with dementia

description: Short RNA seq of post-mortem sample


title: Mycelium grown in the dark, sampled from the earliest timepoint, 132h, replica 1

description:
Library name: DM_132h_1
QuantSeq 3′ mRNA-Seq library


title: 1670

value: Cerebellum

tag: age in years


title: Proliferating IMR90 5SA YAP dox+ rep2

tag: cell type

tag: genotype

tag: treatment

value: Doxycycline for 11 days (1ug/ml)


title: Senescent IMR90 5SA YAP dox+ rep1

tag: cell line


title: SN5_SN_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

tag: Sex

tag: group

tag: age


title: Senescent IMR90 5SA YAP dox- rep1

value: 9 days after exposure to bleomycin (10 ug/ml for 24 h)


title: Mycelium grown in the dark, sampled from the earliest timepoint, 108h, replica 3

description:
Library name: DM_108h_3
QuantSeq 3′ mRNA-Seq library


title: SLAM-seq_U2OS_DMSO_rep2

value: epithelial osteosarcoma


title: SLAM-seq_U2OS_DMSO_rep1


title: 1500

value: M


title: 1674


title: B1_impk36_3MBiP_ABA-3

first: Jen

last: Sheen

data_processing:
Total RNA (500 ng) was used for making the library. The library was prepared using Illumina TruSeq RNA sample Prep Kit v2 according to the manufacture's  guidelines. The libraries were sequenced for 50 cycles on an Illumina HiSeq 2500 rapid mode using two lanes of a flow cell.
51 nucleotide reads from single-end sequncing in fastq files were aligned to the Arabidopsis genome, TAIR10, with the Tophat aligner.
htseq-count from the HTSeq python library was used to determine numbers of reads per gene
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files contain the counts table output of HTseq analysis

source_name: Seedlings

extract_protocol:
Eight seedlings were pooled and total RNA was isolated using Trizol (Invitrogen).
The library was prepared for sequencing using standrad protocols of Illumina TruSeq RNA sample Prep Kit v2.

value: Seedlings

value: 10 uM 3MBiP/ 20 uM ABA


title: 1488


title: Mycelium grown in the dark, sampled from the earliest timepoint, 108h, replica 2

first: Botond

last: Hegedüs

description:
Library name: DM_108h_2
QuantSeq 3′ mRNA-Seq library


title: SN4_SN_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

tag: brainid

tag: diagnosis

tag: rin


title: Proliferating IMR90 5SA YAP dox+ rep1

value: Lung

value: Fibroblast


title: SN2_SN_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

tag: braak

tag: amyloid

value: A

tag: braaklb


title: Senescent IMR90 5SA YAP dox- rep2

value: hTERT pinducer20 N-terminally Flag tagged YAP5SA


title: 1465


title: Proliferating IMR90 5SA YAP dox- rep2

value: untreated


title: Proliferating IMR90 5SA YAP dox- rep1


title: 1486

value: F


title: 1453


title: Mycelium grown in the dark, sampled from the earliest timepoint, 108h, replica 1

description:
Library name: DM_108h_1
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: IgG control2 HK2

city: Ann Arbor

first: David

last: Turner

state: MI

address: 109 Zina Pitcher Place

department: Michigan Neuroscience Institute

institute: University of Michigan

description:
PAR-CLIP with control IgG
HK2_Ago_crosslinks.bed
matrix_HK2_Ago_crosslink_annot.txt

library_source: other

data_processing:
FASTQ files generated with Illumina’s bcl2fastq v2.20.0.422
Adapter sequences were trimmed, sequences were mapped to hg38 with STAR v2.7.1a, Sequences mapping to ChrM or rRNA sequences were removed. Multiple reads with identical sequence and length were considered duplicates and only a single read was retained.
T to C sequence substitutions relative to the genome were identified with Bambino. Reads with low base quality mismatches or mismatches near ends were filtered, so T to C substitution counts are conservative. T to C substitutions at same genomic position present in multiple Argonaute libraries but not in control libraries were considered crosslinks..
Reads with a deleted base at the position of a consistent T to C substitution were considered crosslinked reads. Consistent crosslinks within 15nt of a position with a greater number of reads with a consistent crosslink were removed, to create a set of predominant crosslinks, which were annotated with BEDTools using GENCODE v27.
6 or 7nt miRNA seed matches with the 5’ base of the match within +/-15nt of a predominant crosslink site were identified, based on miRNAs expressed in HK2 cells.
Assembly: hg38
Supplementary files format and content: HK2_Ago_crosslinks.bed: bed file of predominant crosslink sites for Argonaute (name field = index or crosslink identifier, see matrix file below)
Supplementary files format and content: matrix_HK2_Ago_crosslink_annot.txt: text file with matrix of crosslink counts, miRNA seed matches, gene annotation for each predominant crosslink

molecule: other

source_name: HK2 cell line

growth_protocol: HK2 cells were maintained in DMEM/F12 with 10% fetal bovine serum and 1% Penicillin/Streptomycin (5000 U/mL) at 37 C in the presence of a humidified atmosphere with 5% CO2

extract_protocol:
Crosslinked cells were lysed in low salt buffer. Lysates were sequentially treated with RNase-free DNase and micrococcal nuclease. EGTA was added to stop digestion. Lysates were cleared by centrifugation. Cleared lysates were immunoprecipitated with anti-Argonaute mAb or IgG, RNA was dephosphorylated, then phosphorylated with T4 Polynucleotide Kinase. Protein-RNA complexes (100-150kd) were isolated by SDS-PAGE, digested with Proteinase K, and RNA recovered by acidic phenol/chloroform extraction and ethanol precipitation.
Libraries were prepared using an NEB Small RNA Library Prep Kit according the manufacturer’s directions, with the following modification: after reverse transcription 80 to 150nt cDNA was gel purified and precipitated by with 2-propanol, then used for subsequent steps.

treatment_protocol: Cells were serum starved for 24 hrs, then exposed to TGFb1 at 20 ng/mL for 24 hrs; cells were treated with 100 μM 4SU for the final 20h before harvest, then exposed to 365nm UV light on ice in a UV Stratalinker 1800

tag: antibody

value: IgG

value: HK2 cell line

value: WT

value: control


title: Mycelium grown in the dark, sampled from the earliest timepoint, 84h, replica 2

description:
Library name: DM_84h_2
QuantSeq 3′ mRNA-Seq library


title: Mycelium grown in the dark, sampled from the earliest timepoint, 84h, replica 1

description:
Library name: DM_84h_1
QuantSeq 3′ mRNA-Seq library


title: SN3_SN_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

value: Substantia nigra

value: Male

value: PD

value: Park. dis. with dementia

tag: pmd

tag: pd length

tag: sepsis


title: SN1_SN_Park. dis. with dementia

description: Short RNA seq of post-mortem sample

tag: tissue

value: O

tag: apoe


title: OSCC in the background of OSF_2

city: Manipal

first: Raghu

last: Radhakrishnan

state: Karnataka

address: Madava Nagar, Manipal

department: Oral and Maxillofacial Pathology and Microbiology

institute: Manipal College of Dental Sciences, Manipal

data_processing:
The paired end (PE) fastq files were processed in the Galaxy Server (https://usegalaxy.org/) (version 23.1.rc1).
Briefly, the undesired adapters and low-quality sequences were removed with Cutadapt, and the quality was assessed using MultiQC.
Assembly: Mapping was performed to the human reference assembly (hg19) using RNA STAR to estimate the reads mapped per gene.
Supplementary files format and content: text file includes the Read counts for each sample

source_name: OSCC in the background of OSF

extract_protocol:
The isolation of total RNA  was performed utilizing the mirVana™ miRNA Isolation Kit (Cat. No. AM1560, Invitrogen, Carlsbad, CA, US)
Library preparation was performed using NEBNext RNA Ultra II (NEB #E7775, Massachusetts, US).

value: OSCC in the background of OSF


title: Mycelium grown in the dark, sampled from the earliest timepoint, 60h, replica 3

city: Szeged

address: Temesvári krt. 62

institute: Biological Research Center

description:
Library name: DM_60h_3
QuantSeq 3′ mRNA-Seq library


title: Matched Normal_2

source_name: Matched Normal

value: Matched Normal


title: 1429

value: Cerebellum

value: M

tag: age in years


title: Argonaute HK2_TGF2

description:
PAR-CLIP with anti-Ago antibody
HK2_Ago_crosslinks.bed
matrix_HK2_Ago_crosslink_annot.txt

value: Argonaute

tag: cell line

tag: genotype

tag: treatment


title: Matched Normal_1


title: OSCC in the background of OSF_1


title: 1409

tag: Sex


title: Mycelium grown in the dark, sampled from the earliest timepoint, 60h, replica 2

description:
Library name: DM_60h_2
QuantSeq 3′ mRNA-Seq library


title: Argonaute HK2_TGF1


title: iCtrl, 60d, scRNA-seq

city: Esch sur Alzette

first: Alise

last: Zagare

state: Belval

address: 7 Avenue des Hauts-Fourneaux

country: Luxembourg

institute: University of Luxembourg

data_processing:
The reads were demultiplexed according to the multiplexing index sequencing on Illumina’s BaseCloud platform
Pre-processing of Fastq data were conducted using CeleScope® (v.1.3.0;www.github.com/singleron-RD/CeleScope; Singleron Biotechnologies GmbH) to generate raw data, using default parameters. Low-quality reads were removed.
Sequences were mapped usingSTAR(https://github.com/alexdobin/STAR), and the human reference GRCh38 and genes were annotated using Ensembl 92.
The reads were assigned to genes usingfeatureCount(https://subread.sourceforge.net/) and the cell calling was performed by fitting a negative bimodal distribution and determining the threshold between empty wells and cell-associated wells to generate a count matrix file containing the number of Unique Molecular Identifier (UMI) for each gene within each cell.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and count matrix

source_name: midbrain organoid

growth_protocol: Organoids were generated and culturedas described in Monzel et al. 2017.

extract_protocol:
Midbrain organoids were collected from their culture medium and washed with 1x PBS (phosphate-buffered saline, Gibco, cat. nr. 10010-23). Organoids were digested in 1 ml sCelLive™ Tissue Dissociation Solution (Singleron Biotechnologies, cat. nr. 1190062) in a 15 ml conical tube (Sarstedt, cat. nr. 62.5544.003) and placed in a thermal shaker at 50 rpm at 37°C for 30 minutes. The state of dissociation was checked at regular intervals under a light microscope. Following digestion, the suspension was filtered using a 40-µm sterile strainer (Greiner, cat nr. 542040). The cells were centrifuged at 350xg for 5 minutes at 4°C, and the cell pellets were resuspended in 500µl PBS. Cells were stained with Acridine Orange/Propidium Iodide Stain (Logos Biosystems, cat. nr. F23001), and the cell number and viability were calculated using LUNA-FX7™ Automated Cell Counter (Logos Biosystems, Villeneuve d’Ascq, France).
The single-cell RNA-seq libraries were constructed using GEXSCOPE™ Single Cell RNAseq Library Kit (Singleron Biotechnologies, cat nr. 4161031) according to the manufacturer´s instructions. Briefly, for each library, the concentration of the single-cell suspension was adjusted to 3x105 cells/ml with PBS, and the suspension was loaded onto an SD microfluidic chip to capture 6000 cells. Paramagnetic beads conjugated to oligodT probes that carry a unique molecular identifier (UMI) and a barcode unique to each bead (from the same kit) were loaded, after which the cells were lysed. The beads bound to polyadenylated mRNA were extracted from the chip and reverse transcribed into cDNA at 42°C for 1.5 hours, and the cDNA was amplified by PCR. The cDNA was then fragmented and ligated to indexed Illumina adapters. The fragment size distribution of the final amplified library was obtained on an Agilent Fragment Analyzer.

value: midbrain organoid

tag: subject status

value: isogenic control

tag: source cell_type

value: iPSC

value: GC Miro1 R272Q

value: 60 days culture


title: 1407

value: F


title: Mycelium grown in the dark, sampled from the earliest timepoint, 84h, replica 3

description:
Library name: DM_84h_3
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: Mycelium grown in the dark, sampled from the earliest timepoint, 36h, replica 3

description:
Library name: DM_36h_3
QuantSeq 3′ mRNA-Seq library


title: Mycelium grown in the dark, sampled from the earliest timepoint, 60h, replica 1

description:
Library name: DM_60h_1
QuantSeq 3′ mRNA-Seq library


title: 1442


title: Argonaute HK2_1

value: HK2 cell line

value: WT

value: control


title: 1266


title: HK2TGFb_48hrs_4 miRNA

data_processing:
FASTQ files generated with Illumina’s bcl2fastq v2.20.0.422
Insert sequences had adaptor sequences trimmed and inserts <18 nt or >30nt were removed
Sequences were  mapped to mature miRNA sequences in miRBase 21 using a custom Python script. Unmapped sequences were discarded. Counts for sequences with equivalent mappings to multiple miRNA sequences were divided among the matches.
Read counts for miRNAs were normalized to input library size; the most frequent sequence for each mature miRNA was determined.
Assembly: miRbase21
Supplementary files format and content: matrix file of miRNA counts in each sample (counts per million), as well as most frequent sequence (MFS) for each miRNA in HK2_1 sample.

extract_protocol:
Total RNA was extracted using TRIzol, then denatured and separated on a 15% TBE urea gel.18-30 nt small RNA was recovered from a gel slice.
Gel purified small RNA from 1 µg total RNA was used to prepare a small RNA library using a NEB Next Multiplex Small RNA Library Prep Kit (New England Biolabs) according the manufacturer’s directions, with the following modification: after reverse transcription, the reaction was denatured, separated on a 10% TBE urea gel; a gel slice corresponding to 60 to 80 nt was isolated (based on size markers in an adjacent lane: low range ssRNA ladder, NEB). The reverse transcribed product in the gel slice was eluted, precipitated by adding 2-propanol, suspended in Tris-Hcl buffer, and then used in subsequent steps.

treatment_protocol: Cells were serum starved for 24 hrs, then exposed to TGFb1 at 20 ng/mL for 24 or 48 hrs as indicated (control no treatment); all cells were treated with 100 μM 4SU for the final 20h before harvest.

value: TGF-beta, 48hrs


title: 1324


title: 1285


title: Mycelium grown in the dark, sampled from the earliest timepoint, 36h, replica 2

description:
Library name: DM_36h_2
QuantSeq 3′ mRNA-Seq library


title: PBMCs, scRNA-seq, sublibrary 15

city: Stanford

first: Leslie

last: Chan

state: CA

address: 300 Pasteur Dr Bldg S131, Grant

institute: Stanford University

data_processing:
ParseBiosciences-Pipeline.1.0.3p was used to identify barcodes, align sequencing reads, assign transcript counts to genes, and generate a cell-by-gene count matrix
After running each sublibrary through the pipeline, the outputs of each sublibrary were combined into a single dataset
Assembly: Custom genome containing the human genome (HG38) and the annotated Wuhan-Hu-1 SARS-CoV-2 reference sequence (NC_045512.2)
Supplementary files format and content: .mtx file containing expression matrix

source_name: Peripheral blood

extract_protocol:
PBMCs were fixed using Parse fixation reagents, frozen at -80°C for less than 6 months, and prepped according to Parse Evercode WT Mega v2 protocol. In this combinatorial split pool barcoding process, samples were first loaded into a 96-well plate and underwent reverse transcription with barcoded primers, pooled, split and barcoded again, followed by cell lysis using Parse reagents.
According to Parse Evercode WT Mega v2 protocol. First, cDNA was amplified, then underwent fragmentation, adaptor ligation, sublibrary index PCR, and double-sided size selection. Sequencing was performed on a NovaSeq S4 instrument (Illumina; Chan Zuckerberg Biohub). The read structure was paired-end with i7 index, i5 index, and the 4th barcode (6bp) that tags each sublibrary acting as a standard Illumina index.

value: Peripheral blood

tag: cell type

value: Cryopreserved PBMCs

tag: participant group

value: Pooled PBMCs


title: IgG control1 HK2

value: IgG


title: Mycelium grown in the dark, sampled from the earliest timepoint, 12h, replica 3

description:
Library name: DM_12h_3
QuantSeq 3′ mRNA-Seq library


title: PD, 60d, scRNA-seq

value: Parkinson's disease patient

value: PD Miro1 R272Q


title: Ctrl, 60d, scRNA-seq

value: midbrain organoid

value: healthy control

value: Ctrl


title: HK2TGFb_48hrs_3 miRNA


title: Mycelium grown in the dark, sampled from the earliest timepoint, 36h, replica 1

description:
Library name: DM_36h_1
QuantSeq 3′ mRNA-Seq library


title: HK2TGFb_24hrs_2 miRNA

value: TGF-beta, 24hrs


title: 1259

value: Cerebellum

value: M


title: PBMCs, scRNA-seq, sublibrary 14


title: 1185


title: Mycelium grown in the dark, sampled from the earliest timepoint, 12h, replica 2

description:
Library name: DM_12h_2
QuantSeq 3′ mRNA-Seq library

value: Vegetative mycelium


title: HK2TGFb_24hrs_1 miRNA

value: HK2 cell line


title: PBMCs, scRNA-seq, sublibrary 13


title: Mycelium grown in the dark, sampled from the earliest timepoint, 12h, replica 1

description:
Library name: DM_12h_1
QuantSeq 3′ mRNA-Seq library


title: Argonaute HK2_2

value: Argonaute

value: WT


title: HK2_4 miRNA

value: control


title: PBMCs, scRNA-seq, sublibrary 16

value: Peripheral blood


title: Germinating basidiospores, 12h, replica 3

description:
Library name: BS_12h_3
QuantSeq 3′ mRNA-Seq library

source_name: Basidiospore

value: Basidiospore


title: 1101

value: F


title: PBMCs, scRNA-seq, sublibrary 12

value: Cryopreserved PBMCs

value: Pooled PBMCs


title: 1063


title: PBMCs, scRNA-seq, sublibrary 11


title: HK2_3 miRNA


title: 1052


title: HK2_2 miRNA


title: 1027


title: Germinating basidiospores, 12h, replica 1

description:
Library name: BS_12h_1
QuantSeq 3′ mRNA-Seq library


title: 1038


title: Germinating basidiospores, 12h, replica 2

description:
Library name: BS_12h_2
QuantSeq 3′ mRNA-Seq library


title: PBMCs, scRNA-seq, sublibrary 9


title: Germinating basidiospores, 8h, replica 3

description:
Library name: BS_8h_3
QuantSeq 3′ mRNA-Seq library


title: PBMCs, scRNA-seq, sublibrary 10


title: HK2TGFb_1 RNA

data_processing:
FASTQ files generated with Illumina’s bcl2fastq v2.20.0.422
Sequences were mapped to hg38 with STAR v2.7.1a.
Mapped reads were annotated to genes in GenCode v27 using DESeq2
Assembly: hg38
Supplementary files format and content: Matrix file of reads per gene (rpkm) for each sample

extract_protocol:
Total RNA was extracted using TRIzol.
NEBNext Ultra Directional RNA Library Prep Kit was used for making the libraries according to the manufacturer's directions.

treatment_protocol: Cells were serum starved for 24 hrs, then exposed to TGFb1 at 20 ng/mL for 24 hrs; cells were treated with 100 μM 4SU for the final 20h before harvest.


title: PBMCs, scRNA-seq, sublibrary 8


title: 1025

data_processing: Methylation Module in GenomeStudio

extract_protocol: Genomic DNA from cerebellum samples were extracted using Proteinase K Phenol-chloroform method


title: HK2TGFb_2 RNA


title: PBMCs, scRNA-seq, sublibrary 7


title: Germinating basidiospores, 8h, replica 1

description:
Library name: BS_8h_1
QuantSeq 3′ mRNA-Seq library


title: HK2_2 RNA


title: 814


title: PBMCs, scRNA-seq, sublibrary 6


title: Germinating basidiospores, 4h, replica 3

description:
Library name: BS_4h_3
QuantSeq 3′ mRNA-Seq library


title: 777


title: 771


title: Germinating basidiospores, 4h, replica 2

description:
Library name: BS_4h_2
QuantSeq 3′ mRNA-Seq library


title: HK2_1 RNA


title: LCL_pV_ICF2 [RNA-Seq]

city: Paris

first: Guillaume

last: Velasco

address: 35 rue Hélène Brion

department: UMR7216 Epigenetics and Cell Fate

country: France

institute: Université Paris Cité

data_processing:
Paired end (2 × 75) sequencing was performed on an Illumina NextSeq 500 platform, demultiplexing and quality control were performed with the AOZAN software (based on bcl2fastq v2.20 and FastQC modules / v0.11.5).
The quality of raw data has been evaluated with FastQC. Poor quality sequences have been trimmed or removed with Trimmomatic software. Star v2.5.3a has been used to align reads on reference genome (mm10/hg38) using standard options.
Quantification of gene and isoform abundances has been done with rsem 1.2.28, prior to normalisation on library size with DESEq2 bioconductor R package. Finally, differential analysis has been conducted with edgeR bioconductor R package.
Assembly: mm10 or hg38
Supplementary files format and content: bigWig files for visualization of RNA-seq tracks

source_name: LCLs

growth_protocol: mESCs  were maintained in the absence of feeder cells, on plates coated with 1x Laminin in serum-free 2i medium containing  Dulbecco’s modified Eagle’s medium (DMEM) F12 Glutamax supplemented with  50% Neurobasal medium , N2 and B27 Supplements, penicillin/streptomycin, non-essential amino acids, 2-mercaptoethanol, CHIR99201, PD032552 inhibitors and Leukemia Inhibitory Factor. Cells were passaged every two days and maintained at 37ºC with 8% CO2 in a humidified chamber. Human Lymphoblastoid Cell Lines (LCLs) from healthy donors and ICF2 patients were cultured in RPMI 1640 supplemented with 15% FCS and antibiotics.

extract_protocol:
Total RNAs from cell lines were isolated using TRI Reagent according to manufacturer’s instructions. Contaminant genomic DNA was eliminated with TURBO DNA-free Kit . RNA quality was verified using the Bioanalyzer RNA 6000 Nano kit.
The libraries were prepared following the TruSeq Stranded Total RNA protocol from Illumina, starting from 1 µg of high-quality total RNA (RIN > 7)

treatment_protocol: For in vitro differentiation, mESCs were grown in bacteriological Petri dish with differentiation medium containing 25% Advanced DMEM, 25% DMEM/F12 GlutaMAX, 50% Neurobasal medium, penicilline/streptavidin, β-mercatoethanol and 11% of knock out serum, at 37ºC with 5% CO2. The differentiation medium was changed every day and embryoid bodies were collected by centrifugation and resuspended in fresh medium.

value: LCLs

value: lymphobalstoid cells

value: ZBTB24 mutant

value: Male


title: PBMCs, scRNA-seq, sublibrary 5


title: 754


title: HK2_1 miRNA


title: Germinating basidiospores, 4h, replica 1

description:
Library name: BS_4h_1
QuantSeq 3′ mRNA-Seq library


title: Germinating basidiospores, 0h, replica 3

description:
Library name: BS_0h_3
QuantSeq 3′ mRNA-Seq library


title: 616


title: LCL_pD_ICF2 [RNA-Seq]


title: PBMCs, scRNA-seq, sublibrary 4


title: PBMCs, scRNA-seq, sublibrary 3


title: Germinating basidiospores, 0h, replica 2

description:
Library name: BS_0h_2
QuantSeq 3′ mRNA-Seq library


title: Germinating basidiospores, 8h, replica 2

description:
Library name: BS_8h_2
QuantSeq 3′ mRNA-Seq library


title: LCL_2591 [RNA-Seq]