title: E14.5 mouse embryonic maxillary prominence, scRNA seq

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
After extracting read one without poly T tails, cell barcode or UMI, raw sequencing reads of scRNA-Seq libraries were trimmed by fastp V1 to remove adapters and poly A tails before aligning read two to GRCm38 with ensemble version 92 gene annotation (fastp 2.5.3a and featureCounts 1.6.2). The number of UMIs per gene per cell was estimated by counting the reads with the same cell barcode and UMI. The UMI count tables of each cellular barcode were imported for downstream analysis.
Cell type identification and clustering analysis was performed using Seurat program (http://satijalab.org/seurat/). Cell-by-gene counts expression matrices were imported to Seurat. Cells with <200 unique genes and 1500 unique molecular identifiers (UMI) or >3000 unique genes and 15,000 UMI were excluded from downstream analysis.
The expression data were then log transformed, normalized, and scaled for sequencing depth by following the standard Seurat processing pipeline. Clustering of maxillary cells was performed on 111384 cells from E14.5 maxillary prominences, respectively, in Seurat at a resolution of 0.8. The identities of the resultant clusters were inferred using literature-derived marker genes.
Cell cycle analysis was performed using the CellCycleScoring function in Seurat and a list of cell cycle markers from a previous study (Tirosh et al., Science, 2016). Due to the strong influences of cell cycle states on clustering. G1 stage mesenchymal cells at E14.5 were selected for further clustering analysis using resolutions of 0.5, 0.6 and 0.6, respectively. The G1 mesenchymal cells from all stages were then combined and clustered at a resolution of 0.6. Marker genes associated with each mesenchymal cell subpopulation were identified using the FindAllMarkers function in Seurat.
Genome_build: GRCm38
Supplementary_files_format_and_content: rds

source_name: maxillary prominence

extract_protocol:
Fresh maxillary prominence tissues were conserved in the GEXSCOPE® Tissue Preservation Solution (Singleron) until library preparation. scRNA-seq libraries were constructed using a microwell-based system (Zhang K, et al., Nucleic Acids Research, 2018). Briefly, the specimens were washed 3 times with Hanks Balanced Salt Solution (HBSS, Gibco, Cat. No.14025-076), shredded into 1–2 mm pieces, and then digested with 2ml GEXSCOPE® Tissue Dissociation Solution (Singleron) at 37℃ for 15min in a 15ml centrifuge tube (Falcon, Cat. No.352095) with sustained agitation. After digestion, cells were filtered through 40-micron sterile strainers (Falcon, Cat. No.352340) and centrifuged (Eppendorf, 5810R) at 1,000rpm for 5 minutes. The supernatant was removed, and the pellets were resuspended in 1ml PBS (Hyclone, Cat. No.SA30256.01). To remove the red blood cells, 2 mL RBC lysis buﬀer (Roche, Cat. No. 11 814 389 001) was added to the cell suspension according to the manufacturer’s protocol. Cells were collected by centrifugation at 500g for 5 min and resuspend in PBS (Hyclone, Cat. No.SA30256.01). An aliquot from the cell mixture was stained with trypan blue (Bio-RAD, Cat. No.#1450013) and counted on an ECLIPSE Ts2 cellcounter (Nikon). The concentration of the single-cell suspension was adjusted to 1×10e5 cells/mL using PBS.
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPETM protocol by GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X Ten with 150 bp paired end reads.
scRNA seq

treatment_protocol: On Embryo 14.5, pregnant C57BL/6 females were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: embryo 14.5

value: wild type

value: maxillary prominence


title: whole body discarding last third from the cloaca, 23dph, rep1

status: Public on Feb 15 2023

type: SRA

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

library_source: transcriptomic

data_processing:
Reads were mapped to turbot genome assembly using STAR alignment software
Number of aligned reads overlapping each gene was calculated using HTseq-count software
Count matrix was normalized using median of ratios methos with DESEq R package
Assembly: Turbot genome: http://ftp.ensembl.org/pub/release-107/fasta/scophthalmus_maximus/dna/
Supplementary files format and content: Gene counts from Htseq-count
Supplementary files format and content: bigWig format for displaying in a genome browser track

molecule: total RNA

organism: Scophthalmus maximus

extract_protocol:
Total RNA of each developmental stage was isolated using Rneasy Mini Kit (Qiagen) with Dnase digestion treatment (Qiagen)
Library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

tag: tissue

tag: developmental stages

value: 23 days post hatching


title: YH9,NA_3,Day0

city: HeFei

first: Yaohua

last: Cheng

address: Changjiang West Road 130

country: China

institute: Anhui  Agricultural University

description: Camellia. sinensis var. assamica cv. ‘Yinghong 9’

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10

organism: Camellia sinensis var. assamica

source_name: tissue culture of tea seedlings(height of 4-5 cm)

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: cultivar

tag: treatment

value: normal temperature (25°C daytime, 20°C night)


title: FECD case 9

type: genomic

city: Umeå

first: Ida Maria

last: Westin

address: NUS, 6M

department: Medical Biosciensces

country: Sweden

institute: Umeå University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: HiScan array reader (Illumina)

data_processing: Normalization was done with BMIQ version 1.3 (Teschendorff, A.E. et al. 2013) and annotation and pre-filtering was done in R version 3.6.2. The pre-filtering steps excluded CpGs with detection p-value > 0.05, CpG probes that aligned to multiple loci in the genome or were located less than 5 bp from a known single nucleotide polymorphism (Zhou, W. et al. 2017) and CpGs probes identified as meQTLs (Gaunt, T. R. et al. 2016, McClay, J. L. et al. 2015).

molecule: genomic DNA

organism: Homo sapiens

source_name: corneal endothelium

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from human corneal endothelium was extracted using NucleoSpin Tissue XS (Macherey-Nagel, Düren, Germany)

treatment_protocol: EZ DNA Methylation kit (Zymo Research, Irvine, USA) was applied for bisulfite conversion of genomic DNA from corneal endothelium

tag: relative age

value: elderly

tag: disease

value: FECD


title: BJR_P0_KO6

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

institute: CNB-CSIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.76 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method), considering only those genes for which expression was at least 1 count per million (CPM) in at least 3 samples.
Genome_build: GRCm38.76
Supplementary_files_format_and_content: NormCounts.xlsx: TMM-normalized counts (CPM) for genes with expression level of at least 1 count per million (CPM) in at least 3 samples.

organism: Mus musculus

source_name: Perinatal heart

extract_protocol:
Total RNA from P0 hearts of wild type (WT) and cardiomyocyte-specific RXRab-/- newborns was prepared with RNeasy Mini kit (Qiagen) by standard protocols from 3-4 biological replicates.
cDNA was synthesized and amplified from total RNA (1-10 ng) using the Ovation® RNA-seq System v2 (NuGEN® Technologies). Sequencing was performed using the Illumina HiSeq-2500 system (1x61 reads).

value: Total heart

tag: strain

tag: genotype

value: edKO

tag: age


title: whole body discarding last third from the cloaca, 15dph, rep1

value: 15 days post hatching


title: BJR_P0_WT2

value: Wild-type


title: E12.5 mouse embryonic maxillary prominence, scRNA seq

city: Shanghai

data_processing:
After extracting read one without poly T tails, cell barcode or UMI, raw sequencing reads of scRNA-Seq libraries were trimmed by fastp V1 to remove adapters and poly A tails before aligning read two to GRCm38 with ensemble version 92 gene annotation (fastp 2.5.3a and featureCounts 1.6.2). The number of UMIs per gene per cell was estimated by counting the reads with the same cell barcode and UMI. The UMI count tables of each cellular barcode were imported for downstream analysis.
Cell type identification and clustering analysis was performed using Seurat program (http://satijalab.org/seurat/). Cell-by-gene counts expression matrices were imported to Seurat. Cells with <200 unique genes and 1500 unique molecular identifiers (UMI) or >3000 unique genes and 15,000 UMI were excluded from downstream analysis.
The expression data were then log transformed, normalized, and scaled for sequencing depth by following the standard Seurat processing pipeline. Clustering of maxillary cells was performed on 5291, 6522, and 5277 cells from E10.5, E11.5 and E12.5 maxillary prominences, respectively, in Seurat at a resolution of 0.8. The identities of the resultant clusters were inferred using literature-derived marker genes.
Cell cycle analysis was performed using the CellCycleScoring function in Seurat and a list of cell cycle markers from a previous study (Tirosh et al., Science, 2016). Due to the strong influences of cell cycle states on clustering. G1 stage mesenchymal cells at E10.5, E11.5 and E12.5 were selected for further clustering analysis using resolutions of 0.5, 0.6 and 0.6, respectively. The G1 mesenchymal cells from all stages were then combined and clustered at a resolution of 0.6. Marker genes associated with each mesenchymal cell subpopulation were identified using the FindAllMarkers function in Seurat.
Genome_build: GRCm38
Supplementary_files_format_and_content: rds

growth_protocol: C57BL/6 mice were purchased from Shanghai Jihui Laboratory Animal Care Co.Ltd. All mice were maintained in SPF conditions at the Animal Center of the Ninth People’s hospital affiliated to Shanghai Jiaotong University School of medicine. Female and male mice between the ages of 8 to 12 weeks were used.

extract_protocol:
Fresh maxillary prominence tissues were conserved in the GEXSCOPE® Tissue Preservation Solution (Singleron) until library preparation. scRNA-seq libraries were constructed using a microwell-based system (Zhang K, et al., Nucleic Acids Research, 2018). Briefly, the specimens were washed 3 times with Hanks Balanced Salt Solution (HBSS, Gibco, Cat. No.14025-076), shredded into 1–2 mm pieces, and then digested with 2ml GEXSCOPE® Tissue Dissociation Solution (Singleron) at 37℃ for 15min in a 15ml centrifuge tube (Falcon, Cat. No.352095) with sustained agitation. After digestion, cells were filtered through 40-micron sterile strainers (Falcon, Cat. No.352340) and centrifuged (Eppendorf, 5810R) at 1,000rpm for 5 minutes. The supernatant was removed, and the pellets were resuspended in 1ml PBS (Hyclone, Cat. No.SA30256.01). To remove the red blood cells, 2 mL RBC lysis buﬀer (Roche, Cat. No. 11 814 389 001) was added to the cell suspension according to the manufacturer’s protocol. Cells were collected by centrifugation at 500g for 5 min and resuspend in PBS (Hyclone, Cat. No.SA30256.01). An aliquot from the cell mixture was stained with trypan blue (Bio-RAD, Cat. No.#1450013) and counted on an ECLIPSE Ts2 cellcounter (Nikon). The concentration of the single-cell suspension was adjusted to 1×10e5 cells/mL using PBS.
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPETM protocol by GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X Ten with 150 bp paired end reads.

treatment_protocol: One embryo 10.5(E10.5), 11.5, or 12.5, pregnant C57BL/6 female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: embryo 12.5


title: Lens epithelial explants, Immediate collection ATAC_IMD_B

city: OXFORD

first: Anil

last: Upreti

state: OH

address: 501 E High St, Oxford, OH 45056

department: Biology

country: USA

institute: Miami University

data_processing:
Raw reads were trimmed using Cutadapt 3.4 and Trim Galore 0.6.5-1 with the trimming parameters -q 20 --phred33 --length 20.
Alignment of raw reads to the Mus musculus genome GRCm39 was performed with Bowtie2 using the parameters -X 2000 --very-sensitive-local --no-mixed --no-discordant --no-dovetail.
Peaks were called for samples individually with MACS2 using parameters -f BAMPE -g mm -q 0.05. Peaks aligning to the mitochondrial chromosome were discarded.Differential expression testing of peak regions and peak summits was performed with DESeq2.
ATAC coverage tracks were visualized using the Integrative Genomics Viewer.Prior to visualization, BAM files were converted to BIGWIG format and normalized using the bamCoverage --binSize 1 and --scaleFactor parameter using the inverse of DESeq2 size factors.
Differential expression testing was performed with DESeq2.
Assembly: GRCm39 v.M27
Supplementary files format and content: ATAC_seq_normalized_count.csv

source_name: Lens Epithelium

growth_protocol: Lens epitheliall explants were maintained in 35mm culture dish with either pre-calibrated M-199 media supplemented with 1% antibiotic-antimycotic solution  and 0.1% bovine serum albumin  henceforth referred to as “culture medium (CM)” or cultured in vitreous, diluted by CM to 50% concentration, henceforth referred to as “differentiation medium (DM)”, for 1 day or 5 days at 37 °C and 5% CO2.

extract_protocol:
Chromatin was extracted using ATAC-seq kit from Active motif (53150) as per the manufacturers instructions.
ATAC-seq library preparation was performed using ATAC-Seq kit (53150) per the manufacturer’s instructions

value: Lens Epithelium

value: FVB/N

value: Immediate Collection


title: whole, 3dpf, rep2

source_name: whole animal

value: whole animal

value: 3 days post fertilization


title: E11.5 mouse embryonic maxillary prominence, scRNA seq

value: embryo 11.5


title: BJR_P0_WT1


title: YH9,NA_1,Day0

value: tissue culture of tea seedlings(height of 4-5 cm)


title: E10.5 mouse embryonic maxillary prominence, scRNA seq

value: embryo 10.5

value: wild type

value: maxillary prominence


title: whole, 3dpf, rep1


title: 4330_G1E-GATA1(V205M)-ER_-E2_LDB1_rep2

status: Public on Feb 14 2023

city: Philadelphia

first: Marit

middle: W.

last: Vermunt

state: PA

address: 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Phildelphia

library_source: genomic

data_processing:
Bowtie 1.2.1.1 was used to align sequences. Reads with more than one mismatch or multiple alignments were excluded.
Significantly enriched regions were called using MACS2 version 2.1.0 with the following parameters: P = 10−5, extsize = 300 and local lambda = 100,000 using whole-cell extract input controls.
Reads were RPM normalized for  bigwigs.
Assembly: mm9
Supplementary files format and content: bigwig files

source_name: G1E-ER4 V205M

growth_protocol: G1E, G1E-ER4 and G1E-GATA1(V205M)-ER cells were grown in IMDM media (Corning, 10-016-CV) with 15% fetal calf serum (Gemini, lot A08H00K), 2% penicillin/streptomycin (Gibco, 15140-122), 140 μm 1-thioglycerol (Sigma, M6145), 2 units/ml epoetin (Amgen) and conditioned medium from a kit ligand-producing CHO cell line. Cells were grown at a cell density of 100,000 to 1,000,000 cells/ml.

extract_protocol:
Cells were crosslinked in 1% formaldehyde in PBS/2mM EDTA at room temperature for 10 minutes. Reaction was quenched with glycine. Cell pellets were washed in PBS, resuspended in 1 ml cell lysis buffer (Methods) and incubated on ice for 20 minutes. Nuclei were pelleted and resuspended in 1 ml nuclear lysis buffer, incubated on ice for 20 minutes and sonicated for 45 minutes at 4 degrees Celsius. After sonication, samples were spun at 21130×g for 5 minutes at 4C. Supernatant (~ 1 ml) was diluted using 4 ml IP Dilution Buffer (Methods). Samples were precleared using 50 ug of isotope-matched IgG and 50 ul A/G agarose beads. IP reactions were set up by adding A/G beads pre-bound with antibody of interest and rotated overnight at 4 degrees Celsius. On the second day, beads were washed and eluted twice with 100 ul Elution Buffer. After reverse crosslinking, DNA was purified using the QIAquick PCR Purification kit per the manufacturer’s instructions.
ChIP-seq libraries were prepared using Illumina’s TruSeq ChIP sample preparation kit (Illumina, Cat#IP-202-1012) according to manufacturer’s protocol.

treatment_protocol: Erythroid maturation experiments were performed by plating cells at a cell density of ~200,000 cells/ml in fresh G1E medium containing 100 nm estradiol (Sigma, E2758) for durations indicated for each experiment.

tag: cell type

value: G1E-ER4 V205M

tag: antibody

value: Santa Cruz sc-365074

value: G1E cells expressing GATA1(V205M)-ER


title: 4329_G1E-ER4_+E2_24_hours_LDB1_rep2

value: Estradiol (E2) for 24 hours

value: G1E cells expressing GATA1-ER


title: 4331_G1E-GATA1(V205M)-ER_+E2_13_hours_LDB1_rep2

value: Estradiol (E2) for 13 hours


title: 4328_G1E-ER4_+E2_13_hours_LDB1_rep2


title: 4327_G1E-ER4_-E2_LDB1_rep2


title: 4148_G1E-ER4_-E2_LDB1_rep1


title: 4179_G1E-GATA1(V205M)-ER_+E2_13_hours_MTA2_rep1

value: Abcam #ab8106


title: 4108_G1E-GATA1(V205M)-ER_+E2_13_hours_LDB1_rep1


title: 4107_G1E-GATA1(V205M)-ER_-E2_LDB1_rep1


title: 4410_G1E-GATA1(V205M)-ER_+E2_24_hours_MTA2_rep1


title: whole body discarding last third from the cloaca, 15dph, rep2

value: 15 days post hatching


title: 4149_G1E-ER4_+E2_13_hours_LDB1_rep1


title: 4332_G1E-GATA1(V205M)-ER_+E2_24_hours_LDB1_rep2


title: 4343_G1E-GATA1(V205M)-ER_+E2_13_hours_MTA2_rep2


title: 4178_G1E-GATA1(V205M)-ER_-E2_MTA2_rep1


title: FECD case 1

value: elderly

value: FECD


title: 4344_G1E-GATA1(V205M)-ER_+E2_24_hours_MTA2_rep2


title: FECD case 2


title: FECD case 3


title: 4407_G1E-ER4_+E2_24_hours_MTA2_rep1


title: 4340_G1E-ER4_+E2_13_hours_MTA2_rep2


title: 4341_G1E-ER4_+E2_24_hours_MTA2_rep2


title: 4155_G1E-ER4_+E2_13_hours_MTA2_rep1


title: FECD case 4


title: 4338_G1E-GATA1(V205M)-ER_+E2_24_hours_CHD4_rep2

value: Abcam #ab70469


title: 4176_G1E-GATA1(V205M)-ER_+E2_13_hours_CHD4_rep1


title: 4339_G1E-ER4_-E2_MTA2_rep2


title: 4175_G1E-GATA1(V205M)-ER_-E2_CHD4_rep1


title: 4154_G1E-ER4_-E2_MTA2_rep1


title: 4337_G1E-GATA1(V205M)-ER_+E2_13_hours_CHD4_rep2


title: 4411_G1E-GATA1(V205M)-ER_+E2_24_hours_CHD4_rep1


title: YH9,NA_2,Day0

value: normal temperature (25°C daytime, 20°C night)


title: 4336_G1E-GATA1(V205M)-ER_-E2_CHD4_rep2


title: 4335_G1E-ER4_+E2_24_hours_CHD4_rep2


title: 4334_G1E-ER4_+E2_13_hours_CHD4_rep2


title: 4157_G1E-ER4_-E2_CHD4_rep1


title: 4333_G1E-ER4_-E2_CHD4_rep2


title: 4535_MFL_KITlo(0)CD71hi

description: Lineage negative hematopoietic cells isolated from E13.5 mouse fetal liver , cultured for 2 days in expansion medium as per McIver et al., 2018. Sorted based on KIT(CD117) and CD71 levels.

source_name: Mouse fetal liver

growth_protocol: Lineage negative hematopoietic cells were isolated from E13.5 mouse fetal liver and expanded according to McIver et al., 2018.

extract_protocol:
Cells were crosslinked in 1% formaldehyde prior to sorting in PBS/2mM EDTA at room temperature for 10 minutes. Reaction was quenched with glycine. Cell pellets were washed in PBS, resuspended in 1 ml cell lysis buffer (Methods) and incubated on ice for 20 minutes. Nuclei were pelleted and resuspended in 1 ml nuclear lysis buffer, incubated on ice for 20 minutes and sonicated for 45 minutes at 4 degrees Celsius. After sonication, samples were spun at 21130×g for 5 minutes at 4C. Supernatant (~ 1 ml) was diluted using 4 ml IP Dilution Buffer (Methods). Samples were precleared using 50 ug of isotope-matched IgG and 50 ul A/G agarose beads. IP reactions were set up by adding A/G beads pre-bound with antibody of interest and rotated overnight at 4 degrees Celsius. On the second day, beads were washed and eluted twice with 100 ul Elution Buffer. After reverse crosslinking, DNA was purified using the QIAquick PCR Purification kit per the manufacturer’s instructions.
ChIP-seq libraries were prepared using Illumina’s TruSeq ChIP sample preparation kit (Illumina, Cat#IP-202-1012) according to manufacturer’s protocol.

value: Mouse fetal liver

value: anti-H3K27ac Active Motif #39133


title: 4546_MFL_KIThi(100)CD71hi_Input


title: 4619_MFL_KITlo(0)CD71med

description: Lineage negative hematopoietic cells isolated from E13.5 mouse fetal liver , cultured for 4 days in expansion medium as per McIver et al., 2018. Sorted based on KIT(CD117) and CD71 levels.


title: 4536_MFL_KITlo(20)CD71hi


title: 4540_MFL_KIThi(100)CD71hi


title: 4618_MFL_KIThiCD71med

description: Lineage negative hematopoietic cells isolated from E13.5 mouse fetal liver , cultured for 1 day in expansion medium as per McIver et al., 2018


title: 4538_MFL_KITmed(60)CD71hi


title: 4539_MFL_KIThi(80)CD71hi


title: 4408_G1E-ER4_+E2_24_hours_CHD4 _rep1


title: 4409_G1E-GATA1(V205M)-ER_+E2_24_hours_LDB1_rep1


title: 4158_G1E-ER4_+E2_13_hours_CHD4_rep1


title: 4406_G1E-ER4_+E2_24_hours_LDB1_rep1


title: G1E_ER4_cloneC_subclone_del49kb#1_-E2_4C_+5kb_viewpoint

data_processing:
4C mapping was done as described here https://github.com/deWitLab/4C_mapping
PeakC was used to call 4C peaks https://github.com/deWitLab/peakC
Assembly: mm9
Supplementary files format and content: wig
Library strategy: 4C-seq

extract_protocol: 4C-seq protocol was performed as previously described: Krijger et al., 2020. 4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis.

value: expressing GATA1-ER


title: G1E_ER4_cloneC_subclone_del49kb#1_+E2_13_hours_4C_+5kb_viewpoint


title: G1E_ER4_cloneC_subclone_Ctr#1_-E2_4C_+5kb_viewpoint


title: G1E_ER4_cloneB_subclone_Ctr#1_+E2_13_hours_4C_+5kb_viewpoint


title: G1E_ER4_cloneA_subclone_del49kb#1_-E2_4C_+5kb_viewpoint


title: G1E_ER4_cloneB_subclone_del49kb#1_-E2_4C_+5kb_viewpoint


title: G1E_ER4_cloneA_subclone_del49kb#1_+E2_13_hours_4C_+5kb_viewpoint


title: G1E_ER4_cloneB_subclone_Ctr#1_-E2_4C_+5kb_viewpoint


title: G1E_ER4_cloneA_subclone_Ctr#1_-E2_4C_+5kb_viewpoint


title: Retina WT rep4 [WT-c4]

city: Boston

first: Gracia

last: Bonilla

state: MA

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Illumina software used for basecalling.
Reads were mapped using the STAR aligner (Dobin, Davis et al. 2013) and the mm9 assembly of the mouse genome.
Read counts for individual transcripts were obtained using HTSeq (Anders, Pyl et al. 2014) and the GENCODE M1 (NCBIM37) gene annotation.
Analysis of differential expression was performed using only genes with normalized counts (CPM) >=1 for at least one sample
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Retina

extract_protocol:
Retinas were dissected in ice-cold PBS and embryonic hylaoid blood vessels were removed. Retinas were immediately transfered to 1 ml of RNA STAT-60 and the retinal tissue was homogenized using 26 guage needle syringe and RNA was harvested using as recommended by the manufacturer (amsbio, LLC). As recommended by the manufacturer (New England BioLabs, Inc) poly (A) mRNA was isolated (using NEBNext®) and 500ng of RNA was used for construction of sequencing libraries (using NEBNext ultra II directional library prep kit for Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: post natal day 5

value: wild type


title: Retina C3 KO rep4 [KO-c8]

value: C3 KO


title: 4537_MFL_KITmed(40)CD71hi


title: Retina C3 KO rep3 [KO-c7]


title: 4342_G1E-GATA1(V205M)-ER_-E2_MTA2_rep2

value: G1E-ER4 V205M

value: G1E cells expressing GATA1(V205M)-ER


title: Retina C3 KO rep2 [KO-c6]


title: Retina C3 KO rep1 [KO-c5]


title: Retina WT rep3 [WT-c3]


title: Retina WT rep2 [WT-c2]


title: Retina WT rep1 [WT-c1]


title: G1E_ER4_cloneB_subclone_del49kb#1_+E2_13_hours_4C_+5kb_viewpoint


title: G1E_ER4_cloneC_subclone_Ctr#1_+E2_13_hours_4C_+5kb_viewpoint


title: 3770_G1E-ER4_Kit_cDNA_-E2_10%_clone2_Input

data_processing:
Bowtie 1.2.1.1 was used to align sequences. Reads with more than one mismatch or multiple alignments were excluded.
Significantly enriched regions were called using MACS2 version 2.1.0 with the following parameters: P = 10−5, extsize = 300 and local lambda = 100,000 using whole-cell extract input controls.
Reads were RPM normalized for  bigwigs.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

source_name: G1E-ER4 Kit cDNA

value: G1E-ER4 Kit cDNA

tag: genotype/variation

value: G1E-ER4 cells transduced with and selected for MigR1-Kit cDNA-YFP retrovirus. GATA motif within enhancer was deleted using CRISPR-Cas9 mediated genome editing


title: 3771_G1E-ER4_Kit_cDNA_-E2_0%_clone2_Input


title: G1E_ER4_cloneA_subclone_Ctr#1_+E2_13_hours_4C_+5kb_viewpoint

value: Estradiol (E2) for 13 hours


title: 4616_MFL_KIThiCD71lo

description: Lineage negative hematopoietic cells isolated from E13.5 mouse fetal liver


title: 3767_G1E-ER4_Kit_cDNA_+E2_24_hours_Input

value: Estradiol (E2) for 24 hours

value: G1E-ER4 cells transduced with and selected for MigR1-Kit cDNA-YFP retrovirus


title: 3769_G1E-ER4_Kit_cDNA_-E2_0%_clone1_Input


title: 3768_G1E-ER4_Kit_cDNA_-E2_10%_clone1_Input


title: 1990_G1E-ER4_+E2_24_hours_Input

value: G1E cells expressing GATA1-ER


title: 3766_G1E-ER4_Kit_cDNA_-E2_Input


title: 1989_G1E-ER4_+E2_13_hours_Input


title: FECD case 5

value: elderly

value: FECD


title: 1988_G1E-ER4_-E2_Input


title: 3674_G1E-ER4_Kit_cDNA_-E2_H3K27me3_0%_clone1

value: Cel signaling #9733S


title: 3005_G1E-ER4_Kit_cDNA_-E2_H3K27me3_0%_clone2


title: 1924_G1E_Input


title: 3003_G1E-ER4_Kit_cDNA_-E2_H3K27me3_10%_clone2


title: 3238_G1E-ER4_Kit_cDNA_-E2_H3K27me3


title: 3673_G1E-ER4_Kit_cDNA_-E2_H3K27me3_10%_clone1


title: 3002_G1E-ER4_Kit_cDNA_-E2_H3K27ac_10%_clone2

value: Active Motif #39133


title: 3004_G1E-ER4_Kit_cDNA_-E2_H3K27ac_0%_clone2


title: 3764_G1E-ER4_Kit_cDNA_-E2_H3K27ac_10%_clone1


title: 3237_G1E-ER4_Kit_cDNA_-E2_H3K27ac


title: 3239_G1E-ER4_Kit cDNA_+E2_24_hours_H3K27ac


title: Series_1_Month.Time_0_Light.Biorep_02

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

country: France

institute: École Normale Supérieure

data_processing:
Trimming ("trimmomatic-0.38 PE -threads 8 -phred33 -validatePairs ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20")
Mapping (STAR v.2.7.9a --alignIntronMax 5000 --alignIntronMin 20 --outFilterMismatchNmax 2 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outMultimapperOrder Random )
Read count (htseq-count v0.13.5 -s reverse --nonunique all -f bam -r pos -i transcriptId -t exon -a 0)
Fragilariopsis cylindrus is a non-model organism whose genome assembly and annotation have been made recently available. The assembly and annotation were released as a public web portal available at http://genome.jgi-psf.org/Fracy1/Fracy1.home.html
Assembly: CCMP1102
Supplementary files format and content: table with raw read counts

molecule: polyA RNA

organism: Fragilariopsis cylindrus

source_name: Cell culture

growth_protocol: The cultures of F. cylindrus CCMP 3323 were kept in 80 Liter custom-made borosilicate glass cylinders in Aquil media made from artificial sea water. The triplicate culture systems were kept inside a cold laboratory at 0 ± 1°C. Light intensity was adjusted at 30 µmol quanta m-2 s-1.

extract_protocol:
RNA was isolated following the protocol of the manufacturer using the RNeasy Mini Kit (Qiagen).
Library preparation was made using illumina TruSeq Stranded mRNA Library Prep including poly-A selection, performed at the biotechnology company Fasteris.

treatment_protocol: Samples for RNAseq were collected and centrifuged and rinced twice with marine PBS. Pellets were flash freezed in liquid Nitrogen and kept in -80 before extraction.

value: Cell culture

tag: cell line

value: Acclimated to full light


title: Series_1_Month.Time_0_Light.Biorep_03


title: Series_1_Month.Time_0_Light.Biorep_01


title: Series_1_Month.Return_to_Light_7days.Biorep_03

value: 7 days after the light return


title: Series_1_Month.Return_to_Light_24h.Biorep_02

value: 1 day after the light return


title: Series_1_Month.Return_to_Light_7days.Biorep_02


title: Series_1_Month.Return_to_Light_7days.Biorep_01


title: Series_1_Month.Return_to_Light_6h.Biorep_03

value: 6h after the light return


title: Series_1_Month.Return_to_Light_6h.Biorep_01


title: Series_1_Month.Return_to_Light_6h.Biorep_02


title: Series_1_Month.Return_to_Light_30min.Biorep_03

value: 30 min after the light return


title: Series_1_Month.Return_to_Light_24h.Biorep_01


title: 3240_G1E-ER4_Kit cDNA_+E2_24_hours_H3K27me3


title: Series_1_Month.Dark_1Month.Biorep_02

value: 1 month in darkness


title: 3765_G1E-ER4_Kit_cDNA_-E2_H3K27ac_0%_clone1

value: G1E-ER4 Kit cDNA


title: Series_1_Month.Dark_1Month.Biorep_03


title: Series_1_Month.Return_to_Light_30min.Biorep_02


title: Series_1_Month.Return_to_Light_30min.Biorep_01


title: Return_to_Light_7days.Biorep2


title: Return_to_Light_7days.Biorep3


title: Series_1_Month.Dark_1Month.Biorep_01


title: Return_to_Light_5days.Biorep2

value: 5 days after the light return


title: Return_to_Light_3days.Biorep2

value: 3 days after the light return


title: Return_to_Light_5days.Biorep3


title: Return_to_Light_48h.Biorep3

value: 2 days after the light return


title: Return_to_Light_7days.Biorep1


title: Return_to_Light_3days.Biorep3


title: Series_1_Month.Return_to_Light_24h.Biorep_03


title: Return_to_Light_48h.Biorep1


title: Return_to_Light_48h.Biorep2


title: Return_to_Light_24h.Biorep3


title: Return_to_Light_12h.Biorep2

value: 12h after the light return


title: Return_to_Light_12h.Biorep3


title: Return_to_Light_5days.Biorep1


title: Return_to_Light_24h.Biorep1


title: Return_to_Light_12h.Biorep1


title: Return_to_Light_6h.Biorep2


title: Return_to_Light_24h.Biorep2


title: Return_to_Light_6h.Biorep3


title: Return_to_Light_2h.Biorep3

value: 2h after the light return


title: Return_to_Light_3days.Biorep1


title: Return_to_Light_2h.Biorep1


title: Return_to_Light_30m.Biorep2


title: Return_to_Light_30m.Biorep1


title: Return_to_Light_2h.Biorep2


title: Return_to_Light_6h.Biorep1


title: Dark_2Months.Biorep3

value: 2 months in darkness


title: Dark_2Months.Biorep2


title: 16_103713_M137-15_Neuts_S55

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Alignment was performed using STAR version 2.5.2b
Transcript abundance estimates were calculated internal to the STAR aligner using the algorithm of htseq-count. The column corressponding to the unstranded counts from the STAR ReadsPerGene output file was used to create an htseq-count-like file.
Assembly: MacaM v7 (MacaM_Rhesus_Genome_v7.fasta,MacaM_Rhesus_Genome_Annotation_v7.8.2.gtf) (https://www.unmc.edu/rhesusgenechip/index.htm).
Supplementary files format and content: tab delimited text file containing  gene symbol and raw read counts for each annotated transcript

organism: Macaca fascicularis

source_name: Lung

extract_protocol:
RNA was isolated using RNeasy Micro Kits (Qiagen) with on-column DNase Digestion (Qiagen). RNA quality and quantity were determined using a Bioanalyzer RNA Pico chip (Agilent).
RNA was converted to cDNA and amplified using the Clontech SMART-Seq v4 Ultra Low Input RNA kit (Takara Bio) according to the manufacturer’s instructions. Amplified cDNA was fragmented and appended with dual-indexed bar codes using the NexteraXT DNA Library Preparation kit (Illumina). Libraries were validated by capillary electrophoresis on an Agilent 4200 TapeStation, pooled at equimolar concentrations

value: Lung

value: Neutrophil

tag: infection


title: 20_103799_M138-15_Neuts_S59


title: 18_103799_M138-15_IntMac_S57

value: Interstitial Macrophage


title: 19_103799_M138-15_AlvMac_S58

value: Alveolar Macrophage


title: Dark_2Months.Biorep1

value: Cell culture


title: 14_103713_M137-15_IntMac_S53


title: Dark_1Month.Biorep3


title: 13_103713_M137-15_Lung_S52

value: Whole lung


title: 12_103712_M136-15_Neuts_S51


title: Dark_1Month.Biorep1


title: 10_103712_M136-15_IntMac_S49


title: 15_103713_M137-15_AlvMac_S54


title: 11_103712_M136-15_AlvMac_S50


title: Dark_6_days.Biorep3

value: 6 days of darkness


title: Dark_6_days.Biorep1


title: 8_103711_M135-15_Neuts_S47


title: Dark_6_days.Biorep2


title: 17_103799_M138-15_Lung_S56


title: 9_103712_M136-15_Lung_S48


title: 6_103711_M135-15_IntMac_S45


title: Dark_3_days.Biorep3

value: 3 days of darkness


title: Dark_3_days.Biorep2


title: 5_103711_M135-15_Lung_S44


title: Dark_3_days.Biorep1


title: 7_103711_M135-15_AlvMac_S46


title: 4_103709_M133-15_Neuts_S43


title: Dark_24h.Biorep3

value: 1 day in darkness


title: 2_103709_M133-15_IntMac_S41


title: Dark_24h.Biorep2


title: Dark_6h.Biorep3

value: 6h of darkness


title: Dark_1Month.Biorep2

value: 1 month in darkness


title: Dark_6h.Biorep2


title: Dark_6h.Biorep1


title: 30_M59-16_IntMac_S69

value: uninfected


title: 29_M59-16_Lung_S68


title: 31_M59-16_AlvMac_S70


title: Time_0_Light.Biorep1

value: Acclimated to full light


title: Time_0_Light.Biorep2


title: 28_M163-10_Neuts_S67


title: Time_0_Light.Biorep3


title: 26_M163-10_IntMac_S65


title: SAM24363370 Spleen R3

city: South San Francisco

first: Joaquin

last: Pechuan jorge

state: CA

address: 1 dna way

department: Cancer Immunology

institute: Genentech

data_processing:
Exome capture libraries were sequenced on HiSeq 2500 (Illumina) to generate 2 × 75 bp paired-end data, from the sequenced reads, variants were called using the following workflow. Sequencing reads were mapped to UCSC mouse genome (GRCm38) using BWA software (Li 2009) set to default parameters. Local realignment, duplicate marking, and raw variant calling were performed according to GATK best practices (Depristo 2011). Somatic variant calling on tumor and its matched normal BAM file was performed using Strelka (Saunders 2012).
Assembly: GRCm38
Supplementary files format and content: Strelka calls restricted to the variants presnt in the KPP-EGFP cell line with the spleen samples as a reference.

source_name: Spleen

extract_protocol: Each tissue biopsy was transferred to a separate 1.5 mL tube (Eppendorf, Germany) containing 0.25 mL Invitrogen TRIzol Reagent (Thermo Fisher Scientific, MA, USA). Biopsies were incubated in TRIzol for 5 min with intermittent vortexing. 50 µL chloroform (MilliporeSigma, MA, USA) was added to the homogenate, vortexed for 20 sec, and incubated at 20-25°C for 2-3 min. To accelerate phase separation, samples were centrifuged at 10,000xg for 18 min at 4°C. The aqueous (top) phase was removed by aspiration and transferred to a clean 1.5 mL tube (Eppendorf, Germany). A volume of 100% RNAse-free ethanol (MilliporeSigma, MA, USA). equal to the volume of the aqueous layer was added, and the RNA was further isolated using a RNeasy Micro Kit (Qiagen, Germany). Alternatively, an individual tumor biopsy was immersed in RNA later and the RNA further extracted using a RNeasy Mini Kit (Qiagen, Germany).

treatment_protocol: To rule out the possibility that tumor immune phenotypes could be explained by pre-existing major subclones within the KPP-EGFP cell line, the tumor cell line genetic heterogeneity was assessed by whole exome sequencing before implantation and three weeks post implantation. A spleen sample from the wild type mice strain used in the experiments was used as the reference matched normal genome to perform variant calling in tumor cells. The analysis post tumor implantation was restricted to the tumor variants detected in the KPP-EGFP cell line in order to alleviate the effect of any potential genetic variability within mice captured from the different TME components of the different biopsies.

value: Spleen

value: Tissue

tag: primary tissue

value: Normal


title: Return_to_Light_30m.Biorep3

value: 30 min after the light return


title: SAM24363369 Spleen R2


title: 25_M163-10_Lung_S64

value: Lung


title: 27_M163-10_AlvMac_S66


title: 22_M139-15_IntMac_S61


title: Dark_24h.Biorep1


title: SAM24363368 Spleen R1


title: SAM24354696 2-3-D

source_name: Tumor

value: Tumor

value: KPP-EGFP

value: Skin

value: Desert


title: SAM24354695 2-2-E

value: Excluded


title: 23_M139-15_AlvMac_S62

value: Alveolar Macrophage


title: SAM24354694 2-1-I

value: Inflamed


title: 1_103709_M133-15_Lung_S40

value: Whole lung


title: 3_103709_M133-15_AlvMac_S42


title: 32_M59-16_Neuts_S71

value: Neutrophil


title: vil1 27°C H3K27me3 ChIP-seq IP (replicate 2)

city: Austin

first: Sibum

last: Sung

state: TX

institute: University of Texas at Austin

data_processing:
Reads generated by Illumina NextSeq 500 platform were checked for quality using FastQC.
After quality assessment, reads were aligned on TAIR10 genome using Bowtie2 for ChIP-seq.
SAM files generated from mapping were then converted into BAM files and sorted using Samtools.
For the gene counting bedtools program was used which generates raw count using BAM files.
Genome_build: TAIR10
Supplementary_files_format_and_content: .bw (IGV)

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Tissue (7-day-old seedlings) was harvested for experiment at ZT-6.

extract_protocol:
ChIP experiments.
Library was prepared using NEB Illumina library preparation kit.

treatment_protocol: Plants were grown in short day (8-hour light, 16-hour dark) at 22°C or 27°C.

value: Seedling

tag: temperature

value: 7 days

tag: chip antibody


title: SAM24354688 KPP-GFP 3-K-2-B

source_name: Cell Line

tag: tissue

value: Cell Line

value: Pancreas

value: Culture


title: SAM24354691 1-3-I


title: vil1 27°C H3K27me3 ChIP-seq input


title: vil1 27°C H3K27me3 ChIP-seq IP (replicate 1)


title: SAM24354687 KPP-GFP 3-K-2


title: vil1 22°C H3K27me3 ChIP-seq IP (replicate 2)


title: vil1 22°C H3K27me3 ChIP-seq IP (replicate 1)


title: DU145 cells, GALNT7 OE, biol rep 2

city: Newcastle upon Tyne

first: Jennifer

last: Munkley

state: Tyne & Wear

address: International Centre for Life

country: United Kingdom

institute: Newcastle University

data_processing:
Analysis was conducted in R version 3.5.3 (2019-03-11)
Quality control was performed with FastQC
Reads were quantified using Salmon
Differential gene expression analysis was performed with DeSeq2
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Prostate cancer

extract_protocol:
RNEasy Kit following manufacturer's protocol (Qiagen)
TruSeq Stranded mRNA Sequencing Library Prep Kit following manufacturer's protocols.

value: Prostate cancer

value: GALNT7 overexpression


title: 24_M139-15_Neuts_S63

value: Lung

value: uninfected


title: Col-0 27°C H3K27me3 ChIP-seq IP (replicate 2)

tag: ecotype

value: WT


title: Col-0 27°C H3K27me3 ChIP-seq IP (replicate 1)


title: DU145 cells, OEControl, biol rep 3

value: Lenti-ORF control


title: DU145 cells, GALNT7 OE, biol rep 3


title: DU145 cells, OEControl, biol rep 2


title: DU145 cells, GALNT7 OE, biol rep 1


title: Col-0 22°C H3K27me3 ChIP-seq IP (replicate 1)


title: SAM24354692 1-4-E

value: Tumor

value: KPP-EGFP

value: Skin


title: 21_M139-15_Lung_S60


title: CWR22Rv1 cells, GALNT7 KD, biol rep 3

value: GALNT7 knockdown


title: arp6vil1 22°C H2AZ ChIP-seq IP (replicate 1)

data_processing:
Reads generated by Illumina NextSeq 500 platform were checked for quality using FastQC
After quality assessment, reads were aligned on TAIR10 genome using HISAT2 for RNA-seq and Bowtie2 for ChIP-seq
SAM files generated from mapping were then converted into BAM files and sorted using Samtools
For the gene counting bedtools program was used which generates raw count using BAM files
Raw count was then fed into R for differential gene expression analysis using edgeR and data visualization
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel file containing raw read count of each sample and RPKM normalized read count of each sample
Supplementary_files_format_and_content: .bw (IGV)

growth_protocol: Plants were grown in long day (16-hour light, 8-hour dark) and short day (8-hour light, 16-hour dark) at 22°C or 27°C.

extract_protocol:
Total RNAs were extracted by using TRIzol (Invitrogen) and treated with DNase I enzyme (Promega) to eliminate traces of genomic DNA
Library was prepared using NEB illumina library preparation kit

treatment_protocol: Tissue (14 days old seedlinds) was harvested for experiment at ZT-6

value: 14 days old seedling


title: CWR22Rv1 cells, GALNT7 KD, biol rep 2


title: Col-0 27°C H3K27me3 ChIP-seq input


title: DU145 cells, OEControl, biol rep 1


title: CWR22Rv1 cells, GALNT7 KD, biol rep 1


title: CWR22Rv1 cells, shControl, biol rep 2

value: Lenti-shControl


title: arp6vil1 22°C H2AZ ChIP-seq IP (replicate 2)


title: arp6 22°C H2AZ ChIP-seq IP (replicate 2)


title: CWR22Rv1 cells, shControl, biol rep 1


title: CWR22Rv1 cells, shControl, biol rep 3


title: SAM24354686 KPP-GFP 3-K-1-B


title: smrna_hela_set5_sidrosha_r2

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

data_processing:
After careful validation of the quality of each individual dataset, we merged our fastq files from different sets that carried the same name for subsequent analyses. To account for varying read numbers and simplify data normalization in the following, we randomly subsampled all samples to 30 million reads. The subsampled fastq files and their processed datasets were also deposited to GEO. For random subsampling, the following command was used:   for f in *.fastq;  do   cat "$f" | awk '{ printf("%s",$0); n++; if(n%4==0) {  printf("\n");} else { printf("\t");} }' |  awk -v k=30000000 'BEGIN{srand(systime() + PROCINFO["pid"]);}{s=x++<k?x-1:int(rand()*x);if(s<k)R[s]=$0}END{for(i in R)print R[i]}' |   awk -F"\t" '{print $1"\n"$2"\n"$3"\n"$4}' > "${f%.fastq}"_30mio.fastq  done;
subsampled files were treated as described previously:  Sequencing reads were trimmed for adapter (AAAAAAAAAA) as recommend by SMARTer smRNA-seq kit (Takara, #635030) protocol using Cutadapt (v1.18) and reads shorter than 17 bp were omitted. Reads were aligned against human elements in RepBase (v23.08) with STAR (v2.5.3a) and the unmapped output then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.

molecule: cytoplasmic RNA

source_name: HeLa

growth_protocol: HeLa cell lines containing stable shRNA were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS and puromycin (2 μg/ml). Knockdowns were induced by adding of 1 μg/ml doxycycline (Dox) into the culture medium daily for 3 days.

extract_protocol:
Cells were fractionated into nucleus and cytoplasm according to Bhatt et al., Cell 2012, https://doi.org/10.1016/j.cell.2012.05.043. Nuclear RNA was extracted using Trizol reagent  (Thermo Fisher Scientific, #15596026), cytoplasmic RNA using Trizol LS reagent (Thermo Fisher Scientific #10296028) according to the manufacturer’s instructions. Genomic DNA was removed by Turbo DNAse treatment
Small RNA libraries were prepared using the SMARTer smRNA-seq kit (Takara, #635030) with 700 ng of total RNA; 5% (35 ng) of Drosophila RNA were added as spike-in

value: cervical adenocarcinoma

tag: cell source

tag: modification

value: Tet-pLKO_shINTS6 stable cells

tag: ip antibody

tag: nucleotide alteration


title: vil1 22°C H3K27me3 ChIP-seq input

value: Seedling

value: 7 days


title: smrna_hela_set5_sidrosha_r1


title: smrna_hela_set5_sicontrol_r2

molecule: nuclear RNA


title: vil1-1 27°C H2AZ ChIP-seq IP (replicate 2)


title: Col-0 22°C H3K27me3 ChIP-seq input


title: arp6 22°C H2AZ ChIP-seq IP (replicate 1)


title: vil1-1 22°C H2AZ ChIP-seq IP (replicate 2)


title: vil1-1 27°C H2AZ ChIP-seq input


title: vil1-1 27°C H2AZ ChIP-seq IP (replicate 1)


title: arp6 22°C H2AZ ChIP-seq input


title: vil1-1 22°C H2AZ ChIP-seq IP (replicate 1)


title: smrna_hela_set4_eq_r2

description: shGFP

value: Tet-pLKO_shGFP stable cells


title: vil1-1 22°C H2AZ ChIP-seq input


title: smrna_hela_set4_wt_r1

description: shGFP


title: smrna_hela_set4_wt_r2

description: shGFP


title: Col-0 27°C H2AZ ChIP-seq IP (replicate 2)

value: wildtype


title: Col-0 27°C H2AZ ChIP-seq IP (replicate 1)


title: smrna_hela_set4_eq_r1

description: shGFP


title: arp6vil1 22°C H2AZ ChIP-seq input


title: smrna_hela_set4_shints11_r2

description: siDrosha

growth_protocol: Unmodified HeLa cells were maintained at 37°C with 5% CO2 in DMEM supplemented with 10% FBS and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. 2 x 105 cells were seeded in a 6-well plate and transfected with 20nM siRNA using Lipofectamine RNAiMAX (Invitrogen, Cat#  13778075). Medium was changed after 16h and cells were harvested after 3 days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific, #15596026) according to the manufacturer’s instructions. Genomic DNA was removed by Turbo DNAse treatment (Invitrogen, #AM1907).
Small RNA libraries were prepared using the SMARTer smRNA-seq kit (Takara, #635030) with 800 ng of total RNA

value: siDrosha (s26491, Cat# 4390824) transfection


title: smrna_hela_set4_shints11_r1

description: siDrosha


title: Col-0 27°C H2AZ ChIP-seq input


title: smrna_hela_set4_shcontrol_nodox_r2

description: siControl, No Dox

value: siControl (No1, Cat# 4390844) transfection, No Dox


title: Col-0 22°C H2AZ ChIP-seq IP (replicate 1)


title: Col-0 22°C H2AZ ChIP-seq IP (replicate 2)


title: smrna_hela_set4_shcontrol_nodox_r1

description: siControl, No Dox


title: smrna_hela_set4_shcontrol_r2

description: siControl

value: siControl (No1, Cat# 4390844) transfection


title: Col-0 22°C H2AZ ChIP-seq input


title: smrna_hela_set4_shcontrol_r1

description: siControl


title: Col-0 22°C H3K27me3 ChIP-seq IP (replicate 2)

value: WT


title: arp6vil1 22°C RNA-seq (replicate 2)


title: smrna_hela_set3_shints6_r2


title: smrna_hela_set3_shints6_r1


title: arp6vil1 22°C RNA-seq (replicate 1)

description: arpvil


title: smrna_hela_set3_shcontrol_r2

description: WT


title: smrna_hela_set2_shints7_r2

value: Tet-pLKO_shINTS11 stable cells


title: smrna_hela_set3_shcontrol_r1

description: WT


title: vil1-1 27°C RNA-seq (replicate 1)


title: vil1-1 22°C RNA-seq (replicate 2)


title: arp6 22°C RNA-seq (replicate 1)


title: vil1-1 27°C RNA-seq (replicate 2)


title: smrna_hela_set2_shints3_r2

value: Tet-pLKO_shINTS7 stable cells


title: vil1-1 22°C RNA-seq (replicate 1)


title: smrna_hela_set2_shints3_r1


title: smrna_hela_set2_shints7_r1


title: smrna_hela_set2_shcontrol_r2


title: Col-0 27°C RNA-seq (replicate 2)


title: smrna_hela_set2_shcontrol_r1


title: Col-0 27°C RNA-seq (replicate 1)


title: Col-0 22°C RNA-seq (replicate 2)


title: shTSC1_3

city: Guangzhou

first: Xinghong

last: Luo

address: No 366 Jiangnan Avenue South

department: Department of Endodontics

institute: Stomatological Hospital, School of Stomatology, Southern Medical University

data_processing:
After qualified library inspection, the library was pooled for Illumina SE50 sequencing according to the requirements of effective concentration and target offline data amount.
The sequencing process was controlled by the data collection software provided by Illumina that performed real‐time data analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Rattus norvegicus

extract_protocol:
Total RNA was isolated from the samples by using the exoRNeasy Midi/Max Kit (Qiagen, USA) according to the manufacturer’s protocol. The extracted total RNA was analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
After the total RNA was quantified, the sequencing RNA library was constructed with the Small RNA Sample Pre Kit, which included the following steps: addition of a 3’-end linker, addition of a 5’-end linker, reverse transcription, amplification, cDNA library size selection, and purification. Qubit 2.0 was used for preliminary quantification, and then, an Agilent 2100 was used to measure the insert size of the library. After qualified library inspection, the library was pooled for Illumina SE50 sequencing according to the requirements of effective concentration and target offline data amount. The sequencing process was controlled by the data collection software provided by Illumina that performed real‐time data analysis.

value: Exosomes derived from shTSC1 transfected MDPC-23


title: smrna_hela_set1_shints11_r2

value: Tet-pLKO_shINTS3 stable cells


title: smrna_hela_set1_shints11_r1


title: Col-0 22°C RNA-seq (replicate 1)


title: smrna_hela_set1_shints1_r2

value: Tet-pLKO_shINTS1 stable cells


title: shTSC1_2


title: smrna_hela_set1_shints1_r1


title: smrna_hela_set5_sicontrol_r1


title: smrna_hela_set1_shcontrol_r2

description: shGFP


title: shTSC1_1


title: Rapa_3

value: Exosomes derived from rapamycin treated MDPC-23


title: arp6 22°C RNA-seq (replicate 2)

value: 14 days old seedling


title: smrna_hela_set1_shcontrol_r1

description: shGFP

value: cervical adenocarcinoma


title: Rapa_2


title: Rapa_1


title: MDPC_2

value: Exosomes derived from MDPC-23


title: MDPC_1


title: Crosslinked HEK293T, OE RPS19 WT IP, rep2

city: La Jolla

first: Gene

middle: W

last: Yeo

address: 2880 Torrey Pines Scenic Dr

department: Cellular & Molecular Medicine

institute: University of California San Diego

data_processing:
library strategy: eCLIP
Data was processed using Skipper, available at: http://github.com/yeolab/skipper
Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper
Assembly: GRCh38
Supplementary files format and content: reproducible enriched window files contain p values, q values, enrichment, and annotations for significantly bound transcriptome tiled windows
Supplementary files format and content: reproducible enriched re files contain p values, q values, enrichment, and annotations for significantly bound repetitive elements

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and complexes were immunoprecipitated with V5 antibody from Bethyl Laboratories for IP samples
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

treatment_protocol: IP samples were transfected with plasmids expressing V5-tagged mutant or WT RPS19. IN samples were untransfected.

value: OE RPS19 WT

value: V5 antibody (Bethyl Laboratories)


title: Crosslinked HEK293T, OE RPS19 R62W IP, rep3

value: OE RPS19 R62W


title: Crosslinked HEK293T, OE RPS19 WT IP, rep1


title: MDPC_3


title: RPE1 cells, STM2457, rep2

city: Würzburg

first: Julian

last: Konig

address: Am Hubland

country: Germany

institute: Würzburg University

data_processing:
Quality control: FastQC (v0.11.8)
Trimming: Cutadapt (v1.18) with non-default parameters: cutadapt -a file:NexteraPE-PE.fa --minimum-length 50 (additional parameter used for C643, HEK293T, RPE1, male mESC samples: --cut 1)
Mapping: STAR (v2.7.3a) with non-default parameters: STAR --runMode alignReads --outFilterMismatchNoverLmax 0.04 --outFilterMismatchNmax 999 --outStd SAM --outSAMattributes NH HI AS nM MD --outSJfilterReads Unique --outSAMunmapped Within --runThreadN 4 --readFilesCommand zcat --sjdbOverhang READLENGTH-1
Filter/remove secondary hits: Samtools (v1.9) with parameters: samtools view -F 256
Counts per gene: Subread (v2.0.0) with non-default parameters: featureCounts --donotsort -s2 -t exon (default used for -g gene_id)
Assembly: human: GRCh38.p12 (Gencode release 31) (+ ERCC spike-ins in C643, HEK293T, RPE1)
Assembly: mouse: GRCm38.p6 (Gencode release M23) (+ ERCC spike-ins in male mESC)
Supplementary files format and content: tab-delimited text (.tsv) files include absolute read counts per gene for each sample

growth_protocol: For C643 and HEK293T: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, Life Technologies), 1% L-glutamine (Life Technologies) and 1% penicillin/streptomycin (P/S Life Technologies). For RPE1: Cells were cultured in DMEM/F12 (Life Technologies) supplemented with 10% foetal bovine serum (FBS, Life Technologies), 1% penicillin/streptomycin (P/S, Life Technologies), 1% L-Glutamin and 0.04% Hygromycin B (Life Technologies). Cells were grown at 37◦C with 5% CO2. For male and female mESC: Female mouse embryonic stem cells (mESC) were taken from a previous publication (PMID: 24506884). Single clones were picked and cultured until confluency. Male mESC were taken from a previous publication (PMID: 25569111).  Cells were cultured in 2i/LIF medium. Briefly, 500 ml medium was generated by adding 235 ml of each DMEM/F12 and neurobasal (Gibco; 21331020, 21103049), 7.5 ml BSA solution (7.5%, ThermoFisher; 11500496), 5 ml penicillin-streptomycin (Gibco; 15140-122), 2 mM L-Glutamin (ThermoSci; 25030024), 100 µM β-mercaptoethanol (Gibco; 21985023), 5 ml mM nonessential amino acids (Gibco; 11140050), 2.5 ml N2 supplement (Gibco; 17502048), 5 ml B27 supplement (Gibco; 17504044), 3 µM CHIR99021 (Sigma; SML1046), 1 µM PD 0325901 (Biomol; 13034-1), 10 ng/ml LIF (IMB Protein Production core facility). Cells were cultured at 37°C  with 5% CO2. Cell culture dishes were coated using 0.1% gelatin (Sigma; ES-006-B). The medium was exchanged every day and cells were passaged every second day.

extract_protocol:
For RNA extraction, cells were washed twice with ice cold 1x PBS and collected on ice. For total RNA isolation the RNeasy Plus Mini Kit (Qiagen) was used following the manufacturer’s instructions.
RNA-seq: All NGS library preps were performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation Reference Guide (June 2020) (Document # 1000000124518 v00). For RNA-seq in HEK293T and C643 cells: Libraries were prepared with a starting amount of 350 ng for C643 samples and 1000 ng for HEK293T samples and amplified in 11 PCR cycles and 10 cycles respectively. For normalization, 2μl of a 1:300 dilution of ERCC spike-ins (Ambion) were added to the starting material for C643 samples and for HEK293T samples 2μl of a 1:100 dilution. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 80 cycles plus 10 cycles for the index read plus 1 dark cycle upfront Read 1. For RNAseq in male mESC cells upon 24 h of STM2457 treatment: Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. For normalization, 2μl of a 1:100 dilution of ERCC spike-ins (Ambion) were added to the starting material. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 155 cycles plus 10 cycles for the index read and 1 dark cycle upfront Read 1. For RNAseq in RPE1 cells: Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. For normalization, 2μl of a 1:100 dilution of ERCC spike-ins (Ambion) were added to the starting material. Libraries were profiled in a HS DNA chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 80 cycles plus 10 cycles for the index read and 1 dark cycle upfront Read 1. For RNAseq in male mESC upon STM2457 timecourse 3h-12 h: Libraries were prepared with a starting amount of 1000 ng and amplified in 10 cycles. For normalization, 2μl of a 1:100 dilution of ERCC spike-ins (Ambion) were added to the starting material. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All samples were pooled in equimolar ratio and sequenced on 2 NextSeq500 Highoutput FC, SR for 1x 80 cycles plus 10 cycles for the index read plus 1 dark cycle upfront Read 1.  For RNAseq in female mESC single clones: Libraries were prepared with a starting amount of 500 ng and amplified in 10 PCR cycles. Two post PCR purification steps were performed to exclude residual primer and adapter dimers. Libraries were profiled in a DNA 1000 chip on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All 12 samples were pooled in equimolar ratio and sequenced on 1 NextSeq500 Highoutput FC, SR for 1x 79 cycles plus 10 cycles for the index read and 2 dark cycles upfront Read 1.

treatment_protocol: Cells were cultured in respective medium supplemented with Mettl3 inhibitor STM2457 or DMSO as negative control for 3h and up to 24h.

value: Human retinal pigment epithelial-1 cells

tag: treatment

tag: gender

value: female


title: RPE1 cells, DMSO, rep1

value: DMSO


title: RPE1 cells, DMSO, rep3


title: RPE1 cells, STM2457, rep1


title: RPE1 cells, STM2457, rep3


title: RPE1 cells, DMSO, rep4


title: Crosslinked HEK293T, OE RPS19 WT IP, rep3

tag: genotype


title: Crosslinked HEK293T, OE RPS19 R101H IP, rep2

value: OE RPS19 R101H


title: Crosslinked HEK293T, OE RPS19 R62W IP, rep2


title: HEK293T cells, STM2457, rep2

tag: cell type

value: Human embryonic kidney 293T cell line


title: HEK293T cells, STM2457, rep1


title: RPE1 cells, STM2457, rep4


title: HEK293T cells, STM2457, rep3


title: HEK293T cells, DMSO, rep4


title: Crosslinked HEK293T, RPS19 size-matched IN, rep3

value: control

tag: antibody

value: none (input)


title: Crosslinked HEK293T, RPS19 size-matched IN, rep1


title: Crosslinked HEK293T, RPS19 size-matched IN, rep2


title: HEK293T cells, DMSO, rep3


title: HEK293T cells, DMSO, rep2


title: C643 cells, STM2457, rep4

value: Human Thyroidea Carcinoma cell line

value: male


title: RPE1 cells, DMSO, rep2


title: dcre_wnt_91_d7_1

city: Heidelberg

first: Bryce

last: Lim

address: In Neuenheimer Feld 280

institute: DKFZ

description:
human_wnt_notch_norm_counts.tsv
human_wnt_notch_raw_counts.tsv

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence
Filtered reads were mapped to hg38 with STAR to generate raw counts files
Differential expression and normalised counts were determined using DESeq2 (R package version 1.28.1)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file with raw counts for all samples
Supplementary files format and content: Tab-delimited text file with DESeq2 output for all conditions (sample-collapsed)
Supplementary files format and content: Tab-delimited text file with normalised counts for all samples

source_name: NGN2-induced neurons

growth_protocol: H1 (male) human ES cells (WiCell) were maintained feeder-free in mTeSR Plus medium (Stem Cell Technologies) and one allele of human MYT1L (ENSG00000186487) was targeted by  homologous recombination to flank exon 7 with loxP sites. Cre-mediated recombination deleted exon 7 resulting in a frameshift starting in exon 8 at amino acid (aa) 19 and terminating in a premature STOP at aa 69 in exon 9 (p.V19AfsX51). Heterozygous targeting was confirmed by Sanger sequencing that showed insertion of loxP sites within one allele for each clone (+/fl) and MYT1L protein depletion was confirmed by Western blot directly in induced human neurons. WNT and NOTCH inhibition was performed by supplementing  media from day 1 to day 4 with either 10 µM N-[N-(3,5-difluorophenacetyl)-l-alanyl]-S-phenylglycine t-butyl ester (DAPT), 15 µM Tetrahydro-2-[4-(trifluoromethyl)phenyl]-4H-thiopyrano[4,3-d]pyrimidin (XAV939), or both.

extract_protocol:
Cultures were harvested by addition of TRIzol to the cultures (Invitrogen) and RNA was isolated using the RNA Miniprep kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentivirus encoding doxycycline-inducible Ngn2 and either cre-recombinase or an inactive truncated delta-cre-recombinase, both under control of the ubiquitin promoter, were used to transduce conditional MYT1L knockout cells (+/fl). On day 0, Doxycycline (2 mg/ml, Sigma) was added to induce Ngn2 expression and retained in the medium until day 14. On day 1, cells were treated with Accutase (Gibco) and plated on Matrigel (Corning)-coated 6-well plates in DMEM/F12 containing N2-supplement, non-essential amino acids (all from Invitrogen), human BDNF (10 ng/ml, PeproTech), human NT-3 (10 ng/ml, PeproTech), and mouse Laminin-1 (0.2 mg/ml, Invitrogen) containing 10 µM Y-27632 (Axon Medchem) and puromycin (2 µg/ml c.f.) was added for 3 days to select infected cells. On day 4, iN cells were treated with Accutase and replated in Neurobasal-A medium supplemented with B27/glutamax (Invitrogen) containing BDNF, NT3, and Laminin-1, and Ara-C (2 µM, Sigma). For day 7 harvest, iN cells were seeded on Matrigel-coated 12-well plates without addition of glia. For functional maturation, iN cells were seeded on Matrigel-coated coverslips together with primary mouse glia with media changes every 2 days. After 1 week media was gradually exchanged with MEM supplemented with 0.5% glucose, 0.02% NaHCO3), 2 µM Ara-C (all Sigma), Transferrin (100 µg/ml c.f.; Merck), 5% FBS, B27, 0.5 mM L-glutamine (all Invitrogen), following media changes every 3–4 days for the duration of the experiment. All cells were grown at 37 °C and 5% CO2.

tag: donor cell line

value: neuron

tag: harvest day

value: dcre

tag: clone

value: wnt


title: C643 cells, STM2457, rep3

tag: cell line


title: dcre_wnt_90_d7_2


title: Crosslinked HEK293T, OE RPS19 R62W IP, rep1


title: C643 cells, STM2457, rep2


title: dcre_wnt_90_d7_1


title: dcre_W+N_91_d7_1


title: dcre_W+N_90_d7_2


title: C643 cells, DMSO, rep1


title: C643 cells, STM2457, rep1


title: C643 cells, DMSO, rep3


title: dcre_W+N_91_d7_2


title: dcre_W+N_90_d7_1


title: Crosslinked HEK293T, OE RPS19 R101H IP, rep1


title: dcre_null_91_d7_2


title: dcre_null_91_d7_1


title: dcre_null_90_d7_2


title: HEK293T cells, STM2457, rep4


title: dcre_null_90_d7_1


title: dcre_wnt_91_d7_2


title: totalrna_hela_sicontrol_r1

description: siControl

data_processing:
Adapter trimming:   Small_RNA:  FASTQ data were processed with Cutadapt v1.18, adapter trimmed (AAAAAAAAAA) and reads smaller 17 bp were discarded.  Total RNA-seq: FASTQ data were processed with Trimmomatic v0.32 to remove adapters and low-quality reads.   eCLIP: Double adapter trimming was performed using Cutadapt v1.14.
Small_RNA: Reads were aligned against human elements in RepBase (v23.08) with STAR37 (v2.5.3a) and the unmapped output then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.   RNA-seq: reads were aligned to the hg19 human genome using STAR aligner v2.5.3a with default parameters and RSEM v1.2.31 to obtain expected gene counts against the human Ensembl reference (release 87).   eCLIP: Data was processed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810 - https://github.com/YeoLab/eclip
s4U small RNA-seq and RIP small rna-seq were treated as described in Reichholf B, Herzog VA, Fasching N, Manzenreither RA, Sowemimo I, Ameres SL. Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis. Mol Cell. 2019 Aug 22;75(4):756-768.e7. doi: 10.1016/j.molcel.2019.06.018. Epub 2019 Jul 23. PMID: 31350118; PMCID: PMC6713562. )https://github.com/breichholf/smRNAseq)
Genome_build: hg19
Supplementary_files_format_and_content: Small_RNA and RNA-seq: the processed data files are in bigWig format normalized by Count Per Million (CPM) produced from DeepTools2.
Supplementary_files_format_and_content: eCLIP: strand specific bigwig files;  clipper v1.1 output (bed files, col1: chrom, col2: chromStart, col3: chromEnd, col4: -log10 pvalue, col5: log2 fold enrichment above input, col6: strand)) contains clusters of Ints11 binding

extract_protocol:
Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific, #15596026) according to the manufacturer’s instructions. Genomic DNA was removed by Turbo DNAse treatment (Invitrogen, #AM1907).
Total RNA-seq libraries were produced using Stranded Total RNA library prep kit (Illumina, #20020596) with 500 ng of DNAse-treated Input RNA.

value: cervical adenocarcinoma

value: siControl (No1, Cat# 4390844) transfection


title: dcre_null_82_d7_3


title: totalrna_hela_sidrosha_r1

description:
siDrosha
176_precursor_cleaned_hg19.bed

value: siDrosha (s26491, Cat# 4390824) transfection


title: totalrna_hela_sidrosha_r2

description:
siDrosha
176_precursor_cleaned_hg19.bed


title: C643 cells, DMSO, rep2


title: dcre_null_82_d7_2


title: totalrna_hela_shints11_dox_r1

value: Tet-pLKO_shINTS11 stable cells


title: totalrna_hela_shints7_dox_r2

value: Tet-pLKO_shINTS7 stable cells


title: dcre_null_82_d7_1


title: dcre_notch_91_d7_1

value: notch


title: dcre_notch_91_d7_2


title: dcre_notch_90_d7_2


title: totalrna_hela_shints7_dox_r1


title: totalrna_hela_shints3_dox_r2

value: Tet-pLKO_shINTS3 stable cells


title: dcre_notch_90_d7_1


title: dcre_dmso_91_d7_1

value: dmso


title: dcre_dmso_91_d7_2


title: totalrna_hela_shcontrol_dox_r2

description: shGFP

value: Tet-pLKO_shGFP stable cells


title: totalrna_hela_shints1_dox_r1

value: Tet-pLKO_shINTS1 stable cells


title: totalrna_hela_sicontrol_r2

description:
siControl
176_precursor_cleaned_hg19.bed


title: totalrna_hela_shints11_dox_r2


title: dcre_dmso_90_d7_2


title: totalrna_hela_shints1_dox_r2


title: totalrna_hela_shints3_dox_r1


title: totalrna_hela_shcontrol_dox_r1

description: shGFP


title: cre_null_90_d7_2

description:
human_wnt_notch_cre_null_vs_dcre_null_deseq.tsv
human_wnt_notch_norm_counts.tsv
human_wnt_notch_raw_counts.tsv

value: cre


title: cre_null_91_d7_2


title: cre_null_82_d7_2


title: cre_null_91_d7_1


title: cre_W+N_91_d7_2

description:
human_wnt_notch_cre_W.N_vs_cre_null_deseq.tsv
human_wnt_notch_norm_counts.tsv
human_wnt_notch_raw_counts.tsv


title: cre_null_90_d7_1


title: cre_W+N_90_d7_2


title: cre_null_82_d7_1


title: cre_W+N_91_d7_1


title: cre_W+N_90_d7_1


title: smrna_hela_sicontrol_r2_30mio

description: siControl


title: smrna_hela_shints7_r2_30mio


title: smrna_hela_shints1_r2_30mio


title: smrna_hela_shints3_r1_30mio


title: smrna_hela_sicontrol_r1_30mio

description: siControl


title: smrna_hela_shints3_r2_30mio


title: smrna_hela_shints7_r1_30mio


title: smrna_hela_sidrosha_r1_30mio

description: siDrosha


title: smrna_hela_shints1_r1_30mio


title: Hashtags_DRENEA_5

city: Darlinghurst

first: Drew

last: Neavin

state: New South Wales

address: 384 Victoria St

department: Cellular Science

country: Australia

institute: Garvan Institute of Medical Research

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in DRENEA_5

library_source: transcriptomic single cell

data_processing:
cellranger was used to process the reads for quality, aligning to the genome and counting the UMIs per gene per cell
Assembly: hg38
Supplementary files format and content: cellranger filtered matrxi output

extract_protocol:
Approximately 32,000 cells were loaded onto the Chromium Single Cell Chip B (10X Genomics; Catalog Number: PN-1000073) in order to capture 20,000 single cells with the Gel Bead Kit V3.0 (10x Genomics; Catalog Number: PN-1000076). GEM generation, barcoding, cDNA amplification, and library construction were performed according to the 10x Genomics Chromium User Guide (CG000183).
Libraries were prepared with the Single Cell 3' V3.0 Library and Gel Bead Kit (10x Genomics; Catalog Number: PN-1000077 and PN-1000078).

tag: cell lines

tag: hashtag antibodies

tag: time

value: Village

tag: cryopreserved

value: Fresh


title: Hashtags_DRENEA_6

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in DRENEA_6


title: Hashtags_Village_B_1_week_Hashtags

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in Village_B_1_week_Hashtags

value: Cryopreserved


title: Hashtags_DRENEA_4

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in DRENEA_4


title: Hashtags_Village_A_Baseline

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in Village_A_Baseline

value: Uni-culture


title: smrna_hela_sidrosha_r2_30mio

description: siDrosha

tag: cell source


title: C643 cells, DMSO, rep4

value: Human Thyroidea Carcinoma cell line

value: DMSO

value: male


title: Hashtags_DRENEA_1

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in DRENEA_1


title: Hashtags_DRENEA_3

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in DRENEA_3


title: iPSC_Village_P4

description:
10X Genomics Chromium Controller
Single cell sequencing sequencing of genotype pooled samples (18 lines)

source_name: iPSCs

value: iPSCs


title: iPSC_Village_P8


title: Hashtags_DRENEA_2

description:
10X Genomics Chromium Controller
Hashtag antibodies corresponding to the cells sequenced in DRENEA_2


title: iPSC_Village_B_1_week

description:
10X Genomics Chromium Controller
Single cell sequencing sequencing of genotype and hashtag pooled samples


title: iPSC_DRENEA_6


title: iPSC_DRENEA_3


title: sample4 peri-tumor tissues

city: Zhengzhou

first: Ke

last: Shi

address: No.8, Shuanghu Avenue, Longhu Town, Xinzheng, Zhengzhou, Henan Province

institute: Henan Medical College

data_processing:
10X Chromium sequenced single cell RNA-Seq data
bcl2fastq
Genome alignment and gene-level count summarization was done with Cell Ranger (v6)
Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: cell x gene matrix in txt with transcript counts

source_name: esophageal cancer

extract_protocol:
Sinlge cell droplet was generated by 10X Genomics Chromium, and cDNAs with UMIs were generated at single-cell level.
Illumina adapters with unique index were added to the cDNAs of each sample with Chromium Next GEM Single Cell 3’ mRna Library Construction Kit v3.1

tag: tissue

value: peri-tumor


title: sample2 tumor tissues

value: tumor


title: sample2 peri-tumor tissues


title: iPSC_Village_P1


title: iPSC_Village_A_Baseline


title: iPSC_DRENEA_5


title: sample1 peri-tumor tissues


title: iPSC_DRENEA_2


title: sample1 tumor tissues


title: iPSC_DRENEA_4


title: sample4 tumor tissues


title: iPSC_DRENEA_1


title: eclip_hela_ip_igg_r1

data_processing:
Library strategy: eclip-seq
Adapter trimming:   Small_RNA:  FASTQ data were processed with Cutadapt v1.18, adapter trimmed (AAAAAAAAAA) and reads smaller 17 bp were discarded.  Total RNA-seq: FASTQ data were processed with Trimmomatic v0.32 to remove adapters and low-quality reads.   eCLIP: Double adapter trimming was performed using Cutadapt v1.14.
Small_RNA: Reads were aligned against human elements in RepBase (v23.08) with STAR37 (v2.5.3a) and the unmapped output then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.   RNA-seq: reads were aligned to the hg19 human genome using STAR aligner v2.5.3a with default parameters and RSEM v1.2.31 to obtain expected gene counts against the human Ensembl reference (release 87).   eCLIP: Data was processed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810 - https://github.com/YeoLab/eclip
s4U small RNA-seq and RIP small rna-seq were treated as described in Reichholf B, Herzog VA, Fasching N, Manzenreither RA, Sowemimo I, Ameres SL. Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis. Mol Cell. 2019 Aug 22;75(4):756-768.e7. doi: 10.1016/j.molcel.2019.06.018. Epub 2019 Jul 23. PMID: 31350118; PMCID: PMC6713562. )https://github.com/breichholf/smRNAseq)
Genome_build: hg19
Supplementary_files_format_and_content: Small_RNA and RNA-seq: the processed data files are in bigWig format normalized by Count Per Million (CPM) produced from DeepTools2.
Supplementary_files_format_and_content: eCLIP: strand specific bigwig files;  clipper v1.1 output (bed files, col1: chrom, col2: chromStart, col3: chromEnd, col4: -log10 pvalue, col5: log2 fold enrichment above input, col6: strand)) contains clusters of Ints11 binding

growth_protocol: Unmodified HeLa cells were maintained at 37°C with 5% CO2 in DMEM supplemented with 10% FBS and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations.

extract_protocol:
eCLIP was performed according to Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810, with initial increased RNase concentrations of 1:5, resulting in higher digestion and miRNA resolution
libraries were prepared as described in Van Nostrand, E., Pratt, G., Shishkin, A. et al. Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods 13, 508–514 (2016). https://doi.org/10.1038/nmeth.3810

value: cervical adenocarcinoma

tag: modification

tag: ip antibody

value: rabbit IgG isotype control (Invitrogen, 02-6102)


title: eclip_hela_input_igg_r2

tag: nucleotide alteration


title: eclip_hela_input_igg_r1


title: 𝚫rrpA/B  48-h mycelium 1

city: Jena

first: Matthew

middle: George

last: Blango

address: Adolf-Reichwein-Str. 23

department: Junior Resaerch Group RNA Biology of Fungal Infections

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
Biological Replicate 1
C10

data_processing:
Preprocessing of raw reads including quality control and gene abundance estimation was done with the GEO2RNaseq pipeline (v0.9.12; (https://doi.org/10.1101/771063)) in R (version 3.5.1). Quality analysis was done with FastQC (v0.11.8) before and after trimming. Read-quality trimming was done with Trimmomatic (v0.36).
Reads were rRNA-filtered using SortMeRNA (v2.1) with a single rRNA database combining all rRNA databases shipped with SortMeRNA.
Reference annotation was created by extracting and combining exon features from corresponding annotation files. Reads were mapped against the reference genome of A. fumigatus (Af293, ASM265v1) using HiSat2 (v2.1.0, paired-end mode). Gene abundance estimation was done with featureCounts (v1.28.0) in paired-end mode with default parameters. MultiQC version 1.7 was finally used to summarize and assess the quality of the output of FastQC, Trimmomatic, HiSat, featureCounts and SAMtools. The count matrix with gene abundance data without and with median-of-ratios normalization (MRN; (https://doi.org/10.1186/gb-2010-11-10-r106)) were extracted.
Assembly: A. fumigatus (Af293, ASM265v1)
Supplementary files format and content: The processed data file is an excel .xlsx file containing four tabs, including read counts for each gene, MRN-normalized counts, RPKM-normalized counts, and TPM-normalized counts.

organism: Aspergillus fumigatus

source_name: Mycelium

growth_protocol: A. fumigatus strains were grown on Aspergillus minimal medium (AMM) agar plates (70 mM NaNO3, 11.2 mM KH2PO4, 7 mM KCl, 2 mM MgSO4, 1% (w/v) glucose and 1 μl/ml trace element solution (pH 6.5)). The trace element solution was composed of 1 g FeSO4 • 7 H2O, 8.8 g ZnSO4 • 7 H2O, 0.4 g CuSO4 • 5 H2O, 0.15 g MnSO4 • H2O, 0.1 g NaB4O7 • 10 H2O, 0.05 g (NH4)6Mo7O24 • 4 H2O, and ultra-filtrated water to 1000 ml. Spores were harvested after 5 days with 10 ml of sterile distilled water using a T-shaped inoculation spreader and spore suspensions were filtered through a 30-µm cell strainer (MACS, Miltenyi Biotec GmbH, Germany) to exclude mycelium.

extract_protocol:
Total RNA was isolated from three biological replicates of CEA17ΔakuBKU80, ΔppdA/B, ΔdclA/B, and ΔrrpA/B knockout strains from conidia, 24-h-, and 48-h-old mycelium. For A. fumigatus conidia, the spores were first homogenized in a bead beater (0.5 mm beads; FastPrep-24, MP Biomedicals) in Trizol. Fungal mycelium was collected from liquid culture using Miracloth (Millipore) and disrupted in liquid nitrogen using a precooled mortar and pestle. Roughly 0.5 g of homogenized mycelium was transferred into a 2-ml Eppendorf tube. 800 µl TRIzol was added to the ground mycelia and vortexed vigorously. Tubes were frozen briefly for 5 sec in liquid nitrogen and allowed to thaw on ice. To all samples, chloroform was added to the fungal samples in TRIzol, vortexed, and centrifugated for 5 min at 4°C at full speed. The aqueous upper phase was transferred to a fresh 2-ml tube without disturbing the interphase. RNA extraction from aqueous phase was done with 1 volume of phenol/chloroform/isoamyl alcohol (25:24:1, v/v). Brief vortexing preceded centrifugation for 5 min at 4°C. RNA was precipitated using 400 µl isopropanol for 20 min, followed by pelleting by centrifugation for 20 min at 4°C. The pellet was washed with 700 µl 70% ethanol and air dried at 37°C for 5 min prior to resuspension in RNase free water. The RNA isolation was followed by a DNase treatment using 2 units of TURBO DNase (Thermo Fisher) per 10 µg RNA for 30 min at 37°C in 100 µl total volume. Total RNA was then collected using the RNA Clean and Concentrator-25 kit (Zymo Research) according to the manufacturer’s instructions.
Poly-(A) selection and directional sequencing of mRNA was performed by Novogene using paired-end 150-bp read sequencing on a NovaSeq 6000.

value: Mycelium

value: CEA17 delta_akuB::KU80

tag: growth condition

value: Aspergillus minimal media


title: 𝚫rrpA/B  48-h mycelium 2

description:
Biological Replicate 2
C11

tag: genotype


title: 𝚫rrpA/B  48-h mycelium 3

description:
Biological Replicate 3
C12


title: cre_notch_90_d7_1

description:
human_wnt_notch_cre_notch_vs_cre_null_deseq.tsv
human_wnt_notch_norm_counts.tsv
human_wnt_notch_raw_counts.tsv

tag: cell type

value: neuron

value: notch


title: cre_notch_91_d7_1

value: cre


title: cre_wnt_91_d7_2

description:
human_wnt_notch_cre_wnt_vs_cre_null_deseq.tsv
human_wnt_notch_norm_counts.tsv
human_wnt_notch_raw_counts.tsv

value: wnt


title: cre_notch_90_d7_2


title: cre_notch_91_d7_2


title: cre_dmso_90_d7_1

value: dmso


title: cre_dmso_91_d7_1


title: cre_wnt_90_d7_1


title: cre_wnt_91_d7_1


title: eclip_hela_ip_igg_r2


title: dcre_dmso_90_d7_1

value: dcre


title: 𝚫ppdA/B  48-h mycelium 3

description:
Biological Replicate 3
C9


title: eclip_hela_ip_cpsf73_r2

value: CPSF73 (Bethyl, A301-091A)


title: cre_dmso_90_d7_2


title: cre_dmso_91_d7_2


title: treated_HMEC_TGF-B_siControl_rep2

city: Stockholm

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

institute: Karolinska Institutet

data_processing:
Single end RNA-seq reads were aligned to the human genome (hg19) using TopHat (Trapnell et al. 2009) (version 2.0.9) with the default options. Paired end RNA-seq reads were mapped to human reference (Hg19) genome using STAR (Dobin and Gingeras, 2016) version 2.3 with parameters ( --outFilterMismatchNmax 2 --clip3pAdapterSeq AAAAAA –outSJfilterReads Unique --alignSJDBoverhangMin 3 --alignSJoverhangMin 5 --outSJfilterOverhangMin 30 12 12 12 --outSJfilterCountUniqueMin 5 1 1 1 --outSJfilterIntronMaxVsReadN 50000 100000 200000  --sjdbScore 2 --outFilterType BySJout --outSAMstrandField intronMotif  --seedSearchStartLmax 50 ). The aligned reads files were converted and processed to bam files using Samtools (Li et al., 2009)version 1.1 (Li et al., 2009) and the signal was normalized to Human genome using bamcoverage. Deeptools version 2.0 (Ramírez et al., 2016), after splitting alignments into forward and reverse strand, for visualization purposes. Transcripts were quantified using Salmon 0.7.2 (Patro et al., 2017), using k-mer length 31 and H sapiens GRCh37 ENSG75 annotation. Normalized TPM values were used as input for SUPPA 2.0.
Genome_build: hg19
Supplementary_files_format_and_content: All_samples_ZNF.ENSG75.TPM includes tab-delimited text file with the TPM values for each gene in each replicate, ENSEMBL75 GRCh37, from paired-end RNA-seq data. All_samples_SE_ZNF.ENSG72.TPM includes tab-delimited text file withT the PM value for each gene, in each replicate ENSEMBL752GRCh37, from single-end HMEC RNA-seq data.  All_samples_HMEC_TPM.ENS72.txt contains transcript-level TPM for HMEC samples. Supplementary files from the paper include excel files with the alternative splicing events called from the RNA-seq (not included here).

source_name: cell line

growth_protocol: HMECs were obtained from Lonza and cultured according to the manufacturer’s guidelines. HMLE cells were a kind gift from Christina Scheel (Helmholtz Zentrum Munich) and cultured in LONZA primary cell culture medium.

extract_protocol:
Phenol chloroform extraction, followed by ethanol precipitation
HMEC RNA-seq- PolyA Library type, HMLE RNA-seq samples-Ribozero library

treatment_protocol: 4 nM TGF-β added each alternate day for 4 days to induce EMT

value: HMEC

tag: genotype/variation

tag: treatment

value: TGF-B


title: treated_HMEC_TGF-B_siZnf827_rep2


title: treatedTGF-B_siControl_HMLE_rep3

value: HMLE


title: treatedTGF-B_siZnf827_HMLE_rep2


title: treatedTGF-B_siControl_HMLE_rep1


title: treatedTGF-B_siZnf827_HMLE_rep3


title: treatedTGF-B_siZnf827_HMLE_rep1


title: treated_HMEC_TGF-B_siControl_rep1


title: eclip_hela_ip_cpsf73_r1


title: 𝚫ppdA/B  48-h mycelium 2

description:
Biological Replicate 2
C8


title: Untreated_HMLE_rep3

value: no transfection

value: untreated


title: Untreated_HMLE_rep2


title: 𝚫ppdA/B  48-h mycelium 1

description:
Biological Replicate 1
C7


title: treated_HMEC_TGF-B_siZnf827_rep1


title: treatedTGF-B_siControl_HMLE_rep2


title: eclip_hela_input_cpsf73_r1

value: cervical adenocarcinoma


title: eclip_hela_input_cpsf73_r2


title: Untreated_HMLE_rep1


title: eclip_hela_ip_ints11_r2

value: INTS11 (Sigma, HPA029025)


title: eclip_hela_ip_ints11_r1


title: Wild-type 48-h mycelium 3

description:
Biological Replicate 3
C3

value: Mycelium

value: Wild type


title: 𝚫dclA/B 48-h mycelium 2

description:
Biological Replicate 2
C5

value: CEA17 delta_akuB::KU80

value: Aspergillus minimal media


title: 𝚫dclA/B  48-h mycelium 1

description:
Biological Replicate 1
C4


title: eclip_hela_input_ints11_r2


title: eclip_hela_input_ints11_r1


title: Wild-type 48-h mycelium 2

description:
Biological Replicate 2
C2


title: Wild-type 48-h mycelium 1

description:
Biological Replicate 1
C1


title: totalrna_hela_shints6_dox_r2

value: Tet-pLKO_shINTS6 stable cells


title: 𝚫rrpA/B  24-h mycelium 3

description:
Biological Replicate 3
B12


title: 𝚫dclA/B  48-h mycelium 3

description:
Biological Replicate 3
C6


title: totalrna_hela_shints6_dox_r1


title: PA21A092, Time 48h, Rep 4

type: RNA

city: Frederick

first: Shivendra

middle: G

last: Tewari

state: MD

address: 2405 Whittier Drive, Suite 200

institute: Biotechnology HPC Software Applications Institute

description: Gene expression data

hyb_protocol: The eight time course samples were hybridized (along with the manufacturer’s RNA spike-in controls) according to standard protocol to the 8 sectors of an Agilent 8x15K platform microarray (AMADID 037237) with separate microarray slides used for each biological replicate.

scan_protocol: Arrays were scanned with the Agilent G2600D SureScan microarray scanner using scan protocol AgilentHD_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data.

data_processing: Txt files from Agilent’s Feature Extraction Software were transferred to Partek Genomics Suite software (v7.0). Within Partek, the gProcessedSignal was imported and the intensity values were normalized using Quantile Normalization and Log Tranformation Base 2.0 after import.

organism: Plasmodium falciparum

source_name: PA92-treated Dd2-A211V, Time 48, Rep 4

label_protocol: From 100 ng of total RNA, Cyanine-3 labeled cRNA was prepared using the Low Input Quick Amp Labeling Kit One-Color (Agilent).

extract_protocol: For each data point, RNA was extracted from 50 µL of packed RBC culture with Trizol Reagent and the PureLink Mini Kit (Invitrogen/Thermo Fisher Scientific). 1ml Trizol was added to each sample, followed by high-speed disruption in tubes containing Lysing Matrix D (MP Biomedical) in a FastPrep 120 Instrument at speed 6 for 20 seconds. Homogenates were subsequently processed according to the PureLink Mini Kit manufacturer’s (Invitrogen/Thermo Fisher Scientific) protocol, including on-column DNase treatment.

treatment_protocol: Sublethal doses of KAE609 (30 pM) or PA21A092 (400 nM) was added to control RPMI medium at 0 h of the experiment, which was determined using blood smears of the parasite cultures (described in the paper).

value: Blood-stage Dd2-A211V P. falciparum parasites cultured in human erythrocytes at 2% hematocrit and 400 nM PA21A092

tag: replicate

value: Rep 4


title: totalrna_hela_shcontrol_forints6_dox_r2

description: shGFP

value: Tet-pLKO_shGFP stable cells


title: totalrna_hela_shcontrol_forints6_dox_r1

description: shGFP


title: PA21A092, Time 32h, Rep 4

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 32, Rep 4


title: 𝚫rrpA/B  24-h mycelium 1

description:
Biological Replicate 1
B10


title: 𝚫rrpA/B  24-h mycelium 2

description:
Biological Replicate 2
B11


title: PA21A092, Time 8h, Rep 4

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 8, Rep 4


title: 𝚫ppdA/B  24-h mycelium 3

description:
Biological Replicate 3
B9


title: PA21A092, Time 40h, Rep 4

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 40, Rep 4


title: PA21A092, Time 0h, Rep 4

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 0, Rep 4


title: PA21A092, Time 24h, Rep 4

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 24, Rep 4


title: rip_ago2_shints11_24h_noS4U_r2

description:
shINTS11
control_nos4u_rip_shints11_mirna_quantification.tsv

growth_protocol: HeLa cell lines containing stable shRNA were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. DMEM medium was supplemented with 10% FBS and puromycin (2 μg/ml). Knockdowns were induced by adding of 1 μg/ml doxycycline (Dox) into the culture medium daily for 2 days. In addition, 4-Thiouridine (Cayman chemical, 16373) was added for the indicated timepoints to 200 µM.

extract_protocol:
RIP was performed in the dark from s4U treated cells at the indicated timepoints. Before RNA extraction, 2 pmol synthetic ath-miR-159a was spiked-in and RNA was extracted using Trizol reagent (Thermo Fisher Scientific, #15596026) according to the manufacturer’s instructions. All samples were treated with Iodoacetamide (+IAA) for thiol modification. Genomic DNA was removed by Turbo DNAse treatment (Invitrogen, #AM1907).
Small RNA libraries were prepared using the SMARTer smRNA-seq kit (Takara, #635030) with RNA resulting from RIP (typically 200-400 ng)

value: Tet-pLKO_shINTS11 stable cells

value: Ago2 (abcam, ab57113)

value: IAA


title: PA21A092, Time 24h, Rep 3

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 24, Rep 3

value: Rep 3


title: PA21A092, Time 16h, Rep 4

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 16, Rep 4


title: PA21A092, Time 48h, Rep 3

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 48, Rep 3


title: PA21A092, Time 0h, Rep 3

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 0, Rep 3


title: 𝚫ppdA/B  24-h mycelium 2

description:
Biological Replicate 2
B8


title: PA21A092, Time 8h, Rep 3

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 8, Rep 3


title: PA21A092, Time 40h, Rep 2

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 40, Rep 2

value: Rep 2


title: PA21A092, Time 48h, Rep 2

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 48, Rep 2


title: rip_ago2_shints11_24h_noS4U_r1

source_name: HeLa


title: PA21A092, Time 16h, Rep 3

description: Gene expression data

source_name: PA92-treated Dd2-A211V, Time 16, Rep 3