title: KM12 Parental "covalent 2788"

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: km12 covalent peaks.txt

data_processing:
Sequencing data was processed with a custom script (location available from the manuscript) to transfer the first 8bp of a each sequence to the readID of the FastQ file (UMI, unique molecular identifier). In addition, up to and including 3 T bases were removed from the 5'-end following the UMI transfer. The resulting FastQ files were trimmed with Trim Galore (v0.6.5) to remove read-through contamination with the Illumina standard adapter as well as poor base call qualities (cutoff: Phred 20). Trimmed reads were then aligned to the relevant genomes using Bowtie2 (v2.4.1) in --local mode. Following the alignments, reads were de-duplicated taking UMIs as well as mapping position into account, using UmiBam (v0.2.0; https://github.com/FelixKrueger/Umi-Grinder).
Samples were imported into Seqmonk v1.48, truncated to a single base, peaks called using MACS2 and quantified in appropriate sets
Assembly: GRCh38
Supplementary files format and content: Text file of peaks called by MACS2
Library strategy: TrAEL-seq

extract_protocol:
½ an agarose plug of cells was equilibrated once in 100 µl 1x TdT buffer (NEB) for 30 min at room temperature, then incubated for 2 h at 37°C in 100 µl 1x TdT buffer containing 4 µl 10 mM ATP and 2 µl Terminal Transferase (NEB M0315L). Plugs were rinsed with 1 ml tris buffer (10 mM Tris HCl pH 8.0), equilibrated in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000 for 1 hour at room temperature then incubated overnight at 25°C in 100 µl 1x T4 RNA ligase buffer (NEB) containing 40 µl 50% PEG 8000, 1 µl 10 pM/µl TrAEL-seq adaptor 1 ([App]YYYYNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGUAGCA/iBiodT/TGCUACACTCTTTCCCTACACGACGCTCTTCCG) and 1 µl T4 RNA ligase 2 truncated KQ (NEB M0373L). Plugs were then rinsed with 1 ml tris buffer, transferred to 15 ml tubes and washed three times in 10 ml tris buffer with rocking at room temperature for 1-2 hours each, then washed again overnight under the same conditions. Plugs were pooled, equilibrated for 15 min with 1 ml agarase buffer (10 mM Bis-Tris-HCl, 1 mM EDTA pH 6.5), then the supernatant removed and 50 µl agarase buffer added per plug. Plugs were melted for 20 min at 65°C, transferred for 5 min to a heating block pre-heated to 42°C, 1 µl per plug β-agarase (NEB M0392S) was added and mixed by flicking without allowing sample to cool, and incubation continued at 42°C for 1 h. DNA was ethanol precipitated with 25 µl 10 M NH4OAc, 1 µl GlycoBlue, 330 µl of ethanol per plug and resuspended in 10 µl 0.1xTE. 40 µl reaction mix containing 5µl Isothermal amplification buffer (NEB), 3 µl 100 mM MgSO4, 2µl 10 mM dNTPs and 1µl Bst 2 WarmStart DNA polymerase (NEB M0538S) was added and sample incubated 30 min at 65°C before precipitation with 12.5 µl 10 M NH4OAc, 1 µl GlycoBlue, 160 µl ethanol and re-dissolving pellet in 130 µl 1xTE.
The DNA was transferred to an AFA microTUBE (Covaris 520045) and fragmented in a Covaris E220 using duty factor 10, PIP 175, Cycles 200, Temp 11, then transferred to a 1.5 ml tube containing 8 µl pre-washed Dynabeads MyOne streptavidin C1 beads (Thermo, 65001) re-suspended in 300 µl 2xTN (10 mM Tris pH 8, 2 M NaCl) along with 170 µl water (total volume 600 µl) and incubated 30 min at room temperature on a rotating wheel. Beads were washed once with 500 µl 5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl, 5 min on wheel and once with 500 µl 0.1x TE, 5 min on wheel before re-suspension in 25 µl 0.1x TE. 3.5 μl NEBNext Ultra II End Prep buffer, 1 µl 1 ng/µl sonicated salmon sperm DNA (this is added as a carrier) and 1.5 μl NEBNext Ultra II End Prep enzyme were added and reaction incubated 30 min at room temperature and 30 min at 65°C. After cooling, 1.25 µl 10 pM/µl TrAEL-seq adaptor 2 ([Phos]GATCGGAAGAGCACACGTCTGAACTCCAGTCUUUUGACTGGAGTTCAGACGTGTGCTCTTCCGATC*T ), 0.5 µl NEBNext ligation enhancer and 15 µl NEBNext Ultra II ligation mix were added and incubated 30 min at room temperature. The reaction mix was removed and discarded and beads were rinsed with 500 µl wash buffer (5 mM Tris pH 8, 0.5 mM EDTA, 1 M NaCl) then washed twice with 1 ml wash buffer for 10 min on wheel at room temperature and once for 10 min with 1 ml 0.1x TE. Libraries were eluted from beads with 11 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°C, then again with 10.5 µl 1x TE and 1.5 µl USER enzyme (NEB) for 15 min at 37°, and the two eluates combined.An initial test amplification was used to determine the optimal cycle number for each library. For this, 1.25 μl library was amplified in 10 µl total volume with 0.4 µl each of the NEBNext Universal and any NEBNext Index primers with 5 µl NEBNext Ultra II Q5 PCR master mix. Cycling program: 98°C 30s then 18 cycles of [98°C 10 s, 65°C 75 s], 65°C 5 min. Test PCR was cleaned with 8 µl AMPure XP beads (Beckman A63881) and eluted with 2.5 µl 0.1x TE, of which 1 µl was examines on a Bioanalyser high sensitivity DNA chip (Agilent 5067-4626). Ideal cycle number should bring final library to final concentration of 1-3 nM, noting that the final library will be 3 cycles more concentrated than the test anyway. 21 µl of library was then amplified with 2 µl each of NEBNext Universal and chosen Index primer and 25 µl NEBNext Ultra II Q5 PCR master mix using same conditions as above for calculated cycle number. Amplified library was cleaned with 40 µl AMPure XP beads (Beckman A63881) and eluted with 26 µl 0.1x TE, then 25 µl of this was again purified with 20µl AMPure XP beads and eluted with 11µl 0.1x TE.

treatment_protocol: 1-2x106 cells were washed once in 5 ml L buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl) and resuspended in 60 µl L buffer in a 2 ml tube. Samples were heated to 50°C for 2-3 min before addition of 40 µl molten CleanCut agarose (Bio-Rad 1703594), vortexing vigorously for 5 s before pipetting in plug mould (Bio-Rad 1703713) and solidifying 15-30 min at 4°C. Each plug was transferred to a 2 ml tube containing 500 µl digestion buffer (10 mM Tris HCl pH 7.5, 100 mM EDTA, 20 mM NaCl, 1% sodium N-lauroyl sarcosine, 0.1 mg/ml Proteinase K) and incubated overnight at 50°. Plugs were washed three times with 1 ml TE for 1-2 hours at room temperature with rocking, 10 mM PMSF was added to the second and third washes from 100 mM stock (Merck 93482). Plugs were then digested 1 h at 37°C with 1 µl 1000 U/ml RNase T1 (Thermo EN0541) in 200 µl TE.

value: colorectal carcinoma

value: covalent 2788


title: miR-449b-5p transfected HSVEC Rep1

status: Public on Jan 10 2025

type: SRA

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

library_source: transcriptomic

data_processing:
Gene quantification (read count and FPKM) was obtained using RSEM (options: -bowtie2 -pairedend), based on human  GRCh38 genome annotation and GENCODE transcriptome annotation (Release 25)
Assembly: GRCh38
Supplementary files format and content: Count.csv: csv file containing read count for each gene in the different samples
Supplementary files format and content: FPKM.csv: csv file containing the FPKM (fragments per kilobase of transcript per million mapped reads) expression value for each gene in the different samples

molecule: total RNA

organism: Homo sapiens

source_name: Human saphenous vein endothelial cells

growth_protocol: HSVECs were obtained by enzymatic collagenase digestion of human saphenous veins and maintained in EC growth medium (EGM-2 BulletKit™) (Lonza) supplemented with foetal bovine serum (10%, Life Technologies) and Penicillin-Streptomycin (100U/ml) (Gibco).

extract_protocol:
RNA was extracted and DNAse treated using the miRNeasy mini kit (Qiagen)
Library preparation was prepared after polyA mRNA selection using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB).

treatment_protocol: Transient transfection of the 7 miRNA mimics (Dharmacon, ThermoFisher)  or the miRNA control (miR-CTRL-miRIDIAN microRNA Mimic Negative Control #1) was performed with Lipofectamine RNAiMAX (Life Technologies) following the manufacturer’s guidelines, for 6 hours in Opti-MEM (Life Technologies).

tag: cell line

value: Human saphenous vein endothelial cells

tag: replicate/patient

tag: mimic transfection


title: Braf Q241R/+ ;Cre, hippocampus, No8 [PR1825_02]

city: Maebashi

first: Hiroshi

last: Ohnishi

state: Gunma

address: 3-39-22 Showa-machi

department: Department of Laboratory Sciences

country: Japan

institute: Gunma University Graduate School of Health Sciences

description:
n-Braf Q241R/+_2
PR1825_02

data_processing:
Sequencing analysis were performed NovaSeq Control Software v1.6.0, Real Time Analysis v3.4.4 and bcl2fastq2 v2.20.
Sequence reads were processed by the use of fastp program (v0.20.1) for quality control, adapter trimming, quality filtering, and pre-read quality cutting.
Trimmed sequence reads were aligned to GRCm/mm10 using Spliced Transcripts Alignment to a Reference (STAR) software (v2.7.6a).
Aligned data were quantified by RNA-Seq Expectation Maximization (RSEM) software (v1.3.3).
The count data were statistically processed and normalized using edgeR software (v3.36.0).
Assembly: mm10
Supplementary files format and content: Comma separated values file contain row counts sample for each samples and statistical processing data.

organism: Mus musculus

source_name: Hippocampus

growth_protocol: Mice were bred and maintained under specific-pathogen-free conditions. They were housed in an air-conditioned room with a 12-h light, 12-h dark cycle.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 10.0 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMART-Seq®Stranded Kit and SMART-Seq®Stranded Kit Unique Dual Index Kit following SMART-Seq®Stranded Kit User Manual (022819).

tag: tissue

value: Hippocampus

value: male

tag: cell type

value: 32 weeks of age

tag: genotype

value: Braf Q241R/+ ;CaMKII-Cre

tag: strain background


title: Braf Q241R/+ ;Cre, hippocampus, No7 [PR1825_01]

description:
n-Braf Q241R/+_1
PR1825_01

value: 33 weeks of age


title: KM12 Parental "untreated"

description: km12 covalent peaks.txt

library_source: genomic

molecule: genomic DNA

tag: treatment

value: untreated


title: DRB treated Wild Type mouse ES rep-3

type: genomic

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

hyb_protocol: Genomic DNA (300–800 ng) was converted with sodium bisulfite using the EZ DNA Methylation Kit (Zymo Research), and it was hybridized with the Illumina MouseMethylation BeadChip array according to the manufacturer’s protocol.

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting.

data_processing: Raw Infinium MouseMethylation data were preprocessed as followed: CpG probes of low quality (detection p-value threshold of 0.05) were removed from the analysis and Beta-values were computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction.

source_name: DRB treated Wild Type mouse ES

label_protocol: Standard Illumina Protocol

growth_protocol: ESCs were cultured on tissue culture plates coated with 0.1% gelatin and feeder cells, in high glucose DMEM-containing 15% FBS, 1 mM sodium pyruvate, 1% non-essential amino acids, 1% glutaMAX™, 0.1 mM β-mercaptoethanol, and 1000 units/ml recombinant mouse LIF at 37°C under 5% CO2. To generate EBs, 4 × 106 ESCs were seeded in 15 ml EB medium (without LIF) and maintained for 8 days. Cells were precipitated by gravity, resuspended, and cultured with fresh medium every two days.

extract_protocol: Genomic DNA was extracted with the QIAamp DNA Mini Kit (from QIAGEN) following the manufacturer’s protocol.

treatment_protocol: (Mettl3KO) Mettl3 knockout J1 ESCs were generated by Howard Y. Chang, Stanford University, USA (Batista et al, Cell Stem Cell, 2014). (Mettl14KO and rescue) Mettl14 KO E14TG2a mouse ESCs were gifted by Laixin Xia, Southern Medical University, Guangzhou, China. For Mettl14-rescued cells, a Mettl14WT or Mettl14ΔRGG cDNA was cloned into plasmid pLV-EF1a-IRES (Blasticidin S resistant) and used, along with packaging vectors (pMD2.G and psPAX2), to co-transfect HEK293/T cells with Lipofectamine™ 3000, according to the manufacturer's protocol. Supernatant containing lentivirus particles was collected 48 and 72 hours post-transfection, supplemented with polybrene, and used to infect Mettl14 KO ESCs. After two rounds of infection, cells were selected for 7 days with 10 μg/ml blasticidin S48 and the surviving cells were pooled as stably rescued cell lines.  (Mettl3i) ESCs were treated with Mettl3 inhibitor STM-2457 at 50 μM or with its vehicle control and collected 24 h post-treatment for further analysis.  (Dnmt1KO) Dnmt1 KO mouse ESCs were gifted by Fabio Spada, Ludwig Maximilians University, Germany.  (Differentiation).The transition from naïve to formative pluripotency was adapted from previous protocols5,7. Briefly, 2×10⁶ naïve pluripotent ESCs were cultured on tissue culture plates coated with 0.1% gelatin, in “naïve medium” (2i/LIF serum-free N2B27 medium, see “Cell lines” section). After 12 hours, the medium was replaced with FBS-containing medium (high-glucose DMEM containing 15% FBS, 1 mM sodium pyruvate, 1% non-essential amino acids, 1% glutaMAX™, 1% penicillin and streptomycin, 0.1mM β-mercaptoethanol (Gibco)) to induce formative pluripotency. Cells cultured under these conditions were collected after 3 or 24 hours for further analysis.

tag: genotype or drug

value: DRB

tag: es strain

tag: replicate


title: Spl.KO.2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using STAR and the UCSC mm10 known gene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor.
Assembly: mm10
Supplementary files format and content: csv file of RPKM normalized read counts for each detected gene

molecule: polyA RNA

source_name: spleen

extract_protocol:
Cells were FACS sorted into RLT + 1%BME and snap frozen using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
Purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara) and used as an input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

value: spleen

value: T regulatory cells

tag: age

value: 25 week old

value: Foxp3-YFPcre Srebf2-flox/flox

tag: Sex


title: miR-323a-3p transfected HSVEC Rep2


title: Braf Q241R Neo/+, hippocampus, No61 [PR1825_06]

description:
Braf Q241R Neo/+_3
PR1825_06

value: 31 weeks of age

value: Braf Q241R Neo/+


title: miR-323a-3p transfected HSVEC Rep3


title: Untreated Wild Type mouse ES rep-2

source_name: Untreated Wild Type mouse ES


title: Braf Q241R Neo/+, hippocampus, No21 [PR1825_05]

description:
Braf Q241R Neo/+_2
PR1825_05


title: Untreated Wild Type mouse ES rep-3


title: HCT116 C9 ISG4 cl4 "doxy"

description: HCT116 doxy peaks.txt

value: doxy


title: Delta RGG rescued Mettl14 knocked out mouse EB rep-3


title: miR-323a-3p transfected HSVEC Rep1


title: Braf Q241R Neo/+, hippocampus, No9 [PR1825_04]

description:
Braf Q241R Neo/+_1
PR1825_04


title: HCT116 C9 ISG4 cl4 "covalent 2788"

description: HCT116 covalent peaks.txt

value: colorectal carcinoma


title: HeLa-WT-4-RNA

description: RNA WT HeLa Cells

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to human tRNA and rRNA sequences with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences. The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
The processed fastq reads were mapped to a human reference transcriptome that includes Ensembl v85 transcripts and long noncoding from LNCipedia v5.2 using the "RSEM" tool.
Assembly: GRCh37/hg19
Supplementary files format and content: Gene-specific FPKM, TPM and expected count text file

source_name: HeLa cells WT Rep-4

growth_protocol: HeLa cells were cultured at 37°C under 5% CO2 in DMEM (Gibco) media supplemented with 10% FBS and 1% 100X Pen Strep (Gibco).

extract_protocol:
Total RNA was extracted with RNeasy kit according to the manufacturer's instructions. Residual DNA removal was performed using the RNase-Free DNase Set.
Ribo depleted Total RNA
The library preparation was performed using TruSeq Stranded Total RNA with Ribo-Zero Gold following the manufacturer’s instructions.

treatment_protocol: HeLa METTL3 KO cell lines were generated with the CRISPR-Cas9 nuclease system via homology-directed repair (HDR) as previously described. Briefly, sgRNAs were designed to target the start codon (ATG) and the first intron of METTL3 using the guidelines described in the online tool (http://crispor.tefor.net). Then they were cloned into the pX461 vector (Addgene). In parallel, a donor vector (pUC18) containing gene sequences homologous to those flanking the sgRNA targeting sites bordering a selectable marker (either mCherry or puromycin resistance gene) and mammalian transcriptional terminator (bGH, synthesized by GENEWIZ) was constructed. Next, the co-transfection of the donor vectors and gRNAs was performed by using Lipofectamine™ 2000 according to the manufacturer’s instructions (Invitrogen). After 24 hours, cells were selected by puromycin at a concentration of 2 µg/ml for at least 10 days, and sorted into 96-well plates (1 cell per well) by fluorescence-activated cell sorting (FACS). After proliferation, clones were analysed for the METTL3 KO by quantitative reverse transcription PCR (RT-qPCR) and western blotting. Subsequently, the CRISPR-Cas9-targeted genomic regions were PCR-amplified and sequenced in positive clones.

value: HeLa

value: WT


title: miRCTRL transfected HSVEC Rep3

value: Human saphenous vein endothelial cells

value: miRCTRL


title: miRCTRL transfected HSVEC Rep2


title: BrM, replicate 3

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment to the mouse reference genome mm10 (Ensembl 93) 3.1.0 (July 24, 2019), gene counting and aggregation was performed using Cell Ranger software v4.0.
Assembly: mm10 (Ensembl 93) 3.1.0 (July 24, 2019)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain tumor

extract_protocol:
Fresh tumor tissue was collected from sacrificed mice following microdissection, and all the subsequent steps were performed on ice, if not stated otherwise. Tumor tissue was placed in serum-free media and chopped into small pieces with scissors. The Tumor Dissociation Kit for mouse (Miltenyi, Cat# 130-096-730) was used to generate a single cell suspension. After the tissue digestion, cells were filtered through a 40 μm mesh filter and washed. Samples were stained with mouse Fc block and afterwards with anti-CD11b (M1/70) and anti-CD45 (30-F11). Dead cells were excluded using DAPI (Thermo Fisher Scientific, Cat# 62247) and viable cells were additionally stained with RedDot™1 Far-Red Nuclear Stain (Chemie Brunschwig Cat# BIO40060-1) following the manufacturer’s instruction manual. Total immune cells were sorted as CD45+ DAPI- RedDot-1+ cells using an Aria II (SORP) instrument (BD) into 1.5 ml tubes containing 8 μl cold HBSS. Sorted cells were counted and a total of 16,000 total cells were loaded onto the 10x Chromium Controller following the manufacturer’s instruction manual. For the generation of Gel Beads in Emulsion (GEM), Chromium Single Cell 3ʹ GEM Kit v3 (10x, 1000077) and the Chromium Single Cell B Chip Kit (10x, 1000074) were used.
Gene expression libraries were prepared using the Chromium Single Cell 3ʹ Library Kit v3 (10x 1000078) following the manufacturer’s instruction manual. The quantity of constructed libraries was determined with the Qubit Fluorometric Quantification (Thermo Fisher Scientific, Q32851). Library quality was determined using High Sensitivity Next-Generation-Sequencing Fragment Analysis (Agilent Technologies, DNF-474-0500) and the sequencing was performed by Genewiz Services (http://www.genewiz.com/) on an Illumina HiSeq 2500 or Illumina NovaSeq6000 S4 Flow Cell using a 10x sequencing configuration. Targeted sequencing depth was > 20,000 reads per cell.

value: Brain tumor

value: CD45+ immune cells

value: female

value: 10-12 weeks old


title: miRCTRL transfected HSVEC Rep1


title: HeLa-M3KO-0h-1

description: ActinoD METTL3-KO HeLa Cells

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to human tRNA and rRNA sequences with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences. The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
The processed fastq reads were mapped to the human reference genome (GRCh37/hg19) using the "STAR" algorithm with reference transcriptome includes Ensembl v85 and long noncoding from LNCipedia v5.2. Gene expression was evaluated using "HTseq" count.
Assembly: GRCh37/hg19
Supplementary files format and content: HTSeq count file

source_name: HeLa cells METTL3KO 0h Rep-1

extract_protocol:
Total RNA was extracted with RNeasy kit according to the manufacturer's instructions. Residual DNA removal was performed using the RNase-Free DNase Set.
The library preparation was performed using TruSeq Stranded Total RNA with Ribo-Zero Gold following the manufacturer’s instructions.

treatment_protocol: WT and METTL3 KO HeLa cells were treated with 1 μg/ml Actinomycin D or vehicle for 0, 4, 6, and 8 hours.

tag: cellline

value: Human HeLa cell line

tag: knockedout


title: Delta RGG rescued Mettl14 knocked out mouse ES rep-3


title: HeLa-WT-3-RNA

description: RNA WT HeLa Cells

source_name: HeLa cells WT Rep-3


title: Mettl14 knocked out mouse EB rep-3

source_name: Mettl14 knocked out mouse EB


title: DRB treated Wild Type mouse ES rep-1

value: DRB


title: MFP, replicate 3

description: 10x Genomics

source_name: Mammary fat pad tumor

value: Mammary fat pad tumor


title: HSVEC  untransfected Rep3

value: No


title: HeLa-WT-2-RNA

description: RNA WT HeLa Cells

source_name: HeLa cells WT Rep-2


title: Full length rescued Mettl14 knocked out mouse ES rep-3


title: HSVEC  untransfected Rep2


title: MFP, replicate 2

description: 10x Genomics


title: BrM, replicate 2

description: 10x Genomics


title: Mettl14 knocked out mouse ES rep-3

source_name: Mettl14 knocked out mouse ES


title: Wild Type mouse EB (Mettl14 KO control) rep-3

source_name: Wild Type mouse EB (Mettl14 KO control)


title: HeLa-METTL3KO-4-RNA

description: RNA METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Rep-4


title: MFP, replicate 1

description: 10x Genomics


title: HeLa-WT-1-RNA

description: RNA WT HeLa Cells

source_name: HeLa cells WT Rep-1


title: HeLa-METTL3KO-3-RNA

description: RNA METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Rep-3


title: HSVEC  untransfected Rep1

source_name: Human saphenous vein endothelial cells


title: LNCaP WDR77 R1881 Input Rep 2

city: Buffalo

first: Tao

last: Liu

state: NY

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

data_processing:
*library strategy: CUT&RUN
Raw fastq files of paired-end reads were aligned to human genome hg38 using bwa-mem (bwa version 0.7.17).
After alignment, duplicate reads were marked by Picard `MarkDuplicates` function. Then duplicated reads and low quality (Q<30) reads after alignment were removed using samtools with flag `-F 3340 -f 3`.
The pileup profiles for each replicate (either with antibody or input) were generated using MACS3 (version 3.0.0) with command `macs3 pileup -f BAMPE` on the cleaned BAM files with duplicate reads being removed.
Assembly: hg38
Supplementary files format and content: bigwig format, for raw paired-end sequence fragments pileup

source_name: prostate

extract_protocol:
CUT&RUN was performed using a kit from Cell Signalling Technologies (CUT&RUN Assay Kit #86652) as per the manufacturer's protocol. 250,000 cells were used as starting material.
Sequencing libraries were prepared using NEBNext Ultra II DNA libray prep kit (13 cycles for library amplification).

treatment_protocol: In a first experiment, LNCaP cells were seeded in RPMI1640 medium supplemented with 9% FBS without added antibiotics. The next day, cells were transfected with siRNAs targeting WDR77 or non-targeting control siRNA. The next day, medium was changed to medium supplemented with 9% charcoal-stripped FBS. After 80hours, medium was refreshed and cells were treated with 5nM R1881 or vehicle (ethanol) for another 16h. In a second experiment, LNCaP cells were seeded in RPMI1640 medium supplemented with 9% charcoal-stripped FBS.  Two days later, medium was refreshed and cells were treated with 5nM R1881 or vehicle (ethanol) for another 16h.

value: prostate

value: LNCaP

value: prostate cancer


title: Wild Type mouse ES (Mettl14 KO control) rep-3

source_name: Wild Type mouse ES (Mettl14 KO control)


title: lung_chip2_mRNA

city: Beijing

last: Cai

address: No. 7 Science Park Road, Zhongguancun Life Science Park

country: China

institute: National Institute Of Biological Sciences, Beijing (NIBS)

description:
message RNA
read2 for the cell barcodes
lung_chip2_barcodes.txt

data_processing:
The sRNA analysis procedures were adapted from the method in the publication(S. Mi and T. Cai et al., Cell 133, 116, 2008). Briefly, the small RNA sequences, cell barcodes, and molecules UMI were extracted from the raw reads using customized scripts. The small RNA sequences with the length of 16nt~39nt were kept and mapped to the reference genome with no mismatch (bowtie v1.2.2). The small RNAs were annotated according to the databases including miRbase (release v22.1), EBI RNAcenter database (release v11), and EBML CDS database (ENSEMBL release v96). For small RNA genes, UMIs were counted as the measurement of small RNA expression. The computational pipeline can be found at GitHub (https://github.com/biocaitao/PSCSR-seq).
For the mRNA analysis, the reads index tag, cell barcodes, and inserted sequences were extracted from raw reads using customized scripts. then, the inserted sequences were mapped to the genome using the STAR program (v2.6.1) using default parameters. The mapped sequences were annotated according to the gene features of the GENCODE database.  To measure the expression of mRNAs, mapped reads with the same index tag or adjacent index tag (1 mismatch) were collapsed into UMI. After that, the UMI counts were weighted by the number of mapped locations. The UMIs were summed as the measurement of small RNA expression. Then, mRNA expression values for each cell were normalized and log-transformed. The computational pipeline can be found at GitHub (https://github.com/biocaitao/PSCSR-seqII).
For the cell barcodes file, the single cells in PSCSR-seq were selected using TaKaRa ICell8 system protocol (“StandardCellSettings-V5” or “PBMCv4”). The cell barcodes of selected cells were exported. The valid cells were filtered from the background according to the exported barcodes (allowing 2 mismatches) (refer to https://github.com/biocaitao/PSCSR-seq ).
Assembly: hg38 and mm10
Supplementary files format and content: The processed files contain: plain text files for cell barcodes and estimated expression of miRNAs and mRNAs;

source_name: lung

growth_protocol: A549 cells were cultured in DMEM/F-12 (11320082, Gibco), Hela, and HEK293T cells were cultured in DMEM-basic (C11965500BT, Gibco) and K562 cells were cultured in RPMI Medium 1640 basic(1X) (C22400500BT, Gibco). All the cultured media were supplemented with 10% (v/v) fetal bovine serum (26140079, Gibco) and 1% penicillin-streptomycin (15140122, Gibco). Cells were cultured at 37°C in a 5% CO2 humidified incubator.  C57BL/6 mice were maintained under specific pathogen-free (SPF) conditions with free access to food and water. Mice were group-housed under a 12-h light: dark cycle in IVC cages (Lingyunboji, Beijing).

extract_protocol:
Cultured cancer cells were harvested and dissociated, fresh cells were resuspended with 1 x Dulbecco's phosphate-buffered saline (DPBS, C14190500BT, Thermo Fisher Scientific).  Mice were euthanized using carbon dioxide and lung tissues were collected and cut into small pieces of 2-4 mm. These pieces were dissociated into single-cell suspensions with PythoN® Tissue Dissociation System following the manufacturer’s instructions (MD1101001, Singleron Biotechnologies).
Single-cell suspensions were dispensed into the ICELL8 nanowell chip for cell imaging and screening. Selected single live cells were lysed to release total RNA; then, small RNAs were ligated with 3' adapters, and mRNAs were reverse transcribed and linked to adapters using template switching oligos. Next, the remaining 3' adapters were removed, and 5' adapters were ligated to small RNAs. The ligated small RNAs were then reverse transcribed. Cell barcodes were introduced by PCR to label individual cells (PCR-1). Next, small RNA and mRNA libraries were separately collected according to their size ranges. Then, the libraries were amplified for high-throughput sequencing (PCR-2). Additionally, by-products in small RNA libraries were removed.
PSCSR-seq V2

value: lung

value: tissue dissociated cells

tag: strain

value: C57BL/6 mice


title: Mettl14 knocked out mouse EB rep-2


title: HeLa-METTL3KO-2-RNA

description: RNA METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Rep-2

value: HeLa


title: BrM, replicate 1

description: 10x Genomics


title: Spl.KO.1

source_name: spleen

value: spleen

value: T regulatory cells

value: 25 week old

value: Foxp3-YFPcre Srebf2-flox/flox

value: male


title: lung_chip2_sRNA

description:
small RNA
lung_chip2_barcodes.txt


title: HeLa-METTL3KO-1-RNA

description: RNA METTL3-KO HeLa Cells

source_name: HeLa cells METTL3KO Rep-1


title: lung_chip1_mRNA

description:
message RNA
read2 for the cell barcodes
lung_chip1_barcodes.txt


title: Untreated Wild Type mouse ES rep-4

source_name: Untreated Wild Type mouse ES


title: HCT116 C9 ISG4 cl4 "untreated"

description: HCT116 doxy peaks.txt

value: colorectal carcinoma

value: untreated


title: LNCaP WDR77 Vehicle Rep 2

tag: antibody

value: Ethanol


title: Delta RGG rescued Mettl14 knocked out mouse EB rep-2


title: Full length rescued Mettl14 knocked out mouse EB rep-2


title: LNCaP WDR77 R1881 Rep 2

tag: cell line


title: OPTT98-Biological replicate 2 [18170XR.01.23]

city: PHILADELPHIA

first: Devraj

last: Basu

state: PENNSYLVANIA

address: 3400 SPRUCE STREET, 5 RAVDIN

department: Otorhinolaryngology

institute: Perelman School of Medicine, University of Pennsylvania

data_processing:
The raw sequences were aligned to combined genome from hg38, mm10 and HPV genomes (including all high-risk types: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68) using STAR with default parameters.
After STAR first-pass alignment, all the reads that are mapped to mm10 were removed and reads aligned to hg38 and HPV genomes were kept.
STAR first-pass alignment detected the most abundant splice junctions, which were then used in the second-pass alignment.
All of the quantification and analyses were based on the second-pass alignment.
Genome_build: hg38; HPV genomes (including all high-risk types: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66 and 68)
Supplementary_files_format_and_content: normalized abundance measurements

source_name: HPV+ OPSCC PDXs

growth_protocol: PDXs were grown in the subcutaneous flank of NOD/SCID/IL-2Rγ-/- mice. The 8 PDXs were harvested for RNA sequencing in triplicate upon reaching an approximate volume of 1 cm3.

extract_protocol:
RNA isolation was performed with the Qiagen RNA Kit (Qiagen, Hilden, Germany). Sample quality was assessed using Agilent RNA 6000 Nano Reagent on Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and quantified by Qubit RNA HS assay (ThermoFisher, Waltham, MA). Ribosomal RNA depletion was performed with Ribo-zero rRNA Removal Kit, HMR (Illumina Inc., San Diego, CA).
Library preparation was performed with the NEBNext Ultra II Non-directional Synthesis Module (New England Biolabs, Ipswich, MA).
Average final library size is between 400-430 bp. Illumina 8-nt dual-indices were used for multiplexing. Samples were pooled and sequenced on Illumina NextSeq High Output sequencer for 75 bp read length in single-read mode, with an output of 50 million reads per sample.

treatment_protocol: No Treatment

tag: tissue id

value: HPV+ Patient Derived Xenografts (PDXs)

tag: hpv type

value: HPV16 +ve

tag: disease/cell type

value: oropharyngeal squamous cell carcinoma (OPSCC)


title: LNCaP AR R1881 siWDR77 Input Rep 2

tag: tissue

value: prostate

value: LNCaP

tag: cell type


title: OPTT98-Biological replicate 1 [18170XR.01.22]


title: sgTut1-9, RNA-seq

first: wei

middle: zi

last: guo

state: Beijing

address: ZhongGuanCun

institute: tsinghua university

data_processing:
The adapters of paired-end reads were trimmed and quality control check were carried out using trim-galore (version 0.6.4)
Reads were aligned to mouse genome mm10 and Drosophila genome dm6 from GENCODE using STAR (version 2.7.1a).
Aligned reads stored in BAM format were filtered using SAMtools (version 1.9) with parameter is “samtools view –b –h –F 4 –f 3”.
featureCounts (version 1.6.4) counted reads stored in BAM format to exon sites of genes included in GTF file from GENCODE.
Bigwig files were created with deepTools (bamCoverage). We calculated differentially expressed regions by EdgeR.
Assembly: mm10
Supplementary files format and content: bigwig files were generated using deeptools

source_name: healthy pancreas

growth_protocol: Pancreatic cancer cells were cultured at 37℃ in DMEM medium, supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin.   We used AAV to deliver control or high efficiency Tut1 sgRNAs to mice harboring Pdx1-Cre; LSL-Cas9-eGFP alleles  and collected acinar cells for mRNA sequencing experiment.

extract_protocol:
RNA was extracted with TRIzol (Invitrogen, 15596018) according to the manual
500ng RNA of each sample was used to prepare libraries. Total RNA-seq libraries were prepared using the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (Vazyme, NR611).

treatment_protocol: 1μg/mL doxycycline was added into medium for 72hr before harvesting cells to induced dCas9-KRAB expression

value: healthy pancreas cells

value: treated with TUT1 KO in acinar

tag: genotype

value: TUT1 knockout


title: lung_chip1_sRNA

description:
small RNA
lung_chip1_barcodes.txt

value: lung

value: tissue dissociated cells

value: C57BL/6 mice


title: OPTT98-Biological replicate 3 [18170XR.01.24]


title: LNCaP AR vehicle siWDR77 Input Rep 2

value: prostate cancer

tag: treatment


title: LNCaP AR R1881 Input Rep 2


title: sgTut1-5, RNA-seq


title: Delta RGG rescued Mettl14 knocked out mouse ES rep-2

tag: genotype or drug


title: OPTT88-Biological replicate 3 [18170XR.01.21]


title: Wild Type mouse EB (Mettl14 KO control) rep-2

tag: es strain


title: sgRosa2, RNA-seq

value: untreated in acinar

value: control


title: Mettl14 knocked out mouse ES rep-2

tag: replicate


title: OPTT88-Biological replicate 2 [18170XR.01.20]


title: LNCaP AR vehicle Input Rep 2


title: miR-892b transfected HSVEC Rep1

value: Human saphenous vein endothelial cells

tag: replicate/patient

tag: mimic transfection


title: OPTT88-Biological replicate 1 [18170XR.01.19]


title: sgRosa1, RNA-seq


title: sgTut1-2 TUT1KD, RNA-seq

source_name: pancreatic ductal adenocarcinoma

value: pancreatic ductal adenocarcinoma cells

value: treated with TUT1 KD in PDAC

value: TUT1 knockdown


title: OPTT82-Biological replicate 3 [18170XR.01.18]

value: HPV+ Patient Derived Xenografts (PDXs)

value: HPV16 +ve


title: sg9270 TUT1KD, RNA-seq

value: untreated in PDAC


title: OPTT82-Biological replicate 2 [18170XR.01.17]

value: oropharyngeal squamous cell carcinoma (OPSCC)


title: Full length rescued Mettl14 knocked out mouse EB rep-1


title: Wild Type mouse EB (Mettl14 KO control) rep-1


title: OPTT82-Biological replicate 1 [18170XR.01.16]


title: sgTut1-1 TUT1KD, RNA-seq


title: LNCaP AR vehicle Rep 2

value: prostate

value: LNCaP

value: AR

value: Ethanol


title: OPBT75-Biological replicate 3 [18170XR.01.15]


title: LNCaP WDR77 R1881 Input Rep 1


title: LNCaP AR R1881 Rep 2


title: Mettl14 knocked out mouse ES rep-1


title: Full length rescued Mettl14 knocked out mouse ES rep-2


title: LNCaP WDR77 vehicle Input Rep 1


title: OPBT75-Biological replicate 2 [18170XR.01.14]


title: sgT3, 3'-seq

data_processing:
The adapters of reads were trimmed and quality control check were carried out using trim-galore (version 0.6.4)
Reads were aligned to mouse genome mm10 from GENCODE using Bowtie2.
Only reads that were properly paired and uniquely mapped were used for next analyses.
BPM normalized bigwig files were created with deepTools (bamCoverage).
Assembly: mm10
Supplementary files format and content: bigwig files were generated using deeptools
Library strategy: PRO-seq

growth_protocol: Pancreatic cancer cells were cultured at 37℃ in DMEM medium, supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin.

extract_protocol:
Nascent RNA was extracted as previously described (Mahat et al., 2016)
The libraries were prepared using the Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300) according to the manual

treatment_protocol: 1μg/mL doxycycline was added into medium for 72hr before harvesting cells to induced dCas9-KRAB expression and nascent RNA labeled with biotin-NTPs was carried out as previously described (Mahat et al., 2016)

value: treated with TUT1 KD


title: Full length rescued Mettl14 knocked out mouse EB rep-3


title: OPBT75-Biological replicate 1 [18170XR.01.13]


title: LNCaP AR siWDR77 R1881 Rep 2


title: sg4841 TUT1KD, RNA-seq


title: LNCaP WDR77 R1881 Rep 1


title: sg4841, 3'-seq

value: untreated


title: sgT2, 3'-seq


title: OPTT61-Biological replicate 2 [18170XR.01.11]


title: OPTT61-Biological replicate 3 [18170XR.01.12]


title: LNCaP AR R1881 siWDR77 Input Rep 1

value: prostate cancer


title: LNCaP AR siWDR77 vehicle Rep 2


title: Mettl14 knocked out mouse EB rep-1

source_name: Mettl14 knocked out mouse EB


title: OPTT61-Biological replicate 1 [18170XR.01.10]


title: sg9270, 3'-seq


title: Wild Type mouse ES rep-2

source_name: Wild Type mouse ES

value: WT


title: R23G12-Gal4 Drgx knockdown3

city: Regensburg

first: Mathias

last: Rass

address: Universitätsstraße 31

department: Developmental Biology

country: Germany

institute: University of Regensburg

description: RNA-sequencing following Drgx knockdown in Drosophila T4/T5 neurons

data_processing:
STAR was used to align reads to the Drosophila transcriptome and to generate count matrices from each library. Gene count matrices from different libraries were combined into one single matrix in R and DEseq2 was used to perform differential gene expression analyses. Genes without an unique Flybase gene ID were excluded from these analyses.
Assembly: BDGP 6.32
Supplementary files format and content: results from DESeq2 stored in xlsx table
Supplementary files format and content: gene count matrix as comma seperated values

organism: Drosophila melanogaster

source_name: T4/T5 neurons

growth_protocol: development at 25°C until climbing L3 larval stage.

extract_protocol:
Brains were dissected in cold Drosophila Schneider medium. Brains were dissociated with Papain and Liberase into a single cell solution. T4/T5 neurons were expressing GFP and  sorted out from the single cell solution with a FacsAria Ilu sorter into TRL Plus Buffer of the RNeasy Plus Micro Kit. Total RNA was extracted using the RNeasy Plus Micro kit according to the manufacturer's protocol.
libraries were prepared with SMART-Seq v4

value: T4/T5 neurons


title: Mettl3 knocked out mouse ES rep-2

source_name: Mettl3 knocked out mouse ES


title: OPTT59-Biological replicate 3 [18170XR.01.09]


title: Delta RGG rescued Mettl14 knocked out mouse ES rep-1


title: LNCaP AR R1881 Input Rep 1


title: OPTT59-Biological replicate 2 [18170XR.01.08]


title: R23G12-Gal4 Drgx knockdown1


title: Wild Type mouse ES (Mettl14 KO control) rep-1


title: LNCaP AR vehicle Input Rep 1


title: Delta RGG rescued Mettl14 knocked out mouse EB rep-1


title: R23G12-Gal4 ctrl3


title: OPTT59-Biological replicate 1 [18170XR.01.07]


title: Wild Type mouse ES (Dnmt1 KO control) rep-2

source_name: Wild Type mouse ES (Dnmt1 KO control)


title: R23G12-Gal4 Drgx knockdown2


title: LNCaP AR siWDR77 R1881 Rep 1


title: OPBT25-Biological replicate 3 [18170XR.01.06]


title: R23G12-Gal4 ctrl2


title: OPBT25-Biological replicate 2 [18170XR.01.05]


title: Full length rescued Mettl14 knocked out mouse ES rep-1


title: LNCaP AR R1881 Rep 1


title: Drgx-Dam 3

description: Identification of genome-wide binding sites of Drgxl in Drosophila T4/T5 neurons using Targeted DamID

data_processing:
*library strategy: DamID-Seq
uncut DamID adaptors and reads containing an initial or internal GATC site were removed with fastq-filter and seqkit. bam files with extended reads for Dam only controls or Drgx-Dam fusion samples generated by the damidseq pipeline were merged with samtoolslog2(DamPolII/Dam) in bedgraph format have been generated by DamIDseq_pipeline provided by Marshall and Brand (2015).
Assembly: BDGP 6.32
Supplementary files format and content: drgx-dam/dam track in bedgraph format
Supplementary files format and content: peak file in bed format

growth_protocol: development at 18°C until L3 larval stage. L3 larvae were shifted to 29°C for 24h.

extract_protocol:
Brains were dissected in cold PBS  and frozen in liquid nitrogen. For gDNA extraction and sample preparation the protocol of  Marshall et al. (2016) was used.
libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina


title: OPBT25-Biological replicate 1 [18170XR.01.04]


title: LNCaP AR vehicle Rep 1


title: HeLa-WT-INPUT

description: INPUT for WT HeLa cells

data_processing:
Raw sequencing data were first analysed with "FastQC". Low-complexity reads were removed with the "AfterQC" tool with default parameters. To get rid of reads originating from rRNA or tRNA, the reads were mapped to human tRNA and rRNA sequences with "Bowtie2". Reads that did not map to tRNA or rRNA sequences were then further processed with "Trimmomatic" using default parameters to remove adapter sequences. The resulting fastq data were again analysed with "FastQC" to ensure that no further processing was needed.
The processed fastq reads were mapped to the human reference genome (GRCh37/hg19) using the "STAR" algorithm with reference transcriptome includes Ensembl v85 and long noncoding from LNCipedia v5.2. Gene expression was evaluated using "HTseq" count on input samples. m6A sites were identified by applying the "m6aViewer" peak-calling tool onto immunoprecipitated (IP) samples, using their input counterpart to estimate background noise. Sites showing significant enrichment in all replicates and present on genes showing an expression level of at least 1TPM were considered for further analyses.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include list of reproducible peaks across replicates for genes expressed at at least 1 TPM

source_name: HeLa cells WT INPUT

extract_protocol:
(RNA purification) Total RNA was extracted with RNeasy kit according to the manufacturer's instructions. Residual DNA removal was performed using the RNase-Free DNase Set. Polyadenylated RNA was enriched from 500 µg total RNA by one round of oligo-dT selection using the GenElute mRNA miniprep kit (Sigma-Aldrich). (m6A-immunoprecipitation) RNA was fragmented by mixing 90 µl RNA (at 0.9 µg/µl) and 10 µl fragmentation buffer 10X (100 mM Tris-HCl and 100 mM ZnCl2) in thin-walled 200-μl PCR tubes, then incubated at 94°C for 40 s in a pre-heated thermocycler block with the heated lid opened. 10 µl of 0.5 M EDTA was added and the tubes were placed on ice. RNA was then subjected to sodium acetate precipitation and resuspended in 300 μl RNase-free water. RNA fragmentation size was assessed by running 0.25 µg RNA on a 2100 Bioanalyzer (Agilent) with the RNA Nano kit (Agilent). Furthermore, 2-5 µg of fragmented RNA was kept at -80°C to later serve as input control. The RNA was denatured by heating (70°C for 5 min, then put on ice) and the immunoprecipitation mix was prepared as follows: polyA enriched fragmented RNA from cultured cells in 290 µl, 10µl proteinases inhibitors (Roche), 5 µl (200 units) RNasin® Ribonuclease Inhibitors (Promega), 5 µl of 200 mM Ribonucleoside Vanadyl Complex (RVC) (Sigma), 100 µl IP buffer 5X (50 mM Tris-HCl, 750 mM NaCl, 0.5% (vol/vol) Igepal), 3.5 µl anti-m6A antibody (Synaptic System, #202003) and 86.5 µl RNase-free water. The mix was incubated overnight at 4°C on a rotating wheel. The next day, 50 µl Dynabeads™ Protein G (Invitrogen, #10004D) were washed twice with IP buffer 1x supplemented with antiproteases (Roche) and blocked by incubating the beads in wash buffer supplemented with 0.5 mg/ml BSA for 1 h on a rotating wheel. The beads were washed again twice, then added to the immunoprecipitation mix and incubated for 2 h at 4°C on a rotating wheel. Then, the beads were washed three times with 1 ml washing buffer supplemented with 10 µl RNasin® and 10 µl RVC, and elution was performed by TriPure (Roche) extraction, so the RNA was resuspended in 9 µl RNase-free water.
The sequence library was prepared with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) for both input and IP samples.
m6A-seq

value: HeLa

tag: library

value: INPUT

tag: rip antibody


title: cells_chip2_mRNA

description:
message RNA
read2 for the cell barcodes
cells_chip2_barcodes.txt

value: mixed cell culture


title: Drgx-Dam 1


title: LNCaP AR vehicle siWDR77 Input Rep 1


title: Wild Type mouse ES (Dnmt1 KO control) rep-3


title: LNCaP AR siWDR77 vehicle Rep 1


title: HeLa-WT-3-m6A

description: m6A-seq for WT HeLa cells Rep-3

source_name: HeLa cells WT-3 m6A-seq

value: IP

value: anti-m6A antibody (Synaptic System, #202003)


title: Drgx-Dam 2


title: R23G12-Gal4 ctrl1


title: cells_chip2_sRNA

description:
small RNA
cells_chip2_barcodes.txt


title: Dnmt1 knocked out mouse ES rep-3

source_name: Dnmt1 knocked out mouse ES


title: R23G12-Gal4 Dam3


title: HeLa-WT-2-m6A

description: m6A-seq for WT HeLa cells Rep-2

source_name: HeLa cells WT-2 m6A-seq


title: Dnmt1 knocked out mouse ES rep-1


title: Mettl3 knocked out mouse ES rep-3


title: HeLa-WT-1-m6A

description: m6A-seq for WT HeLa cells Rep-1

source_name: HeLa cells WT-1 m6A-seq


title: R23G12-Gal4 Dam2


title: cells_chip1_mRNA

description:
message RNA
read2 for the cell barcodes
cells_chip1_barcodes.txt


title: THP-1 cells, GSK-LSD1-H3K4me1, CUT&RUN biol rep 2

status: Public on Jan 09 2025

city: Oxford

first: Yang

last: Shi

address: Old Road Campus Research Building off Roosevelt Drive

department: Nuffield Department of Medicine

institute: Ludwig Institute for Cancer Research, University of Oxford

data_processing:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for b-catenin and IRF7 in  THP-1 cell line.
nf-core CUT&RUN pipeline (v3.0.0) with SEACR with a standard peak threshold of 0.05 and spike-in calibration performed with S.cerevisiae genome
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: blood

extract_protocol:
Briefly, Cell were washed in 1 mL of wash buffer (HEPES pH=7.5 20mM, Spermidine 0.5mM, NaCl 120mM) and centrifuged at 600g at room temperature for three times and the pellet were resuspended in 100 μL of wash buffer per reaction. Following this, 10 μL of activated Concavalin A beads per reaction were added, and the mixture were incubated at room temperature for 10 minutes with intermittent shaking. Captured cells were resuspended in 50 μL of antibody binding buffer (wash buffer with digitonin 0.05%, EDTA). Primary antibodies, including negative and positive controls, were added, and the tubes were nutated overnight at 4°C. On the following day, the samples were washed twice in dig wash buffer (Wash buffer with 0.05% digitonin), and a master mix of pAG-Mnase was prepared and added to each sample. After nutating at 4°C for 1 hour, the samples were washed to remove unbound pAG-Mnase. Tubes were cooled to 0°C for 5 minutes, then supplemented with CaCl2 to promote MNase digestion at 4°C for 2 hours followed by the addition of 2X STOP buffer (NaCl 340mM, EDTA 20mM, EGTA 4mM, digitonin 0.05%) and incubation at 37°C for 10-15 minutes. Following a brief spin and magnetic separation, the supernatant containing enriched target-bound chromatin was proceeded directly with DNA cleanup with Zymo DNA Clean&Concentrator-5 kit (Zymo research). DNA libraries were prepared by NEBNext Ultra II DNA library kit (E7645S) as per manufacturer’s instructions.
CUT&RUN DNA libraries were prepared by NEBNext Ultra II DNA library kit (E7645S) as per manufacturer’s instructions,
The supernatant containing enriched target-bound chromatin was proceeded directly with DNA cleanup with Zymo DNA Clean&Concentrator-5 kit (Zymo research). DNA libraries were prepared by NEBNext Ultra II DNA library kit (E7645S) as per manufacturer’s instructions.

value: blood

value: human leukemia monocytic cell line

tag: cut&run antibody

value: Mono-Methyl-Histone H3 (Lys4) (D1A9) XP® Rabbit mAb (cell signaling#5326)


title: THP-1 cells, combo-H3K4me1, CUT&RUN biol rep 2

value: Combination of GSK-LSD1 and LY2090315


title: THP-1 cells, combo-H3K4me1, CUT&RUN biol rep 1


title: THP-1 cells, LY-H3K4me1, CUT&RUN biol rep 1


title: LNCaP WDR77 Vehicle Rep 1

source_name: prostate

value: prostate

value: LNCaP

tag: antibody


title: THP-1 cells, CTRL-H3K4me1, CUT&RUN biol rep 1

tag: cell line

value: Vehicle


title: THP-1 cells, CTRL-H3K4me1, CUT&RUN biol rep 2


title: THP-1 cells, GSK-LSD1-H3K4me1, CUT&RUN biol rep 1


title: Wild Type mouse ES (Dnmt1 KO control) rep-1


title: THP-1 cells, Combo R3, RNA-seq biol rep 3

data_processing:
The RNA-seq analysis was conducted using EdgeR-limma workflow.
Reads were quantified using featureCounts50, creating the raw gene count matrix.
Data quality metrics were investigated, and the limma voom normalization was applied to obtain counts per million (CPM) normalization and trimmed means of M (TMM) values and normalization to finalize the differential expression analysis.
The normalization accounted for sequencing depth.
Assembly: hg38
Supplementary files format and content: featurecounts.txt contains a featurecounts matrix with all samples.
Supplementary files format and content: LCPM.csv and CPM.csv contain log and count per million normalised values for all samples, respectively.

growth_protocol: Colony forming unit (CFU) assays Leukemia Cell Lines: Approximately 1000 cells (for human leukemia cell lines) were initially plated in triplicates in the methylcellulose medium (MethoCultTM GF H4435; StemCell Technologies) pre-added with Vehicle, GSK-LSD1, LY2090314 or combination of inhibitors. For serial replating, cells isolated from colonies in the previous plating were seeded again in the same semi-solid medium. CFUs were scored every 7 to 10 /days’ post seeding.

extract_protocol:
For freshly cultured cells, total RNA isolation and DNaseI treatment was performed using Direct-zol(TM) RNA MiniPrep kit (Zymo Research, R2053) as per manufacturer’s protocol.
Library preparation was conducted using the NEBNext UltraII RNA library kit (NEB#E7770S/L). Sequencing was conducted on an Illumina NextSeq 2000.


title: THP-1 cells, Control R3, RNA-seq biol rep 3


title: cells_chip1_sRNA

description:
small RNA
cells_chip1_barcodes.txt


title: WT mouse ES rep-3

source_name: WT mouse ES


title: ER-HoxA9_cells_Combo_rep3

city: Philadelphia

first: Andres

last: Blanco

state: PA

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

data_processing:
Fastq reads were aligned to the mouse genome (mm10) using STAR 2.7.0f
Read counts were mapped to genes using featureCounts
Only genes with > 10 total counts when summed across all samples were considered.
Differential analysis of gene expression was performed using DESeq2
Assembly: mm10
Supplementary files format and content: text files of read count data

growth_protocol: ER-HoxA9 cells were grown in RPMI-1640 medium supplemented with 10% of fetal bovine serum (FBS), 100 ng/ml stem cell factor (SCF) (Stemcell Technologies, 78064), 4mM glutamine, 1% penicillin/streptomycin, and 0.5mM beta-estradiol (Sigma Aldrich, E4389)

extract_protocol:
Total RNA isolation and DNaseI treatment was performed using Direct-zol(TM) RNA MiniPrep kit (Zymo Research, R2053) as per manufacturer’s protocol
Library preparation was conducted using the NEBNext UltraII RNA library kit (NEB#E7770S/L)

value: Combo


title: THP-1 cells, LY2090314 R2, RNA-seq biol rep 2


title: THP-1 cells, Combo R2, RNA-seq biol rep 2


title: THP-1 cells, Control R1, RNA-seq biol rep 1


title: Wild Type mouse ES rep-1


title: THP-1 cells, GSK-LSD1 R2, RNA-seq biol rep 2


title: ER-HoxA9_cells_GSK-LSD1_rep3


title: ER-HoxA9_cells_LY20903014_rep3


title: THP-1 cells, LY2090314 R1, RNA-seq biol rep 1


title: THP-1 cells, GSK-LSD1 R1, RNA-seq biol rep 1


title: THP-1 cells, LY2090314 R3, RNA-seq biol rep 3


title: Mettl3 knocked out mouse ES rep-1


title: Wild Type mouse EB (day 8) replicate 3

source_name: Wild Type EB

growth_protocol: ESCs were cultured on tissue culture plates coated with 0.1% gelatin and feeder cells, in high glucose DMEM-containing 15% FBS, 1 mM sodium pyruvate, 1% non-essential amino acids, 1% glutaMAX™, 0.1 mM β-mercaptoethanol, and 1000 units/ml recombinant mouse LIF at 37°C under 5% CO2. To generate EBs, 4 × 10^6 ESCs were seeded in 15 ml EB medium (without LIF) and maintained for 8 days. Cells were precipitated by gravity, resuspended, and cultured with fresh medium every two days.

treatment_protocol: Mettl3 knockout J1 ESCs were generated by Howard Y. Chang, Stanford University, USA (Batista et al, Cell Stem Cell, 2014)

tag: strain

value: EB cells

tag: differentiation days


title: Dnmt1 knocked out mouse ES rep-2


title: R23G12-Gal4 Dam1


title: THP-1 cells, GSK-LSD1 R3, RNA-seq biol rep 3


title: THP-1 cells, Control R2, RNA-seq biol rep 2


title: ER-HoxA9_cells_GSK-LSD1_rep2


title: METTL3 knocked out mouse EB (day 8)  replicate 3

source_name: METTL3 knocked out EB


title: ER-HoxA9_cells_Vehicle_rep2


title: ER-HoxA9_cells_Vehicle_rep3


title: ER-HoxA9_cells_Combo_rep2


title: THP-1 cells, LY-IRF7, CUT&RUN biol rep 2

description:
LY2090314
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for b-catenin and IRF7 in  THP-1 cell line.

data_processing:
nf-core CUT&RUN pipeline (v3.0.0) with SEACR with a standard peak threshold of 0.05 and spike-in calibration performed with S.cerevisiae genome
Assembly: hg38
Supplementary files format and content: bigWig

value: IRF-7, D8V1J (Cell Signaling, #72073)


title: ER-HoxA9_cells_Combo_rep1


title: METTL3 knocked out mouse EB (day 8)  replicate 2

data_processing: Raw Infinium MouseMethylation data were preprocessed as followed: CpG probes of low quality (detection p-value threshold of 0.05) were removed from the analysis and Beta-values were computed using the following formula: Beta-value = M/[U+M] where M and U are the raw “methylated” and “unmethylated” signals, respectively. Beta-values were corrected for type I and type II bias using the peak-based correction.


title: ER-HoxA9_cells_LY20903014_rep1


title: THP-1 cells, LY-IRF7, CUT&RUN biol rep 1


title: THP-1 cells, LY-b-cat, CUT&RUN biol rep 2

value: B-Catenin, D10A8 (Cell Signaling, #8480)


title: ER-HoxA9_cells_GSK-LSD1_rep1


title: Wild Type mouse EB (day 8) replicate 1

value: WT


title: LNCaP WDR77 vehicle Input Rep2

value: prostate cancer

value: Ethanol


title: METTL3 knocked out mouse EB (day 8)  replicate 1


title: ER-HoxA9_cells_Vehicle_rep1


title: THP-1 cells, LY-b-cat, CUT&RUN biol rep 1


title: THP-1 cells, GSK-LSD-IRF7, CUT&RUN biol rep 1

description:
GSK-LSD1
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for b-catenin and IRF7 in  THP-1 cell line.


title: THP-1 cells, GSK-LSD-b-cat, CUT&RUN biol rep 2


title: Wild Type mouse EB (day 8) replicate 2


title: THP-1 cells, GSK-LSD-IRF7, CUT&RUN biol rep 2


title: S119 with asparagine replicate-4

city: Jerusalem

first: Abhinay

last: Sharma

address: Hadassah Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

description: Processed data columns: A,B - gene details; C-J - normalized counts; K-O - DESeq2 results table

data_processing:
Raw reads were trimmed with Cutadapt, v2.10, using parameters -q32,32 -O 1 --allow-read-wildcards -m 15 and the adapter sequence to trim.
Processed reads were aligned with bowtie2, v2.3.4.3, using default parameters.
Quantification was done with htseq-count, v0.6.0, using parameter -s 'reverse' and counting only CDS genes.
Differential expression was done with DESeq2, v1.26.0, after removing genes with less than 10 counts, using default parameters.
Assembly: GCA_900608505.1
Supplementary files format and content: An Excel file with normalized counts and DESeq2 results, comparing samples with Asn to ones without Asn.

organism: Streptococcus pyogenes

source_name: Bacteria

growth_protocol: GAS was grown in 24-well plates in a humidified environment with 5% CO2 at 37oC in CDM with or without asparagine (10 µg/ml).

extract_protocol:
RNA was harvested according to the protocol by Livak and Schmittgen, 2001. RNA purification was conducted using the Direct-zol RNA miniprep kit (Zymo Research). A total of 1 µg of RNA was used to construct sequencing libraries.
RNA quality was determined by Agilent 2200 TapeStation analysis. For mRNA library preparation: KAPA Stranded mRNA-Seq Kit was used (Kapa Biosystems, KK8421)

treatment_protocol: GAS was treated with or without asparagine (10 µg/ml) in CDM

value: Bacteria

value: Gram-positive bacteria

value: With asparagine (10 ug/ml)


title: S119 with asparagine replicate-3


title: S119 without asparagine replicate-4

value: Without asparagine


title: THP-1 cells, GSK-LSD-b-cat, CUT&RUN biol rep 1

value: blood

value: human leukemia monocytic cell line


title: S119 with asparagine replicate-2


title: S119 without asparagine replicate-2


title: THP-1 cells, CTRL-IRF7, CUT&RUN biol rep 2

description:
Vehicle
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for b-catenin and IRF7 in  THP-1 cell line.


title: THP-1 cells, CTRL-IRF7, CUT&RUN biol rep 1


title: S119 with asparagine replicate-1


title: S119 without asparagine replicate-3


title: THP-1 cells, CTRL-b-cat, CUT&RUN biol rep 2


title: THP-1 cells, CTRL-b-cat, CUT&RUN biol rep 1


title: S119 without asparagine replicate-1


title: THP-1 cells, CONTROL, CUT&RUN biol rep 2

value: IgG, DA1E (Cell Signaling, #66362)


title: THP-1 cells, CONTROL, CUT&RUN biol rep 1


title: sort_seq__Fig2_fig_suppl_3_198copy_17549_fob1_rep2_S

city: Seattle

first: Antonio

last: Bedalov

state: WA

address: 1100 Fairview Ave N

department: Translational Science and Therapeutics Division

institute: Fred Hutch Cancer Center

description: Library name: Fig2_fig_suppl_3_198copy_17549_fob1_rep2_S_231109

data_processing:
align with bwa using the -n option set to 1; this option specifies that, if a read can be aligned to more than one genomic locations, it is aligned to just one of those location, and that one is chosen at random
picard CleanSam
picard SortSam
picard FixMateInformation
picard AddOrReplaceReadGroups
Assembly: sacCer3
Supplementary files format and content: bedgraph; includes coverage of only library inserts that are 151-200 base pairs; the entire fragment is inferred; e.g if there are two 50 bp reads that define the borders of a 170 bp library insert, the entire 170 bp insert will be reflected in the coverage

organism: Saccharomyces cerevisiae

extract_protocol:
MNase seq  We carried out MNase-Seq as previously described (Foss 2019). Briefly, cells grown to log phase in rich medium, Yeast Peptone Agar with 2% glucose (YEPD), from an overnight 25 mL culture were synchronized with 3 μM alpha-factor for 1.5 hrs. at 30 ° C. Arrested cells were crosslinked with 1% formaldehyde for 30 min at room temperature water bath with shaking. Formaldehyde was quenched with 125 mM glycine and cells were centrifuged at 3000 rpm for 5 min. Cells were washed twice with water and resuspended in 1.5 mL Buffer Z (1 M sorbitol, 50 mM Tris-HCl pH 7.4) with 1 mM beta-mercaptoethanol (1.1 μL of 14.3 M beta-mercaptoethanol diluted 1:10 in Buffer Z) per 25 mL culture. Cells were treated with 100 μL 20 mg/ mL zymolyase at 30 ° C for 20–30 min. Spheroplasts were centrifuged at 5000 rpm for 10 min and resuspended in 5 mL NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) supplemented with 500 μM spermidine, 1 mM beta-mercaptoethanol and 0.075% NP-40. Nuclei were aliquoted in tubes with varying concentrations of micrococcal nuclease (Worthington), mixed via tube inversion, and incubated at room temperature for 20 mins. Chromatin digested with 1.9 U– 7.5 U micrococcal nuclease per 1/5th of spheroplasts from a 25 mL culture yielded appropriate mono-, di-, tri- nucleosome protected fragments for next-generation sequencing. Digestion was stopped with freshly made 5x stop buffer (5% SDS, 50 mM EDTA) and proteinase K was added (0.2 mg/ml final concentration) for an overnight incubation at 65 ° C to reverse crosslinking. DNA was extracted with phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation. Sequencing libraries were prepared as described below for ChEC.  Chromatin Endogenous Cleavage (ChEC)  ChEC-seq was carried out as previously described (Foss et al. 2019; Foss et al. 2021). Briefly, MNase was activated by addition of CaCl2 to cells that were permeabilized with digitonin. DNA was extracted from cells using phenol and chloroform, precipitated using salt and ethanol and used to construct sequencing libraries without size fractionation. Cells were centrifuged at 1,500 x g for 2 mins, and washed twice in cold Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA) without additives. Washed cells were carefully resuspended in 570 μL Buffer A with additives (0.2 mM spermidine, 0.5 mM spermine, 1 mM PMSF, ½ cOmplete ULTRA protease inhibitors tablet, Roche, per 5 mL Buffer A) and permeabilized with 0.1% digitonin in 30 ° C water bath for 5 min. Permeabilized cells were cooled at room temperature for 1 min and 1/5th of cells were transferred in a tube with freshly made 2x stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA)/1% SDS solution for undigested control. Micrococcal nuclease was activated with 5.5 μL of 200 mM CaCl2 at various times (5 mins, and 10 mins) and the reaction stopped with 2x stop buffer/1% SDS. Once all time points were collected, proteinase K was added to each of the collected time points and incubated at 55 ° C water bath for 30 mins. DNA was extracted using phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation. Library was prepared as previously described used using total DNA, without any fragment size selection (Foss et al. 2019; Foss et al. 2021).  Chromatin immunoprecipitation followed by sequencing (ChIP-seq)  Cells were grown to log phase in rich medium, YEPD (1% Yeast Extract, 2% Peptone, 2% glucose), synchronized with 3 μM alpha-factor for 1.5 hrs. at 30°C. G1 arrested cells were released into 200 mM hydroxyurea (HU) YEPD and grown for 1hr. Cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 125 mM glycine for 5 minutes, and centrifuged at 3000 rpm for 5 minutes. Cell pellets were washed three times with TBS (20 mM Tris-HCl, pH 7.6, 150 mM NaCl). Cell pellets were flash frozen.  Chromatin Preparation  The cell pellet was thawed in 300 μL Breaking Buffer (100 mM Tris- HCl, pH 8.0, 20% Glycerol) supplemented with protease inhibitors (Pierce Protease inhibitor EDTA-free tablets [Thermo Scientific A32965] and 1 mM PMSF). 300 μL acid-washed glass beads were added to the mixture. Cells were lysed using a BioSpec Mini-Bead-beater in a cold room: 5x 30-second pulses with 1-minute on ice between rounds. The supernatant was transferred to a new tube and added 600 μL FA buffer (50 mM Hepes-KOH, pH 7.6, 150 mM NaCl, 5 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate) with protease inhibitors. The chromatin was sonicated with a F60 Sonic Dismembrator 10 times for 10 seconds at setting 4, with 1-minute rests on ice between rounds. The sonicated chromatin was centrifuged at 14,000 rpm for 15 minutes at 4°C. The supernatant was transferred and spun again at 14,000 rpm for 15 minutes at 4°C.  Immunoprecipitation (IP)  For IP, 20 μL of Dynabeads Protein G beads (Invitrogen 10004D) were washed three times with 500 μL PBS-T (0.8% NaCl, 0.144% Na2HPO4, 0.02% KCl, 0.024% KH2PO, 0.1% Tween 20, pH 7.1), resuspended in PBS-T, and incubated with 5 μL of FLAG M2 (Sigma F1804) antibody for 60 minutes at room temperature. The antibody-conjugated beads were washed and resuspended in 20 μL FA buffer with protease inhibitors. IP chromatin samples (1 μg) were brought up to 400 μL with FA buffer with protease inhibitors and incubated with antibody- conjugated beads for 90 minutes at room temperature. Beads were washed three times with FA buffer with protease inhibitors, twice with FA-HS buffer (50 mM Hepes-KOH, pH 7.6, 500 mM NaCl, 5 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate with protease inhibitors), and once with RIPA buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 0.5% NP-40, 0.5% Sodium deoxycholate, 5 mM EDTA with protease inhibitors). Input sample was generated by adding 0.1 μg chromatin in 40 μL FA buffer to 40 μL 2X Stop buffer (20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS, 2% Tween 20) and reversed crosslinks by overnight incubation at 65°C.  Elution and Crosslink Reversal  Bound chromatin was eluted by incubating the beads in 80 μL 2X Stop buffer at 75°C for 10 minutes. The eluate was collected, and crosslinks were reversed by overnight incubation at 65°C. The IP and Input were treated with 4 μL of 20 mg/mL RNase A and incubated at 55°C for 1 hour, followed by 4 μL of 20 mg/mL Proteinase K and incubation at 55°C for at least 3 hours. DNA was purified using a MinElute PCR Purification Kit  Paired-Ends NGS  Chromatin immunoprecipitation samples were prepared for sequencing following the protocol for the Kapa Hyper Kit. For Input samples, 2 ng were processed for End Repair. For IP samples, the entire volume was used. PCR amplification was performed with 10- 14 cycles based on DNA quantity.  Quantification of rDNA replication using the thymidine analogue EdU  Cells were grown to log phase in rich YEPD medium from a 50 mL culture and synchronized in G1 using 3 μM alpha factor for 2 hours at 30°C. Using 500 μg/mL pronase, arrested cells were released into rich media containing 200 mM hydroxyurea and 130 μM EdU (5-Ethynyl-2’- deoxyuridine). Cells were harvested in G1 and after 60 minutes released into HU. DNA was extracted using YeaStar Genomic DNA Kit (Zymo Research) and sonicated. Separate sequencing primers were ligated to each of the samples. Samples were pooled together, and subjected to click chemistry reaction in 10 mM Tris pH 7.4, 50mM NaCl, 20 μM biotin-TEG azide (Vector Laboratories), 5mM THPTA (tris-hydroxypropyltriazolylmethylamine) (Vector Laboratories), 1mM copper sulfate, and 15 mM sodium ascorbate (total volume 200 μL). Click reaction proceeded for 30 minutes at room temperature prior to DNA ethanol precipitation. Streptavidin magnetic beads (New England Biolabs) were washed 3 times with B&W buffer I (100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.05% Tween20, 0.5% SDS) before adding 100 μL of bead suspension to 180 μL DNA plus B&W buffer I. After a 30-minute incubation at room temperature while gently inverting tubes, bead bound DNA was washed with 200 μL B&W buffer I followed by 100 μL Stringency wash buffer (0.1% SDS, 0.1% SSC buffer) and 200 μL Wash Buffer II (100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.05% Tween 20). DNA was eluted off the beads by denaturation at 98°C for 5 minutes, followed by cooling at 25°C. Edu-labeled DNA was PCR amplified post-pulldown and subjected to sequencing.  Hydoxyurea ChEC time course experiment  Cells grown in synthetic media to logarithmic phase were arrested in G1 using alpha factor for 90 minutes, centrifuged, washed in water to remove alpha factor, and released into media containing 200 mM Hydroxyurea. Cells were harvested in G1 and at indicated time points following release into HU-containing media, chilled at 4 degrees and analyzed by ChEC as described above.
MNase seq  We carried out MNase-Seq as previously described (Foss 2019). Briefly, cells grown to log phase in rich medium, Yeast Peptone Agar with 2% glucose (YEPD), from an overnight 25 mL culture were synchronized with 3 μM alpha-factor for 1.5 hrs. at 30 ° C. Arrested cells were crosslinked with 1% formaldehyde for 30 min at room temperature water bath with shaking. Formaldehyde was quenched with 125 mM glycine and cells were centrifuged at 3000 rpm for 5 min. Cells were washed twice with water and resuspended in 1.5 mL Buffer Z (1 M sorbitol, 50 mM Tris-HCl pH 7.4) with 1 mM beta-mercaptoethanol (1.1 μL of 14.3 M beta-mercaptoethanol diluted 1:10 in Buffer Z) per 25 mL culture. Cells were treated with 100 μL 20 mg/ mL zymolyase at 30 ° C for 20–30 min. Spheroplasts were centrifuged at 5000 rpm for 10 min and resuspended in 5 mL NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) supplemented with 500 μM spermidine, 1 mM beta-mercaptoethanol and 0.075% NP-40. Nuclei were aliquoted in tubes with varying concentrations of micrococcal nuclease (Worthington), mixed via tube inversion, and incubated at room temperature for 20 mins. Chromatin digested with 1.9 U– 7.5 U micrococcal nuclease per 1/5th of spheroplasts from a 25 mL culture yielded appropriate mono-, di-, tri- nucleosome protected fragments for next-generation sequencing. Digestion was stopped with freshly made 5x stop buffer (5% SDS, 50 mM EDTA) and proteinase K was added (0.2 mg/ml final concentration) for an overnight incubation at 65 ° C to reverse crosslinking. DNA was extracted with phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation. Sequencing libraries were prepared as described below for ChEC.  Chromatin Endogenous Cleavage (ChEC)  ChEC-seq was carried out as previously described (Foss et al. 2019; Foss et al. 2021). Briefly, MNase was activated by addition of CaCl2 to cells that were permeabilized with digitonin. DNA was extracted from cells using phenol and chloroform, precipitated using salt and ethanol and used to construct sequencing libraries without size fractionation. Cells were centrifuged at 1,500 x g for 2 mins, and washed twice in cold Buffer A (15 mM Tris pH 7.5, 80 mM KCl, 0.1 mM EGTA) without additives. Washed cells were carefully resuspended in 570 μL Buffer A with additives (0.2 mM spermidine, 0.5 mM spermine, 1 mM PMSF, ½ cOmplete ULTRA protease inhibitors tablet, Roche, per 5 mL Buffer A) and permeabilized with 0.1% digitonin in 30 ° C water bath for 5 min. Permeabilized cells were cooled at room temperature for 1 min and 1/5th of cells were transferred in a tube with freshly made 2x stop buffer (400 mM NaCl, 20 mM EDTA, 4 mM EGTA)/1% SDS solution for undigested control. Micrococcal nuclease was activated with 5.5 μL of 200 mM CaCl2 at various times (5 mins, and 10 mins) and the reaction stopped with 2x stop buffer/1% SDS. Once all time points were collected, proteinase K was added to each of the collected time points and incubated at 55 ° C water bath for 30 mins. DNA was extracted using phenol/chloroform and precipitated with ethanol. Micrococcal nuclease digestion was analyzed via gel electrophoresis prior to proceeding to library preparation. Library was prepared as previously described used using total DNA, without any fragment size selection (Foss et al. 2019; Foss et al. 2021).  Chromatin immunoprecipitation followed by sequencing (ChIP-seq)  Cells were grown to log phase in rich medium, YEPD (1% Yeast Extract, 2% Peptone, 2% glucose), synchronized with 3 μM alpha-factor for 1.5 hrs. at 30°C. G1 arrested cells were released into 200 mM hydroxyurea (HU) YEPD and grown for 1hr. Cells were crosslinked with 1% formaldehyde for 30 min at room temperature, quenched with 125 mM glycine for 5 minutes, and centrifuged at 3000 rpm for 5 minutes. Cell pellets were washed three times with TBS (20 mM Tris-HCl, pH 7.6, 150 mM NaCl). Cell pellets were flash frozen.  Chromatin Preparation  The cell pellet was thawed in 300 μL Breaking Buffer (100 mM Tris- HCl, pH 8.0, 20% Glycerol) supplemented with protease inhibitors (Pierce Protease inhibitor EDTA-free tablets [Thermo Scientific A32965] and 1 mM PMSF). 300 μL acid-washed glass beads were added to the mixture. Cells were lysed using a BioSpec Mini-Bead-beater in a cold room: 5x 30-second pulses with 1-minute on ice between rounds. The supernatant was transferred to a new tube and added 600 μL FA buffer (50 mM Hepes-KOH, pH 7.6, 150 mM NaCl, 5 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate) with protease inhibitors. The chromatin was sonicated with a F60 Sonic Dismembrator 10 times for 10 seconds at setting 4, with 1-minute rests on ice between rounds. The sonicated chromatin was centrifuged at 14,000 rpm for 15 minutes at 4°C. The supernatant was transferred and spun again at 14,000 rpm for 15 minutes at 4°C.  Immunoprecipitation (IP)  For IP, 20 μL of Dynabeads Protein G beads (Invitrogen 10004D) were washed three times with 500 μL PBS-T (0.8% NaCl, 0.144% Na2HPO4, 0.02% KCl, 0.024% KH2PO, 0.1% Tween 20, pH 7.1), resuspended in PBS-T, and incubated with 5 μL of FLAG M2 (Sigma F1804) antibody for 60 minutes at room temperature. The antibody-conjugated beads were washed and resuspended in 20 μL FA buffer with protease inhibitors. IP chromatin samples (1 μg) were brought up to 400 μL with FA buffer with protease inhibitors and incubated with antibody- conjugated beads for 90 minutes at room temperature. Beads were washed three times with FA buffer with protease inhibitors, twice with FA-HS buffer (50 mM Hepes-KOH, pH 7.6, 500 mM NaCl, 5 mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate with protease inhibitors), and once with RIPA buffer (10 mM Tris-HCl, pH 8.0, 0.25 M LiCl, 0.5% NP-40, 0.5% Sodium deoxycholate, 5 mM EDTA with protease inhibitors). Input sample was generated by adding 0.1 μg chromatin in 40 μL FA buffer to 40 μL 2X Stop buffer (20 mM Tris-HCl, pH 8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS, 2% Tween 20) and reversed crosslinks by overnight incubation at 65°C.  Elution and Crosslink Reversal  Bound chromatin was eluted by incubating the beads in 80 μL 2X Stop buffer at 75°C for 10 minutes. The eluate was collected, and crosslinks were reversed by overnight incubation at 65°C. The IP and Input were treated with 4 μL of 20 mg/mL RNase A and incubated at 55°C for 1 hour, followed by 4 μL of 20 mg/mL Proteinase K and incubation at 55°C for at least 3 hours. DNA was purified using a MinElute PCR Purification Kit  Paired-Ends NGS  Chromatin immunoprecipitation samples were prepared for sequencing following the protocol for the Kapa Hyper Kit. For Input samples, 2 ng were processed for End Repair. For IP samples, the entire volume was used. PCR amplification was performed with 10- 14 cycles based on DNA quantity.  Quantification of rDNA replication using the thymidine analogue EdU  Cells were grown to log phase in rich YEPD medium from a 50 mL culture and synchronized in G1 using 3 μM alpha factor for 2 hours at 30°C. Using 500 μg/mL pronase, arrested cells were released into rich media containing 200 mM hydroxyurea and 130 μM EdU (5-Ethynyl-2’- deoxyuridine). Cells were harvested in G1 and after 60 minutes released into HU. DNA was extracted using YeaStar Genomic DNA Kit (Zymo Research) and sonicated. Separate sequencing primers were ligated to each of the samples. Samples were pooled together, and subjected to click chemistry reaction in 10 mM Tris pH 7.4, 50mM NaCl, 20 μM biotin-TEG azide (Vector Laboratories), 5mM THPTA (tris-hydroxypropyltriazolylmethylamine) (Vector Laboratories), 1mM copper sulfate, and 15 mM sodium ascorbate (total volume 200 μL). Click reaction proceeded for 30 minutes at room temperature prior to DNA ethanol precipitation. Streptavidin magnetic beads (New England Biolabs) were washed 3 times with B&W buffer I (100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.05% Tween20, 0.5% SDS) before adding 100 μL of bead suspension to 180 μL DNA plus B&W buffer I. After a 30-minute incubation at room temperature while gently inverting tubes, bead bound DNA was washed with 200 μL B&W buffer I followed by 100 μL Stringency wash buffer (0.1% SDS, 0.1% SSC buffer) and 200 μL Wash Buffer II (100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.05% Tween 20). DNA was eluted off the beads by denaturation at 98°C for 5 minutes, followed by cooling at 25°C. Edu-labeled DNA was PCR amplified post-pulldown and subjected to sequencing.  Hydoxyurea ChEC time course experiment  Cells grown in synthetic media to logarithmic phase were arrested in G1 using alpha factor for 90 minutes, centrifuged, washed in water to remove alpha factor, and released into media containing 200 mM Hydroxyurea. Cells were harvested in G1 and at indicated time points following release into HU-containing media, chilled at 4 degrees and analyzed by ChEC as described above.

value: haploid

value: Mat A, Fob1::KanMX, YDR110W, 11,C11, hml::HYG (Final count of rDNA:198 copies)


title: THP-1 cells, combo-IRF-7, CUT&RUN biol rep 2

description:
Combination of GSK-LSD1 and LY2090315
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for b-catenin and IRF7 in  THP-1 cell line.


title: sort_seq__Fig2_fig_suppl_3_191copy_17550_fob1_rep3_S

description: Library name: Fig2_fig_suppl_3_191copy_17550_fob1_rep3_S_231109

value: Mat A, Fob1::KanMX, YDR110W, 11,C11, hml::HYG (Final count of rDNA:191 copies)


title: THP-1 cells, combo-b-cat, CUT&RUN biol rep 2

description:
Combination of GSK-LSD1 and LY2090314
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) for b-catenin and IRF7 in  THP-1 cell line.


title: sort_seq__Fig2_fig_suppl_3_191copy_17550_fob1_rep3_G1

description: Library name: Fig2_fig_suppl_3_191copy_17550_fob1_rep3_G1_231109


title: THP-1 cells, combo-IRF-7, CUT&RUN biol rep 1


title: sort_seq__Fig2_fig_suppl_3_158copy_17548_fob1_fun30_sir2_rep1_S

description: Library name: Fig2_fig_suppl_3_158copy_17548_fob1_fun30_sir2_rep1_S_231109

value: Mat A, Fob1::KanMX, YDR110W, 11,C11 fun30::HYG, hml::NAT, sir2::LEU (Final count of rDNA:158 copies)


title: sort_seq__Fig2_fig_suppl_3_152copy_17477_fob1_fun30_rep2_S

description: Library name: Fig2_fig_suppl_3_152copy_17477_fob1_fun30_rep2_S_231201

value: Mat A, Fob1::KanMX, YDR110W, 11,C11 fun30::HYG, hml::NAT (Final count of rDNA:152 copies)


title: sort_seq__Fig2_fig_suppl_3_158copy_17548_fob1_fun30_sir2_rep1_G1

description: Library name: Fig2_fig_suppl_3_158copy_17548_fob1_fun30_sir2_rep1_G1_231109


title: THP-1 cells, combo-b-cat, CUT&RUN biol rep 1


title: RPMI+pEtn-3

city: Pittsburgh

first: Greg

last: Delgoffe

address: 5115 Centre Ave.

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench for adapter trimming, alignment and differential gene expression analysis
GSEA for gene set enrichment analysis
Assembly: GENCODE M30 (GRCm39)
Supplementary files format and content: count matrix

source_name: CD8+ T cell

growth_protocol: SIINFEKL activated CD8+ T cells from OT-I mice were cultured with IL-2 in either RPMI supplemented with 10% FBS or RPMI supplemented with 10% FBS and  o-phosphoethanolamine (470uM) for 5 days

extract_protocol:
The CD8+ T-cell samples were sorted into lysed buffer and went through direct cDNA extraction.
cDNA was generated using the Takara SmartSeq Kit (Takara: 634438) using 15 cycles of whole genome amplification.

value: OT-I mice

value: CD8+ T cell

value: RPMI based media supplemented with pEtn


title: RPMI+pEtn-4


title: sort_seq__Fig2_fig_suppl_3_122copy_17542_fob1_fun30_rep1_G1

description: Library name: Fig2_fig_suppl_3_122copy_17542_fob1_fun30_rep1_G1_231109

value: Mat A, Fob1::KanMX, YDR110W, 11,C11 fun30::HYG (Final count of rDNA:113 copies), hml::NAT


title: RPMI-3

value: RPMI based media


title: RPMI-2


title: RPMI-4


title: RPMI+pEtn-1


title: RPMI-1


title: sort_seq__Fig2_fig_suppl_3_152copy_17477_fob1_fun30_rep2_G1

description: Library name: Fig2_fig_suppl_3_152copy_17477_fob1_fun30_rep2_G1_231201


title: sort_seq__Fig2_fig_suppl_3_119copy_16630_fob1_rep1_S

description: Library name: Fig2_fig_suppl_3_119copy_16630_fob1_rep1_S_231010

value: Mat A, Fob1::KanMX, YDR110W, 11,C11


title: sort_seq__Fig2_fig_suppl_3_119copy_16630_fob1_rep1_G1

description: Library name: Fig2_fig_suppl_3_119copy_16630_fob1_rep1_G1_231010


title: sort_seq__Fig2_fig_suppl_3_177copy_17561_fob1_sir2_rep5_G1

description: Library name: Fig2_fig_suppl_3_177copy_17561_fob1_sir2_rep5_G1_231201

value: Mat A, Fob1::KanMX, YDR110W, 11,C11, hml::HYG, sir2::LEU Final count of rDNA:177 copies)


title: sort_seq__Fig2_fig_suppl_3_198copy_17549_fob1_rep2_G1

description: Library name: Fig2_fig_suppl_3_198copy_17549_fob1_rep2_G1_231109


title: sort_seq__Fig2_fig_suppl_3_122copy_17542_fob1_fun30_rep1_S

description: Library name: Fig2_fig_suppl_3_122copy_17542_fob1_fun30_rep1_S_231109


title: THP-1 cells, Combo R1, RNA-seq biol rep 1

value: Combination of GSK-LSD1 and LY2090315


title: sort_seq__Fig2_fig_suppl_3_177copy_17561_fob1_sir2_rep5_S

description: Library name: Fig2_fig_suppl_3_177copy_17561_fob1_sir2_rep5_S_231201


title: sort_seq__Fig2B_sir2_S_16668_rep3

description: Library name: Fig2B_sir2_S_16668_rep3_160304

value: Mat a  his3 leu2 met15 ura3 sir2::Kanmx, hml:HYG


title: SW480, shEIF2B4, induced, repl 3 [2B4_2_plus_RPF_3_c]

city: Berlin

first: Chiara

last: Giacomelli

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center for Molecular Medicine

description:
2B4_2_plus_RPF_3_c
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv

library_source: other

data_processing:
Processing of all ribosome profiling data was carried out using scripts publicly available the https://github.com/Bushell-lab/Ribo-seq GitHub package. All R scripts were carried out using R version 4.3.1.
For cytoplasmic RNA samples: Cutadapt (version 1.18) was used to remove adaptors, trim 3’ bases with quality scores below 20 and discard reads less than 30 bases after trimming. Reads are deduplicated using cd-hit-dup and then UMIs are removed with cutadapt (v 1.18). BBmap (version 38.18) was used to align reads to a FASTA file containing rRNA, tRNA, and mitochondrial encoded RNA reads (GENECODE v38). Transcript isoform and gene level quantification were then carried out using with RSEM (with bowtie2 as alignment algorythm (version 2.3.5.1)). Custom R script and python script were then used to calculate the most abundant transcript per gene, and to create the FASTA to which RPFs were subsequently aligned to.
For Ribosome Protected Fractments (RPFs): Cutadapt (version 1.18) was used to remove adaptors, trim 3’ bases with quality scores below 20 and discard reads less than 30 and more than 50 bases after trimming. Reads are deduplicated using cd-hit-dup and then UMIs are removed with cutadapt (v 1.18). BBmap (version 38.18) was used to align reads to a FASTA file containing rRNA, tRNA, and mitochondrial encoded RNA reads (GENECODE v38). All unaligned reads were then aligned to a filtered protein coding FASTA, containing the most abundant transcript per gene (calculated from cytoplasmic RNA samples). The resulting BAM files were sorted with samtools (version 1.9). The number of reads in which the 5’ end is at each position of every transcript is then counted and the correct offset for each read length is calculated and applied, to collapse all reads into a single frame. Total counts across the entire CDS, excluding the first 20 and last 10 codons are then summed together.
Assembly: GENCODE v38 Protein-coding transcript sequences, filtered to contain only transcripts that have both a 5’ and 3’ UTR, with a CDS equally divisible by 3 and an nUG start codon, a stop codon and that have been manually annotated by HAVANA. All PAR_Y transcripts were also removed.
Supplementary files format and content: Totals_2B1_2B4_NTCcorrected_normalised_counts.csv contains gene-level and transcript-level counts, normalised using the DESeq2 packge Regularized log transformation (rlog(dds)). Only genes with an average of 10 reads across all samples are included
Supplementary files format and content: RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv contains gene-level and transcript-level counts aligned to the coding sequences and summed as described above. Normalisation is done using the regularised log transformation formula (rlog(dds)) from DESeq2 package. Only genes with an average of 10 reads across all samples are included

molecule: other

source_name: Colon

growth_protocol: SW480 cells were cultured in RPMI 1640 (#21875091, Thermo Fisher Scientific), supplemented with 10 % heat-inactivated FBS (#FBS-11A, Capricorn Scientific) and 1% penicillin/streptomycin (#P4333, Sigma).

extract_protocol:
Pellets were resuspended in non-denaturing lysis buffer (15 mM Tris-Cl pH 7.5, 150 mM NaCl, 15 mM MgCl2, 100 μg/ml cycloheximide, 1% Triton X-100, 0.05% Tween-20, 2% n-Dodecyl-beta-Maltoside Detergent (DDM), 0.5 mM DTT, 5 mM NaF, 1x cOmplete mini (#04693124001, Roche)). For RPFs: Lysates were digested with 8 μl of RNAseI (#AM2295, Lot# 00791236, Ambion) at 22°C for 20 min. Digestion was stopped with 16 μl of SUPERaseIn (#AM2696, Invitrogen). Digested lysates were run on a 10-50% sucrose gradients where fractions corresponding to monosomes and disomes were collected. RNA from these fractions was extracted by acid phenol-chloroform extractions, further processed to select for ribosome protected frament (RPF) size, treated with T4 Polynucleotide Kinase (NEB M0201S) and size checked on an Agilent Bioanalyzer small RNA chip. For total cytoplasmic RNA: prior to digesting the lysate for RPF extraction, an aliquot was kept aside and mixed with 1 ml of TRIzol™ Reagent (Invitrogen, 15596026). RNA extraction from TRIzol was performed according to manufacturer's instruction, with a further Ethanol precipitation to eliminate all impurities. Average eRIN value of total cytoplasmic RNAs was 9.7, as checked by RNA screen tape on a TapeStation (Agilent)
Total cytoplasmic RNAs were depleted of rRNA with RiboCop v2 (Lexogen) and then libraries were prepared using the CORALL kit (Lexogen), all following the manufacturer’s instructions. 900 μg of total cytoplasmic RNAs were used as input for the RiboCop. 13 PCR cycles were used in the library amplification stage. For RPFs: Libraries were prepared with the NEXTflex small RNA kit v3 (Perkin Elmer) following the manufacturer’s instructions, using 10.5 ng of input and 11 PCR cycles in the amplification step. Alternative step F and Step H2 were used.

treatment_protocol: SW480 cells  transduced with inducible non-targeting control (CTRL), EIF2B1, or EIF2B4 shRNAs were grown in the absence (DMSO) or presence of 1 µg/ml doxycycline for five days. Two 15 cm dishes per condition were then harvested in cold PBS, washed twice in cold PBS, and the resulting pellet was snap-frozen in liquid nitrogen. One additional 15 cm dish per condition was harvested in parallel to check efficient knockdown by immunoblotting. The experiment was performed four times in separate weeks.

value: Colon

tag: shRNA

value: inducible shEIF2B4

value: Adenocarcinoma; Colorectal; Dukes' type B

value: induced (Doxycicline)


title: sort_seq__Fig2B_sir2_S_16669_rep5

description: Library name: Fig2B_sir2_S_16669_rep5_160304

value: haploid


title: SW480, shEIF2B4, induced, repl 4 [2B4_2_plus_RPF_4]

description:
2B4_2_plus_RPF_4
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv

tag: tissue


title: RPMI+pEtn-2

tag: cell type


title: SW480, shEIF2B4, induced, repl 2 [2B4_2_plus_RPF_2]

description:
2B4_2_plus_RPF_2
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: SW480, shEIF2B4, induced, repl 1 [2B4_2_plus_RPF_1]

description:
2B4_2_plus_RPF_1
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_sir2_S_15984_rep1_1

description: Library name: Fig2B_sir2_S_15984_rep1_1_150624

tag: genotype

value: Mat@ lys2 amn1::Nat sir2::Hyg


title: sort_seq__Fig2B_sir2_G1_16669_rep6

description: Library name: Fig2B_sir2_G1_16669_rep6_160304


title: SW480, shEIF2B4, uninduced, repl 3 [2B4_2_min_RPF_3_c]

description:
2B4_2_min_RPF_3_c
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv

tag: treatment

value: uninduced (DMSO)


title: SW480, shEIF2B4, uninduced, repl 4 [2B4_2_min_RPF_4]

description:
2B4_2_min_RPF_4
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_sir2_G1_16669_rep5

description: Library name: Fig2B_sir2_G1_16669_rep5_160304


title: SW480, shEIF2B4, uninduced, repl 1 [2B4_2_min_RPF_1]

description:
2B4_2_min_RPF_1
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_sir2_G1_16668_rep3

description: Library name: Fig2B_sir2_G1_16668_rep3_160304


title: SW480, shEIF2B1, induced, repl 4 [2B1_3A_plus_RPF_4]

description:
2B1_3A_plus_RPF_4
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv

value: inducible shEIF2B1


title: sort_seq__Fig2B_sir2_G1_16668_rep4

description: Library name: Fig2B_sir2_G1_16668_rep4_160304


title: SW480, shEIF2B1, induced, repl 3 [2B1_3A_plus_RPF_3_c]

description:
2B1_3A_plus_RPF_3_c
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_sir2_G1_16560_rep2

description: Library name: Fig2B_sir2_G1_16560_rep2_160304

value: Mat A his3 leu2 met15 ura3m, hml:HYG, sir2::NAT


title: SW480, shEIF2B1, induced, repl 2 [2B1_3A_plus_RPF_2]

description:
2B1_3A_plus_RPF_2
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: THP-1 cells, LY-H3K4me1, CUT&RUN biol rep 2

value: blood

value: human leukemia monocytic cell line

value: Mono-Methyl-Histone H3 (Lys4) (D1A9) XP® Rabbit mAb (cell signaling#5326)


title: sort_seq__Fig2B_sir2_G1_15984_rep1_2

description: Library name: Fig2B_sir2_G1_15984_rep1_2_150624


title: sort_seq__Fig2B_sir2_G1_15984_rep1_1

description: Library name: Fig2B_sir2_G1_15984_rep1_1_150624


title: sort_seq__Fig2B_fun30_sir2_S_17263_rep1

description: Library name: Fig2B_fun30_sir2_S_17263_rep1_230728

value: Mat A his3 leu2 met15 ura3, hml:HYG, fun30::URA sir2::LEU


title: sort_seq__Fig2B_fun30_sir2_G1_17263_rep2

description: Library name: Fig2B_fun30_sir2_G1_17263_rep2_230728


title: SW480, shEIF2B1, uninduced, repl 3 [2B1_3A_min_RPF_3_c]

description:
2B1_3A_min_RPF_3_c
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_sir2_S_16560_rep2

description: Library name: Fig2B_sir2_S_16560_rep2_160304


title: sort_seq__Fig2B_fun30_sir2_S_17263_rep2

description: Library name: Fig2B_fun30_sir2_S_17263_rep2_230728


title: SW480, shEIF2B1, uninduced, repl 1 [2B1_3A_min_RPF_1]

description:
2B1_3A_min_RPF_1
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_fun30_sir2_G1_17263_rep1

description: Library name: Fig2B_fun30_sir2_G1_17263_rep1_230728


title: SW480, shEIF2B4, uninduced, repl 2 [2B4_2_min_RPF_2]

description:
2B4_2_min_RPF_2
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_sir2_S_15984_rep1_2

description: Library name: Fig2B_sir2_S_15984_rep1_2_150624


title: SW480, shCTRL, induced, repl 4 [NTC_plus_RPF_4]

description:
NTC_plus_RPF_4
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv

value: inducible shCTRL


title: sort_seq__Fig2B_fun30_S20A_S28A_S_17114_rep2

description: Library name: Fig2B_fun30_S20A_S28A_S_17114_rep2_231010

value: Mat A his3 leu2 met15 ura3m, hml, Fun 30 S20A; S28A; sir2::LEU.        colony 2


title: sort_seq__Fig2B_fun30_S20A_S28A_S_17113_rep1

description: Library name: Fig2B_fun30_S20A_S28A_S_17113_rep1_231010

value: Mat A his3 leu2 met15 ura3m, hml, Fun 30 S20A; S28A; sir2::LEU.    colony 1


title: SW480, shCTRL, induced, repl 2 [NTC_plus_RPF_2]

description:
NTC_plus_RPF_2
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: SW480, shCTRL, induced, repl 3 [NTC_plus_RPF_3_c]

description:
NTC_plus_RPF_3_c
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_fun30K603R_sir2_S_17345_rep2

description: Library name: Fig2B_fun30K603R_sir2_S_17345_rep2_230728

value: Mat A his3 leu2 met15 ura3 hml:HYG with #877 (pml104 + FUN30 K603R gRNA oligo) and FUN30 K603R gBlock repair template. No URA3 plasmid. sir2::LEU


title: SW480, shCTRL, induced, repl 1 [NTC_plus_RPF_1]

description:
NTC_plus_RPF_1
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv

value: Colon


title: SW480, shCTRL, uninduced, repl 4 [NTC_min_RPF_4]

description:
NTC_min_RPF_4
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_fun30_S20A_S28A_G1_17113_rep1

description: Library name: Fig2B_fun30_S20A_S28A_G1_17113_rep1_231010


title: sort_seq__Fig2B_fun30K603R_sir2_S_17345_rep1

description: Library name: Fig2B_fun30K603R_sir2_S_17345_rep1_221123


title: SW480, shCTRL, uninduced, repl 2 [NTC_min_RPF_2]

description:
NTC_min_RPF_2
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_fun30_S20A_S28A_G1_17114_rep2

description: Library name: Fig2B_fun30_S20A_S28A_G1_17114_rep2_231010


title: SW480, shCTRL, uninduced, repl 3 [NTC_min_RPF_3_c]

description:
NTC_min_RPF_3_c
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: SW480, shEIF2B1, induced, repl 1 [2B1_3A_plus_RPF_1]

description:
2B1_3A_plus_RPF_1
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: SW480, shEIF2B1, uninduced, repl 4 [2B1_3A_min_RPF_4]

description:
2B1_3A_min_RPF_4
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_fun30K603R_sir2_G1_17345_rep1

description: Library name: Fig2B_fun30K603R_sir2_G1_17345_rep1_221123


title: SW480, shCTRL, uninduced, repl 1 [NTC_min_RPF_1]

description:
NTC_min_RPF_1
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv


title: SW480, shEIF2B4, induced, repl 4 [2B4_2_plus_Tot_4]

description:
2B4_2_plus_Tot_4
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv

molecule: cytoplasmic RNA

value: inducible shEIF2B4


title: SW480, shEIF2B1, uninduced, repl 2 [2B1_3A_min_RPF_2]

description:
2B1_3A_min_RPF_2
RPFs_2B1_2B4_NTCcorrected_normalised_counts.csv

value: Adenocarcinoma; Colorectal; Dukes' type B


title: sort_seq__Fig2B_WT_S_15691_rep5_2

description: Library name: Fig2B_WT_S_15691_rep5_2_150624

value: amN1::Nat  Mat a lys2  created from 15690


title: ER-HoxA9_cells_LY20903014_rep2


title: SW480, shEIF2B4, induced, repl 1 [2B4_2_plus_Tot_1]

description:
2B4_2_plus_Tot_1
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv

value: induced (Doxycicline)


title: sort_seq__Fig2B_WT_S_15691_rep5_1

description: Library name: Fig2B_WT_S_15691_rep5_1_150624

value: haploid


title: SW480, shEIF2B4, induced, repl 2 [2B4_2_plus_Tot_2]

description:
2B4_2_plus_Tot_2
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_WT_S_15213_rep4

description: Library name: Fig2B_WT_S_15213_rep4_160511

value: BY parent from Tonibelle's amn1::Nat Plates  Mat@ lys2 amn1::Nat


title: SW480, shEIF2B4, induced, repl 3 [2B4_2_plus_Tot_3_c]

description:
2B4_2_plus_Tot_3_c
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq__Fig2B_WT_G1_15691_rep5_2

description: Library name: Fig2B_WT_G1_15691_rep5_2_150624


title: sort_seq__Fig2B_WT_G1_15691_rep5_1

description: Library name: Fig2B_WT_G1_15691_rep5_1_150624


title: sort_seq__Fig2B_WT_G1_15213_rep4

description: Library name: Fig2B_WT_G1_15213_rep4_160511


title: SW480, shEIF2B4, uninduced, repl 2 [2B4_2_min_Tot_2]

description:
2B4_2_min_Tot_2
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv

value: uninduced (DMSO)


title: sort_seq__Fig2B_fun30K603R_sir2_G1_17345_rep2

description: Library name: Fig2B_fun30K603R_sir2_G1_17345_rep2_230728


title: SW480, shEIF2B4, uninduced, repl 1 [2B4_2_min_Tot_1]

description:
2B4_2_min_Tot_1
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq_Fig2A_sir2_G1_16668

description: Library name: Fig2A_sir2_G1_16668_160511

value: Mat a  his3 leu2 met15 ura3 sir2::Kanmx, hml:HYG


title: sort_seq_Fig2A_WT_S_16535

description: Library name: Fig2A_WT_S_16535_160304

value: Mat A his3 leu2 met15 ura3, hml::HYG


title: SW480, shEIF2B1, induced, repl 3 [2B1_3A_plus_Tot_3_c]

description:
2B1_3A_plus_Tot_3_c
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv

value: inducible shEIF2B1


title: SW480, shEIF2B1, induced, repl 2 [2B1_3A_plus_Tot_2]

description:
2B1_3A_plus_Tot_2
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv


title: sort_seq_Fig2A_WT_G1_16535

description: Library name: Fig2A_WT_G1_16535_160304


title: sort_seq_Fig2A_sir2_S_16668

description: Library name: Fig2A_sir2_S_16668_160511


title: MNase_seq_Figure_6_figure_supplement_1_17248_fun30_G1

description: Library name: Figure_6_figure_supplement_1_17248_G1_Mnase_20U_AA21_S10

value: Mat A his3 leu2 met15 ura3m, hml:HYG, fun30::URA


title: SW480, shEIF2B4, uninduced, repl 4 [2B4_2_min_Tot_4]

description:
2B4_2_min_Tot_4
Totals_2B1_2B4_NTCcorrected_normalised_counts.csv