title: CHP134 RNA-seq C6 1 day rep2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
641-1D2

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 or mm10 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
SLAM-seq was processed using SLAMdunk.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: SLAM-seq: tab-delimited text file include raw counts for each Sample

growth_protocol: Media for all cell lines was supplemented with 100 IU/ml Penicillin and 100 μg/ml streptomycin.

extract_protocol:
ChIP-seq assays (performed as described in Weissmiller, et. al. Nat Commun,10, Article number: 2014 (2019)): Briefly, cross-linking was carried out with 0.75% formaldehyde (Sigma-Aldrich; in PBS pH 7.4) at room temperature for 10 minutes. The reaction was quenched with 125 mM glycine for 10 minutes at room temperature, after which cells were washed twice with ice-cold PBS. Nuclei were prepared by incubating cells in Nuclear Lysis Buffer A (1 M HEPES pH 7.9, 1 M KCl, 0.5 M EDTA, 0.4% NP-40, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 5 minutes on ice, after which they were collected by centrifugation. Nuclei were then lysed in Formaldehyde Lysis Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1% SDS, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 15 minutes on ice. Chromatin was sheared by 17–24 minute sonication (BioRuptor UCD-200, Diagenode; on highest setting, alternating between 30 seconds on and 30 seconds off) to yield a mean chromatin size of ~250 bp. After sonication, debris was cleared by centrifugation, and sheared chromatin diluted 10-fold in Formaldehyde Lysis Buffer without SDS. Chromatin from 107 cells was used per immunoprecipitation reaction. Immunoprecipitation reactions were performed with either 0.8 µL of IgG or 4.0 µL of α-WDR5 antibody as indicated. Immune complexes were recovered on Protein A agarose beads (Roche) and washed sequentially with Low Salt Wash buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), High Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), LiCl Wash buffer (10 mM Tris pH 8.9, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail) and TE (10 mM Tris pH 8.0, 1 mM EDTA, supplemented with PMSF and Complete Protease Inhibitor Cocktail). Protein–DNA complexes were de-crosslinked overnight at 65°C in 50 µL Elution Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.1% SDS, and 20 µg Proteinase K (740506, Clontech).  ---   RNA-seq assays: CHP134 cells were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ.   ---   SLAM-seq assays: Nascent RNA was labeled using the SLAMseq Kinetics Kit–Anabolic Kinetics Module (061, Lexogen).  LoVo cells were pretreated with 25 uM C6, C6nc, or 0.1% DMSO prior to a three hour labeling with 1 mM 4-Thiouridine (S4U). Following the manufacturer's instructions, total RNA was isolated, alkylated with iodoacetamide, flash frozen, and shipped to Lexogen for analysis.
For analysis of ChIP-Seq, de-crosslinked DNA samples from three ChIP reactions were pooled (a total of 3 x 107 cellular equivalents per sample), and DNA purified by phenol-chloroform extraction and recovered by ethanol precipitation. Indexed libraries were then made using the DNA Ultra II Library Prep Kit for Illumina (E7645, New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subject to 75 bp single sequencing according to the manufacturer’s protocol (Illumina NextSeq500). Sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Shared Resource. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.   ---   RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. RNA-Seq for CHP-134 cells was completed with three biological replicates.   ---    For analysis of SLAM-seq: After quality control analyses, libraries were prepared (250 ng RNA per sample) using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the User Guide (015UG009V0251) recommendations. Sequencing was performed by Lexogen on an Illumina NextSeq 500 system, using the SR75 High Output Kit. The SLAMdunk analysis pipeline (34) was used to analyze SLAMseq sequencing data. SLAM-Seq completed with three biological replicates.

tag: treatment

value: 5 uM C6

tag: time

value: 1 day


title: CHP134 RNA-seq C6 1 day rep1

status: Public on Jan 17 2020

type: SRA

country: USA

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
641-1D1

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: CHP134 RNA-seq C6 4 day rep1

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
641-4D1

value: 4 day


title: CHP134 RNA-seq C6 4 day rep2

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
641-4D2


title: CHP134 RNA-seq DMSO 4 day rep3

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
DMSO-4D3

value: DMSO


title: CHP134 RNA-seq DMSO 4 day rep2

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
DMSO-4D2


title: CHP134 RNA-seq C6 4 day rep3

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
641-4D3


title: KO1

city: Vancouver

first: Pauline

last: Johnson

state: BC

address: 2350 Health Sciences Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

data_processing:
Sequencing was performed on the Illumina NextSeq 500 with paired end 42bp × 42bp reads.
De-multiplexed read sequences were then aligned to the Mus musculus (mm10) reference sequence using Spliced Transcripts Alignment to a Reference, STAR, alignersm through Cufflinks Assembly.
Cuffdiff analysis was used for FPKM calculations as per Illumina basespace software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for the genes in all 6 samples. The columns WTBAL_FPKM & KOBAL_FPKM include the replicate averages.

organism: Mus musculus

source_name: Alveolar Macrophage

extract_protocol:
RNA extraction performed according to manufacturer's instructions using the Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were isolated from mice using bronchoalveolar lavage, using PBS and 2mM EDTA, then treated with RBC lysis buffer

tag: genotype

tag: strain

tag: Sex

value: female

tag: cell type

value: alveolar macrophage

tag: age

value: 6-10 weeks


title: CHP134 RNA-seq C6 1 day rep3

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
641-1D3


title: CHP134 RNA-seq DMSO 1 day rep3

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
DMSO-1D3


title: CHP134 RNA-seq DMSO 4 day rep1

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
DMSO-4D1


title: CHP134 RNA-seq DMSO 1 day rep2

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
DMSO-1D2


title: Dorsal Raphe Nucleus, RbV, Set 2

city: Boston

first: Kee Wui

last: Huang

state: MA

address: 200 Longwood Ave, WAB 347

department: Neurobiology

institute: Harvard Medical School

description: Contains libraries DRM2.2, DRM3.2, DRF3.2, DRF4.3. Please see README file containing library barcodes for demultiplexing.

data_processing:
All processing steps performed on sequencing fastq files to generate count matrices were performed using a custom pipeline for inDrops data analysis available at https://github.com/indrops/indrops (Klein et al., 2015).
Reads were filtered by expected structure and sorted by library index (see README file containing library information). Valid reads were then trimmed (Trimmomatic version 0.33; parameters: LEADING: "28" SLIDINGWINDOW: "4:20" MINLEN: "16") before demultiplexing and sorting by cell barcodes. Cell barcodes containing fewer than 250 total reads were discarded.
Remaining reads were aligned using Bowtie (version 1.2.2; parameters: m = 200, n = 1, l = 15, e = 100) to a custom-built reference transcriptome, which is based on GRCm38.87 with the addition of genes from SAD B19 rabies viruses and transgenes.
Aligned reads were quantified as UMI-filtered mapped read (UMIFM) counts. The UMIFM count matrix (counts per gene per cell) for a single library (e.g. DRF3.1) were exported as a gunzipped TSV file for downstream analysis.
Genome_build: GRCm38.87, modified to include sequences from G-deleted SAD B19 rabies viruses (B19N, B19P, B19M, B19L, EGFP, tdTomato, AmCyan1).
Supplementary_files_format_and_content: Processed files are compressed TSV files containing UMIFM count matrices from a single library.

molecule: polyA RNA

source_name: Microdissected brain tissue containing dorsal raphe nucleus

growth_protocol: Mice were pair-housed in standard 12:12 light-dark cycles (7:00 AM - 7:00 PM) with ad-libitum food and water.

extract_protocol:
Mice were transcardially perfused with an ice-cold choline cutting solution containing neuronal activity blockers (10 µM (R)-CPP, 1 µM tetrodotoxin). Brains were rapidly dissected out and sliced into 250 µm thick coronal sections on a vibratome in a chilled cutting chamber filled with choline cutting solution.
Coronal slices containing the DRN were then transferred to a chilled dissection dish containing a choline-based cutting solution for microdissection. Dissected tissue chunks were transferred to cold HBSS-based dissociation media with an inhibitor cocktail (0.9 mM kynurenic acid, 10 µM (R)-CPP, 1 µM tetrodotoxin, 10 µM triptolide, 5 µg/ml actinomycin D, 30 µg/ml anisomycin) and kept on ice.
Dissected tissue chunks for each sample were pooled into a single tube for dissociation. Tissue chunks were mixed with a digestion cocktail (dissociation media with 20 U/ml papain, 1 mg/ml pronase, 0.05 mg/mL DNAse I, 10 µM triptolide, 5 µg/ml actinomycin D, 30 µg/ml anisomycin) and incubated at 34 °C for 90 min with gentle rocking. Digestion was quenched by adding dissociation media with 0.2% BSA and 10 mg/ml ovomucoid inhibitor, and samples were kept chilled for the rest of the dissociation procedure.
Tissue chunks were then mechanically triturated using fine-tip plastic micropipette tips of progressively decreasing size. Triturated cell suspension was filtered in two stages using a 70 µm cell strainer and 40 µm pipette tip filter and washed in two repeated centrifugation (5 min, 300 g) and re-suspension steps to remove debris before a final re-suspension in dissociation media containing 0.04% BSA and 15% OptiPrep.
Cell density was calculated based on hemocytometer counts and adjusted to approximately 100,000 cells/ml. Single-cell encapsulation and RNA capture on the InDrop platform was performed at the Harvard Medical School ICCB Single Cell Core using v3 chemistry hydrogels based on previously described protocols (Zilionis et al., 2017).
Libraries were constructed following the protocols described in Zillionis et al. (2017) for inDrop v3 hydrogels. Libraries were pooled for sequencing and demultiplexed using library barcodes (see README file). R1 is the biological read, R2 is the first half of the hydrogel barcode, R3 is the library index, and R4 contains the second half of the hydrogel barcode, UMI, and fraction of the polyA tail.

treatment_protocol: Mice received intracranial injections of glycoprotein-deleted rabies viruses (B19G-SADdG-EGFP or B19G-SADdG-tdTomato) 7 days prior to tissue collection. Each mouse received a pair of injections (Str and dLGN, or NAc and SN) under general anesthesia following protocols approved by the Harvard Standing Committee on Animal Care in accordance with NIH guidelines. All injections were placed in the right hemisphere, and virus titers used were approximately 1E+9 to 1E+10 IU/mL. See README file for information regarding the injection sites for each sample.

value: 8-10 weeks

tag: condition

value: RbV (injected)


title: Dorsal Raphe Nucleus, RbV, Set 6

description: Contains libraries DRM3.8, DRF3.6. Please see README file containing library barcodes for demultiplexing.


title: Dorsal Raphe Nucleus, RbV, Set 5

description: Contains libraries DRM3.6, DRM3.7, DRF3.5, DRF4.6. Please see README file containing library barcodes for demultiplexing.


title: Dorsal Raphe Nucleus, RbV, Set 4

description: Contains libraries DRM2.4, DRM3.4, DRF3.4, DRF4.5. Please see README file containing library barcodes for demultiplexing.


title: Dorsal Raphe Nucleus, RbV, Set 1

description: Contains libraries DRM2.1, DRM3.1, DRF3.1, DRF4.2. Please see README file containing library barcodes for demultiplexing.


title: 3T3 ChIP-seq WDR5 rep3

description: NIH3T3 (male) cell lines were maintained in DMEM with 10% Bovine Serum.

library_source: genomic

molecule: genomic DNA

tag: chip antibody

value: Cell Signaling WDR5 (D9E1I)


title: 3T3 ChIP-seq WDR5 rep2


title: Patient 14.region d

city: New York

first: Augusto

last: Villanueva

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Cell counter: Cell Ranger
Data filtering: Seurat 2.0.0
Data normalization: Seurat 2.0.0
Genome_build: Hg19
Supplementary_files_format_and_content: tsv and mtx files are tab-separated plain-text tables

source_name: Tumor sample

extract_protocol:
The cell density was determined using a C-Chip DHC-N01 disposable hemocytometer. A mixture of 5 μl of 0.04% trypan blue (BioRad) and 5 μl of the single cell suspension was loaded unto the hemocytometer and examined at 10X magnification, using the Invitrogen Evos FL Cell Imaging System-digital inverted microscope. The single-cell chip loading, GEM generation & barcoding, post GEM-RT & cDNA amplification, and library construction were performed according to the ChromiumTM Single Cell 3’ Protocol - Chemistry v2. For GEM generation an input of 10,000 cells total, at 1,000 cells/uL density, was targeted for each sample, with a target cell recovery of 6,000 cells.
Library construction, enzymatic fragmentation, End-repair and A-tailing were performed as follows: pre-cool block at 4°C hold, fragmentation at 32°C for 5 minutes; End repair and A-tailing 65°C for 30 minutes and held at 4°C. Post reaction cleanup was performed, followed by Adaptor ligation. Adaptor ligation incubation was done at 20°C for 15 minutes. Post adaptor ligation cleanup was then performed, followed by sample index PCR with the following parameters: 98°C for 45 seconds; followed by 14 cycles: 98°C for 20 seconds; 54°C for 30 seconds; and 72°C for 20 seconds; followed by 72°C for 1 minute and held at 4°C. Quantification of the constructed libraries was evaluated using Qubit dsDNA HS Assay Kit (Thermo Fisher), Agilent cDNA High Sensitivity Kit, and Kapa DNA Quantification Kit for Illumina platforms, following the manufacturer's instructions.
Generated libraries were sequenced on the Illumina HiSeq2500, using the paired-end 2 x 125bp sequencing protocol. Sequencing run parameters were set up according to version 2 chemistry, the number of cycles for each read as follows: Read 1: 26 cycles, i7 index: 8 cycles, i5 index: 0 cycles and Read 2: 98 cycles.

tag: subject id

value: Patient 14

tag: subject status

value: hepatocellular carcinoma patient

tag: tissue type

value: tumor


title: 3T3 ChIP-seq WDR5 rep1


title: BC_6

type: RNA

city: Brussels

first: Sandra

last: Schmitz

address: Avenue Hippocrate, 54

department: Medical Oncology

country: Belgium

institute: Universite catholique de louvain

hyb_protocol: 250 ng of RNA was amplified and labeled using the Affymetrix  GeneChip® 3’ IVT Express Kit. RNA was hybridized  overnight to Affymetrix GeneChip HG-U133 Plus 2.0  (High Wycombe, UK), then stained and washed on an  Affymetrix Gene Chip® Fluidics Station 450.

scan_protocol: The array was then scanned to produce an image data file (DAT) and  a cell intensities data file (CEL).

data_processing: The dataset was normalized using the GCRMA method.

label: biotin

extract_protocol: Total RNA was extracted using the miRNeasy Mini  Kit from Qiagen (Venlo, Netherlands).

treatment_protocol: Cetuximab two weeks before surgery

tag: disease state

value: HNSCC

value: before treatment

tag: sample id

tag: tumor site

value: OC

tag: tumor loc

value: Tongue

tag: clinical staging

tag: tabac (uap)

tag: alcool (units)


title: WT1

tag: genotype


title: Patient 14.region b


title: Patient 14.region a


title: Patient 14.region c


title: Dorsal Raphe Nucleus, RbV, Set 3

description: Contains libraries DRM2.3, DRM3.3, DRF3.3, DRF4.4. Please see README file containing library barcodes for demultiplexing.

tag: strain


title: Patient 13.region b

value: Patient 13


title: Patient 13.region a


title: Patient 13.region c


title: CHP134 RNA-seq DMSO 1 day rep1

description:
CHP134 (male) cell lines were cultured in RPMI-1640 media with 10% FBS.
CHP134-count.txt
DMSO-1D1

tag: cell line

tag: treatment

tag: time

value: 1 day


title: MC38 ChIP-seq IgG rep3

description: MC38 (female) cell lines were maintained in DMEM with 10% Bovine Serum.

value: Cell Signaling IgG (2729S)


title: MC38 ChIP-seq WDR5 rep2


title: 3T3 ChIP-seq IgG rep1


title: MC38 ChIP-seq WDR5 rep1


title: MC38 ChIP-seq IgG rep2


title: MC38 ChIP-seq WDR5 rep3


title: hnRNPFH_CLIP_Mock1_IgG

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

data_processing:
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcodes were separated using Novobarcode
Sequences were aligned to mm10 genome using STAR
Normalized abundance was generated by RSEM
Peaks were called by HOMER
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet includes 30nt peaks called at FDR <0.00001

source_name: Mouse Embryonic Stem Cells

growth_protocol: E14 mESCs were maintained on standard mESC protocol from Jaenisch lab

extract_protocol:
Clip-seq libraries were made from RNA isolated using Trizol + isopropanol precipitation. Antibody against hnNRNPF/H was used for irCLIP. Antibody: sc-32310
Libraries were prepared using protocol described in Zarnegar et al. 2016 Nature Methods
irCLIP-seq

treatment_protocol: Cells were transfected with LNA containing oligos antisense to tRF-GG or Mock transfected


title: hnRNPFH_CLIP_tGG1_IgG


title: hnRNPFH_CLIP_Mock2


title: hnRNPFH_CLIP_Mock1


title: 3T3 ChIP-seq IgG rep2


title: hnRNPFH_CLIP_tGG1


title: hnRNPFH_CLIP_tGG2


title: MC38 ChIP-seq IgG rep1


title: Csf1r_het replicate1

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
Kallisto (v0.43.1) software was employed to determine the read count and transcripts per kilobase million (TPM) for each gene that was annotated in the GENCODE database (vM15). Genes  with an average TPM >1 were selected and then analyzed using the software DESeq2 to detect differentiall expressed genes at false discovery rate < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts in each sample

source_name: Isolated Tmem119+ microglia

extract_protocol:
Tmem119+ microglia were isolated by sorting directly into Qiagen RNeasy lysis buffer.The RNA was extracted the same day using a Rneasy Plus Micro Kit and stored at -80°C prior to processing.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

tag: cell type

value: cerebral microglia

tag: age

value: 20 months old


title: Mettl3_KO1_mNET_r2

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

country: China

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) using HISAT (version 2.1.0) with ‘--rna-strandness F’ parameters. Annotation files (version M19, 2018-08-30, in gtf format) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on different regions of each GENCODE annotated gene were counted using featureCounts.
Escaping Index was calculated as sense reads around TSS (the interval [TSS-50, TSS+250]) devided by sense reads on genebody (the interval [TSS+500, TES])  (Takayuki Nojima et al., 2015, Cell ).
Genome_build: mm10
Supplementary_files_format_and_content: Escapping Index for each gene and each sample.

source_name: Embryonic stem cells

growth_protocol: Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2.

extract_protocol:
Isolated chromatin was washed in 100 l of 1x Micrococcal Nuclease (MNase) buffer (NEB) and then incubated with MNase (40 u/ml) on Thermomixer (eppendorf, 1,400 rpm) at 37 oC for 90 s. In order to inactivate MNase, EGTA (25 mM) was added immediately after the reaction and soluble-digested chromatin was collected by 13,000 rpm centrifuge for 5 min. The supernatant was diluted with 9 ml of NET-2 buffer (50 mM Tris-Hcl, pH 7.4, 150 mM NaCl, 0.05% NP40) and Pol II antibody-conjugated beads were added. 40 g of Pol II antibody was used for each mNET-seq experiment. Immunoprecipitation was performed at 4 oC for 1 hr. The beads were washed with 1ml of NET-2 buffer six times and with 500 l of 1xPNKT (1xPNK buffer and 0.1% Triton X-100) buffer once in the cold room. The washed beads were incubated in 100 l of PNK reaction mix (1xPNKT, 1 mM ATP and 0.05 U/ml T4 PNK 3’ phosphatase minus (NEB) on Thermomixer (1,400 rpm) at 37 oC for 6 min. After, the reaction beads were washed with 1ml of NET-2 buffer once and RNA was extracted with Trizol reagent. RNA was resolved on 8% denaturing acrylamide 7M urea gels for size purification. 35–100 nt fragments were eluted from the gel using RNA elution buffer (1 M NaOAc and 1 mM EDTA) and RNA was precipitated in 75% Ethanol.
RNA libraries were prepared according to the manual of NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

treatment_protocol: The cells were lysed with ice-cold 4 ml of HLB/NP40 buffer (10 mM Tris-Hcl, pH 7.5, 10 mM NaCl, 0.5% NP40, and 2.5 mM MgCl2) and incubated on ice for 5 min. After the incubation, 1 ml of ice-cold HLB/NP40/Sucrose buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.5% NP40, 2.5 mM MgCl2, and 10% Sucrose) was under-laid and then the nuclei were collected under 1,400 rpm centrifuge at 4 oC for 5 min. Isolated nuclei were resuspended in 125 ml of NUN1 solution (20 mM Tri-HCl, pH 8.0, 75 mM NaCl, 0.5 mM EDTA, 50% Glycerol and proteinase inhibitor 1xComplete (Roche) followed by 1.2 ml NUN2 buffer (20 mM HEPES-KOH pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 300 mM NaCl, 1 M Urea, 1% NP40, proteinase inhibitor 1xComplete and phosphatase inhibitor 1xPhosStop [Roche]). 15 min incubation was carried out on ice with mixing by max speed vortex for 5 s every 4 min and then chromatin pellets were precipitated under 13,000 rpm centrifuge at 4 oC for 10 min.

value: mouse embryonic stem cells

tag: antibody

value: mouse anti-RNA Polymerase II


title: Mettl3_Control_mNET_r2


title: Mettl3_KO2_mNET_r2


title: Mettl3_KO2_mNET_r1


title: Ythdc1_cKO_6h_r2

description: non-ribosome RNA

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38 and aligned to mouse genome (mm10, version M19, 2018-08-30) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with default parameters.
Reads on each GENCODE annotated gene were counted using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

extract_protocol:
The nuclear fraction was separated and total RNA was purified by Trizol. Before purified non-ribosome RNA with RiboMinus transcriptome isolation kit, ERCC RNA spike-in control (Ambion) was added to each sample (0.1 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.

treatment_protocol: Six 6-cm plates of mESCs were seeded and controlled to afford the same amount of cells. After 48 h, actinomycin D was added to 5 μg ml–1 at 6 h, 3 h, and 0 h before trypsinization collection.

tag: treatment time point (h)

tag: agent

value: actinomycin D


title: Ythdc1_cKO_6h_r1

description: non-ribosome RNA


title: Ythdc1_cKO_0h_r2

description: non-ribosome RNA


title: Mettl3_KO_JARID2_b3.r2

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, and then uniquely mapped to mouse genome (mm10, version M19, 2018-08-30) and Drosophila melanogaster chromatin (Spike-in Chromatin) using bowtie (version 1.2.2) allowing one mismatch.
Peaks were called using HOMER with '-style factor -F 2 -L 2' parameters
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations reported by HOMER for each sample.

extract_protocol:
The cells were then collected in lysis buffer (0.1% SDS, 2 mM EDTA, 1 x protease inhibitors, 20 mM Tris–HCl, pH 8.0, 150 mM NaCl, 1% Triton) and the lysates were sonicated by a Bioruptor UCD-200 (Diagenode) to result in DNA fragments of 200 to 500 bp in length. Cellular debris was removed by centrifugation and the lysates were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, 1 x protease inhibitors, 16.7 mM Tris–HCl, pH 8.0). Take 1% of sonicated chromatin as Input control. Washed Protein G Magnetic beads (Invitrogen) two times with ChIP buffer, eluted beads in 1 mL of ChIP buffer, added antibody and incubated the mixture 2 hours on rotating platform at 4 °C. The washed the antibody-coated beads with ChIP buffer three times. Chromatin solutions were incubated overnight at 4 °C with rotation with antibodies-coated beads. The beads were washed sequentially for 3 min by rotation with 1 ml of the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris–HCl, pH 8.0), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris–HCl, pH 8.0) and LiCl wash buffer (0.25 M LiCl, 1% Nonidet P-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris–HCl, pH 8.0). Finally, the beads were washed twice with 1 ml TE buffer (1 mM EDTA, 10 mM Tris–HCl, pH 8.0). The immuno-complexes and Input were then eluted by adding 400 μl of elution buffer (100 mM NaHCO3, 1% SDS) plus 18 μl 5 M NaCl and incubating for 4 hrs at 65 °C to reverse protein-DNA crosslinks. The remaining proteins were digested by adding 5 μl of proteinase K (Promega) and incubating overnight at 65 °C. The DNA was recovered by phenol/chloroform/isoamyl alcohol (25:24:1) extractions and precipitated with 0.1 volume of 3 M sodium acetate, pH 5.2, and 3 volumes of ethanol using glycogen as carrier.
Library preparation was performed by using KAPA HyperPlus Kits (Kapabiosystems) according to the manufacturer’s protocols.

treatment_protocol: mESCs were resuspended in growth media with a concentration of 10e6 ml-1 and cross-linked by adding 1% formaldehyde directly to the media, slow shaked 20 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature with slowly shaking. The media was removed and the cells were washed twice with ice-cold PBS.

value: rabbit anti-JARID2 (NB100-2214, Novus Biologicals)


title: Ythdc1_cKO_3h_r1

description: non-ribosome RNA


title: Ythdc1_cKO_3h_r2

description: non-ribosome RNA


title: Ythdc1_Control_6h_r2

description: non-ribosome RNA


title: Mettl3_KO_JARID2_b3.r1


title: Identification of HMGA2 knockout (#2) target genes in TE-8

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

country: Japan

institute: Chiba University

description: HMGA2 knockout with CRISPR/Cas9

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 12.1.1.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA or siRNA transfection using Lipofectamine RNAiMAX (Invitrogen). Gene knockdown was performed using Alt-R CRISPR-Cas9 System (Integrated DNA Tecnologies).

value: esophageal cancer

tag: transfection

value: no transfection

source_name: HMGA2 knockout (#2) cell line


title: Identification of HMGA2 knockout (#8) target genes in TE-8 2

description: HMGA2 knockout with CRISPR/Cas9

source_name: HMGA2 knockout (#8) cell line


title: Ythdc1_Control_6h_r1

description: non-ribosome RNA


title: Identification of si-HMGA2-2 target genes in TE-8

source_name: siHMGA2-2 transfected cell line


title: Identification of si-HMGA2-2 target genes in TE-8 1


title: Identification of si-SERPINH1-2 target genes in MKN45

value: gastric cancer

source_name: si-SERPINH1-2 transfected cell line


title: Identification of HMGA2 knockout (#8) target genes in TE-8 1

description: HMGA2 knockout with CRISPR/Cas9


title: Identification of si-HMGA2-3 target genes in TE-8 2

source_name: siHMGA2-3 transfected cell line


title: Ythdc1_Control_3h_r2

description: non-ribosome RNA


title: Mettl3_KO_Input_b3.r2


title: Identification of si-SERPINH1-1 target genes in MKN45

source_name: si-SERPINH1-1 transfected cell line


title: Mettl3_KO1_mNET_r1


title: Mettl3_KO_Input_b3.r1


title: Mettl3_Control_JARID2_b3.r2


title: Mettl3_Control_mNET_r1


title: Ythdc1_Control_3h_r1

description: non-ribosome RNA


title: Ythdc1_cKO_0h_r1

description: non-ribosome RNA


title: Mettl3_Control_Input_b3.r2


title: Mettl3_Control_JARID2_b3.r1


title: Mettl3_KO_EP300_b2.r1

value: rabbit anti-KAT3B/P300 (ab14984, Abcam)


title: WT mCh- Colon Stem Cell FLAG-Ascl2 ChIP-seq

first: Ramesh

last: Shivdasani

address: 450 Brookline Ave. Dana 720D

institute: Dana Farber Cancer Institute

data_processing:
RNA-seq: STAR aligner, version 2.5.3a.
RNA-seq raw read counts: HTSeq
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression
Alignment: ATAC-seq and ChIP-seq: Bowtie2.
ATAC-seq differential region identification: diffReps; Peak calling: MACS2;
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags

extract_protocol:
Colonic epithelial cells were isolated in 10mM EDTA in DMEM, digested in a mixture of Accumax, Dispase, TrypLE , and sorted based on mCherry or GFP. RNA was extracted with Trizol reagent (ThermoFisher) for RNA-seq. Whole nuclei were used for chromatin transposition with Nextera Tn5 Transposase (Illumina) for ATAC-seq and ChiP-seq.
SMARTer® Universal Low Input RNA Kit (TAKARA Bio) for RNA library and high-fidelity 2X PCR Master Mix (NEB) for ChIP and ATAC library were used.

treatment_protocol: 2mg tamoxifen on 1st and 2nd day and 1mg tamoxifen on 3rd day was intraperitoneally administered to knockout Ascl2. Diphtheria toxin (50 ug/kg) was intraperitoneally administered every other day 4 times to ablate stem cells

tag: strain background

value: C57BL/6 129/Sv mixed

tag: genotype/variation

value: wild type

tag: tissue

value: mouse colon epithelium

value: Mouse colon stem cells

tag: cell population

tag: chip antibody

value: FLAG (Sigma-Aldrich, F1804, lot SLBN5629V)


title: WT mCh+ Colon Stem Cell FLAG-Ascl2 ChIP-seq

value: Ascl2(mCh); Lgr5Dtr-Egfp


title: Ythdc1_Control_0h_r2

description: non-ribosome RNA

tag: genotype


title: Mettl3_KO_EP300_b2.r2

tag: strain


title: Regenerating Cell FLAG-Ascl2 ChIP-seq

source_name: Regenerating Cell FLAG-Ascl2 ChIP-seq

value: Mouse regenerating colon cells


title: Ythdc1_Control_0h_r1

description: non-ribosome RNA


title: Ascl2 KO Colon Stem Cell RNA-seq replicate2

source_name: Ascl2 KO Colon Stem Cell RNA-seq

value: Ascl2 KO

value: Mouse Ascl2 KO colon stem cells

value: Ascl2Fl/Fl; Lgr5EGFP-Cre+


title: Mettl3_KO_Input_b2.r2

value: mouse embryonic stem cells


title: Ascl2 KO Colon Stem Cell RNA-seq replicate1


title: Mettl3_KO_Input_b2.r1


title: Regenerating Cell RNA-seq replicate2

source_name: Regenerating Cell RNA-seq

value: Mouse colon regenerating cells

value: Ascl2(mCh); Lgr5Dtr-Egfp+


title: Mettl3_Control_Input_b2.r2


title: Mettl3_Control_Input_b2.r1


title: Regenerating Cell RNA-seq replicate1


title: Mettl3_Control_EP300_b2.r1


title: WT Colon Stem Cell RNA-seq replicate3

source_name: WT Colon Stem Cell RNA-seq


title: WT Colon Stem Cell RNA-seq replicate1


title: Mettl3_Control_EP300_b2.r2


title: Mettl3_KO_YY1_b1.r2

value: rabbit anti-YY1 (ab109237, Abcam)


title: WT Colon Stem Cell RNA-seq replicate2


title: Mettl3_Control_Input_b3.r1


title: LYVE1_rep2

description: processed data file: Rawgenescounts.csv

data_processing:
All bulk RNAseq data was analyzed using the VIPER pipeline
It was aligned to the mouse reference genome Mm10 using the STAR aligner
Genome_build: mm10
Supplementary_files_format_and_content: Rawgenescounts file was generated using the VIPER pipeline, aligned to the mm10 reference genome using STAR aligner, which also produced gene counts.

source_name: CD31+LYVE1+ intestinal mesenchymal cells murine

extract_protocol: Cells were isolated from entire small intestinal tissues, muscle stripped, epithelium denuded via 20 minutes in warm 10 mM EDTA/HBSS (at 37degrees C), and tissue was further minced by fine scalpels. Digestion of tissue was performed using 1.5mg/ml collagenase II (Worthington) in 10%FBS/DMEM at 37 degrees C. Supernatants were collected every 20 minutes for one hour, and washed twice to remove debris. Antibody-labelling was performed prior to FACS. FACS-sorted cells were spun at 1200 rcf for 2 min., and trizol reagent (ThermoFisher) was applied to resultant cellular pellet. RNA isolates were purified using the RNeasy Microkit (Qiagen). Total RNA (5-10ng) was used to prepare libraries with the SMART-Seq v4 Ultra Low Input RNA kit (Clontech) and libraries sequenced on an Illumina NextSeq500 instrument.

value: primary cells

tag: cell subtype

value: Intestinal lymphatic endothelial cells

value: positive CD31 (1:100, BD 551262), positive LYVE1 (1:100, AngioBio 11-034)


title: CD31_rep2

description: processed data file: Rawgenescounts.csv

source_name: CD31+LYVE1- intestinal mesenchymal cells murine

value: Intestinal endothelial cells

value: positive CD31 (1:100, BD 551262), negative LYVE1 (1:100, AngioBio 11-034)


title: Mettl3_KO_Input_b1.r2


title: LYVE1_rep1

description: processed data file: Rawgenescounts.csv


title: Mettl3_Control_YY1_b1.r2


title: CD31_rep1

description: processed data file: Rawgenescounts.csv


title: PDGFRAlo_rep2

description: processed data file: Rawgenescounts.csv

source_name: GFPLo cells from PDGFRAH2BEGFP murine transgenic

value: transgenic PDGFRAH2BEGFP mouse (Jackson, #007669)

value: PDGFRAlo stromal cells


title: Telocyte_rep2

description: processed data file: Rawgenescounts.csv

source_name: GFPHi cells from PDGFRAH2BEGFP murine transgenic

value: Telocyte cells


title: PDGFRAlo_rep1

description: processed data file: Rawgenescounts.csv


title: Mettl3_Control_Input_b1.r1


title: Mettl3_Control_YY1_b1.r1


title: Telocyte_rep1

description: processed data file: Rawgenescounts.csv


title: Mettl3_Control_Input_b1.r2


title: Mettl3_KO2_60m_b2.r2

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to mouse genome and transcriptome (mm10, version M19, 2018-08-30) together with external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with ‘--rna-strandness R’ parameters. Annotation files (version M19, 2018-08-30, in gtf format for mouse) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

extract_protocol:
Total RNA was purified by Trizol and nascent RNA was captured by using Click-iT Nascent RNA Capture Kit (Invitrogen). Before constructing libraries ERCC RNA spike-in control (Ambion) was added to each sample (0.01 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.

treatment_protocol: Eight 6-cm plates of mESCs were seeded and controlled to afford the same amount of cells. After 48 h, 5-ethynyl Uridine (EU) was added to 0.5 mM at 60 min, 30 min, 20 min and 10 min before trypsinization collection.

value: embryonic stem cells

tag: eu treatment time (min)


title: Mettl3_KO2_60m_b2.r1


description:
Eed_KO_Day30_Adult_ISC_RNA Biological Replicate 2
supplementary file: Read_Counts_All_Cells.txt

data_processing:
ChIP-seq:bowtie2 version 2.3.4.3. For 150bp paired-end data, reads from the 'Read1' file were trimmed to 75bp and used for further analysis, RNA-seq: STAR aligner version 2.5.3a
ChIP-seq peak calling: SICER v0.0.1
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types

source_name: mouse intestinal villus cells

extract_protocol: Total RNA was extracted with TRIzol reagent (Life Technologies) followed by DNase treatment with the RNeasy kit (Qiagen).

treatment_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4C followed by digestion in TrypLE solution at 37C for 30 min to generate single-cell suspensions and FACS to isolate GFP+ ISCs. Cells were frozen in TRIzol reagent and stored at -80C for subsequent RNA isolation.
Mice were injected with 1-2mg Tamoxifen for 5 consecutive days and every alternate day after that to activate tamoxifen-inducible Cre and recombine conditional alleles.

value: B6;129 mixed background

value: Adult Epitheial cells; proximal 1/3 of intestine

value: Eed F/F; Lgr5EGFP-IRES-CreERT


description:
Eed_KO_Day30_Adult_ISC_RNA Biological Replicate 1
supplementary file: Read_Counts_All_Cells.txt


description:
Eed_KO_Day21_Adult_ISC_RNA Biological Replicate 2
supplementary file: Read_Counts_All_Cells.txt


title: Mettl3_KO2_20m_b2.r2

source_name: Embryonic stem cells


title: Mettl3_KO2_30m_b2.r1


title: Mettl3_KO_YY1_b1.r1


title: Mettl3_KO2_20m_b2.r1


title: Mettl3_KO2_10m_b2.r2


description:
Eed_KO_Day14_Adult_ISC_RNA Biological Replicate 1
supplementary file: Read_Counts_All_Cells.txt


title: Mettl3_KO2_10m_b2.r1


description:
Eed_KO_Day9_Adult_ISC_RNA Biological Replicate 1
supplementary file: Read_Counts_All_Cells.txt


title: Eed_KO_Day9_Adult_ISC_RNA Biological Replicate 3

description:
Eed_KO_Day9_Adult_ISC_RNA Biological Replicate 2
supplementary file: Read_Counts_All_Cells.txt


title: Eed_KO_Day9_Adult_ISC_RNA Biological Replicate 2


title: Eed_KO_Day14 Adult ISC H3K27me3 ChIP Rep1

description: Eed_KO_Day14 Adult ISC H3K27me3 ChIP Biological Replicate 1

source_name: mouse ISCs

extract_protocol:
Whole cell lysates were sonicated and incubated with H3K27me3 antibody overnight (EMD Millipore 07-449) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4C followed by digestion in TrypLE solution at 37C for 30 min to generate single-cell suspensions and FACS to isolate GFP+ ISCs. Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.


title: Mettl3_KO_Input_b1.r1


title: Mettl3_Control_30m_b2.r1


description:
Eed_KO_Day21_Adult_ISC_RNA Biological Replicate 1
supplementary file: Read_Counts_All_Cells.txt


title: Eed_KO_Day9 Adult ISC H3K27me3 ChIP Rep2

description: Eed_KO_Day9 Adult ISC H3K27me3 ChIP Biological Replicate 2


title: Mettl3_Control_60m_b2.r1


title: Mettl3_Control_60m_b2.r2


title: Eed_KO_Day9 Adult ISC H3K27me3 ChIP Rep1

description: Eed_KO_Day9 Adult ISC H3K27me3 ChIP Biological Replicate 1


title: WT Adult ISC H3K27me3 ChIP Rep1

description: WT Adult ISC H3K27me3 ChIP Biological Replicate 1

value: Eed +/+; Lgr5EGFP-IRES-CreERT


title: Ezh2 KO Adult Intestinal Villus H3K27me3  ChIP Rep2

description: Ezh2 KO Adult Intestinal Villus H3K27me3 ChIP Biological Replicate 2

treatment_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4C. Villi were isolated using 70uM filter and snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.

value: Ezh2 F/F; Villin-CRE


title: Mettl3_Control_20m_b2.r2


title: Mettl3_Control_30m_b2.r2


title: Mettl3_Control_20m_b2.r1


title: Mettl3_Control_10m_b2.r2


title: Mettl3_KO2_30m_b2.r2


title: Ezh2 KO Adult Intestinal Villus H3K27me3 ChIP Rep1

description: Ezh2 KO Adult Intestinal VIllus H3K27me3 ChIP Biological Replicate 1


title: Eed KO Adult Intestinal Villus H3K27me3  ChIP Rep2

description: Eed KO Adult Intestinal Villus H3K27me3 ChIP Biological Replicate 2

value: Eed F/F; Villin-CRE


title: Mettl3_Control_10m_b2.r1


title: Eed KO Adult Intestinal Villus H3K27me3 ChIP Rep1

description: Eed KO Adult Intestinal VIllus H3K27me3 ChIP Biological Replicate 1


title: WT Adult Intestinal Villus H3K27me3 ChIP Rep1

description: WT Adult Intestinal Villus H3K27me3 ChIP Biological Replicate 1

value: Eed +/+; Villin-CRE


title: mESCs_tGG30_4sU2

description:
processed data file:
Boskovic_Table_S1.xlsx

data_processing:
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcodes were separated using Novobarcode
Sequences were aligned to mm10 genome using Tophat/Bowtie2 with default settings
Normalized abundance was generated by RSEM
Genome_build: mm10, hg19 for hESCs
Supplementary_files_format_and_content: Excell sheet with FPKM for all genes

source_name: mESCs_LNA against tRF-GG

growth_protocol: E14 mESCs were maintained on standard mESC protocol from Jaenisch lab. H9 hESCs were maintained feeder free using recommended protocol from StemCell Technologies using mTESR1.

extract_protocol:
RNAs were extracted using Trizol. ATACseq follows standard protocol.
RNAseq libraries were prepared using protocol described in Heyer et a. 2015 NAR. ATAC-seq uses standard tagmentation protocol. Ribomethseq used NEB small-RNA library construction kit.

treatment_protocol: E14 cells were transfected with LNA or siRNAs or small RNAs. hESCs were treated with LNAs using nucleofection

value: mouse embryonic stem cells E14

tag: transfected with

value: LNA against tRF-GG


title: Mettl3_KO1_60m_r2

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to mouse genome (mm10, version M19, 2018-08-30) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with default parameters. Annotation
Reads on each GENCODE annotated gene were counted using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

value: mouse embryonic stem cells


title: Mettl3_KO1_30m_r2


title: mESCs_tGG30_4sU1


title: Mettl3_KO1_30m_r1


title: mESCs_tGG30_total2


title: mESCs_tGG15_4sU


title: Mettl3_KO1_20m_r2


title: mESCs_tGG30_total1


title: Mettl3_KO1_10m_r1


title: Mettl3_KO1_10m_r2


title: Mettl3_Control_60m_r1


title: Mettl3_Control_60m_r2


title: mESCs_GFP30_4sU2

source_name: mESCs_esiRNA against GFP

value: esiRNA against GFP


title: Mettl3_Control_30m_r1


title: mESCs_GFP30_total2


title: Regenerating Colon Cells (Day 8) Single Cell RNA-seq

data_processing:
RNA-seq: STAR aligner, version 2.5.3a.
RNA-seq raw read counts: HTSeq
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression
Single Cell RNA: aligned with 10x CellRanger, version 3.0.2
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types

source_name: Mouse regenerating colon cells

extract_protocol:
Colonic epithelial cells were isolated in 10mM EDTA in DMEM, digested in a mixture of Accumax, Dispase, TrypLE , and sorted based on expression of mCherry and absence of GFP.
About 104 cells were loaded onto Chromium Chip B using the 3’ GEM Library & Gel Bead Kit v3, followed by reverse transcription, cDNA amplification, and library preparation according to the 10X Genomics recommendations. Libraries were sequenced on a HiSeq4000 instrument.

value: mouse colon epithelium

value: C57BL/6 129/Sv  mix background

value: Ascl2(mCh); Lgr5Dtr-Egfp+


title: mESCs_GFP30_total1


title: Mettl3_Control_20m_r2


title: mESCs_GFP30_4sU1


title: mESCs_tGG4_RBM

description:
processed data file:
All_Ribomethseq_replicates_coverage.xlsx

data_processing:
library strategy: RiboMethseq
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcodes were separated using Novobarcode
Sequences were aligned to mm10 genome using Tophat/Bowtie2 with default settings
Normalized abundance was generated by RSEM
Genome_build: mm10, hg19 for hESCs
Supplementary_files_format_and_content: Excell sheet with FPKM for all genes


title: 3T3 ChIP-seq IgG rep3

description: NIH3T3 (male) cell lines were maintained in DMEM with 10% Bovine Serum.

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ChIP-seq reads were aligned to the hg19 or mm10 genome assembly using Bowtie2 after adapter trimming.
Peaks were called by MACS2 with a q-value of 0.01.
Differential binding peaks were identified using DiffBind.
SLAM-seq was processed using SLAMdunk.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: ChIP-seq: one peak file per Sample
Supplementary_files_format_and_content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary_files_format_and_content: SLAM-seq: tab-delimited text file include raw counts for each Sample

extract_protocol:
ChIP-seq assays (performed as described in Weissmiller, et. al. Nat Commun,10, Article number: 2014 (2019)): Briefly, cross-linking was carried out with 0.75% formaldehyde (Sigma-Aldrich; in PBS pH 7.4) at room temperature for 10 minutes. The reaction was quenched with 125 mM glycine for 10 minutes at room temperature, after which cells were washed twice with ice-cold PBS. Nuclei were prepared by incubating cells in Nuclear Lysis Buffer A (1 M HEPES pH 7.9, 1 M KCl, 0.5 M EDTA, 0.4% NP-40, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 5 minutes on ice, after which they were collected by centrifugation. Nuclei were then lysed in Formaldehyde Lysis Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1% SDS, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 15 minutes on ice. Chromatin was sheared by 17–24 minute sonication (BioRuptor UCD-200, Diagenode; on highest setting, alternating between 30 seconds on and 30 seconds off) to yield a mean chromatin size of ~250 bp. After sonication, debris was cleared by centrifugation, and sheared chromatin diluted 10-fold in Formaldehyde Lysis Buffer without SDS. Chromatin from 107 cells was used per immunoprecipitation reaction. Immunoprecipitation reactions were performed with either 0.8 µL of IgG or 4.0 µL of α-WDR5 antibody as indicated. Immune complexes were recovered on Protein A agarose beads (Roche) and washed sequentially with Low Salt Wash buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), High Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), LiCl Wash buffer (10 mM Tris pH 8.9, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail) and TE (10 mM Tris pH 8.0, 1 mM EDTA, supplemented with PMSF and Complete Protease Inhibitor Cocktail). Protein–DNA complexes were de-crosslinked overnight at 65°C in 50 µL Elution Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.1% SDS, and 20 µg Proteinase K (740506, Clontech).  ---   RNA-seq assays: CHP134 cells were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ.   ---   SLAM-seq assays: Nascent RNA was labeled using the SLAMseq Kinetics Kit–Anabolic Kinetics Module (061, Lexogen).  LoVo cells were pretreated with 25 uM C6, C6nc, or 0.1% DMSO prior to a three hour labeling with 1 mM 4-Thiouridine (S4U). Following the manufacturer's instructions, total RNA was isolated, alkylated with iodoacetamide, flash frozen, and shipped to Lexogen for analysis.
For analysis of ChIP-Seq, de-crosslinked DNA samples from three ChIP reactions were pooled (a total of 3 x 107 cellular equivalents per sample), and DNA purified by phenol-chloroform extraction and recovered by ethanol precipitation. Indexed libraries were then made using the DNA Ultra II Library Prep Kit for Illumina (E7645, New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subject to 75 bp single sequencing according to the manufacturer’s protocol (Illumina NextSeq500). Sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Shared Resource. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.   ---   RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. RNA-Seq for CHP-134 cells was completed with three biological replicates.   ---    For analysis of SLAM-seq: After quality control analyses, libraries were prepared (250 ng RNA per sample) using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the User Guide (015UG009V0251) recommendations. Sequencing was performed by Lexogen on an Illumina NextSeq 500 system, using the SR75 High Output Kit. The SLAMdunk analysis pipeline (34) was used to analyze SLAMseq sequencing data. SLAM-Seq completed with three biological replicates.

tag: cell line

tag: treatment

value: Cell Signaling IgG (2729S)


title: Mettl3_Control_20m_r1

tag: cell type


title: Mettl3_KO1_60m_r1


title: mESCs_tGG3_RBM


title: Mettl3_Control_10m_r2


title: Mettl3_Control_10m_r1


title: mESCs_tGG1_RBM


title: Mettl3_KO1_20m_r1


title: mESCs_tGG2_RBM


title: WT_Mettl3_IP_r2

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, and then uniquely mapped to mouse genome (mm10, version M19, 2018-08-30) and Drosophila melanogaster chromatin (Spike-in Chromatin) using bowtie (version 1.2.2) allowing one mismatch.
METTL3 peaks were called using HOMER in factor style with parameter ‘-F 1’ and ‘-L 1’ separately.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations together with peak summit and pvalue reported by HOMER for each sample.

extract_protocol:
The cells were then collected in lysis buffer (0.1% SDS, 2 mM EDTA, 1 x protease inhibitors, 20 mM Tris–HCl, pH 8.0, 150 mM NaCl, 1% Triton) and the lysates were sonicated by a Bioruptor UCD-200 (Diagenode) to result in DNA fragments of 200 to 500 bp in length. Cellular debris was removed by centrifugation and the lysates were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl, 1 x protease inhibitors, 16.7 mM Tris–HCl, pH 8.0). Take 1% of sonicated chromatin as Input control. Washed Protein G Magnetic beads (Invitrogen) two times with ChIP buffer, eluted beads in 1 mL of ChIP buffer, added METTL3 antibody (Abcam) and incubated the mixture 2 hours on rotating platform at 4 °C. The washed the antibody-coated beads with ChIP buffer three times. Chromatin solutions were incubated overnight at 4 °C with rotation with antibodies-coated beads. The beads were washed sequentially for 3 min by rotation with 1 ml of the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris–HCl, pH 8.0), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 500 mM NaCl, 20 mM Tris–HCl, pH 8.0) and LiCl wash buffer (0.25 M LiCl, 1% Nonidet P-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris–HCl, pH 8.0). Finally, the beads were washed twice with 1 ml TE buffer (1 mM EDTA, 10 mM Tris–HCl, pH 8.0). The immuno-complexes and Input were then eluted by adding 400 μl of elution buffer (100 mM NaHCO3, 1% SDS) plus 18 μl 5 M NaCl and incubating for 4 hrs at 65 °C to reverse protein-DNA crosslinks. The remaining proteins were digested by adding 5 μl of proteinase K (Promega) and incubating overnight at 65 °C. The DNA was recovered by phenol/chloroform/isoamyl alcohol (25:24:1) extractions and precipitated with 0.1 volume of 3 M sodium acetate, pH 5.2, and 3 volumes of ethanol using glycogen as carrier.
Library preparation was performed by using KAPA HyperPlus Kits (Kapabiosystems) according to the manufacturer’s protocols.

tag: antibody

value: Rabbit anti-METTL3 (ab195352, Abcam)


title: mESCs_tGG15_total


title: mESCs_GFP15_4sU


title: mESCs_Mock4_RBM

value: Mock


title: mESCs_Mock3_RBM


title: WT_Input_r2


title: Mettl3_Control_30m_r2


title: mESCs_Mock2_RBM


title: WT_Mettl3_IP_r1


title: mESCs_GFP15_total


title: mESCs_Mock1_RBM


title: mESCs_tGG48_2

description:
processed data file:
tRFGG_Mock_48_10kb.bed


title: Mettl3_KO2_Input_r1

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, and then uniquely mapped to mouse genome (mm10, version M19, 2018-08-30) and Drosophila melanogaster chromatin (Spike-in Chromatin) using bowtie (version 1.2.2) allowing one mismatch.
Peaks were called usin MACS2 with default paramters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations together with peak summit and pvalue reported by MACS2 for each sample.

extract_protocol:
Chromatin immunoprecipitation was performed using Auto iDeal ChIP-seq kit for Histone (diagenode) with spike-in Chromatin (Active Motif) and spike-in Antibody (Active Motif) following the manufacturer’s protocols.
Library preparation was performed by using KAPA HyperPlus Kits (Kapabiosystems) according to the manufacturer’s protocols.

treatment_protocol: mESCs were resuspended in growth media with a concentration of 10e6 ml-1 and cross-linked by adding 1% formaldehyde directly to the media, slow shaked 10 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature with slowly shaking. The media was removed and the cells were washed twice with ice-cold PBS.


title: Mettl3_KO2_Input_r2


title: mESCs_Mock48_2


title: Mettl3_KO2_H3K4me3_r2

value: rabbit anti-H3K4me3 (ab8580, Abcam)


title: mESCs_Mock48_1


title: mESCs_tGG24_2

description:
processed data file:
tRFGG_Mock_24_1kb.bed


title: Mettl3_KO2_H3K4me3_r1


title: Mettl3_KO2_H3K27ac_r2

value: rabbit anti-H3K27ac (ab4729, Abcam)


title: mESCs_tGG24_1


title: Mettl3_KO2_H3K27ac_r1


title: mESCs_Mock24_2


title: Mettl3_KO1_Input_r2


title: Mettl3_KO1_Input_r1


title: mESCs_Mock24_1


title: mESCs_siH2

description:
processed data file:
Boskovic_Table_S4.xlsx

source_name: mESCs_HNRNPH1 siRNA

value: HNRNPH1 siRNA


title: mESCs_siH3


title: WT_Input_r1


title: mESCs_siFH3

source_name: mESCs_HNRNPF+H siRNA

value: HNRNPF+H siRNA


title: mESCs_siFH2


title: mESCs_siFH1


title: Mettl3_KO1_H3K4me3_r1


title: Mettl3_KO1_H3K4me3_r2


title: mESCs_siC3

source_name: mESCs_control siRNA

value: control siRNA


title: Mettl3_Control_Input_r1


title: Mettl3_Control_Input_r2


title: Mettl3_KO1_H3K27ac_r1


title: Mettl3_KO1_H3K27ac_r2


title: mESCs_tGG48_1


title: Mettl3_Control_H3K4me3_r2


title: mESCs_siC2


title: mESCs_siC1


title: Mettl3_Control_H3K4me3_r1


title: Mettl3_Control_H3K27ac_r2


title: Immunized twice 2nd-SP

city: Newark

first: GyuLee

last: Kim

address: South orange ave 205

institute: Rutgers University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Spleen

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: The mice were immunized with pneumococcal whole cell vaccine (pep27 deletion mutant)

tag: cell

value: Spleen cell

value: Balb/c


title: Non-immunized C-SP


title: Immunized once 1st-SP


title: Immunized third 3rd-SP


title: Immunized third 3rd-L

source_name: Lung

value: Lung cell


title: Mettl3_Control_H3K27ac_r1


title: Immunized twice 2nd-L


title: Immunized once 1st-L


title: Non-immunized C-L


title: Same as sample 3, but TEX treated before sequencing

city: Muenster

first: Ulrich

last: Dobrindt

state: NRW

address: Mendelstrasse 7

department: Institute of Hygiene

country: Germany

institute: University of Münster

description: total RNA from Sample 3, TEX treated

data_processing:
Raw sequence reads were quality checked using quality control tool FastQC.
Reads were mapped using bwa with standard parameters (doi: 10.1093/bioinformatics/btp324)
Further analysis were carried out using ReadXplorer 2.2.3 (doi: 10.1093/bioinformatics/btw541)
Genome_build: The reads were mapped to the genome sequence of E. coli M1/5. The genome sequence is currently been submitted (accession number is pending).
Supplementary_files_format_and_content: Excel files including TPM values for each sample

organism: Escherichia coli

source_name: RNA-seq

growth_protocol: Bacteria where grown in Greiner 96-well Flat Bottom white polystyrol plates in 150µl M9-medium with 1g L‑1 casein hydrolysate, using a Tecan Infinite 200 Reader (Tecan Group), 37°C, shaking for 10min with amplitude 2 in 15min intervals. Bacterial cultures with OD600nm of 0.4 (three biological triplicates with eight technical replicates, 140µl each), were pooled and harvested in late exponential growth phase by centrifugation.

extract_protocol:
The suspension was centrifuged (5 min, 4 °C) and the bacterial pellet was resuspended in 35 µL lysis buffer (lysozyme in TE buffer, 85 mg/mL). After 10 min incubation at RT and gentle vortexing every 10 s, 1 mL TRizol ® (Thermo Fisher Scientific) was added and the isolation process was continued according to the manufacturer's protocol. 10 µg of isolated total RNA were used for DNA digestion, using the Turbo DNase (Turbo-DNA-free™ Kit, Thermo Fisher Scientific) according to the manufacturer's instructions.
The RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3' adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified (11 PCR cycles) to about 10-20 ng/µl using a high fidelity DNA polymerase. The TruSeq barcode sequences AGGATAGG or TCAGAGCC, which are part of the 5' TruSeq sequencing adapter were used. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: 3.36 mL of pooled bacterial culture was mixed with 0.42 mL stop solution (95 % ethanol, 5 % phenol).


title: Constutive clbQ expressing variant

description: total RNA


title: clbR deletion mutant

description: total RNA


title: Reference strain

description: total RNA


title: clbQ deletion mutant

description: total RNA


title: THP1_CTRL_rep1

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: Nascent-RNA profiling with fastGRO was performed in untreated THP1.

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
Alignment (RNAseq, chromatin RNA-seq): STAR
Tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization).

source_name: THP1 cell line

growth_protocol: THP1 cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) of FBS and 2 mM of L-glutamine.

extract_protocol: NEBNext ChIP-Seq ULTRAII RNA Sample Prep Kit (New England Biolabs, Inc.)

tag: experiment

value: fastGRO


title: C9KO-1_3

city: Dresden

first: Jared

last: Sterneckert

state: Saxony

address: Fetscherstraße 105

department: Center for Molecular and Cellular Bioengineering (CMCB)

institute: TU Dresden

data_processing:
bcl2fastq: 2.19.1
alignment: Processed fastq files were aligned with the aligner GSNAP (v. 2017-11-15)  to the human reference hg38 from Ensembl with the support of splice site detection which was done with the Ensembl annotation (gtf file) version 87
genecount: Fragments were assigned to Gene with featureCounts (v1.5.3) and Ensembl annotation (gtf file) version 87 was used to find gene regions
Genome_build: hg38
Supplementary_files_format_and_content: bfx1299.genecounts.csv is a tab separated file which is the featureCounts output. The first columns contain gene information such as Ensembl ID, Strand, Length, Start and End. Afterwards the 9 samples are listed

source_name: iPSC-derived motor neurons

growth_protocol: Neurons were cultured in N2B27 medium with 200 μM ascorbic acid, 10 ng/ml BDNF, and 20 ng/ml GDNF, 200 μM dbcAMP, 1 ng/ml TGFβ3

extract_protocol:
Total RNA was isolated using Qiagen RNeasy columns including a column DNase digest
mRNA was isolated from total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions. Final elution was done in 15ul 2x first strand cDNA synthesis buffer (NEBnext, NEB). Samples were then directly subjected to the workflow for strand specific RNA-Seq library preparation (Ultra Directional RNA Library Prep II, NEB). For ligation custom adaptors were used 1: (Adaptor-Oligo 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligaton adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 1:1. Indexing was done during the following PCR enrichment using custom amplification primers carring the i7 index sequence indicated with ‘NNNNNNNN’. (Primer1: AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T, primer2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T. After two more XP beads purifications (1:1) libraries were quantified.

treatment_protocol: not applicable

value: hexanucleotide repeat expansion in intron of C9ORF72 gene as well as a knockout of the start codon in exon 2


title: THP1_CTRL_rep2


title: THP1_LPS_rep1

description: Nascent-RNA profiling with fastGRO was performed in LPS-treated THP1.

treatment_protocol: THP1 cells were treated with 5 µg/ml of LPS.

value: LPS


title: THP1_LPS_rep2


title: Constutive clbR expressing variant

description: total RNA


title: C9KO-1_1


title: C9KO-1_2


title: C9GC-1_3

value: gene corrected (wild type C9ORF72 protein lacking the ALS mutation)


title: C. elegans was grown with Comamonas sp. 12022 3

city: Montreal

first: Orcun

last: Hacariz

state: Quebec

address: 1001 Boul Décarie, Site Glen Pavilion E / Block E. E02.2143

institute: Research Institute of the McGill University Health Centre

data_processing:
The Illumina control software was HCS 2.2.58, the real-time analysis program was RTA v. 1.18.63. Program bcl2fastq v1.8.4 was used to demultiplex samples and generate fastq reads.
Data analysis was carried out using NetworkAnalyst (https://www.networkanalyst.ca)
Read quality was checked with FASTQC (version 0.72) and adapter related sequences were removed using Trim Galore (version 0.4.3.1) (https://www.bioinformatics.babraham.ac.uk/projects/)
The genome sequence of C. elegans and GTF file (Caenorhabditis_elegans.WBcel235.94.gtf) was obtained from ENSEMBL  (https://www.ensembl.org/).
Reads were aligned to the C. elegans genome with HISAT2 (Galaxy version 2.1.0) and read counts were obtained using HTSeq (version 0.9.1) with the intersection-strict mode.
Genome_build: WBcel235.94
Supplementary_files_format_and_content: Raw read counts for genes were obtained using HTSeq

organism: Caenorhabditis elegans

source_name: Whole tissue

growth_protocol: Approximately 200 synchronized L1 of C. elegans were grown to the L4-young adult stage with E. coli OP50 or bacteria of interest (Chryseobacterium sp. CHNTR56 or Comamonas sp. 12022), for 48 hours at 21˚C, as triplicate.

extract_protocol:
The NGM plates containing L4-young adult stage larvae were washed twice with 1X M9 buffer and centrifuged at 1,000 g for 2 minutes.  A total of 200 µl of Trizol (Ambion, USA) was added to the worm pellet. The worm pellet was snap-frozen in liquid nitrogen, which was followed by a quick thaw. These two steps were repeated once.
RNA libraries were prepared with standard Illumina protocols

treatment_protocol: Individual bacterium was seeded on NGM plates and C. elegans was grown on the plates

value: Comamonas sp. 12022

tag: age

value: adult day 1 stage


title: C9GC-1_2


title: C. elegans was grown with Comamonas sp. 12022 2


title: C9GC-1_1


title: C. elegans was grown with Comamonas sp. 12022 1


title: C9-1_3

value: untargetted cells containing hexanucleotide repeat expansion in intron of C9ORF72


title: C. elegans was grown with Chryseobacterium sp. CHNTR56 3

value: Chryseobacterium sp. CHNTR56


title: C9-1_2


title: C. elegans was grown with Chryseobacterium sp. CHNTR56 1


title: C. elegans was grown with Chryseobacterium sp. CHNTR56 2


description:
SUDHL10_UNC1999_Day6_RNAseq Biological Replicate 2
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt

data_processing:
ChIP-seq:bowtie2 version 2.3.4.3. For 150bp paired-end data, reads from the 'Read1' file were trimmed to 75bp and used for further analysis, RNA-seq: STAR aligner version 2.5.3a
ChIP-seq peak calling: SICER v0.0.1
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
scRNA-Seq – reads were processed using Cell Ranger v3.0.2
Genome_build: mm9
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types
Supplementary_files_format_and_content: scRNA-Seq: raw gene-cell count matrix files

source_name: human lymphoma cell line

extract_protocol:
Cultured cells were collected by centrifugation
Total RNA was extracted with TRIzol reagent (Life Technologies) followed by DNase treatment with the RNeasy kit (Qiagen).
TruSeq RNA Sample Preparation Kit V2 (Illumina) was used according to the manufacturer's instructions and 50 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Cells were treated with PRC2 uinhibitors UNC1999 or MAK-683 at 5uM concentration and cells were collected at indicated days

value: lymphoma cell line


title: C9-1_1


title: CCRF-CEM-SLFN11 KO 12h 3

city: Tsuruoka

first: Junko

last: Murai

state: Yamagata

address: 246-2 Kakuganji Mizugami

institute: Keio University

hyb_protocol: Four replicates of each group were hybridized to Affymetrix human Gene ST 2.0 GeneChip (Platform GPL19251) in Affymetrix hybridization oven at 45C, 60rpm for 16 hrs.

scan_protocol: Wash and stain were performed on Affymetrix Fluidics Station 450 and scanned on Affymetrix GeneChip scanner 3000 with AutoLoader.

data_processing: Data were collected using Affymetrix AGCC software. Statistical and clustering analysis was performed with Partek Genomics Suite software using RMA normalization algorithm.  Differentially expressed genes were identified with ANOVA analysis.  Genes that are up- or down-regulated more than 2 fold and with a p<0.001 were considered significant.

source_name: CCRF-CEM-SLFN11 KO treatment for 12h

label_protocol: 100 ng of RNA was reverse transcribed, amplified and sense strand cDNA was fragmented and labeled using Affymetrix’s GeneChip WT Plus Reagent Kit following manufacturer’s suggested protocol.

growth_protocol: All cells were cultured in RPMI1640 medium supplied with 10% FBS

extract_protocol: Total RNA were extracted using TRIzol reagent (Invitrogen), followed by further purification using PureLink RNA Mini Kit (Life Technology) with DNase treatment (Qiagen).

treatment_protocol: Camptothecin (250 nM) or DMSO was added to the medium and cells were incubated for 6 hours or 12 hours

value: leukemia CCRF-CEM

value: camptothecin for 12 hrs

tag: sample type


title: CCRF-CEM-SLFN11 KO 12h 2


title: CCRF-CEM-SLFN11 KO CPT 6h 1

source_name: CCRF-CEM-SLFN11 KO treatment for 6h

value: camptothecin for 6 hrs


title: CCRF-CEM-SLFN11 KO CPT 6h 2


description:
SUDHL10_UNC1999_Day6_RNAseq Biological Replicate 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: C. elegans grown with E. coli OP50 3

value: E. coli OP50


title: CCRF-CEM-SLFN11 KO 3

source_name: CCRF-CEM-SLFN11 KO


title: C. elegans grown with E. coli OP50 2


title: CCRF-CEM-SLFN11 KO CPT 6h 3


description:
SUDHL10_UNC1999_Day5_RNAseq Biological Replicate 2
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: CCRF-CEM-SLFN11 KO CPT 12h 1


title: CCRF-CEM CPT 12h 1

description: SLFN11-proficient parent

source_name: CCRF-CEM CPT treatment for 12h

value: SLFN11-proficient parent


title: DU145-SLFN11KO CPT 12h 2

source_name: DU145-SLFN11KO treatment for 12h

value: prostate DU145


description:
SUDHL10_UNC1999_Day5_RNAseq Biological Replicate 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: DU145-SLFN11KO CPT 12h 1


title: DU145-SLFN11KO CPT 6h 1

source_name: DU145-SLFN11KO treatment for 6h


title: CCRF-CEM CPT 6h 1

description: SLFN11-proficient parent

source_name: CCRF-CEM CPT treatment for 6h


title: CCRF-CEM 3

description: SLFN11-proficient parent

source_name: CCRF-CEM


title: CCRF-CEM 2

description: SLFN11-proficient parent


title: CCRF-CEM CPT 12h 2

description: SLFN11-proficient parent


title: DU145-SLFN11KO CPT 6h 3


title: CCRF-CEM-SLFN11 KO control 1

source_name: CCRF-CEM-SLFN11 KO control


title: CCRF-CEM CPT 6h 2

description: SLFN11-proficient parent


title: DU145-SLFN11KO control 2

source_name: DU145-SLFN11KO control


title: DU145-SLFN11KO control 3


title: DU145-SLFN11KO CPT 12h 3


title: DU145-SLFN11KO CPT 6h 2


title: CCRF-CEM control 1

description: SLFN11-proficient parent

source_name: CCRF-CEM control


description:
SUDHL10_UNC1999_Day3_RNAseq Biological Replicate 2
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: CCRF-CEM CPT 12h 3

description: SLFN11-proficient parent


title: No TAP tag ChIP-exo 5.0 BY4741 Replicate 1

city: State College

first: Chitvan

last: Mittal

state: PA

address: 453 North Frear, University Park

department: BMB

institute: Pennsylvania State University

description: no TAP-tag ChIP-exo 5.0

data_processing:
High-throughput DNA sequencing in paired end mode was performed with Illumina NextSeq 500.
Sequence reads were aligned to the yeast genome (sacCer3) using bwa-mem (v0.7.9a). Reference : https://arxiv.org/pdf/1303.3997.pdf
Aligned reads obtained were filtered to remove PCR duplicates and non-unique alignments.
Genome_build: sacCer3
Supplementary_files_format_and_content: Bedgraph, deduplicated BAM files aligned to sacCer3

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: yeast strains were grown to an O.D600 of ~0.8 at 30°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and Protein-DNA complexes were purified using appropriate antibody.
Libraries were prepared as described in PMID: 30030442

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

value: IgG (Sigma i5006, Lot#SLBM2617V)

tag: cell description

value: GRF88, MATa his4-38, S288C background


title: CCRF-CEM-SLFN11 KO 2


description:
SUDHL10_UNC1999_Day1_RNAseq Biological Replicate 2
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: TAP-Lge1 ChIP-exo 5.0 bre1Δ Replicate 1

description: nTAP-Lge1_bre1D ChIP-exo 5.0


title: Reb1-TAP ChIP-exo 5.0 BY4741 Replicate 1

description: Reb1-TAP ChIP-exo 5.0


title: Ythdc1_cKO_RIP_r1

description: Non-ribosome RNA

data_processing:
Library strategy: MeRIP-seq
Illumina Casava software used for basecalling
Raw reads were trimmed with Trimmomatic-0.38 and aligned to mouse genome (mm10, version M19, 2018-08-30) and spike-in genomes including unmodified control RNA (Cypridina Luciferase) and  m6A methylated control RNA (Gaussia Luciferase) (New England Biolabs) using HISAT (version 2.1.0) with default parameters.
Mapped reads were separated by strands with in-house script and m6A peaks on each strand were called using MACS (version 2) with parameter ‘--nomodel’ and ‘--keep-dup 5’ separately.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited peak locations together with peak summit, pvalue and qvalue reported by MACS2 for each sample.

source_name: Embryonic stem cells

extract_protocol:
Total RNA was isolated from chromatin-associated fraction of mESCs. Non-ribosome RNA was further enriched from total RNA by using RiboMinus transcriptome isolation kit (Invitrogen). 1 μL 1:1000 diluted m6A spike-in from EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610S) was added to 1 μg non-ribosome RNA, followed by fragmentation according to previously published protocols. m6A-IP was performed using EpiMark N6-Methyladenosine Enrichment Kit following the manufacturer’s protocols.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.

value: mouse embryonic stem cells

tag: m6a antibody


title: Ythdc1_cKO_RIP_r2

description: Non-ribosome RNA

value: EpiMark N6-Methyladenosine Enrichment Kit


title: CCRF-CEM CPT 6h 3

description: SLFN11-proficient parent


title: Ythdc1_Control_RIP_r2

description: Non-ribosome RNA


title: Mettl3_KO2_RIP_r2

description: Non-ribosome RNA


description:
SUDHL10_UNC1999_Day1_RNAseq Biological Replicate 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: Ythdc1_Control_RIP_r1

description: Non-ribosome RNA


title: Mettl3_KO2_RIP_r1

description: Non-ribosome RNA


title: Lge1-TAP ChIP-exo 5.0 bre1Δ Replicate 1

description: Lge1-TAP_bre1D ChIP-exo 5.0


title: DU145-SLFN11KO control 1


title: DU145 CPT 12h 3

description: SLFN11-proficient parent

source_name: DU145 CPT treatment for 12h


title: DU145 CPT 12h 1

description: SLFN11-proficient parent


title: SUDHL10_MAK683_Day5_RNAseq Biological Replicate 1

description:
SUDHL10_MAK683_Day5_RNAseq Biological Replication 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: C. elegans grown with E. coli OP50 1


title: DU145 CPT 12h 2

description: SLFN11-proficient parent


title: Mettl3_KO1_RIP_r2

description: Non-ribosome RNA


title: TAP-Lge1 ChIP-exo 5.0 BRE1-WT Replicate 1

description: nTAP-Lge1 ChIP-exo 5.0


title: SUDHL10_MAK683_Day3_RNAseq Biological Replicate 1

description:
SUDHL10_MAK683_Day3_RNAseq Biological Replication 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: Lge1-TAP ChIP-exo 5.0 BRE1-WT Replicate 1

description: Lge1-TAP ChIP-exo 5.0


title: Mettl3_Control_RIP_r1

description: Non-ribosome RNA


title: Mettl3_KO1_RIP_r1

description: Non-ribosome RNA


title: SUDHL10_MAK683_Day1_RNAseq Biological Replicate 1

description:
SUDHL10_MAK683_Day1_RNAseq Biological Replication 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: Ythdc1_cKO_Input_r2

description: Non-ribosome RNA


title: Ythdc1_cKO_Input_r1

description: Non-ribosome RNA


title: Ythdc1_Control_Input_r2

description: Non-ribosome RNA


title: SUDHL10_NonTreated_Day5_RNAseq_Biological Replicate 2

description:
SUDHL10_NonTreated_Day5_RNAseq_Biological Replication 2
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: H2BK123ub ChIP-exo 5.0 BY4741 Replicate 1

description: BY4741_H2BK123ub ChIP-exo 5.0 rep1

value: H2BK123ub (Cell Signaling, Catalogt# 5546s, Lot#5)


title: H2BK123ub ChIP-exo 5.0 BY4741 Replicate 2

description: BY4741_H2BK123ub ChIP-exo 5.0 rep2


title: DU145 control 3

description: SLFN11-proficient parent

source_name: DU145 control


title: DU145 control 1

description: SLFN11-proficient parent


title: SUDHL10_NonTreated_Day5_RNAseq_Biological Replicate 1

description:
SUDHL10_NonTreated_Day5_RNAseq_Biological Replication 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: Ythdc1_Control_Input_r1

description: Non-ribosome RNA


title: DU145 control 2

description: SLFN11-proficient parent


title: Mettl3_KO2_Input_r1

description: Non-ribosome RNA


title: Mettl3_Control_RIP_r2

description: Non-ribosome RNA


title: H2BK123ub ChIP-exo 5.0 WAC-Lge1CC Replicate 2

description: WAC-lge-CC_H2BK123ub ChIP-exo 5.0 rep2


title: SUDHL10_H3K27me3_ChIP

extract_protocol:
Cultured cells were collected by centrifugation
Whole cell lysates were sonicated and incubated with H3K27me3 antibody overnight (Diagenode, C15410003) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Mettl3_KO2_Input_r2

description: Non-ribosome RNA


title: Mettl3_KO1_Input_r2

description: Non-ribosome RNA


title: Mettl3_KO1_Input_r1

description: Non-ribosome RNA


title: SUDHL10_H3K4me3_ChIP

extract_protocol:
Cultured cells were collected by centrifugation
Whole cell lysates were sonicated and incubated with H3K4me3 antibody overnight (Diagenode, C15410003) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Mettl3_Control_Input_r2

description: Non-ribosome RNA


title: H2BK123ub ChIP-exo 5.0 WAC-Lge1CC Replicate 1

description: WAC-lge-CC_H2BK123ub ChIP-exo 5.0 rep1


title: Mettl3_Control_Input_r1

description: Non-ribosome RNA


description:
SUDHL10_UNC1999_Day3_RNAseq Biological Replicate 1
Supplementary file: SUDHL10_RNAseq_Raw_Read_Counts.txt


title: Mettl3_KO2_r2

description: non-ribosome RNA

data_processing:
Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38 and aligned to mouse genome (mm10, version M19, 2018-08-30) and external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with default parameters.
Reads on each GENCODE annotated gene were counted using HTSeq.
Genome_build: mm10
Supplementary_files_format_and_content: Read counts for each gene and each sample.

extract_protocol:
The nuclear fraction was separated and total RNA was purified by Trizol. Before purified non-ribosome RNA with RiboMinus transcriptome isolation kit, ERCC RNA spike-in control (Ambion) was added to each sample (0.1 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.

treatment_protocol: Six 6-cm plates of mESCs were seeded and controlled to afford the same amount of cells. After 48 h, actinomycin D was added to 5 μg ml–1 at 6 h, 3 h, and 0 h before trypsinization collection.

tag: treatment time point (h)

tag: agent

value: actinomycin D


title: LoVo SLAM-seq C6 rep2

first: Jing

last: Wang

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

description: LoVo (male) cells were cultured in DMEM media supplemented with 10% FBS, 1% L-glutamine, and 1% Nonessential amino acids.

source_name: LoVo

value: LoVo

value: 25 uM C6


title: Mettl3_KO2_r1

description: non-ribosome RNA

tag: genotype


title: H2BK123ub ChIP-exo 5.0 LAF1-Lge1CC Replicate 1

description: Laf1-IDR-lge1-CC_H2BK123ub ChIP-exo 5.0 rep1

tag: strain


title: H2BK123ub ChIP-exo 5.0 LGE1-CC Replicate 2

description: lge1-CC_H2BK123ub ChIP-exo 5.0 rep2


title: DU145 CPT 6h 2

description: SLFN11-proficient parent

source_name: DU145 CPT treatment for 6h


title: Mettl3_KO1_r2

description: non-ribosome RNA


title: H2BK123ub ChIP-exo 5.0 LAF1-Lge1CC Replicate 2

description: Laf1-IDR-lge1-CC_H2BK123ub ChIP-exo 5.0 rep2


title: Mettl3_KO1_r1

description: non-ribosome RNA


title: Mettl3_Control_r2

description: non-ribosome RNA


title: LoVo SLAM-seq C6 rep1


title: LoVo SLAM-seq DMSO rep3

value: DMSO


title: Eed_KO_Day21 Adult ISC H3K27me3 ChIP Rep2

description: Eed_KO_Day21 Adult ISC H3K27me3 ChIP Biological Replicate 2

data_processing:
ChIP-seq:bowtie2 version 2.3.4.3. For 150bp paired-end data, reads from the 'Read1' file were trimmed to 75bp and used for further analysis, RNA-seq: STAR aligner version 2.5.3a
ChIP-seq peak calling: SICER v0.0.1
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with raw read counts for all cell types

source_name: mouse ISCs

extract_protocol:
Whole cell lysates were sonicated and incubated with H3K27me3 antibody overnight (EMD Millipore 07-449) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 150 bp paired-end reads were sequenced on an NovoSeq S4 instrument.

value: B6;129 mixed background

value: Adult Epitheial cells; proximal 1/3 of intestine

value: Eed F/F; Lgr5EGFP-IRES-CreERT


title: H2BK123ub ChIP-exo 5.0 LGE1-CC Replicate 1

description: lge1-CC_H2BK123ub ChIP-exo 5.0 rep1


title: Mettl3_Control_r1

description: non-ribosome RNA


title: LoVo SLAM-seq DMSO rep2


title: H2BK123ub ChIP-exo 5.0 Lge1Δ1-80 Replicate 2

description: lge1D1-80_H2BK123ub ChIP-exo 5.0 rep2


title: DU145 CPT 6h 1

description: SLFN11-proficient parent


title: Eed_KO_Day21 Adult ISC H3K27me3 ChIP Rep1

description: Eed_KO_Day21 Adult ISC H3K27me3 ChIP Biological Replicate 1


title: Eed KO Adult Intestinal Crypt H3K27me3  ChIP Rep2

description: Eed KO Adult Intestinal Crypt H3K27me3 ChIP Biological Replicate 2

source_name: mouse intestinal Crypt cells

treatment_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4C. Villi were seperated using 70uM filter and crypt Cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.

value: Eed F/F; Villin-CRE


title: LoVo SLAM-seq C6 rep3


title: WT Adult ISC H3K27me3 ChIP Rep2

description: WT Adult ISC H3K27me3 ChIP Biological Replicate 2

value: Eed +/+; Lgr5EGFP-IRES-CreERT


title: H2BK123ub ChIP-exo 5.0 Lge1Δ1-80 Replicate 1

description: lge1D1-80_H2BK123ub ChIP-exo 5.0 rep1


title: H2BK123ub ChIP-exo 5.0 NLS-Lge1 IDR Replicate 2

description: NLS-lge1-IDR_H2BK123ub ChIP-exo 5.0 rep2


title: WT Adult Intestinal_Villus H3K27me3 ChIP Rep2

description: WT Adult Intestinal Villus H3K27me3 ChIP Biological Replicate 2

source_name: mouse intestinal villus cells

value: Eed +/+; Villin-CRE


title: H2BK123ub ChIP-exo 5.0 NLS-Lge1 IDR Replicate 1

description: NLS-lge1-IDR_H2BK123ub ChIP-exo 5.0 rep1


title: IgG ChIP-exo 5.0 BY4741

description: IgG ChIP-exo 5.0

value: IgG (Sigma, i5006, Lot#SLBM2617V)


title: STARVATION replicate 2

city: Utrecht

first: Wessel

middle: van

last: Leeuwen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Read alignment using STAR 2.4.0.1 with default parameters
Read count calculation using an in-house Python2.7 script (available upon request) using pysam and the Dm6 annotation file
Differential gene expression between the conditions was determined using EdgeR (3.24.3)
Genome_build: Dm6
Supplementary_files_format_and_content: CSV file containing the differential gene expression between STARVED/FED and the read count table

organism: Drosophila melanogaster

source_name: Krebs Ringer Bicarbonate treated sample

extract_protocol:
RNA extraction using Rneasy mini kit (Qiagen)
rRNA depletion using Illumina RiboZero kit and library preparation using Illumina TruSeq Stranded Total RNA library prep kit

value: 4h Krebs Ringer Bicarbonate


title: STARVATION replicate 1


title: Be2C ChIP-seq WDR5 rep2

city: Nashville

description: Be2C (male) cell lines were cultured in RPMI-1640 media with 10% FBS.

extract_protocol:
ChIP-seq assays (performed as described in Weissmiller, et. al. Nat Commun,10, Article number: 2014 (2019)): Briefly, cross-linking was carried out with 0.75% formaldehyde (Sigma-Aldrich; in PBS pH 7.4) at room temperature for 10 minutes. The reaction was quenched with 125 mM glycine for 10 minutes at room temperature, after which cells were washed twice with ice-cold PBS. Nuclei were prepared by incubating cells in Nuclear Lysis Buffer A (1 M HEPES pH 7.9, 1 M KCl, 0.5 M EDTA, 0.4% NP-40, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 5 minutes on ice, after which they were collected by centrifugation. Nuclei were then lysed in Formaldehyde Lysis Buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 1% SDS, PMSF, Na3VO4, and Complete Protease Inhibitor Cocktail) for 15 minutes on ice. Chromatin was sheared by 17–24 minute sonication (BioRuptor UCD-200, Diagenode; on highest setting, alternating between 30 seconds on and 30 seconds off) to yield a mean chromatin size of ~250 bp. After sonication, debris was cleared by centrifugation, and sheared chromatin diluted 10-fold in Formaldehyde Lysis Buffer without SDS. Chromatin from 107 cells was used per immunoprecipitation reaction. Immunoprecipitation reactions were performed with either 0.8 µL of IgG or 4.0 µL of α-WDR5 antibody as indicated. Immune complexes were recovered on Protein A agarose beads (Roche) and washed sequentially with Low Salt Wash buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), High Salt Wash Buffer (20 mM Tris pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail), LiCl Wash buffer (10 mM Tris pH 8.9, 250 mM LiCl, 1 mM EDTA, 1% Triton X-100, PMSF, and Complete Protease Inhibitor Cocktail) and TE (10 mM Tris pH 8.0, 1 mM EDTA, supplemented with PMSF and Complete Protease Inhibitor Cocktail). Protein–DNA complexes were de-crosslinked overnight at 65°C in 50 µL Elution Buffer (10 mM Tris pH 8.0, 1 mM EDTA, 200 mM NaCl, 0.1% SDS, and 20 µg Proteinase K (740506, Clontech).  ---   RNA-seq assays: CHP134 cells were lysed in Trizol (ThermoFisher), after which RNA was isolated using the Direct-zol RNA MiniPrep Kit (Zymo Research) with on-column DNase digestion, following the manufacturer's instructions. RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ.   ---   SLAM-seq assays: Nascent RNA was labeled using the SLAMseq Kinetics Kit–Anabolic Kinetics Module (061, Lexogen).  LoVo cells were pretreated with 25 uM C6, C6nc, or 0.1% DMSO prior to a three hour labeling with 1 mM 4-Thiouridine (S4U). Following the manufacturer's instructions, total RNA was isolated, alkylated with iodoacetamide, flash frozen, and shipped to Lexogen for analysis.
For analysis of ChIP-Seq, de-crosslinked DNA samples from three ChIP reactions were pooled (a total of 3 x 107 cellular equivalents per sample), and DNA purified by phenol-chloroform extraction and recovered by ethanol precipitation. Indexed libraries were then made using the DNA Ultra II Library Prep Kit for Illumina (E7645, New England Biolabs). Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries quantitated using KAPA Library Quantification Kits (KAPA Biosystems). Pooled libraries were subject to 75 bp single sequencing according to the manufacturer’s protocol (Illumina NextSeq500). Sequencing was performed by the Vanderbilt Technologies for Advanced Genomics (VANTAGE) Shared Resource. Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.   ---   RNA-Seq analysis (with rRNA reduction) was performed at GENEWIZ. Library preparation with rRNA depletion and paired-end 150 base pair sequencing on an Illumina HiSeq was performed by GENEWIZ. RNA-Seq for CHP-134 cells was completed with three biological replicates.   ---    For analysis of SLAM-seq: After quality control analyses, libraries were prepared (250 ng RNA per sample) using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following the User Guide (015UG009V0251) recommendations. Sequencing was performed by Lexogen on an Illumina NextSeq 500 system, using the SR75 High Output Kit. The SLAMdunk analysis pipeline (34) was used to analyze SLAMseq sequencing data. SLAM-Seq completed with three biological replicates.

tag: chip antibody

value: Cell Signaling WDR5 (D9E1I)


title: Be2C ChIP-seq WDR5 rep3


title: FED replicate 2

source_name: Schneider's treated sample

value: 4h Schneider's


title: K562_E669Q_CPT1000_4h [K562E669Q-1000]

data_processing:
Raw reads were trimmed using trimmomatic (v0.39).
Trimmed reads were aligned to the hg19 genome version using the bowtie2 (v2.2.6) aligner.
Aligned reads were sorted using samtools (v1.8), duplicate reads were marked with picard-tools (v2.9.2).
ATAC-seq peaks were called using MACS (v2.1.2) with the "--nomodel", "--shift -37" and "--extsize 73" settings, filtering out peaks with >0.01 FDR p--value.
Alignment files were converted to bigwig format using the BAMscale cov (v0.1) program with default settings (genome scaling).
Genome_build: Human - hg19
Supplementary_files_format_and_content: Bigwig coverage track files for visualization were created with BAMscale
Supplementary_files_format_and_content: Narrow peaks were called using MACS peak caller

extract_protocol:
Fifty thousand cells were treated with DMSO or camptothecin for the indicated time. To prepare nuclei, cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately following the nuclei preparation, the pellet was re-suspended in the transposase reaction mix [25 μl 2x TD buffer, 2.5 μl Transposase (Illumina) and 22.5 μl of nuclease free water], and incubated for 30 minutes at 37 °C. Directly following transposition, the sample was purified using a DNA Clean and Concentrator-5 (ZYMO RESEARCH) and eluted with 25 μl of DNA elution buffer. Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermo-cycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. We amplified the full libraries for 5 cycles, after 5 cycles we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Syber Green at a final concentration of 0.6x. We ran this reaction for 20 cycles, to determine the additional number of cycles needed for the remaining 45 μL reaction. Libraries were amplified for a total of 10–12 cycles and purified using a PCRClean DX yielding a final library concentration of ~30 nM in 20 μl.
Illumina Genomic DNA protocol (Illumina Paired-END DNA Sample Prep Kit).

treatment_protocol: Camptothecin or DMSO was added to the medium and cells were incubated for different time

value: Lymphoblast

tag: genotype/variation

value: E669Q SLFN11 overexpression

value: Camtothecin 1000 nM treatment for 4h

tag: molecule subtype

value: PCR amplified DNA


title: H2BK123ub ChIP-exo 5.0 lge1Δ Replicate 2

description: lge1D_H2BK123ub ChIP-exo 5.0 rep2

value: H2BK123ub (Cell Signaling, Catalogt# 5546s, Lot#5)


title: K562_E669Q_control [K562E669Q-0]

tag: cell line

value: DMSO treatment


title: Be2C ChIP-seq WDR5 rep1

tag: treatment


title: FED replicate 1


title: K562_SLFN11_CPT1000_4h [K562SLFN11-1000]

tag: cell type

value: wild-type SLFN11 overexpression


title: Be2C ChIP-seq IgG rep2

value: Cell Signaling IgG (2729S)


title: Eed KO Adult Intestinal Crypt H3K27me3 ChIP Rep1

description: Eed KO Adult Intestinal Crypt H3K27me3 ChIP Biological Replicate 1

treatment_protocol:
Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4C. Villi were seperated using 70uM filter and crypt cells were snap-frozen in liquid nitrogen and used for subsequent ChIP analysis.
Mice were injected with 1-2mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre and recombine conditional alleles.

value: B6;129 mixed background

value: Adult Epitheial cells; proximal 1/3 of intestine


title: K562_SLFN11_control [K562SLFN11-0]


title: Be2C ChIP-seq IgG rep3


title: LoVo SLAM-seq DMSO rep1

value: LoVo

value: DMSO


title: H2BK123ub ChIP-exo 5.0 lge1Δbre1Δ Replicate 1

description: lge1D-bre1D_H2BK123ub ChIP-exo 5.0 rep1

tag: antibody


title: H2BK123ub ChIP-exo 5.0 lge1Δbre1Δ Replicate 2

description: lge1D-bre1D_H2BK123ub ChIP-exo 5.0 rep2


title: Be2C ChIP-seq IgG rep1


title: H2BK123ub ChIP-exo 5.0 lge1Δ Replicate 1

description: lge1D_H2BK123ub ChIP-exo 5.0 rep1


title: RNA-Seq_MCF7_siCTL_E2_rep2

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19

source_name: breast cancer

growth_protocol: MCF7 cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality. RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: MCF7 cells were maintained in stripping medium (phenol red free) for three days before treating with or without estrogen (E2, 10-7 M) for 6h.

value: estrogen+siCTL


title: RNA-Seq_MCF7_siCARM1-1_CTL_rep2

value: ethanol+siRNA


title: RNA-Seq_MCF7_siCARM1-1_E2_rep2

value: estrogen+siRNA


title: K562_vector_CPT1000_4h [K562Vec-1000]

value: vector control


title: H2BK123ub ChIP-exo 5.0 LGE1-WT Replicate 2

description: LGE1-WT_H2BK123ub ChIP-exo 5.0 rep2