title: Young Myeloid-biased HSCs #3

city: Los Angeles

first: Kenneth

last: Dorshkind

state: California

address: 10833 Le Conte Avenue

department: Pathology and Laboratory Medicine

institute: David Geffen School of Medicine at UCLA

description:
Ly_My_HSCs.genesfpkm.txt
MyYou3

data_processing:
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
The STAR ultrafast universal RNA-seq aligner (v2.5.2b) was used to generate the genome index and perform paired-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCm38 primary assembly) and the exon/intron structure of known gene models (Gencode M12 genome annotation). Alignment files were used to generate strand-specific, gene-level count summaries with STAR's built-in gene counter. Differential expression analysis was performed with DESeq2.
Counts were normalized per-sample in units of FPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of FPKMs

source_name: Hematopoietic stem cell

growth_protocol: Young 8-12 week-old C57BL/6 (B6) were obtained from the Jackson Laboratory or the UCLA Division of Laboratory Animal Medicine. Old B6 mice were obtained from the National Institute on Aging colony and were used at 18 months of age. HSCs were resolved using specific combinations of FITC, PE, PerCP/-7 Cy5.5, PECy7, APC efluor780, Pacific Blue, and 605NC conjugated antibodies as previously described (Montecino-Rodriquez et al., 2016). The lineage cocktail included antibodies to CD3a, CD8a, CD45R(B220), CD48, Gr-1, IgM, NK1.1, TCRb, TCRgd, and TER-119. Lineage negative cells were further resolved by labelling with antibodies to CD117 (c-kit), Sca-1, and CD135. All antibodies were obtained from Life Technologies except for IgM (Southern Biotechnolog), CD135 (Biolegend) and CD150 (Biolegend). HSCs were purified using Aria Cell sorters (BD Biosciences) located in the Jonsson Comprehensive Cancer Center flow cytometry core and analyses were performed on an LSRII (BD Biosciences) located in the Broad Stem Cell Research Center flow cytometry core at UCLA. Ly-HSCs and My-HSCs were resolved on the basis of CD150 intensity

extract_protocol:
RNA was extracted using the Zymo Direct-Zol RNA MiniPrep Plus (cat# R2070, Irvine, CA) as per the manufacturer’s instructions. Total RNA was quantified and 260/280 ratios determined using Nanodrop.
RNA sequencing and library preparation was performed by the UCLA Technology Center for Genomics and Bioinformatics using the KAPA Stranded mRNA-seq kit (Roche Sequencing, cat#KK8421, Pleasanton, CA, USA), according to the manufacturer’s instructions. The work flow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on the HiSeq3000 System for a paired-ended 150bp run (Illumina).

value: Female

tag: age

value: 8-10 weeks

tag: cell type

value: Myeloid-biased HSCs


title: Experiment_2_DAF-mut9_2

status: Public on Feb 21 2019

type: SRA

city: Columbus

first: Emily

middle: Rose

last: Theisen

state: OH

address: 700 Childrens Drive

department: Center For Childhood Cancer and Blood Diseases

country: USA

institute: Nationwide Children's Hospital

library_source: transcriptomic

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to hg19 whole genome using STAR-2.5.1b using --outSAMunmapped within and otherwise default
Raw counts were generated for each sample using htseq-count with -t exon -i gene -r pos
Normalized counts were generated using default settings in ComBat.
Differential expression was calculated using default settings and blind = TRUE in DEseq2.
Genome_build: hg19
Supplementary_files_format_and_content: csv; Counts are organized by gene (row) and sample (column); ComBat counts are the raw counts filtered and normalized with ComBat to correct for batch effects; Differential expression contains information for gene (Ensembl ID and HGNC symbol), the base mean expression level, and the log2(FoldChange), stdev(log2(FoldChange)), and the adjusted p-value (Benjamini-Hochberg) for each construct as compared to the iEF samples as reference control.

molecule: total RNA

organism: Homo sapiens

source_name: A673 cells

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) with on-column DNase digestion.  2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq

treatment_protocol: A673 cells were seeded at 50% confluency and left to adhere overnight (day 0). shRNAs were retrovirally delivered on day 1. Selection in 2 µg/mL puromycin (Sigma P8833) occurred on days 2-5. Cells were infected with retrovirus containing the cDNA in the pMSCV-hygro backbone on day 5. Double selection in puromycin and 400 µg/mL hygromycin B (Thermo Fisher 10687010) began on day 6 and continued until day 16. Cells were subsequently harvested for RNA, protein, and seeded for soft agar assays.

tag: cell line

tag: transduced shrna

value: iEF

tag: transduced cdna

tag: replicate


title: Experiment_2_del22_3


title: Young Lymphoid-biased HSCs #2

description:
Ly_My_HSCs.genesfpkm.txt
LyYou2

organism: Mus musculus

tag: strain

tag: Sex

value: Lymphoid-biased HSCs


title: Young Myeloid-biased HSCs #2

description:
Ly_My_HSCs.genesfpkm.txt
MyYou2


title: Young Myeloid-biased HSCs #1

description:
Ly_My_HSCs.genesfpkm.txt
MyYou1


title: Experiment_2_del22_2


title: Young Lymphoid-biased HSCs #3

description:
Ly_My_HSCs.genesfpkm.txt
LyYou3


title: Young Lymphoid-biased HSCs #1

description:
Ly_My_HSCs.genesfpkm.txt
LyYou1


title: Experiment_2_WT-EF_3

value: wildtype EWS/FLI


title: Old Myeloid-biased HSCs #3

description:
Ly_My_HSCs.genesfpkm.txt
MyOld3

value: 18 months


title: Old Myeloid-biased HSCs #2

description:
Ly_My_HSCs.genesfpkm.txt
MyOld2


title: Old Lymphoid-biased HSCs #3

description:
Ly_My_HSCs.genesfpkm.txt
LyOld3


title: Old Lymphoid-biased HSCs #2

description:
Ly_My_HSCs.genesfpkm.txt
LyOld2


title: Experiment_2_WT-EF_2


title: Old Lymphoid-biased HSCs #1

description:
Ly_My_HSCs.genesfpkm.txt
LyOld1


title: Old Myeloid-biased HSCs #1

description:
Ly_My_HSCs.genesfpkm.txt
MyOld1


title: Experiment_2_del22_1


title: Experiment_2_iEF_3

value: empty vector


title: LM-IFNg 8hpt-rep2

type: RNA

city: Shreveport

first: Seong

middle: K

last: Kim

state: Louisiana

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: LSU Health Sciences Center

description: 2_LM-IFN gamma - 8hpt_(Mouse430_2)_2

hyb_protocol: Biotin labeled cRNA are hybridized with Mouse 430 array using Affymetrix Standard Protocol.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Expression Console (Affymetrix) for MAS5 summarization and Quantile normalization.
affymetrix-algorithm-name = mas5
affymetrix-algorithm-version = 1.0
program_name = q_probeset_summarize.exe

label: Biotin

source_name: LM-IFNg_8h post-treatment

label_protocol: Amplified and biotinylated cRNA was generated from total RNA using 3' IVT PLUS kit from (Affymetrix)

growth_protocol: MH-S cells were maintained at 37°C in RPMI-1640 medium supplemented with 100 U/ml of penicillin, 100 mg/ml of streptomycin, 0.05 mM 2-mercaptoethanol, and 10% fetal bovine serum.  L-M cells were maintained at 37°C in complete Eagle’s Minimum Essential Medium (EMEM) supplemented with 100 U/ml of penicillin, 100 mg/ml of streptomycin, nonessential amino acids, and 5% fetal bovine serum.

extract_protocol: Poly(A)+ RNA was isolated from total RNA using the FastTrack 2.0 kit (Invitrogen, San Diego, CA) according to the manufacturer's instructions.

treatment_protocol: MH-S and L-M cells were treated with 0 or 20 ng/ml of murine IFN-γ (Cell Sciences, Canton, MA). The untreated and treated cells were harvested at 8 h post-treatment. Affymetrix microarray analyses were performed with IFN-g-treated and untreated RNA. Untreated RNAs were used as a control.

value: L-M

value: mouse fibroblast

tag: treatment

value: 20 ng/ml of murine IFN-γ


title: LM-mock 8hpt-rep3

description: 3_LM - 8hpt_(Mouse430_2)

source_name: LM-mock_8h post-treatment

value: none (untreated)


title: LM-IFNg 8hpt-rep3

description: 3_LM-IFN gamma - 8hpt_(Mouse430_2)_2


title: Experiment_2_iEF_1


title: LM-mock 8hpt-rep1

description: 1_LM - 8hpt_(Mouse430_2)


title: Experiment_2_WT-EF_1


title: LM-IFNg 8hpt-rep1

description: 1_LM-IFN gamma - 8hpt_(Mouse430_2)_2


title: H-TO-1uM-1

city: Seoul

first: Jiho

last: Jang

address: 50 Yonsei-ro Seodaemoon-gu

department: Department of Physiology

country: South Korea

institute: Yonsei University College of Medicine

hyb_protocol: Following fragmentation, fragmented cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® HT HG-U133+ PM Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The Robust Multiarray Average (RMA) algorithm implemented in Affymetrix Expression Console software (version1.1) was used to normalize the raw data. Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label: biotin

source_name: Human Dermal fibroblast_TO901317_1uM

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® WT Terminal Labeling and Controls Kit P/N 901525 1, Affymetrix).

growth_protocol: Human fibroblasts were cultured in fibroblast medium made up of Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS; GIBCO, Grand Island, NY, USA), 1 mM glutamine (GIBCO), 1% nonessential amino acids (Invitrogen), and penicillin/streptomycin (Invitrogen) as previously described

extract_protocol: The sample preparation was performed according to the instructions and recommendations provided by the manufacturer. Total RNA was isolated using RNeasy Mini Kit columns (Qiagen, Hilden, Germany). RNA quality was assessed by Agilent 2100 Bioanalyzer using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE, USA).

treatment_protocol: Human fibroblasts (HDF, AMN, and CCALD, respectively) were treated with 25-HC (5 or 10 mM) and TO901317 (1 mM) or vehicle (PBS)

value: fibroblast

tag: diagnosis

value: healthy control


title: Experiment_2_iLuc_3

value: iLuc


title: H-con-2

description: Affymetrix GeneChip® HT HG-U133+ PM Array

source_name: Human Dermal fibroblast_control


title: H-25HC-5uM-2

source_name: Human Dermal fibroblast_25HC_5uM


title: H-con-1


title: MHS-IFNg 8hpt-rep2

description: 2_AM-IFN gamma - 8hpt_(Mouse430_2)

source_name: MHS-IFNg_8h post-treatment

value: MH-S

value: Murine alveolar macrophage


title: Experiment_2_iLuc_2


title: Experiment_2_iEF_2


title: H-25HC-5uM-1


title: MHS-IFNg  8hpt-rep3

description: 3_AM-IFN gamma - 8hpt_(Mouse430_2)


title: H-25HC-10uM-2

source_name: Human Dermal fibroblast_25HC_10uM


title: MHS-mock 8hpt-rep3

description: 3_AM - 8hpt_(Mouse430_2)_2

source_name: MHS-mock_8h post-treatment


title: H-25HC-10uM-1


title: H-TO-1uM-2


title: C-TO-1uM-1

source_name: CCALD fibroblast_TO901317_1uM

value: CCALD


title: Experiment_2_iLuc_1


title: LM-mock 8hpt-rep2

description: 2_LM - 8hpt_(Mouse430_2)


title: C-con-2

source_name: CCALD fibroblast_control


title: MHS-IFNg  8hpt-rep1

description: 1_AM-IFN gamma - 8hpt_(Mouse430_2)


title: Vn-LB3-37-3

status: Public on Feb 22 2019

city: BOSTON

first: Henry

middle: Hung-Yi

last: Lee

state: Massachusetts

address: 77 AVENUE LOUIS PASTEUR, NRB 233

department: Genetics

institute: Harvard Medical School

description:
Directional RNASeq
processed data file: SupplementaryTable6_Transcriptome_Analysis.xlsx

data_processing:
Basecalling and demultiplexing via Basespace (Illumina).
Trimmed UMI with cutadapt <= 1.16.
Alignment with bowtie2 2.2.8 to protein-encoding genes from RAST, organism 691.12 (RefSeq NZ_CP009977, NZ_CP009978).
Transcripts were quantified with Salmon 0.8.1 and counts were summarized with tximport for differential expression analysis with DESeq2.
Genome_build: RAST, organism 691.12 (RefSeq NZ_CP009977.1, NZ_CP009978.1)
Supplementary_files_format_and_content: SupplementaryTable6_Transcriptome_Analysis.xlsx: Excel file including differential expression analysis results and salmon analyses results for each sample.

organism: Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

source_name: microbial culture

growth_protocol: Cultures were grown overnight in LB3 or minimal media with glucose at 37C and subcultured 1:1000 (~10E6 cfu/mL) into 25mL of fresh media in a 250mL baffled flask at ~250rpm until OD600 ~0.3-0.5.

extract_protocol:
Samples were resuspended in RNAProtect (Qiagen) and frozen overnight at -80C, RNA extracted with RNeasy (Qiagen) protocol with lysozyme digestion and DNase on column digestion, rRNA depleted with Ribo-Zero rRNA Removal Kit Bacteria (Illumina).
Prepared according to manufacturer's protocol NEXTflexTM Rapid Directional qRNA-SeqTM Kit - 5130-01D.

tag: media


title: MHS-mock 8hpt-rep2

description: 2_AM - 8hpt_(Mouse430_2)_2


title: Experiment_1_DAF_3

value: DAF


title: C-TO-1uM-2


title: Experiment_1_DAF_1


title: MHS-mock  8hpt-rep1

description: 1_AM - 8hpt_(Mouse430_2)


title: Experiment_1_DAF_2


title: Experiment_1_del22_3


title: Experiment_1_del22_1


title: Experiment_1_del22_2


title: C-25HC-5uM-1

source_name: CCALD fibroblast_25HC_5uM


title: TN1035

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

country: Canada

institute: Princess Margaret Cancer Centre

description: Gene expression from patient mcgill.gq.3

hyb_protocol: The fragmented and labeled DNA target was hybridized on GeneChip Human Gene 1.0 ST Array (Affymetrix) and incubated at 450C in the Genechip Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer's instructions (Affymetrix).

scan_protocol: The microarrays were scanned on a GeneChip scanner 3000 (Affymetrix) using the standard Affymetrix protocol.

data_processing: Used Brainarray CDF package (hugene10sthsentrezgcdf_19.0.0)- Duplicate arrays were averaged. For genes with multiple probes, the probe with the highest IQR was chosen.

source_name: Bulk Tumor Tissue

label_protocol: Sense-strand cDNA was synthesized from 250ng of total RNA using the Ambion WT Expression Kit according to the manufacturer instructions (Life Technologies Corporation). The cDNA was fragmented and labeled with the Affymetrix GeneChip WT Terminal Labeling Kit according to manufacturer instructions (Affymetrix)

extract_protocol: RNA was then extracted from these sections using the AllPrep Mini kit (Qiagen). RNA quality was assessed using an Agilent Bioanalyzer

treatment_protocol: All tissues were snap-frozen in O.C.T. Tissue-Tek Compound within 30 minutes of removal.

tag: lymph node

tag: grade

value: III

tag: death

value: no

tag: recurrence

tag: tumor size

tag: patient


title: A-TO-1uM-1

source_name: AMN fibroblast_TO901317_1uM

value: AMN


title: C-con-1


title: fetal hepatocyte, N3KO, ActD 12h

city: Onna

first: Toru

last: Suzuki

state: Okinawa

address: 1919-1 Tancha

country: Japan

institute: Okinawa Instutue of Science and Technology Graduate University

description: Gene expression data from Cnot3KO mouse fetal hepatocytes which were treated actinomycin D for 12h.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with the Robust Multi-array Average algorithm (RMA) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: fetal hepatocytes from Cnot3LKO mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Genetically modified mice are bred in SPF condition.

extract_protocol: Isogen II extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Fetal hepatocytes are prepared from control or Cnot3KO E16.5 embryos and treated with Actinomycin D for 0, 6 or 12h.

tag: tissue

value: fetal hepatocytes

tag: genotype


title: TN1004

description: Gene expression from patient mcgill.gq.5

tag: age


title: fetal hepatocyte, N3KO

description: Gene expression data from Cnot3KO mouse fetal hepatocytes


title: A-25HC-5uM-2

source_name: AMN fibroblast_25HC_5uM

tag: cell type


title: Experiment_1_WT-EF_3

source_name: A673 cells

tag: cell line

tag: transduced shrna

value: iEF

tag: transduced cdna

value: wildtype EWS/FLI


title: fetal hepatocyte, control, ActD 12h

description: Gene expression data from control mouse fetal hepatocytes which were treated actinomycin D for 12h.

source_name: fetal hepatocytes from control mouse

value: wild type


title: A-25HC-5uM-1


title: A-TO-1uM-2


title: A-25HC-10uM-2

source_name: AMN fibroblast_25HC_10uM


title: A-con-2

source_name: AMN fibroblast_control


title: fetal hepatocyte, N3KO, ActD 6h

description: Gene expression data from Cnot3KO mouse fetal hepatocytes which were treated actinomycin D for 6h.


title: A-25HC-10uM-1


title: A-con-1


title: C-25HC-5uM-2


title: fetal hepatocyte, control

description: Gene expression data from control mouse fetal hepatocytes


title: fetal hepatocyte, control, ActD 6h

description: Gene expression data from control mouse fetal hepatocytes which were treated actinomycin D for 6h.


title: Cnot3KO day3-2

source_name: liver from Cnot3KO mouse

treatment_protocol: Livers are picked up from the mice at embryonic day 16.5 or postnatal day 3

value: liver


title: C-25HC-10uM-1

source_name: CCALD fibroblast_25HC_10uM


title: Experiment_1_WT-EF_2

tag: replicate


title: Experiment_1_WT-EF_1


title: Experiment_1_iEF_3

value: empty vector


title: WT_IL-4C, biological rep 2 (pm)

city: Bethesda

first: Anup

last: Dey

address: 9000 Rockville Pike

department: DDB

institute: NIH/NICHD

description: Gene expression data following in-vivo IL-treament

hyb_protocol: Hybridization cocktail was prepared using the hybridization, wash, and stain kit (Affymetrix) applied to array and incubated at 45C for 16 hours.

scan_protocol: Following hybridization arrays was washed and stained using standard Affymetrix procedures before scanning on the Affymetrix GeneChip scanner

data_processing: Data was extracted using Affymetrix Expression console.

source_name: Peritoneal Macrophages

label_protocol: 200ng total RNA first underwent RT step designed to exclude ribosomal RNA. The sense strand cDNA fragmented and labeled using Affymetrix DNA labeleling reagents (Gene Chip expression analysis  technical mannual , Affymetrix)

growth_protocol: Peritoneal cells were isolated using standard protocol. Peritoneal macrophages were purified with MACS column (Mylteni) using  a negative selection method.

extract_protocol: RNA was isolated and purified using RNeasy kit (QIAGEN) following manufacturere's protocol.

treatment_protocol: For ex-vivo activation, purified macrophages were plated in DMEM F12 culture media in the presence 10% FCS. For stimulation in vivo mice were injected with a complex of IL-4 and anti IL-4 antibody on day 0 and 2 (SJ Jenkins et.al Science 332, 1284, 2011), macrophages were isolated on day 4.

tag: strain

tag: genotype/variation

tag: treatment

value: in-vivo IL4-treament

value: PM


title: WT_IL-4C, biological rep 1 (pm)


title: Experiment_1_iEF_2


title: Control day3-2

source_name: liver from wild type mouse


title: Experiment_1_iLuc_3


title: KO_IL-4C, biological rep 2 (pm)

value: Brd4Floxed :LysM-Cre


title: C-25HC-10uM-2

value: fibroblast

tag: diagnosis


title: Control day3-1


title: Experiment_1_iLuc_2

value: iLuc


title: Experiment_1_iLuc_1


title: KO_IFNg+LPS, biological rep 1 (pm)

description: Gene expression data from peritoneal macrophages following ex-vivo treatment of 14h IFNg (100U/ml)+ 4 hours LPS (100ng/ml)

value: IFNg + LPS


title: KO_IL-4, biological rep 2 (pm)

description: Gene expression data from peritoneal macrophages following ex-vivo treatment of IL-4 (10ng/ml) for 4hours

value: ex-vivo treatment of IL-4


title: Cnot3KO day3-1


title: WT_IL-4, biological rep 1 (pm)


title: Cnot3KO E16-1


title: Experiment_1_iEF_1


title: KO_IL-4C, biological rep 1 (pm)


title: WT_IFNg+LPS, biological rep 2 (pm)


title: KO_IL-4, biological rep 1 (pm)


title: Cnot3KO E16-2


title: Control E16-2


title: WT_IL-4, biological rep 2 (pm)


title: HepG2 shSETD2#2 m6a-rep3 (m6A-seq)

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

description:
HepG2_shSetD2#2_m6A-seq_rep1-3_exomePeak_peak.txt
HepG2_shSetD2#2_m6a_rep1-3_peak.bed

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters; then the processed reads were mapped to hg19 whole genome using TopHat v2.1.1 with default parameters
The m6A enriched regions were calculated by using exomePeak with default parameters.
The cutoff for significantly enriched m6A peak: p-value < 1e-5, FDR < 1e-3, fold_enrichment >= 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include exomePeak peak calling results for each Sample

source_name: HepG2 cells

growth_protocol: The human hepatocellular carcinoma cell line HepG2 (ATCC HB-8065) was maintained in EMEM medium (ATCC) supplemented with 10% FBS (Invitrogen, Carlsbad, CA), 2 mM L-Glutamine and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using Direct-zol RNA MiniPrep Kit (Zymo). mRNA was further purified using Dynabeads mRNA DIRECT Kit (Thermo Fisher). mRNA was then sonicated. For IP samples, RNA was subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Lentivirus were produced in HEK293T cells by co-transfecting individual shRNA construct with packaging vectors (pMD2.G, pMDLg/pRRE and pRSV-Rev) into HEK293T cells in 60 mm cell culture dish using X-tremeGENE HP DNA Transfection Reagent (Roche Diagnostics, Grenzach-Wyhlen, Germany). The lentivirus particles were harvested at 48 and 72 hours after transfection and directly added into HepG2 cells with 4 μg/mL polybrene. After two rounds of infection, cells were selected for at least three passages by adding 1 μg/mL puromycin into growth medium.

tag: shRNA

tag: ip antibody

value: m6A antibody (Synaptic Systems, 202003)

tag: replication


title: Control E16-1


title: glp-4_OP50_C

city: Houston

first: Natalia

middle: V

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

institute: Rice University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data were analyzed with GC-RMA in the R programming language, using the Bioconductor package gcrma. Analysis was performed using default settings.

organism: Caenorhabditis elegans

source_name: glp-4, OP50, NGM (agar), 60h

label_protocol: Affymetrix standard protocol

growth_protocol: glp-4 worms were synchronized by hypochlorite treatment. Arrested L1s were plated on 10 cm NGM plates seeded with E. coli OP50 or E. coli HT115 and grown at 15°C overnight then shifted to 25°C for 44h until they reached sterile young adult stage.

extract_protocol: RNA was extracted using TRI Reagent (Molecular Research Center) according to manufacturer's instructions and purified using an RNeasy column (Qiagen).

treatment_protocol: Animals were grown until young adult stage. No additional treatment (except different E. coli food source) was performed

tag: media

value: NGM, E. coli OP50

value: Whole organism


title: Liver, CNOT3KO mouse 4w 2

description: Cnot3KO 4w 2

source_name: liver from CNOT3KO mouse

treatment_protocol: Livers are picked up from the mice 4 weeks after birth

tag: strain background

value: 4 weeks after birth


title: KO_IFNg, biological rep 2 (pm)

description: Gene expression data from peritoneal macrophages following ex-vivo treatment of  IFNg (100U/ml) for 14hours

value: ex-vivo treatment of  IFNg


title: glp-4_HT115_B

source_name: glp-4, HT115, NGM (agar), 60h

value: NGM, E. coli HT115

tag: tissue


title: WT_IFNg+LPS, biological rep 1 (pm)


title: glp-4_HT115_A


title: HepG2 shSETD2#2 m6a-rep2 (m6A-seq)


title: glp-4_OP50_B


title: HepG2 shSETD2#2 input-rep3 (m6A-seq)


title: glp-4_HT115_C


title: WT_IFNg, biological rep 2 (pm)


title: Liver, CNOT3KO mouse 4w 1

description: Cnot3KO 4w 1


title: KO_IFNg, biological rep 1 (pm)


title: HepG2 shSETD2#2 input-rep2 (m6A-seq)


title: WT_IFNg, biological rep 1 (pm)


title: sample.kidney_28_3months

city: Lugano

first: Pietro

middle: Ernesto

last: Cippa

address: Via Tesserete 46

department: Nephrology

country: Switzerland

institute: Ente Ospedaliero Cantonale

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GTATTTG
all.gene_RPKM.txt
all.gene_counts.txt

data_processing:
Reads were aligned to the Ensemble top-level assemby with STAR, version 2.0.4b
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Transcript counts were produced by Sailfish version 0.6.3
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Gene-level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.

source_name: Kidney allograft biopsy

extract_protocol:
Clontech SMARTer
Clontech SMARTer

tag: patient

value: Patient #28

tag: time point

value: 3 months


title: sample.kidney_29_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/ACTCCAA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #29

value: post


title: sample.kidney_28_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CTGGTGG
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: sample.kidney_29_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TCGAGAT
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2 shSETD2#2 m6a-rep1 (m6A-seq)


title: KO_NT, biological rep 2 (pm)

description: Gene expression data from unstimulated Peritoneal macrophages

value: control

tag: cell type

value: PM


title: glp-4_OP50_A


title: Liver, WT mouse 4w 2

description: Control 4w 2

value: wild type

tag: age

value: liver


title: KO_NT, biological rep 1 (pm)

value: Brd4Floxed :LysM-Cre


title: Liver, CNOT3KO mouse 3

description: Cnot3KO 1w 3

treatment_protocol: Livers are picked up from the mice 1 week after birth

value: 1 week after birth


title: sample.kidney_30_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/ACCTGAA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #30

value: pre


title: sample.kidney_29_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GACACAG
all.gene_RPKM.txt
all.gene_counts.txt


title: Liver, CNOT3KO mouse 4

description: Cnot3KO 1w 4


title: HepG2 shCtrl (for shSETD2#2) m6a-rep3 (m6A-seq)

description:
HepG2_shCont#2_m6A-seq_rep1-3_exomePeak_peak.txt
HepG2_shCont#2_m6a_rep1-3_peak.bed

tag: cell line

value: Non-specific control

value: m6A antibody (Synaptic Systems, 202003)


title: Liver, WT mouse 4w 1

description: Control 4w 1

value: 4 weeks after birth


title: WT_NT, biological rep 1 (pm)


title: Liver, CNOT3KO mouse 1

description: Cnot3KO 1w 1


title: HepG2 shCtrl (for shSETD2#2) m6a-rep2 (m6A-seq)


title: sample.kidney_30_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TGGTCTC
all.gene_RPKM.txt
all.gene_counts.txt


title: sample.kidney_30_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TACTCTA
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2 shSETD2#2 input-rep1 (m6A-seq)


title: WT_NT, biological rep 2 (pm)


title: sample.kidney_30_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GAGTACG
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2 shCtrl (for shSETD2#2) input-rep3 (m6A-seq)


title: Liver, WT mouse 4

description: Control 1w 4


title: KO_IL-4, biological rep 2 (bmdm)

description: Gene expression data from 4 hours IL-4 (10ng/ml) treated macrophages

source_name: Bone marrow derived Macrophages

label_protocol: 200ng total RNA first underwent RT step designed to exclude ribosomal RNA. The sense strand cDNA fragmented and labeled using Affymetrix DNA labeleling reagents (Gene Chip expression analysis technical mannual , Affymetrix)

growth_protocol: Bone marrow cells were cultured in DMEM F12 media with 10% FCS and 20% L929 culture supernatant for 7 days. To maintain optimum growth on day 3 old culture media was replaced with fresh media.

value: BMDM


title: WT_IL-4, biological rep 2 (bmdm)


title: HepG2 shCtrl (for shSETD2#2) input-rep2 (m6A-seq)


title: sample.kidney_31_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TGCCCAT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #31


title: KO_IL-4, biological rep 1 (bmdm)


title: Liver, WT mouse 3

description: Control 1w 3


title: Liver, WT mouse 2

description: Control 1w 2


title: sample.kidney_31_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TGTGCCA
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2 shCtrl (for shSETD2#2) input-rep1 (m6A-seq)


title: WT_IL-4, biological rep 1 (bmdm)


title: LSD1 ChIP non Wnt-Treated

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

institute: Insititut de Recherches Cliniques

library_source: genomic

data_processing:
ChIP-Seq reads were aligned to hg19 using Bowtie2 v2.10
Reads were processed and duplicates were removed using Samtools and a genome coverage file was generated for each sample using Bedtools
Peaks were called from the aligned reads using macs2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: .bw files with normalized read scores of genomic coverage; peak files

molecule: genomic DNA

source_name: K562 Cells

extract_protocol:
Cells were fixed with 1% formaldehyde. Cell lysis was performed using the following buffers: total cell lysis - 5mM PIPES pH 8, 85mM KCl, 0.5% NP-40, 1X protease inhibitor cocktail, 1mM PMSF, and nuclear lysis – 50mM Tris, 10mM EDTA, 1% SDS, 1X protease inhibitor cocktail, 1mM PMSF. After sonication (Covaris E220 sonicator), immunoprecipitation was performed using Protein A/G Dynabeads (Life Technologies)
For ChIP-Seq experiments, sequencing libraries were prepared from immunoprecipitated chromatin using the TruSeq DNA kit from Illumina according to the manufacturer’s instructions and sequenced using the TruSeq PE Clusterkit v3-cBot-HS. For RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS

value: K562 Cells

tag: gender

value: Female

value: Bone Marrow

tag: disease

value: Chronic Myelogenous Leukemia

tag: antibody

tag: agent


title: LSD1 ChIP Wnt-Treated


title: HepG2 shSETD2 Ribo rep2 (Ribo-seq)

description:
HepG2_ribosome-profiling_featureCount_results.txt
HepG2_shSETD2#1_RiboDiff_Differential_Translation_Efficiency.txt

data_processing:
Library strategy: Ribo-seq
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters.
cutadapt v1.13 was used for removing adapters and poly(A) oligos with commands:cutadapt -q 30 -a AGATCGGAAGAGCACACGTCT -u 3 --minimum-length 10
Then the processed reads were mapped to hg19 whole genome using Bowtie v1.1.2 with following parameters: -v 2 -m 20 --best --strata
After mapping to the genome, we used RiboDiff v0.2.1 to calculate the differential translation efficiency of genes.
Genome_build: hg19
Supplementary_files_format_and_content: txt files include running results of featureCounts and RiboDiff

extract_protocol:
For each replicate, 1x107 cells were used and 1 mL lysis buffer (20 mM HEPES pH 7.6, 100 mM KCl, 5 mM MgCl2, 100 μg/ml cycloheximide, 1% Triton X-100) was added supplemented with 1:100 protease inhibitor (Roche), 40 U/mL SUPERNase inhibitor (Ambion). Cells were resuspended and the mixture was rotated at 4 ˚C for 15 min. After centrifuge at 14,000 rpm for 15 min, the supernatant was collected and 8 μL Turbo DNase (Invitrogen) was added. 20% of the lysate was saved as input, from which total RNA and mRNA were isolated. 40 µL 10× MNase buffer and 3 µL MNase (NEB) were added to the rest 80% of the lysate and the mixture was incubated at room temperature for 15 min before 8 µL SUPERNase inhibitor was added. The mixture was then loaded onto a 10/50% (w/v) sucrose gradient prepared in a lysis buffer without Triton X-100 and centrifuged at 4 ˚C for 3 h at 27,500 rpm. The sample was then fractioned and analyzed by Gradient Station (BioCamp) equipped with ECONO UV monitor (BioRad) and fraction collector (Gilson, FC203B). The fractions corresponding to 80S monosome were collected. RNA were isolated from the collected fractions and rRNAs were removed by using RiboMinus Eukaryote kit (Invitrogen). rRNA-depleted RNA was separated on a 15% TBE-Urea gel and the gel band between 20-30 nt was cut. RNA was recovered from the gel by elution buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.1 U/mL SUPERNase inhibitor) by rotating at 4 ˚C overnight and the RNA was purified from the eluent by EtOH precipitation. For input, mRNA was fragmented by using 1× PNK buffer (NEB) by heating at 94 ˚C for 25 min. RNA were then subjected to end repair using T4 PNK (NEB) according to manufacturer’s protocol and then purified by the RNA Clean and Concentrator kit (Zymo).
Libraries were constructed using the NEBNext small RNA library prep kit (E7330S) and sequenced on illumina Hiseq4000.

treatment_protocol: Lentivirus were produced in HEK293T cells by co-transfecting individual shRNA construct with packing vectors (pMD2.G, pMDLg/pRRE and pRSV-Rev) into HEK293T cells in 60 mm cell culture dish using X-tremeGENE HP DNA Transfection Reagent (Roche Diagnostics, Grenzach-Wyhlen, Germany). The lentivirus particles were harvested at 48 and 72 hours after transfection and directly added into HepG2 cells with 4 μg/mL polybrene. After two rounds of infection, cells were selected for at least two passages by adding 1 μg/mL puromycin into growth medium. Cells were grown at around 70% confluence and treated with 100 ug/mL cycloheximide (Sigma) at 37 ˚C for 7 min before collection.

tag: fraction

value: 80S monosome


title: Liver, CNOT3KO mouse 2

description: Cnot3KO 1w 2

tag: genotype/variation


title: sample.kidney_31_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CATTTAG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: Beta-Catenin ChIP Wnt-Treated

value: Beta-Catenin


title: HepG2 shSETD2 Ribo rep1 (Ribo-seq)

tag: shRNA


title: Liver, WT mouse 1

description: Control 1w 1

value: wild type

value: liver


title: Beta-Catenin ChIP non Wnt-Treated


title: sample.kidney_32_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CCAGGCA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #32


title: KO_IFNg+LPS, biological rep 2 (bmdm)

description: Gene expression data from 14h IFNg (100U/ml) + 4 hours LPS (100ng/ml) treated macrophages

tag: strain

value: Brd4Floxed :LysM-Cre

tag: treatment

value: IFNg + LPS


title: WT_IFNg+LPS, biological rep 2 (bmdm)


title: HepG2 shMETTL14 Ribo rep2 (Ribo-seq)

description:
HepG2_ribosome-profiling_featureCount_results.txt
HepG2_shMETTL14_RiboDiff_Differential_Translation_Efficiency.txt


title: WT_IFNg+LPS, biological rep 1 (bmdm)


title: HepG2 shCtrl (for shSETD2#2) m6a-rep1 (m6A-seq)

value: Non-specific control

tag: ip antibody

tag: replication


title: KO_IFNg+LPS, biological rep 1 (bmdm)


title: HepG2 shMETTL14 Ribo rep1 (Ribo-seq)


title: sample.kidney_32_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TTCGCTG
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: Gfi1b ChIP non Wnt-Treated

tag: tissue


title: sample.kidney_32_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AGACTGA
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient


title: sample.kidney_32_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/ACAGATA
all.gene_RPKM.txt
all.gene_counts.txt

tag: time point

value: 1 year


title: sample.kidney_31_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AGGACCT
all.gene_RPKM.txt
all.gene_counts.txt


title: KO_LPS, biological rep 1 (bmdm)

description: Gene expression data from 4 hours LPS (100ng/ml) treated macrophages

value: LPS

tag: cell type

value: BMDM


title: sample.kidney_33_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AAACCTT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #33

value: pre


title: H3K9me2 ChIP Wnt-Treated

data_processing:
ChIP-Seq reads were aligned to hg19 using Bowtie2 v2.10
Reads were processed and duplicates were removed using Samtools and a genome coverage file was generated for each sample using Bedtools
Genome_build: hg19
Supplementary_files_format_and_content: .bw files contain normalized read scores of genomic coverage

value: K562 Cells

value: Female

value: Bone Marrow


title: Input non Wnt-Treated

value: Chronic Myelogenous Leukemia

value: none, Input


title: HepG2 shCtrl Ribo rep2 (Ribo-seq)

description: HepG2_ribosome-profiling_featureCount_results.txt

value: Non specific control

value: 80S monosome


title: HepG2 shCtrl Ribo rep1 (Ribo-seq)


title: WT_LPS, biological rep 2 (bmdm)


title: HepG2 shSETD2 input rep2 (Ribo-seq)

value: input


title: Gfi1b ChIP Wnt-Treated


title: KO_IFNg+LPS, biological rep 2 (pm)

description: Gene expression data from peritoneal macrophages following ex-vivo treatment of 14h IFNg (100U/ml)+ 4 hours LPS (100ng/ml)

value: Brd4Floxed :LysM-Cre

value: PM


title: HepG2 shSETD2 input rep1 (Ribo-seq)


title: WT_LPS, biological rep 1 (bmdm)


title: sample.kidney_33_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AACGGAG
all.gene_RPKM.txt
all.gene_counts.txt


title: KO_IFNg, biological rep 2 (bmdm)

description: Gene expression data from 14 hours IFNg (100U/ml) treated macrophages

value: IFNg


title: sample.kidney_33_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TCCGGGA
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: Input Wnt-Treated


title: H3K4me1 ChIP Wnt-Treated


title: sample.kidney_33_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TTTTCGG
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: HepG2 shMETTL14 input rep1 (Ribo-seq)


title: HepG2 shCtrl input rep2 (Ribo-seq)


title: WT_IFNg, biological rep 2 (bmdm)


title: KO_IFNg, biological rep 1 (bmdm)


title: sample.kidney_34_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TTTCAGA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #34


title: HepG2 shCtrl input rep1 (Ribo-seq)


title: H3K9me2 ChIP non Wnt-Treated


title: sample.kidney_34_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TATCTTA
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: WT_IFNg, biological rep 1 (bmdm)

value: BMDM


title: HepG2 shMETTL14 input rep2 (Ribo-seq)


title: H3 ChIP non Wnt-Treated


title: sample.kidney_34_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CTTGGAA
all.gene_RPKM.txt
all.gene_counts.txt


title: HA-METTL14 rep2 (PAR-CLIP)

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters.
cutadapt v1.13 was used for removing adapters with following parameters: -q 30 -a AGATCGGAAGAGCACACGTCT --minimum-length 10
Then the processed reads were mapped to hg19 whole genome using Bowtie v1.1.2 with following parameters: -v 2 -m 20 --best --strata
After mapping to the genome, we scanned the cross-linking sites with T-C mutation to identify the binding sites of METTL14
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain identified binding sites of METTL14

extract_protocol:
Cells were then harvested and lysed in lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.5% NP-40, 0.5 mM DTT) supplemented with proteinase inhibitors. The lysate was cleared by centrifuge and filter, and was then digested by using 0.2 U/µL RNase T1 at 22 ˚C for 15 min. The reaction was quenched by incubating on ice for 5 min followed by incubating with 30 µL pre-washed HA-beads (88836, Thermo Fisher Scientific) at 4 ˚C for 4 h. Beads were then collected and washed 3 times with wash buffer (50 mM HEPS, pH 7.5, 300 mM NaCl, 0.05% NP-40) supplemented with proteinase inhibitor. 50 µL wash buffer was used to resuspend the beads and the RNA was further digested by using 10 U/µL RNase T1 at 22 ˚C for 6 min. Beads were washed with high salt wash buffer (50 mM Tris-HCl pH 7.4, 500 mM NaCl, 0.05% NP-40) 3 times and end repair was performed by using T4 PNK (M0201S, NEB) according to manufacturer’s protocol. RNA was then released by incubating beads in 100 µL proteinase K buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 0.5% SDS) supplemented with 2 mg/mL proteinase K (Invitrogen, 25530049) and SUPERNase inhibitor at 55 ˚C for 20 min. RNA was extracted by phenol:chloroform, recovered by EtOH precipitation.
Libraries were constructed using NEBNext small RNA library prep kit (E7330S) and sequenced on illumina Hiseq4000.

treatment_protocol: For overexpression, PLJM1 vectors with METTL14 cDNA fused with HA-tag at N-terminal and EGFP at C-terminal, along with 2nd generation packaging vectors (pMD2.G and psPAX2), were co-transfected into HEK293T cells using X-tremeGENE HP DNA Transfection Reagent. The lentivirus particles were harvested at 48 and 72 hours after transfection and were used for infection of target cells with the supplement polybrene. After two rounds of infection, cells were selected with 1 μg/ml puromycin. GFP-high cells were then sorted by flow cytometry to make sure that the stable cells have relatively high expression of METTL14. HepG2 cells with HA-tagged METTL14 were treated with 200 µM of 4-thiouridine for 16 h before subjected to UV crosslinking (365 nm, 0.15 J/cm2) at 4 ˚C for 3 times.


title: H3 ChIP Wnt-Treated


title: sample.kidney_34_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CTCAATG
all.gene_RPKM.txt
all.gene_counts.txt


title: KO_NT, biological rep 2 (bmdm)

description: Gene expression data from unstimulated macrophages

value: control


title: KO_NT, biological rep 1 (bmdm)


title: HA-METTL14 rep1 (PAR-CLIP)


title: HepG2 shSETD2#2 rep3 (m6A-seq)

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters.
cutadapt v1.13 was used for removing adapters and poly(A) oligos with commands:cutadapt -q 30 -a AGATCGGAAGAGCACACGTCT -u 3 --minimum-length 10, cutadapt -q 30 -a "A{50}" --minimum-length 10
Then the processed reads were mapped to hg19 whole genome using Bowtie v1.1.2 with following parameters: -v 2 -m 20 --best --strata
After mapping to the genome, we used m6A motif “RRAC” to scan the cross-linking sites with C-T mutation to identify the m6A sites at single nucleotide resolution
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain identified m6A site

value: replication 3


title: WT_NT, biological rep 2 (bmdm)


title: Input lin37 26C rep2

city: Milwaukee

first: Lisa

middle: N.

last: Petrella

state: WI

address: 1428 W. Clybourn St

department: Biological Sciences

institute: Marquette University

data_processing:
Raw sequence reads from the Illumina HiSeq (50 bp single-end read sequencing for ChIP-seq) were mapped to the C. elegans genome (Wormbase version WS220) using Bowtie 1.1.2 with default settings.
MACS2 was used to call peaks and to create bedgraph files. The broad peak option was used for H3K9me2. The statistical cutoff q=0.01 was used. Further options used were -g ce --bdg —keep-dup=auto.
Custom scripts were used to scale bedgraph files to the same number of total reads (number depended on the histone mark).
Genome_build: ws220 (ce10)
Supplementary_files_format_and_content: bedgraph file for genome browser containing scaled read coverage
Supplementary_files_format_and_content: narrowPeak or broadPeak file with peak calls as determined by MACS2

source_name: Input lin37 26C

growth_protocol: Synchronized N2 or mutant L1s from standard NGM plates were washed off of plates and grown in standard S-basal media liquid culture with HB101 as a food source at 20°C until there were gravid adults. Adult worms were treated with standard bleaching solution to collect embryos, and embryos were incubated for 14 hours in S-basal without food to acquire synchronized L1s.  For 20°C samples F1 synchronized N2 or mutant L1s were grown in standard S-basal media liquid culture with HB101 as a food source at 20°C until there were gravid adult, they were bleached, and the resulting embryos were grown for 14 hours until all L1s then frozen in liquid nitrogen.  For 26°C samples F1 synchronized N2 or mutant L1s were grown in standard S-basal media liquid culture with HB101 as a food source at 20°C until the L4 larval stage at which point the culture was shifted to 26°C and grown until there were gravid adults.  The adults were bleached and the resulting embryos were grown for 14 hours at 26°C until all L1s then frozen in liquid nitrogen

extract_protocol:
Crosslinked samples were resuspended in FA buffer, and sonicated in a Diagenode Bioruptor (60 pulses of 30 seconds at full power with 1 minute rest in between).  Extracts were clarified and protein concentrations determined using a Bradford reagents.  Histone modifications were individually IPed using 1 μg appropriate antibodies on prepared lysates. ChIPs were performed with 0.5 mg of extract, and 2% of the extract was set aside for an input reference control.  Two methods were used for ChIP, see Sample section above to match with sample.  Method 1: ChIPs were incubated overnight at 4°C with 1% sarkosyl. Mouse IgG Dynabeads equilibrated in 100 μL FA buffer were added and incubated for 2 hours at 4°C. ChIPs were washed with the following buffers: twice with FA buffer, once with FA buffer containing 1 M NaCl, once with FA buffer containing 0.5 M NaCl, once with TEL buffer (10 mM Tris-HCl pH 8.0, 0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). 2 elutions of 150 μL elution buffer containing TE plus 1% SDS and 250 mM NaCl were incubated at 65°C. Eluted ChIP and input samples were incubated with RNAse One for 30 min at 37°C and then proteinase K for 1 hour at 55°C. Crosslinks were reversed overnight at 65°C. DNA was purified using a Qiagen PCR clean-up column and eluted in 25 μl of water.  Method 2: ChIPs were performed using an IP-Star Compact Automated System (Diagenode) according to the manufacturers’ instructions with the following settings and reagents: the “indirect method” was used with 100 μL reaction, 80 μL Mouse IgG Dynabeads equilibrated in FA buffer; IP for 12 hr, bead incubation for 2 hr; 10 minute washes at middle speed with FA buffer containing 1 M NaCl, FA buffer containing 0.5M NaCl, TEL buffer, and TE buffer. Samples were eluted in 100 μL Elution Buffer. Eluted samples were incubated with RNAse One for 30 min at 37°C and then proteinase K for 1 hour at 55°C. Crosslinks were reversed overnight at 65°C. DNA was purified by phenol chloroform extraction, ETOH precipitated, and DNA resuspended in 20 μl of water.
Two methods were used for library construction, see Characteristics section.  Method 1: Both ChIP and input DNA samples had the ends blunted and phosphorylated with KlenowDNAP, T4 DNAP, and T4 PNK. 3’-dA overhangs are then added with Klenow Fragment (3’ to 5’exo minus), and Illumina adapters were subsequently ligated to the ends. Next, PCR amplification was performed using Illumina primers, for a total of 16 cycles. Amplified DNA libraries were size-selected on a 2% agarose gel so that fragments sized between 250-350bp were obtained; gel extraction was carried out at room temperature. Method 2: The NEBNext Ultra DNA library Prep Kit (NEB) was used following the manufacturers’ instructions.  1 ng of starting DNA was used, adapters were diluted 1:40, and AMPure beads were used for size selection before amplification to enrich for fragments corresponding to a 200 bp insert size.

treatment_protocol: Frozen late L1s were ground using a mortar and pestle with liquid nitrogen.  The resulting worm powder was resuspended in FA buffer and crosslinked for 10 minutes in 1% formaldehyde.

tag: developmental stage

tag: genotype

tag: temperature

tag: chip antibody

value: Method 1


title: sample.kidney_35_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/ACCATAC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #35

value: pre


title: HepG2 shSETD2#2 rep2 (m6A-seq)

tag: cell line

value: replication 2


title: sample.kidney_35_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GATAGTT
all.gene_RPKM.txt
all.gene_counts.txt


title: Input lin37 26C rep1


title: WT_NT, biological rep 1 (bmdm)


title: H3K4me1 ChIP non Wnt-Treated

value: K562 Cells

tag: gender

value: Female

value: Bone Marrow

tag: disease

value: Chronic Myelogenous Leukemia

tag: antibody

tag: agent


title: sample.kidney_35_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CGAAAGT
all.gene_RPKM.txt
all.gene_counts.txt


title: Input lin37 20C rep3

source_name: Input lin37 20C

value: Method 2


title: HepG2 shSETD2#2 rep1 (m6A-seq)

tag: shRNA

value: replication 1


title: HepG2 shSETD2#1 rep3 (m6A-seq)


title: Input lin37 20C rep2


title: sample.kidney_35_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CAGAGTC
all.gene_RPKM.txt
all.gene_counts.txt


title: non_TFH_Adult_day_10_rep3

city: São Paulo

first: Frederico

middle: Moraes

last: Ferreira

state: SP

address: Av. Dr. Arnaldo, 455

department: Clinical Medicine Department

country: Brazil

institute: University of São Paulo

hyb_protocol: twelve microarray datasets obtained from  hybridization of murine RNAs on Agilent Whole Mouse Genome Oligo Microarrays 8x60K.

scan_protocol: Arrays were scanned with the Agilent microarray scanner system G2505C

data_processing: Raw intensities were extracted with Feature Extraction v10.6 software (detection p-value >0.01),   Integrated, background corrected and log transformed.

label_protocol: Cy3 labeled cRNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays 8x60K (design ID 028005) using Agilent’s recommended hybridization chamber and oven.

growth_protocol: TFH cell populations were sorted at day 10 by flow cytometry, with 3 different sorts per age group performed on different days, pooling inguinal draining LNs of 5 or 16 mice each day for adult or 1wk-old mice, respectively.

extract_protocol: The RNA was isolated from murine T cell samples (subpopulations TFH and non-TFH) of young and adult animals. Quality verification and microarray analysis were performed at Miltenyi (Germany).

treatment_protocol: 1wk-old and adult C57BL/6 mice were immunized with TT/AlOH for comparative transcription profile analysis of TFH and non-TFH cells

tag: strain

tag: age

value: Adult day 10

value: non-TFH


title: sample.kidney_36_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/ACTGGAT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #36


title: non_TFH_Adult_day_10_rep1


title: HepG2 shSETD2#1 rep2 (m6A-seq)

tag: replication


title: non_TFH_1wk_day_10_rep3

value: 1wk day 10


title: sample.kidney_36_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CTCACCC
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: Input lin35 26C rep2

source_name: Input lin35 26C


title: Input lin37 20C rep1


title: sample.kidney_36_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CCGATTA
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: HepG2 shCtrl rep3 (m6A-seq)

value: Non-specific control

value: replication 3


title: HepG2 shCtrl rep2 (m6A-seq)


title: sample.kidney_36_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AAATGCA
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: Input lin35 26C rep1

value: Method 1


title: Input lin35 20C rep1

source_name: Input lin35 20C


title: Input lin35 20C rep2


title: HepG2 shCtrl rep1 (m6A-seq)


title: non_TFH_1wk_day_10_rep2


title: T47D_MK2206_resistant

city: Lexington

first: Binhua

middle: P

last: Zhou

state: KY

address: 789 South Limestone

department: Markey Cancer Center/Biochemistry

institute: University of Kentucky School of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC genome hg38 using Hisat2 (version 2.1.0) with default parameters.
Read counts were generated using featureCounts (versoin 1.6.0) with "--ignoreDup -M -O --fraction  -t exon" options and annotations from GENCODE Release 28 were used.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

growth_protocol: Breast cancer cell line BT474 cells were grown in DMEM/F-12 medium plus 10% FBS and T47D cells were grown in PRMI-1640 plus 10% FBS.

extract_protocol:
Total RNA was extracted with PureLink® RNA Mini Kit (Thermo Fisher), followed by on-column DNase digestion.
Poly(A) RNA was enriched using NEBNext® Poly(A) mRNA Magnetic Isolation Module and libraries were NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (cat# E7765S).

treatment_protocol: MK2206-resistant cancer cells were obtained by stepwise increased concentrations of MK2206. Whenever we subcultured, the cells were incubated with gradual increasing concentration of MK2206 for 2 days. Some aliquots of the cells were stored whenever we subcultured it. Cells that grew at the maximum concentration (20 μM) of MK2206 were used for RNAseq.

value: Breast cancer cell line

tag: genotype/variation

value: MK2206 resistant


title: sample.kidney_37_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GGTGAAT
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient

value: Patient #37


title: HepG2 shSETD2#1 rep1 (m6A-seq)


title: non_TFH_1wk_day_10_rep1


title: non_TFH_Adult_day_10_rep2


title: Input lin15B 26C rep3

source_name: Input lin15B 26C


title: TFH_Adult_day_10_rep2

value: Follicular T helper (T FH ) cells


title: TFH_1wk_day_10_rep2


title: TFH_Adult_day_10_rep1


title: TFH_1wk_day_10_rep3


title: TFH_Adult_day_10_rep3


title: sample.kidney_37_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GCCTCCC
all.gene_RPKM.txt
all.gene_counts.txt

tag: time point


title: sample.kidney_37_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GTATCCT
all.gene_RPKM.txt
all.gene_counts.txt


title: BT474_MK2206_resistant

tag: cell type


title: TFH_1wk_day_10_rep1


title: CHMP3

city: shanghai

first: haomin

last: cui

address: 600 Yishan Road

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People’s  Hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 16 nt.
The clean reads were compared to the miRbase version 21 and Rfam database  to identify known miRNA and other non-coding RNAs.
The raw count for known miRNAs  were summarized and then normalized using reads per million mapped reads (RPM).
Total clean reads were  also mapped to the mice reference genome using the bwa aligner.The mapped reads were further annotated to the repeats and exon regions based on the genome annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: macrophages derived exosome

growth_protocol: Bone-marrow-derived macrophages were isolated from the femurs and tibias of adult mice.Tibias were ﬂushed and bone marrow cells were seeded into 10 cm2 tissue culture plates and cultured in alpha MEM (Gibco) containing 10% FBS and 1% penicillin–streptomycin, supplemented with M-CSF 104 U ml-1 for 24 h. Then bone-marrow-derived macrophages were cultured in alpha MEM containing 10% exosome-free FBS  to produce exosomes.After 72 h macrophage culture, debris and dead cells in the medium were removed by centrifugation at 1000 × g for 10 min and then filtered through a 0.2-mm filter. The medium was then subjected to ultracentrifugation at 100,000 × g for 4–6h at 4 °C. After washing with PBS (100,000 × g for 20 min), the Exo-containing pellet was resuspended in PBS.Cells were routinely maintained in a humidified chamber at 37°C and 5% CO2.

extract_protocol:
After 72 h macrophage culture, debris and dead cells in the medium were removed by centrifugation at 1000 × g for 10 min and then filtered through a 0.2-mm filter. The medium was then subjected to ultracentrifugation at 100,000 × g for 4–6h at 4 °C. After washing with PBS (100,000 × g for 20 min), the Exo-containing pellet was resuspended in PBS.Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen) following the manufacturer’s protocol.RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).
Total RNA was isolated from exosomes using the Trizol (invitrogen) according to the manufacturer's protocol. RNA purity was assessed using the ND-1000 Nanodrop. Each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies, USA) and each sample had the RIN e above 7.0. Briefly, RNAs were ligated with 3’RNA adapter, and followed by 5’adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and diluted to 10 pM for cluster generation in situ on the HiSeq2500 single-end flow cell followed by sequencing (1×50 bp) on HiSeq 2500.

value: Bone-marrow-derived macrophages

value: wild type


title: CHMP2


title: Input lin15B 26C rep2

tag: developmental stage


title: CHMP1

tag: genotype


title: Input lin15B 26C rep1

tag: temperature


title: Input lin15B 20C rep2

source_name: Input lin15B 20C

tag: chip antibody


title: Input lin15B 20C rep1


title: sample.kidney_37_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AATACGC
all.gene_RPKM.txt
all.gene_counts.txt

value: pre


title: sample.kidney_38_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GGCAAGA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #38


title: sample.kidney_38_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GGCAGCG
all.gene_RPKM.txt
all.gene_counts.txt


title: sample.kidney_38_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TCGTGCG
all.gene_RPKM.txt
all.gene_counts.txt


title: Input N2 26C rep2

source_name: Input N2 26C

value: wild-type


title: CORTEX_ERRB4_WT_1

city: Cold Spring Harbor

first: Jesse

last: Gillis

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

data_processing:
bcl2fastq2-v2.16.0.10 was used to generate FASTQ files.
Sequenced reads are trimmed for adaptor sequence using Trimmomatic (v0.32). List of adaptors are in Buenrostro et al (2013).
Reads are mapped to mm9 using Bowtie2 with parameters as in Denny et al (2016) for paired-end reads. No additional parmeters were used for single-end reads.
Duplicate reads were removed by Picard (v1.88). Low quality reads (Mapping quality<30) were also removed.  We extracted reads that are mapped chromosome 1-19,X&Y and then merged technical replicates.
Reads aligned to + strand were offset +4bp and reads aligned to - strand were offset -5 bp (using Qu et al (2015) script). We then randomly sampled 10% of reads for 10 times without replacement. Peaks are called for each sampling replicate using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: A tab delimited file containing the list of TSS and the number of ATAC-seq reads for each sample mapped to TSS+/- 1kb regions.

source_name: Brain

growth_protocol: Mice were group-housed under a 12 h light-dark cycle (7:00 A.M. to 7:00 P.M. light), with food and water freely available. (Penzo et al (2014))

extract_protocol:
Brains were dissected and sectioned at 500 μm on ice in a stainless steel brain matrix (EMS 69090-C). PFC or CeA was microdissected in ice-cold PBS with 1x protease inhibitors (Roche) under a stereomicroscope. The tissue was resuspended in 500µl homogenization buffer containing 300mM sucrose, 60mM KCl, 15mM NaCl, 15mM Tris-HCl, 5mM MgCl2, 0.1mM EGTA, 1 mM DTT, 0.1mM PMSF and 1x protease inhibitors, EDTA-free (Roche), and disrupted using a cordless pestle motor homogenize tissue with 4 bursts of 5 seconds. Nuclei were prepared by a seven minute detergent lysis with the addition of IGEPAL CA-630 (Sigma) to a final concentration of 0.2%, followed by pelleting at 1500rcf and gentle resuspension in PBS containing 2% FBS for FACS sorting. Nuclei were filtered through 40 μm cell strainers and NucBlue was added to SOMErbb4-KO nuclei, while SOMH2B-GFP were gated on GFP. Nuclei were sorted into technical replicates of 50,000 nuclei and immediately proceeded to the ATAC-seq transposition reaction.
For each library, 50,000 sorted nuclei were resuspended in Transposition Reaction Mix then incubated at 37° C. Using Qiagen MinElute Kit we purified 50uL reaction volume. Transposed DNA were stored at -20C. We used the primers in Buenrostro et al (2013) for library construction. ATAC-seq library quality was assessed on an agarose gel with 1X SYBR Gold to view banding. Libraries were quantified by both Bioanalyzer High Sensitivity Chips and the KAPA Illumina Library Quantification kit.

treatment_protocol: Animals were deeply anesthetized and rapidly decapitated.

tag: tissue

value: Cortex

value: Bulk

value: Erbb4-KO in SOM+ cells

tag: treatment

value: Control

tag: Sex

value: F

value: 2-3 months


title: Input N2 26C rep1


title: sample.kidney_38_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/ACGCGGG
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: Input N2 20C rep2

source_name: Input N2 20C

value: Method 1


title: HepG2 shWTAP m6a-rep2 (m6A-seq)

description:
HepG2_shWtap_m6A-seq_rep1-3_exomePeak_peak.txt
HepG2_shWTAP_m6a_rep1-3_peak.bed

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters; then the processed reads were mapped to hg19 whole genome using TopHat v2.1.1 with default parameters
The m6A enriched regions were calculated by using exomePeak with default parameters.
The cutoff for significantly enriched m6A peak: p-value < 1e-5, FDR < 1e-3, fold_enrichment >= 2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited .txt files include exomePeak peak calling results for each Sample

source_name: HepG2 cells

treatment_protocol: Lentivirus were produced in HEK293T cells by co-transfecting individual shRNA construct with packing vectors (pMD2.G, pMDLg/pRRE and pRSV-Rev) into HEK293T cells in 60 mm cell culture dish using X-tremeGENE HP DNA Transfection Reagent (Roche Diagnostics, Grenzach-Wyhlen, Germany). The lentivirus particles were harvested at 48 and 72 hours after transfection and directly added into HepG2 cells with 4 μg/mL polybrene. After two rounds of infection, cells were selected for at least three passages by adding 1 μg/mL puromycin into growth medium.

tag: cell line

value: shWTAP

value: WTAP knockdown

tag: rip antibody

value: m6A antibody (Synaptic Systems, catalog# 202003, lot# 202003/2-75)

tag: replicate


title: HepG2 shWTAP m6a-rep1 (m6A-seq)

tag: shRNA


title: sample.kidney_39_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CGCTACA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #39


title: HepG2 shWTAP input-rep3 (m6A-seq)


title: CORTEX_ERRB4_KO_2

tag: strain

value: M

tag: age


title: HepG2 shWTAP m6a-rep3 (m6A-seq)


title: HepG2 shWTAP input-rep2 (m6A-seq)


title: sample.kidney_39_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/ATGTTCT
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: Input N2 20C rep1


title: CORTEX_ERRB4_WT_2


title: H3K9me2 lin37 26C rep2

source_name: H3K9me2 lin37 26C

value: Fujifilm Wako MABI0307, #302-32369

tag: input control

value: Input lin37 26C rep2


title: HepG2 shSETD2#1 m6a-rep3 (m6A-seq)

description:
HepG2_shSetd2_m6A-seq_rep1-3_exomePeak_peak.txt
HepG2_shSETD2_m6a_rep1-3_peak.bed

value: SETD2 knockdown


title: HepG2 shWTAP input-rep1 (m6A-seq)


title: AMYGDALA_ERRB4_WT_1

value: CeA


title: AMYGDALA_ERRB4_WT_2

value: Bulk


title: sample.kidney_39_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CCGGCAG
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient


title: HepG2 shSETD2#1 m6a-rep2 (m6A-seq)


title: H3K9me2 lin37 20C rep2

source_name: H3K9me2 lin37 20C

value: Input lin37 20C rep2


title: H3K9me2 lin37 26C rep1

value: Input lin37 26C rep1


title: CORTEX_ERRB4_KO_3

value: Cortex

value: Erbb4-KO in SOM+ cells

value: Control


title: sample.kidney_40_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GATGGCC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #40

tag: time point

value: pre


title: AMYGDALA_ERRB4_KO_3

tag: cell type

value: 2-3 months


title: H3K9me2 lin37 20C rep1

tag: developmental stage

value: Input lin37 20C rep1

value: Method 1


title: T47D_Control

value: Breast cancer cell line

tag: genotype/variation

value: Parental cells without MK2206 resistance


title: AMYGDALA_ERRB4_KO_2

tag: genotype

value: M


title: HepG2 shSETD2#1 input-rep3 (m6A-seq)


title: H3K9me2 lin35 26C rep2

source_name: H3K9me2 lin35 26C

tag: temperature

tag: chip antibody

value: Fujifilm Wako MABI0307, #302-32369

value: Input lin35 26C rep2


title: AMYGDALA_ERRB4_KO_1

tag: tissue

value: CeA

tag: treatment


title: sample.kidney_40_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CCATCAT
all.gene_RPKM.txt
all.gene_counts.txt

source_name: Kidney allograft biopsy

value: 3 months


title: HepG2 shSETD2#1 input-rep2 (m6A-seq)

tag: cell line

value: SETD2 knockdown


title: CORTEX_ERRB4_KO_1

value: Bulk

tag: Sex


title: sample.kidney_39_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AGTTATG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #39


title: H3K9me2 lin35 26C rep1

value: Input lin35 26C rep1


title: CORTEX_FEAR_2

value: Cortex

value: Somatostatin positive (SOM+) neurons

value: WT

value: Fear-conditioned

value: F


title: sample.kidney_40_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TGACTCT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #40

value: post


title: KO_LPS, biological rep 2 (bmdm)

description: Gene expression data from 4 hours LPS (100ng/ml) treated macrophages

source_name: Bone marrow derived Macrophages

value: Brd4Floxed :LysM-Cre

value: LPS

value: BMDM


title: HepG2 shSETD2#1 input-rep1 (m6A-seq)

tag: rip antibody

tag: replicate


title: sample.kidney_41_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GTAAAAA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #41


title: sample.kidney_41_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TGGCATA
all.gene_RPKM.txt
all.gene_counts.txt

value: pre


title: CORTEX_FEAR_1

tag: strain

value: M

value: 2-3 months


title: H3K9me2 lin35 20C rep1

source_name: H3K9me2 lin35 20C

value: Fujifilm Wako MABI0307, #302-32369

value: Input lin35 20C rep1

value: Method 1


title: sample.kidney_41_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/CTGCAAT
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: HepG2 shSETD2#1 m6a-rep1 (m6A-seq)

tag: shRNA

value: SETD2 knockdown

value: m6A antibody (Synaptic Systems, catalog# 202003, lot# 202003/2-75)


title: CORTEX_CTRL_2

value: Cortex

value: Somatostatin positive (SOM+) neurons

value: WT

value: Control

tag: age


title: H3K9me2 lin15B 26C rep1

source_name: H3K9me2 lin15B 26C

tag: input control

value: Input lin15B 26C rep1


title: HepG2 shMETTL14 m6a-rep3 (m6A-seq)

description:
HepG2_shMettl14_m6A-seq_rep1-3_exomePeak_peak.txt
HepG2_shMETTL14_m6a_rep1-3_peak.bed

value: METLT14 knockdown


title: CORTEX_CTRL_1


title: H3K9me2 lin15B 26C rep2

value: Input lin15B 26C rep2


title: AMYGDALA_FEAR_2

value: CeA

value: Fear-conditioned

value: F


title: sample.kidney_42_baseline_pre

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AATTCAT
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient

value: Patient #42

tag: time point

value: pre


title: HepG2 shMETTL14 m6a-rep1 (m6A-seq)


title: H3K9me2 lin15B 20C rep2

source_name: H3K9me2 lin15B 20C

tag: developmental stage

value: Fujifilm Wako MABI0307, #302-32369

value: Input lin15B 20C rep2


title: sample.kidney_40_1year

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/GGAGTCC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #40

value: 1 year


title: sample.kidney_42_baseline_post

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/AGGCGAA
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: sample.kidney_42_3months

description:
htcf.wustl.edu/files/zdwR4VMw/Mcmahon_2332_12345/TTTGGCG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: AMYGDALA_CTRL_2

tag: cell type

value: Somatostatin positive (SOM+) neurons

value: 2-3 months


title: H3K9me2 lin35 20C rep2

tag: genotype

value: Input lin35 20C rep2

value: Method 1


title: HepG2 shMETTL14 m6a-rep2 (m6A-seq)

value: METLT14 knockdown

value: m6A antibody (Synaptic Systems, catalog# 202003, lot# 202003/2-75)


title: H3K9me2 lin15B 20C rep1

tag: temperature

value: Input lin15B 20C rep1


title: H3K9me2 N2 26C rep2

source_name: H3K9me2 N2 26C

value: wild-type

tag: chip antibody

value: Input N2 26C rep2


title: HepG2 shMETTL14 input-rep1 (m6A-seq)


title: HepG2 shMETTL14 input-rep2 (m6A-seq)


title: HepG2 shMETTL3 m6a-rep3 (m6A-seq)

description:
HepG2_shMettl3_m6A-seq_rep1-3_exomePeak_peak.txt
HepG2_shMETTL3_m6a_rep1-3_peak.bed

value: METTL3 knockdown


title: sample.kidney_16_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TGCCCAT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #16


title: sample.kidney_16_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TGTGCCA
all.gene_RPKM.txt
all.gene_counts.txt


title: H3K9me2 N2 26C rep1

value: Fujifilm Wako MABI0307, #302-32369

value: Input N2 26C rep1


title: H3K9me2 N2 20C rep2

source_name: H3K9me2 N2 20C

value: Input N2 20C rep2


title: HepG2 shMETTL3 m6a-rep2 (m6A-seq)


title: sample.kidney_16_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GAGTACG
all.gene_RPKM.txt
all.gene_counts.txt

value: pre


title: H3K9me2 N2 20C rep1

value: Input N2 20C rep1


title: HepG2 shMETTL3 m6a-rep1 (m6A-seq)


title: sample.kidney_16_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CATTTAG
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: HepG2 shMETTL3 input-rep3 (m6A-seq)


title: H3K4me3 lin37 26C rep2

source_name: H3K4me3 lin37 26C

value: Fujifilm Wako MABI0304, #305–34819

value: Input lin37 26C rep2

value: Method 2


title: sample.kidney_17_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AGGACCT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #17


title: sample.kidney_17_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TTCGCTG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: sample.kidney_17_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CCAGGCA
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: H3K4me3 lin37 20C rep2

source_name: H3K4me3 lin37 20C

value: Input lin37 20C rep2


title: HepG2 shMETTL3 input-rep2 (m6A-seq)


title: HepG2 shCtrl m6a-rep3 (m6A-seq)

description:
HepG2_shCont_m6A-seq_rep1-3_exomePeak_peak.txt
HepG2_shCtrl_m6a_rep1-3_peak.bed

value: Non-specific control

value: control

value: m6A antibody (Synaptic Systems, catalog# 202003, lot# 202003/2-75)


title: HepG2 shMETTL14 input-rep3 (m6A-seq)

value: METLT14 knockdown


title: AMYGDALA_FEAR_1

tag: tissue

value: CeA

value: Somatostatin positive (SOM+) neurons

value: WT

value: Fear-conditioned

value: M

value: 2-3 months


title: H3K4me3 lin35 26C rep2

source_name: H3K4me3 lin35 26C

value: Fujifilm Wako MABI0304, #305–34819

value: Input lin35 26C rep2


title: H3K4me3 lin35 20C rep1

source_name: H3K4me3 lin35 20C

value: Input lin35 20C rep2

value: Method 2


title: H3K4me3 lin15B 26C rep2

source_name: H3K4me3 lin15B 26C

value: Input lin15B 26C rep2


title: HepG2 shCtrl m6a-rep1 (m6A-seq)


title: HepG2 shMETTL3 input-rep1 (m6A-seq)

value: METTL3 knockdown


title: HepG2 shCtrl m6a-rep2 (m6A-seq)


title: H3K4me3 lin15B 20C rep2

source_name: H3K4me3 lin15B 20C

value: Input lin15B 20C rep2


title: H3K4me3 lin37 26C rep1

value: Input lin37 26C rep1


title: HepG2 shCtrl input-rep3 (m6A-seq)

source_name: HepG2 cells

value: Non-specific control

value: control


title: H3K4me3 N2 26C rep1

source_name: H3K4me3 N2 26C

value: wild-type

value: Input N2 26C rep1


title: HepG2 shCtrl input-rep1 (m6A-seq)


title: sample.kidney_18_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AAACCTT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #18

value: post


title: H3K36me3 lin37 26C rep2

source_name: H3K36me3 lin37 26C

value: Fujifilm Wako MABI0333, #300–952

value: Input lin37 26C rep2

value: Method 1


title: sample.kidney_17_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AGACTGA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #17

value: 1 year


title: sample.kidney_19_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TTTTCGG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #19

value: pre


title: sample.kidney_19_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TTTCAGA
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2 shCtrl input-rep2 (m6A-seq)


title: sample.kidney_19_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TATCTTA
all.gene_RPKM.txt
all.gene_counts.txt


title: HepG2 shSETD2 H3K36me3-rep2 (ChIP-seq)

description:
HepG2_shSetd2_ChIP-seq_rep1-2_MACS_peaks.txt
HepG2_macs_shSetD2_rep1-2_peaks.bed

data_processing:
Illumina Casava1.8 software used for basecalling.
All sequenced reads were checked for quality control by using FastQC v0.11.5 with default parameters; then the processed reads were mapped to hg19 whole genome using Bowtie v1.1.2 with default parameters
The H3K36me3 enriched regions were calculated by using MACS with following parameters: -g hs --nomodel --shiftsize 147 -B -S --call-subpeaks
The cutoff for significantly enriched H3K36me3 peak: p-value < 1e-5, FDR < 0.05
Genome_build: hg19
Supplementary_files_format_and_content: *txt: tab-delimited text files containing peaks generated by MACS.
Supplementary_files_format_and_content: *bed: bed files containing significantly enriched H3K36me3 peaks.

extract_protocol:
Cell lysate was sonicated and clarified by using 0.22 µm filter. Histone-DNA complexes were isolated with H3K36me3 antibody.
Libraries were constructed by using Auto iDeal ChIP-seq kit for Histones (Diagenode, C01010057) following manufacturer's prorocol.

value: SETD2 shRNA

value: SETD2 knockdown

value: H3K36me3 (Abcam, catalog# ab9050, lot# GR166781-1)


title: sample.kidney_20_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CTTGGAA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #20


title: H3K36me3 lin37 20C rep3

source_name: H3K36me3 lin37 20C

value: Input lin37 20C rep3

value: Method 2


title: iCLIP SINV-infected 18hpi

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
RNA-seq data processing: We combined the human genome (version hg38) with SINV sequence as our reference genome. RNAseq reads were then mapped to this reference genome using STAR (Dobin et al., 2013). Reads mapping to each transcript were counted with featureCounts in Subread software package (Liao et al., 2013). Only uniquely mapped reads are considered for counting.
iCLIP-seq data processing: To identify GEMIN5 binding sites on SINV RNAs, reads in the fastq files from sequencing were demultiplexed to separate the samples according to the sample barcodes. Molecular and sample barcodes as well as trailing adapter sequences were trimmed off. Molecular barcode information was stored in the read name. Reads were then mapped to a combined human (GRCh38) and SINV genome (pT7-SVwt (NC_001547.1)) sequence using STAR (Dobin et al., 2013). Uniquely aligned reads were then extracted using SAMtools (Li et al., 2009). Binding sites were determined as the 5'-most base of each uniquely mapped read. PCR duplicates were identified as reads with the same mapping position and molecular barcode and each unique fragment counted just once. The 5'-most base in sequenced reads corresponds to the base directly 3' of the crosslinked base. The number of unique fragment counts per position gives a measure of GEMIN5 interaction strength with that position along the RNA. Due to the sheer abundance of SINV RNA at 18 hpi, some background signal could be observed in GFP control. To account for this background, GFP signal was subtracted from GEMIN5 signal after correction to total SINV reads. Significantly crosslinked sites were determined using iCount peaks (Curk et al., https://icount.readthedocs.io/). iCount peaks was run to generate a background distribution by randomly distributing the crosslinked sites a hundred times along the SINV genome and compare the actual observed distribution to this background to generate a false discovery rate. Since regions corresponding to genomic, subgenomic and 3' end region have different overall abundance, they were indicated as individual gene segments in the calculation to account for potentially higher background. Sites meeting FDR cutoff of 0.01 within 5 nt of each other were then merged using iCount clusters to form binding sites.
Genome_build: hg.38; pT7-SVwt (NC_001547.1)
Supplementary_files_format_and_content: RNA-seq: tsv file that contains read count per gene for all nine samples (three mock replicates, three 4 hpi replicates, three 18 hpi replicates).
Supplementary_files_format_and_content: iCLIP-seq: bed file that contains the predicted GEMIN5 binding sites along SINV genome for different replicates.

growth_protocol: For RNA-seq, we used human embryo kidney 293 cells (HEK293). For iCLIP-seq, HEK293 Tet-on cells expressing eGFP or GEMIN5-eGFP proteins were used. All cells were cultured in DMEM with 10% FBS and 1x penicillin/streptomycin at 37°C with 5% CO2. The media of Flp-In TREx (Tet-on) cells was supplemented with 15 µg/ml Blasticidin S and 100 µg/ml Zeocin.

extract_protocol:
We followed the protocol described in König et al., 2012 and Garcia-Moreno, Noerenberg, Ni, et al. 2019. Briefly, cells were washed with PBS and UV irradiated with 150 mJ/cm2 at 254 nm. Cells were the lysed, sheared by passing through a 27G needle, sonicated for three 10 second pulses in Digenonde bioruptor at level M at 4°C, and centrifuged 17900 g at 4°C for 10 min. The supernatant was collect and used for further analyses.
Briefly, samples were DNase and RNase treated to obtain RNA fragments of suitable length and to degrade DNA. Samples were pre-cleared using control agarose beads and then incubated with GFP_trap_A beads to bind GEMIN5-GFP and GFP proteins and their bound RNA to beads. Following washes, pre-adenylated linker L3 was ligated to dephosphorylated RNA ends, and the protein-RNA complexes size selected from a nictrocellulose membrane after an SDS-PAGE and wet transfer. RNA was released using proteinase K treatment and extracted using phenol-chloroform. Reverse transcription was then carried out using unique barcodes for each sample and the cDNA size selected on a gel. cDNA was extracted, circularized, and re-linearised to generate fragments suitable for sequencing. Samples were the PCR amplified, size selected on a gel and purified. Libraries were pooled for sequencing and processed using single-end sequencing mode with a NextSeq 500/550 High Output v2 kit (75 cycles).
For full details, including product codes, please see the following paper: Garcia-Moreno, Noerenberg, Ni, et al. System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection. 2019.

treatment_protocol: Infection of cells at 80% confluency with SINV at MOI of 10, followed by 4h or 18h incubation. "Mock" samples were not infected with virus. iCLIP-seq samples were induced with doxycycline for 24h (GEMIN5 samples) or 8h (GFP samples) prior to infection.

value: HEK293 Tet-on expressing eGFP

tag: infection

value: SINV

tag: time (hpi)

tag: time (doxycycline)


title: sample.kidney_18_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TCCGGGA
all.gene_RPKM.txt
all.gene_counts.txt

source_name: Kidney allograft biopsy

value: Patient #18


title: BT474_Control

tag: cell line

value: Breast cancer cell line

tag: genotype/variation

value: Parental cells without MK2206 resistance


title: H3K36me3 lin37 26C rep1

value: Fujifilm Wako MABI0333, #300–952

value: Input lin37 26C rep1


title: HepG2 shSETD2 input-rep2 (ChIP-seq)

tag: replicate


title: sample.kidney_18_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AACGGAG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: H3K36me3 lin37 20C rep2

value: Input lin37 20C rep2

value: Method 1


title: HepG2 shCtrl H3K36me3-rep2 (ChIP-seq)

description:
HepG2_shCont_ChIP-seq_rep1-2_MACS_peaks.txt
HepG2_macs_shCont_rep1-2_peaks.bed

tag: shRNA

value: Non-specific control

value: control


title: sample.kidney_20_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CTCAATG
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: HepG2 shCtrl input-rep2 (ChIP-seq)


title: iCLIP SINV-infected 18hpi rep5

value: HEK293 Tet-on expressing GEMIN5-eGFP


title: sample.kidney_20_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/ACCATAC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #20


title: HepG2 shSETD2 H3K36me3-rep1 (ChIP-seq)

value: SETD2 shRNA

value: SETD2 knockdown

value: H3K36me3 (Abcam, catalog# ab9050, lot# GR166781-1)


title: H3K36me3 lin37 20C rep1

value: Input lin37 20C rep1


title: iCLIP SINV-infected 18hpi rep4

value: SINV


title: iCLIP SINV-infected 18hpi rep3


title: H3K36me3 lin35 26C rep2

source_name: H3K36me3 lin35 26C

value: Input lin35 26C rep2


title: sample.kidney_21_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CGAAAGT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #21


title: HepG2 shCtrl H3K36me3-rep1 (ChIP-seq)


title: HepG2 shSETD2 input-rep1 (ChIP-seq)


title: sample.kidney_21_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CAGAGTC
all.gene_RPKM.txt
all.gene_counts.txt


title: iCLIP SINV-infected 18hpi rep2


title: H3K36me3 lin35 20C rep2

source_name: H3K36me3 lin35 20C

value: Fujifilm Wako MABI0333, #300–952

value: Input lin35 20C rep2


title: iCLIP SINV-infected 18hpi rep1


title: H3K36me3 lin35 26C rep1

value: Input lin35 26C rep1


title: RNA-seq SINV-infected 18 hpi rep3

description:
RNAseq-gene-counts.tsv
Hour18_rep3

extract_protocol:
RNA was extracted from whole cell lysates using TRIzol
Libraries were prepared using NEBNext Ultra Directional RNA library Prep Kit for Illumina according to manufacturer instructions. In brief, RNA was fragmented for 15 min at 94⁰C and then reverse transcribed. cDNA and double-stranded cDNA was purified with AMPure XP beads. After end repair, NEBNext Adaptors for Illumina  were ligated onto the cDNA according to the kit manual. Libraries were amplified by 15 cycles of PCR. Multiplexed dibraries with an average length of 320 nt were pooled and sequenced with an Illumina NextSeq instrument, using 78 nt paired-end sequencing mode with a NextSeq 500/550 High Output v2 kit.
For full details, including product codes, please see the following paper: Garcia-Moreno, Noerenberg, Ni, et al. System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection. 2019.


title: sample.kidney_21_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/ACTGGAT
all.gene_RPKM.txt
all.gene_counts.txt

value: 1 year


title: H3K36me3 lin15B 26C rep2

source_name: H3K36me3 lin15B 26C

value: Input lin15B 26C rep3

value: Method 1


title: P_3: control 3

first: Balazs

last: Balint

state: Csongrad

address: Vallalkozok street

country: Hungary

institute: Seqomics Ltd

data_processing:
Reads were quality trimmed using CLC Genomics Workbench Tool (v 11.0). Ambiguous base limit=0, Error probability cutoff value=0.01. Reads shorter than 40 nt were discarded. A custom-masked reference sequence based on E. coli K12 MG1655 reference genome version U00096.3 was used for mapping. Masking was performed keeping only one copy of each analyzed IS type. Reads were mapped using RNA-Seq analysis package 2.16 of CLC Genomics Workbench Tool (v. 11.0). Parameters: min. read length fraction = 0.9, min. read similarity fraction = 0.95. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = Both, Maximum number of hits for a read=30, Count paired reads as two=no, Expression value= Total counts. Trimmed mean of M values (TMM) scale normalization was used. Function: calcNormFactors, Package: edgeR, Version 3.12.1 Voom log2 transformation without quantile normalization was applied. Function: voom normalize.method="none", Package: limma, Version: 3.26.9 List of differentially expressed genes was obtained with limma, using linear modeling with empirical Bayes moderation. Package: limma, Version: 3.26.9.
Genome_build: Reference sequence file: U00096.3_RepMasked.fasta, annotation file: U00096.3_1extra_IS150_IS1_IS3_IS5_IS5y_CrispR.gff3
Supplementary_files_format_and_content: *_CLC_RNA_Seq.csv: RNA-Seq read counts table exported from CLC Genomic Workbench Tool.
Supplementary_files_format_and_content: TMM_Voom_Exp_28Aug2018.csv: Normalized gene expression matrix.
Supplementary_files_format_and_content: U00096.3_RepMasked.fasta: IS_Repeat-masked reference file.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial culture

growth_protocol: The six parallel cultures were grown at 37 oC in Mineral Salts minimal medium (Hall, Mol Biol Evol 15:1) supplemented with 0.2 % glucose and Chloramphenicol to an OD540 value of 1.

extract_protocol:
Total RNA was prepared using the E.Z.N.A. Bacteria RNA Kit (Omega bio-tek, Norcross, GA, USA) following instructions of the manufacturers.
Library construction was performed using TrueSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions with slight modifications. Briefly, RNA quality and quantity measurements were performed using RNA ScreenTape and Reagents on TapeStation (all from Agilent, Santa Clara, CA, USA) and Qubit (Thermo Fisher Scientific, Waltham, MA, USA); only high quality (RIN >8.0) total RNA samples were processed. Next, 1 µg of RNA was DNaseI (Thermo Fisher Scientific, Waltham, MA, USA) treated, the ribosomal RNA depleted using RiboZero Magnetic Kit for Gram-negative bacteria (Epicentre, Madison, WI, USA) and the leftover was ethanol precipitated. The success of rRNA removal was determined by measurement on TapeStation using high-sense RNA ScreenTape and Reagents (all from Agilent, Santa Clara, CA, USA). Next, RNA was purified and fragmented; first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher Scientific, Waltham, MA, USA) followed by second strand cDNA synthesis, end repair, 3’-end adenylation, adapter ligation and PCR amplification. All of the purification steps were performed using AmPureXP Beads (Beckman Coulter, Indianapolis, IN, USA). Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation (all from Agilent, Santa Clara, CA, USA). Concentration of each library was determined using the KAPA Library Quantification Kit for Illumina (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Each culture was treated with the RNAprotect Bacteria Reagent (Qiagen, Leipzig, Germany).

value: bacterial culture

value: carrying plasmid pCRISPath

tag: growth medium

value: glucose minimal medium + Chloramphenicol

tag: od


title: P_2: control 2


title: RNA-seq SINV-infected 18 hpi rep2

description:
RNAseq-gene-counts.tsv
Hour18_rep2


title: sample.kidney_21_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GATAGTT
all.gene_RPKM.txt
all.gene_counts.txt

tag: patient

value: pre


title: sample.kidney_22_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CCGATTA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #22

tag: time point

value: post


title: H3K36me3 lin15B 26C rep1

tag: developmental stage

tag: input control

value: Input lin15B 26C rep1


title: IS_3: IS-knockdown sample 3

value: carrying plasmid pCRISP_ISF


title: RNA-seq SINV-infected 18 hpi rep1

description:
RNAseq-gene-counts.tsv
Hour18_rep1

value: SINV


title: H3K36me3 lin15B 20C rep2

source_name: H3K36me3 lin15B 20C

tag: genotype

value: Input lin15B 20C rep2


title: sample.kidney_22_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AAATGCA
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: HepG2 shCtrl input-rep1 (ChIP-seq)

value: Non-specific control

value: control


title: H3K36me3 lin35 20C rep1

tag: temperature

value: Fujifilm Wako MABI0333, #300–952

value: Input lin35 20C rep1


title: RNA-seq SINV-infected 4 hpi rep2

description:
RNAseq-gene-counts.tsv
Hour4_rep2


title: RNA-seq SINV-infected 4 hpi rep3

description:
RNAseq-gene-counts.tsv
Hour4_rep3


title: H3K36me3 N2 26C rep2

value: wild-type

tag: chip antibody

value: Input N2 26C rep2


title: H3K36me3 lin15B 20C rep1

value: Input lin15B 20C rep1

value: Method 1


title: IS_2: IS-knockdown sample 2

tag: tissue

value: bacterial culture

value: glucose minimal medium + Chloramphenicol


title: sample.kidney_23_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GGTGAAT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #23

value: pre


title: sample.kidney_23_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GCCTCCC
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: sample.kidney_22_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/CTCACCC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #22


title: RNA-seq SINV-infected 4 hpi rep1

description:
RNAseq-gene-counts.tsv
Hour4_rep1

tag: infection

value: SINV


title: AMYGDALA_CTRL_1

source_name: Brain

tag: strain

value: CeA

tag: cell type

value: Somatostatin positive (SOM+) neurons

value: WT

tag: treatment

value: Control

tag: Sex

value: M

tag: age

value: 2-3 months


title: H3K4me3 N2 20C rep2

source_name: H3K4me3 N2 20C

value: wild-type

value: Fujifilm Wako MABI0304, #305–34819

value: Input N2 20C rep2

value: Method 2


title: sample.kidney_23_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GTATCCT
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: IS_1: IS-knockdown sample 1

value: bacterial culture

tag: genotype/variation

value: carrying plasmid pCRISP_ISF

value: glucose minimal medium + Chloramphenicol


title: H3K36me3 N2 26C rep1

value: Fujifilm Wako MABI0333, #300–952

value: Input N2 26C rep1

value: Method 1


title: H3K36me3 N2 20C rep1

value: Input N2 20C rep1


title: RNA-seq mock rep1

description:
RNAseq-gene-counts.tsv
Mock_rep1

extract_protocol:
RNA was extracted from whole cell lysates using TRIzol.
Libraries were prepared using NEBNext Ultra Directional RNA library Prep Kit for Illumina according to manufacturer instructions. In brief, RNA was fragmented for 15 min at 94⁰C and then reverse transcribed. cDNA and double-stranded cDNA was purified with AMPure XP beads. After end repair, NEBNext Adaptors for Illumina  were ligated onto the cDNA according to the kit manual. Libraries were amplified by 15 cycles of PCR. Multiplexed dibraries with an average length of 320 nt were pooled and sequenced with an Illumina NextSeq instrument, using 78 nt paired-end sequencing mode with a NextSeq 500/550 High Output v2 kit.
For full details, including product codes, please see the following paper: Garcia-Moreno, Noerenberg, Ni, et al. System-wide profiling of RNA-binding proteins uncovers key regulators of virus infection. 2019.

tag: cell line

value: Uninfected cells


title: RNA-seq mock rep2

description:
RNAseq-gene-counts.tsv
Mock_rep2


title: sample.kidney_23_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GGCAAGA
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #23

value: 1 year


title: H3K36me3 N2 20C rep2


title: sample.kidney_22_1year

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AATACGC
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #22


title: sample.kidney_24_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/TCGTGCG
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #24

value: pre


title: H3K27me3 lin35 20C rep1

source_name: H3K27me3 lin35 20C

value: Fujifilm Wako MABI0323, #309–95259

value: Input lin35 20C rep1


title: H3K27me3 lin35 26C rep1

source_name: H3K27me3 lin35 26C

value: Input lin35 26C rep1


title: Week 18 fetal kidney

city: Leiden

first: Stefan

last: Semrau

address: Einsteinweg 55

department: Physics

country: Netherlands

institute: Leiden University

data_processing:
Single-cell expression was quantified using unique molecular identifiers (UMIs) by 10x Genomics’ “Cell Ranger” software.
Cells were filtered for having 2000 UMI counts or more
Genome_build: hg19
Supplementary_files_format_and_content: count_matrix: matrix of UMI counts where cells are columns and genes rows; barcode_list: list of 12bp barcodes corresponding to the columns of matrix; gene_list: HUGO and ensembl identifiers corresponding to the rows of matrix

source_name: disociated human embryonic kidney

extract_protocol:
Human fetal embryos were isolated and the kidney dissected in cold saline solution (0.9% NaCl, Versylene Fresenius, France). The obtained kidneys were decapsulated and kept on ice in dissociation buffer (DPBS + Penicillin 100U/ml + Streptomycin 0.1 mg/ml) before cutting it into 1 – 2 mm pieces. The pieces were washed 3 times with washing solution (Advanced DMEM F12 supplemented with: ITS commercial solution (Insulin – Transferrin – Selenium), Glutamax, Penicillin 100 U/ml and Streptomycin 0.1 mg/ml) with brief centrifugation (160g) in order to remove as many red blood cells as possible. The washed kidney tissues were then incubated with digestion solution (Trypsin/EDTA solution 0.25% and Collagenase-II 280 U/ml) and incubated overnight at 4°C. The next day, the digestion solution was removed, the kidneys were rinsed with washing solution and incubated with washing solution for 30 min at 37°C with agitation. Subsequently, the samples were sequentially passed through sterile cell-strainers of 100, 70 and 40 µm pore size with the help of washing solution. The cells were then centrifuged, counted and viability was measured to be 78% (trypan blue assay) before proceeding with single-cell RNA sequencing library preparation.
10X library: Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3' Reagent Kit, Version 2 Chemistry (10x Genomics) according to the manufacturer's protocol.  Libraries were sequenced on a NextSeq500 in Mid Output mode using a version 2, 150 cycles kit (Illumina).

value: Week 18

value: embryonic kidney


title: sample.kidney_24_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/GGCAGCG
all.gene_RPKM.txt
all.gene_counts.txt

value: post


title: Week 13 fetal kidney

value: Week 13


title: RNA-seq mock rep3

description:
RNAseq-gene-counts.tsv
Mock_rep3


title: Week 11 fetal kidney

value: Week 11


title: Week 9 fetal kidney

value: Week 9


title: H3K27me3 lin15B 26C rep1

source_name: H3K27me3 lin15B 26C

value: Input lin15B 26C rep1

value: Method 1


title: sample.kidney_24_3months

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/ACGCGGG
all.gene_RPKM.txt
all.gene_counts.txt

value: 3 months


title: sample.kidney_25_baseline_pre

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/ATGTTCT
all.gene_RPKM.txt
all.gene_counts.txt

value: Patient #25


title: sample.kidney_25_baseline_post

description:
htcf.wustl.edu/files/NeAlDBd2/Mcmahon_2328_5678/AGTTATG
all.gene_RPKM.txt
all.gene_counts.txt