title: RNA-seq_D18-Rep1

city: Dallas

first: Mala

last: Mahendroo

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing:
The raw data were subjected to QC analyses using the FastQC tool.  The reads were then mapped to mouse genome (mm10) using the spliced reader aligner TopHat version 2.0.13.  Transcriptome assembly was performed using cufflinks v.2.2.1 with default parameters48.  The transcripts were merged into two distinct, non-overlapping sets using cuffmerge, followed by cuffdiff to call the differentially regulated transcripts.  The significantly (p <0.05) regulated genes from cells expressing the H2B mutants S36A or E35A were compared to wild-type at the indicated time points.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57BL6/SvEv129 mice were used in this study. Nonpregnant mice were in metestrus for RNAseq. Timed pregnant mice were collected on gestation days 6, 12, 15 and 18 with day of plug considered day 0 and birth on day 19. Each library was generated from an equal pool of RNA from 3 mice.  Proteomic studies- mice were treated with deuterium-labeled drinking water for 3 days prior to cervical tissue collection. Whole cervix was extracted into 3- fractions: 1) SDS-soluble, 2) guanidine-soluble and 3) guanidine-insoluble.


title: RNA-Esrrb_KD1_lowdensity_r2

status: Public on Nov 24 2021

type: SRA

city: Austin

first: Jonghwan

last: Kim

state: TX

address: 2506 Speedway

department: Molecular Biosciences

country: USA

institute: University of Texas at Austin

description: Differentiation in -LIF for 72 hr

library_source: transcriptomic

data_processing:
For ChIP-seq, reads from .fastq files were aligned to the mm10 genome using Bowtie 2 version 2.4.2 using multithreading and default settings.
Peaks were then called using MACS2 version 2.2.7.1 using input as control and an effective genome size of 2652783500. Input represents chromatin-associated DNA from mouse embryonic stem cells that were grown, differentiated, fixed, sheared, washed, etc. the same as samples but without dox treatment (meaning no expression of biotinylated transcription factor).
For RNA-seq, reads were pseudoaligned to the mm10 genome using kallisto version 0.46.1 with sequence bias correction enabled as well as bootstrapping (n = 100) in either single or paired-end mode depending on the samples.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files for ChIP-seq, TPM output for RNA-seq

molecule: polyA RNA

organism: Mus musculus

source_name: Mouse embryonic stem cells, differentiated

growth_protocol: J1 mouse embryonic stem cells were routinely cultured in serum and LIF-containing media (+LIF) for self-renewal or without LIF for differentiation (-LIF). Differentiation was carried out for 72 hr or 96 hr as indicated in sample description. Cells were either seeded at high density (1.9e5 cells/cm^2) in a 6-well plate or low density (2.3e4 cells/cm^2) in a 12-well plate or at the densities indicated in sample name in a 24-well plate.

extract_protocol:
For ChIP-seq, chromatin was sheared from formaldehyde-fixed mouse embryonic stem cells. Protein-DNA complexes of interest were pulled down with magnetic streptaviding beads that were extensively washed in buffer before elution. For RNA-seq, total RNA was isolated using the RNeasy Mini Plus Kit from Qiagen and quantified on a Nanodrop.
For ChIP-seq, libraries were prepared according to the manufacturer's instructions in the NEBNext Ultra™ II DNA Library Prep Kit for Illumina (NEB) and sequenced on a NovaSeq 6000. For RNA-seq, paired-end libraries were prepared according to the manufacturer's instructions in the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB) and sequenced on a NovaSeq 6000. Unpaired libraries were prepared using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB) and sequenced on a NextSeq500.

treatment_protocol: Dox was used at the indicated concentrations for last 48 hr (included in the 72 hr of differentiation). Inducible expression was achieved through transfection with pSB vector containing FLAG-BIO-tagged Esrrb, Tcfl7l1, or beta-catenin in BirA-expressing cells, followed by double selection with puromycin and neomycin. shRNA was transduced using lentivirus (constitutive KD, puromycin selection) with non-targeting shRNA as control.

tag: cell type

value: J1 mouse embryonic stem cells

tag: treatment

value: shRNA against Esrrb


title: RNA-seq_D15-Rep2

tag: strain


title: RNA-swapld1_lowdensity_r1

description: Differentiation in -LIF for 72 hr

value: swap media w high density cells 4 hr


title: nasopharyngeal gene expression of subject M131 at m1 [121144011312]

type: RNA

city: Utrecht

first: Wouter

last: de Steenhuijsen Piters

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Clariom S Human Pico arrays.

scan_protocol: GeneChips were scanned inhouse by Hologic Ltd. UK.

data_processing: The data were analyzed using R/Rstudio. Outliers were identified using raw intensity data using the arrayQualityMetrics package and removed from the dataset. RMA was performed to reduce the data from 300304 probe-level features to 27189 genes. After removing non-annotated genes/control probes, 18526 genes remained, which were for the conclusions in the paper.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: nasopharyngeal cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: N/A; study in human infants.

extract_protocol: RNA was extracted by a TRIzol reagent (Invitrogen)/chlorform method, cleaned using the RNAeasy Micro Kit (Qiagen) (OpenWetWare contributors, 2015)

treatment_protocol: Nasopharyngeal cells were collected in RNAprotect Cell Reagent (Qiagen) at -80 °C until extraction.

tag: subject

tag: time point

tag: age

value: nasopharyngeal cells


title: 201533640031_R04C01

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

hyb_protocol: One hundred and fifty-eight samples from St. Jude Children’s Research Hospital (SJCRH, pediatric) and Stanford Hospital and Clinics (adult) were analyzed using Illumina Methylation BeadChip (EPIC) arrays according to the manufacturer’s instructions. Data were generated from formalin-fixed paraffin-embedded (FFPE) tissue samples. DNA of 158 patients was extracted and hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays.

scan_protocol: Standard Illumina protocol

data_processing: All methylation data were analyzed in R (http://www.r-project.org, version 3.5.3), using a number of packages from Bioconductor and other repositories. Specifically, array data were preprocessed using the minfi package (v.1.28.4) (13). Background correction with dye-bias normalization was performed for all samples using noob (normal-exponential out-of-band) with “single” dye method (14). Filtering was performed to remove probes located on sex chromosomes, probes containing nucleotide polymorphisms (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, or probes mapping to multiple sites on hg19 (allowing for one mismatch), and cross-reactive probes.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: rhabdomyosarcoma

label_protocol: Standard Illumina protocol

tag: molecular group

value: ARMS


title: 201533640024_R02C01

extract_protocol: Data were generated from formalin-fixed paraffin-embedded (FFPE) tissue samples. DNA of 158 patients was extracted and hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays


title: RNA-conld2_lowdensity_r2

description: Differentiation in -LIF for 72 hr


title: RNA-seq_D15-Rep1


title: RNA-conld1_lowdensity_r1

description: Differentiation in -LIF for 72 hr


title: 201533640024_R03C01

value: ERMS


title: nasopharyngeal gene expression of subject M132 at m1 [121144011322]


title: RNA-swaphd2_highdensity_r2

description: Differentiation in -LIF for 72 hr

value: swap media w low density cells 4 hr


title: RNA-seq_D12-Rep2


title: 201533640024_R04C01

value: PRMS


title: RNA-seq_D18-Rep2


title: RNA-seq_D12-Rep1


title: 201533640031_R01C01


title: nasopharyngeal gene expression of subject M130 at m1 [121144011302]


title: nasopharyngeal gene expression of subject M090 at m2 [121145010902]


title: 201533640023_R03C01


title: 201533640024_R05C01


title: RNA-seq_D6-Rep2


title: 201533640023_R04C01


title: RNA-seq_D6-Rep1


title: RNA-seq_NP-Rep2

source_name: NP


title: RNA-seq_NP-Rep1


title: 201533640023_R01C01


title: 201533640023_R06C01


title: RNA-swaphd1_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: 201533640009_R07C01


title: 201533640023_R02C01


title: beta cells sample M_WT_32A4

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

country: Canada

institute: University of British Columbia

data_processing:
Alignment and count extraction with STAR
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: beta cells from mouse islets

extract_protocol:
Groups of 50 islets were dispersed using mild trypsin digest, and FACS purified based on the GFP-positivity of the Ins1Cre-induced nTnG allele.
RNA isolation and library preparation were conducted in accordance with the SMART seq 2 protocol.

value: Ins1cre (C57BL/6J)

tag: Sex

value: M

value: WT


title: nasopharyngeal gene expression of subject M128 at m1 [121144011282]


title: 201533640009_R08C01


title: 201533640023_R08C01


title: nasopharyngeal gene expression of subject M120 at m1 [121144011202]


title: RNA-Tcf7l1_KD_lowdensity_r1

description: Differentiation in -LIF for 72 hr

value: shRNA against Tcf7l1


title: RNA-conhd1_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: RNA-Tcf7l1_KD_lowdensity_r2

description: Differentiation in -LIF for 72 hr


title: RNA-conhd2_highdensity_r2

description: Differentiation in -LIF for 72 hr


title: beta cells sample M_WT_32A3


title: nasopharyngeal gene expression of subject M119 at m1 [121144011192]


title: 201533640009_R04C01


title: 201533640009_R05C01


title: nasopharyngeal gene expression of subject M117 at m1 [121144011172]


title: beta cells sample M_WT_26A8


title: nasopharyngeal gene expression of subject M129 at m1 [121144011292]


title: beta cells sample M_WT_26A7


title: nasopharyngeal gene expression of subject M116 at m1 [121144011162]


title: nasopharyngeal gene expression of subject M126 at m1 [121144011262]


title: nasopharyngeal gene expression of subject M112 at m1 [121144011122]


title: beta cells sample M_WT_23B5


title: beta cells sample M_WT_26A6


title: nasopharyngeal gene expression of subject M114 at m1 [121144011142]


title: nasopharyngeal gene expression of subject M115 at m1 [121144011152]


title: nasopharyngeal gene expression of subject M127 at m1 [121144011272]


title: 201533640023_R05C01


title: 201533640023_R07C01


title: nasopharyngeal gene expression of subject M111 at m1 [121144011112]


title: beta cells sample M_KO_374

value: KO


title: RNA-betacatenin4A-OE-dox_lowdensity_r2

description: Differentiation in -LIF for 72 hr


title: beta cells sample M_KO_27A8


title: RNA-shCon_lowdensity_r1

description: Differentiation in -LIF for 72 hr

value: non-targeting shRNA


title: RNA-betacatenin4A-OE+dox_highdensity_r1

description: Differentiation in -LIF for 72 hr

value: 125 ng/mL dox 48 hr


title: nasopharyngeal gene expression of subject M110 at m1 [121144011102]


title: 201533640009_R02C01


title: RNA-betacatenin4A-OE+dox_highdensity_r2

description: Differentiation in -LIF for 72 hr


title: RNA-Tcf7l1_KD_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: RNA-shCon_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: RNA-Tcf7l1_KD_highdensity_r2

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M109 at m1 [121144011092]


title: 201533620059_R07C01


title: RNA-betacatenin4A-OE-dox_highdensity_r1

description: Differentiation in -LIF for 72 hr


title: beta cells sample M_KO_27A7


title: RNA-betacateninKD2_lowdensity_r2

description: Differentiation in -LIF for 72 hr

value: shRNA against Ctnnb1


title: RNA-betacateninKD2_lowdensity_r1

description: Differentiation in -LIF for 72 hr


title: beta cells sample M_KO_27A6


title: nasopharyngeal gene expression of subject M108 at m1 [121144011082]


title: beta cells sample M_HET_32A6

value: HET


title: RNA-betacateninKD2_highdensity_r1

description: Differentiation in -LIF for 72 hr

value: J1 mouse embryonic stem cells


title: nasopharyngeal gene expression of subject M102 at m1 [121144011022]


title: RNA-betacateninKD2_highdensity_r2

description: Differentiation in -LIF for 72 hr


title: 201533640009_R01C01


title: beta cells sample M_KO_26B8


title: beta cells sample M_HET_32A5


title: RNA-shCon_lowdensity_r3

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M101 at m1 [121144011012]


title: nasopharyngeal gene expression of subject M098 at m1 [121144010982]


title: nasopharyngeal gene expression of subject M100 at m1 [121144011002]


title: RNA-shCon_highdensity_r3

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M096 at m1 [121144010962]


title: nasopharyngeal gene expression of subject M080 at m1 [121144010802]


title: beta cells sample M_HET_27A5


title: beta cells sample M_HET_21bB8


title: ChIP-ES-betacatenin-highdensity_r2

description: Differentiation in -LIF for 72 hr

library_source: genomic

value: 100 ng/mL dox 48 hr


title: beta cells sample M_HET_21bB7


title: ChIP-ES-betacatenin-highdensity_r1

description: Differentiation in -LIF for 72 hr


title: 201533620059_R03C01


title: nasopharyngeal gene expression of subject M078 at m1 [121144010782]


title: beta cells sample F_WT_46A3

value: F


title: ChIP-ES-betacatenin-input_r1

description: Differentiation in -LIF for 72 hr


title: 201533620048_R01C01

source_name: skeletal muscle

value: Control


title: 201533620059_R04C01

value: ARMS


title: nasopharyngeal gene expression of subject M136 at w2 [121143011362]

value: nasopharyngeal cells


title: ChIP-ES-Esrrb-lowdensity_r2

description: Differentiation in -LIF for 72 hr

value: 10 ng/mL dox 48 hr


title: 201533620059_R05C01


title: beta cells sample F_WT_30A2


title: ChIP-ES-Esrrb-lowdensity_r1

description: Differentiation in -LIF for 72 hr


title: 201533620039_R08C01


title: beta cells sample F_WT_25A6


title: 201533620059_R06C01


title: ChIP-ES-Esrrb-highdensity_r2

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M135 at w2 [121143011352]


title: 201533620039_R06C01

value: ERMS


title: beta cells sample F_WT_34B2

value: Ins1cre (C57BL/6J)


title: 201533620048_R03C01


title: nasopharyngeal gene expression of subject M133 at w2 [121143011332]


title: beta cells sample F_WT_23A1


title: 201533620059_R01C01


title: ChIP-ES-Esrrb-highdensity_r1

description: Differentiation in -LIF for 72 hr


title: 201533620039_R07C01


title: beta cells sample F_KO_46A4


title: nasopharyngeal gene expression of subject M131 at w2 [121143011312]


title: 201533620039_R05C01


title: nasopharyngeal gene expression of subject M130 at w2 [121143011302]


title: nasopharyngeal gene expression of subject M132 at w2 [121143011322]


title: ChIP-ES-Tcf7l1-lowdensity_r2

description: Differentiation in -LIF for 72 hr

value: 50 ng/mL dox 48 hr


title: nasopharyngeal gene expression of subject M138 at w2 [121143011382]


title: beta cells sample F_WT_23B3

value: WT


title: nasopharyngeal gene expression of subject M129 at w2 [121143011292]


title: 201533620039_R04C01


title: 201533620012_R07C01


title: 201533620039_R01C01


title: 201533620048_R02C01


title: 201533620012_R08C01


title: beta cells sample F_KO_32C2


title: ChIP-ES-Tcf7l1-lowdensity_r1

description: Differentiation in -LIF for 72 hr


title: ChIP-ES-Tcf7l1-highdensity_r2

description: Differentiation in -LIF for 72 hr


title: beta cells sample F_KO_37A2


title: 201533620039_R03C01


title: ChIP-ES-Esrrb-input_r1

description: Differentiation in -LIF for 72 hr


title: beta cells sample F_KO_32C1


title: ChIP-ES-Tcf7l1-highdensity_r1

description: Differentiation in -LIF for 72 hr


title: nasopharyngeal gene expression of subject M128 at w2 [121143011282]


title: nasopharyngeal gene expression of subject M127 at w2 [121143011272]


title: beta cells sample F_KO_32A1


title: 201533620012_R05C01


title: 201533620012_R06C01


title: beta cells sample F_KO_25A3


title: 201533620012_R04C01


title: nasopharyngeal gene expression of subject M123 at w2 [121143011232]


title: nasopharyngeal gene expression of subject M122 at w2 [121143011222]


title: 201533620012_R03C01


title: nasopharyngeal gene expression of subject M120 at w2 [121143011202]


title: 201533620012_R02C01


title: nasopharyngeal gene expression of subject M119 at w2 [121143011192]


title: HFD1

city: PULLMAN

first: Liang

last: Zhao

state: WA

address: 100 Dairy Road

institute: Washington State University

description: scRNA-seq

data_processing:
Raw sequencing data were pre-processed with Cell Ranger (v3.0.2, 10x Genomics) mapping to the mouse mm10 transcriptome.
Cell transcriptomes were integrated in R using the Seurat package (v3.2.1). Dataset was normalized with a global-scaling normalization method (“LogNormalize”) with default parameters.
Genome_build: mouse mm10 transcriptome (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: mouse embryos

growth_protocol: Female mice were fed with either a control or high-fat diet for 10 weeks before breeding with male mice on a regular chow.

extract_protocol:
After mincing, embryo samples were incubated with TryLE Express dissociation reagent (Life Technology) at 37 °C for 15 min, swirled every two minutes, and the reaction was quenched with heat inactivated serum. After washing, the dissociated single-cell suspensions were re-suspended in PBS with 0.04% BSA and filtered through a 40 μm cell strainer.
After checking the viability and counting, single-cell suspensions of each group were loaded onto the Chromium Controller and cDNA libraries were constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 following the manufacturer’s protocol (10X Genomics, Inc.).

treatment_protocol: Mouse embryos were dissected and collected on embryonic 9.5 day. After removing the portion of head and first 7 somite pairs, the portion starting from the 8th somite pair till the tail end was collected. For each sample, a total of 15 embryos from three litters of maternal obese (MO) or lean (CT) mice respectively were pooled together for the preparation of cell suspension. One sample for the CT or MO was collected on the same day and repeated on a second day.

tag: tissue

value: embryos (8th somite pair to the tail end)

tag: developmental stage

value: embryonic 9.5 day

value: From high-fat diet fed maternal obese mice (MO)


title: ChIP-ES-Tcf7l1-input_r1

description: Differentiation in -LIF for 72 hr


title: beta cells sample F_KO_23B1

value: KO


title: beta cells sample F_HET_34B5


title: ChIP-ES-betacatenin-lowdensity_r1

description: Differentiation in -LIF for 72 hr


title: ChIP-ES-betacatenin-lowdensity_r2

description: Differentiation in -LIF for 72 hr


title: beta cells sample F_KO_21bB1


title: 201533620012_R01C01


title: 201533620011_R02C01


title: 201533620004_R08C01


title: beta cells sample F_HET_46A2


title: HFD2

description: scRNA-seq


title: nasopharyngeal gene expression of subject M116 at w2 [121143011162]


title: beta cells sample F_HET_30A1


title: nasopharyngeal gene expression of subject M114 at w2 [121143011142]


title: 201533620004_R05C01


title: CT2

description: scRNA-seq

value: From control-diet fed maternal lean mice (CT)


title: nasopharyngeal gene expression of subject M115 at w2 [121143011152]


title: beta cells sample F_HET_32A2

value: HET


title: 18294X11 4% STEM

city: Salt Lake City

first: Micah

middle: J

last: Drummond

state: Utah

address: 520 Wakara Way

department: Physical Therapy and Athletic Training

institute: The University of Utah

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 100.
The reference database was created using STAR version 2.7.3a with splice junctions optimized for 150 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.26.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited file with raw counts (featureCount output files combined into a single file).

growth_protocol: At ~ 95% confluency cells were treated with differentiation media (DMEM supplemented with 2% Horse Serum, Pen/Strep), for 5 days to achieve fully mature myotubes.

extract_protocol: Following 24 hour treatment period cells were washed with ice cold PBS and collected and processed for RNA isolation using Trizol and taken to the University of Utah Genomics Core for RNA Sequencing.

treatment_protocol: Upon completion of 5 days of differntiation, media was changed to either Control (DMEM supplemented with 4% Horse Serum, Pen/Strep) or STEM Treatment (DMEM supplemented with 4% STEM, Pen/Strep) for a duration of 24 hours.

tag: cell line

value: Mature Fully Differentiated Myotubes

value: 24 hours of STEM


title: nasopharyngeal gene expression of subject M112 at w2 [121143011122]


title: nasopharyngeal gene expression of subject M111 at w2 [121143011112]


title: beta cells sample F_HET_25A4

value: F


title: nasopharyngeal gene expression of subject M109 at w2 [121143011092]


title: beta cells sample F_HET_25A2


title: beta cells sample F_HET_23B2


title: 18294X10 4% STEM


title: 201533620004_R06C01


title: 18294X8 4% STEM


title: 201533620004_R07C01


title: nasopharyngeal gene expression of subject M110 at w2 [121143011102]


title: 18294X7 4% STEM


title: Patient #11 (Deceased)

city: Ancona

first: Jacopo

last: Sabbatinelli

state: AN

address: Via Tronto 10/A

department: Department of Clinical and Molecular Sciences

country: Italy

institute: Università Politecnica delle Marche

description: COVID-19 patient #11 (Dead)

data_processing:
Raw base-call data generated by the Illumina NextSeq 500 system were demultiplexed using Illumina BaseSpace Sequence Hub (https://basespace.illumina.com/home/index) and converted to FASTQ format.
After a quality check with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), sequence reads were quality trimmed using the cutadapt tool.
Sequence reads were aligned to the miRbase version 21.0 database using the STAR algorithm.
Raw counts from mapped reads were obtained using the htseq-count script from the HTSeq tools (http://www-huber.embl.de/HTSeq/doc/overview.html).
Raw counts were further normalized using DESeq2 bioconductor package (http://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated value (CSV) files including miRNA raw counts (COVID19_serum_hsa_miR_raw_counts.csv) and DESeq2-normalized counts (COVID19_serum_hsa_miR_normalized_counts.csv) for each sample.

source_name: Serum

extract_protocol:
Peripheral blood samples were collected in clot activator gel tubes (BD, United Kingdom). After two subsequent spins, total RNA, including small (< 200 nucleotides) RNAs, was extracted from serum using Norgen’s total RNA Purification Kit (cat. no. 37500, Norgen Biotek Corporation, Canada) according to the manufacturer’s protocol. Purified RNA was stored at −80°C until analysis.
Small RNA sequencing was performed in serum samples from 12 patients with severe COVID-19 (6 survivors, 6 deceased). TruSeq Small RNA Library PrepKit v2 (Illumina; RS-200-0012/24/36/48) was used for library preparation according to the manufacturer’s indications. Briefly, 35 ng purified RNA was linked to RNA 3’ and 5’ adapters, converted to cDNA, and amplified using Illumina primers containing unique indexes for each sample. Each library was quantified using Agilent Bioanalyzer and High Sensitivity DNA Kit (cat. no. 5067-4626, Agilent Technologies, USA) and equal amounts of libraries were pooled together. Size selection allowed keeping 130-160 bp fragments. After ethanol precipitation, the library pool was quantified with Agilent High Sensitivity DNA Kit, diluted to 1.8 pM, and sequenced using NextSeq® 500/550 High Output Kit v2 (75 cycles) (Illumina; FC-404-2005) on the Illumina NextSeq500 platform.

tag: disease

tag: prognosis

value: Death

value: Female


title: nasopharyngeal gene expression of subject M108 at w2 [121143011082]

value: nasopharyngeal cells


title: 201533620004_R01C01


title: Patient #10 (Deceased)

description: COVID-19 patient #10 (Dead)


title: 18294X6 4% Horse Serum Control

source_name: 18294X6 4% Horse Serum Control

value: 24 hours of 4% Horse Serum


title: 201533620004_R04C01

value: ERMS


title: nasopharyngeal gene expression of subject M106 at w2 [121143011062]


title: Patient #09 (Deceased)

description: COVID-19 patient #09 (Dead)


title: nasopharyngeal gene expression of subject M105 at w2 [121143011052]


title: Patient #12 (Deceased)

description: COVID-19 patient #12 (Dead)

value: Male


title: 18294X12 4% STEM


title: 201533620004_R02C01

value: ARMS


title: 18294X5 4% Horse Serum Control

source_name: 18294X5 4% Horse Serum Control


title: 201533620004_R03C01


title: 201533520040_R08C01


title: nasopharyngeal gene expression of subject M102 at w2 [121143011022]


title: nasopharyngeal gene expression of subject M104 at w2 [121143011042]


title: Patient #08 (Deceased)

description: COVID-19 patient #08 (Dead)


title: 18294X4 4% Horse Serum Control

source_name: 18294X4 4% Horse Serum Control


title: Patient #07 (Deceased)

description: COVID-19 patient #07 (Dead)


title: 18294X2 4% Horse Serum Control

source_name: 18294X2 4% Horse Serum Control


title: 201533520048_R03C01


title: 18294X9 4% STEM


title: Patient #06 (Survivor)

description: COVID-19 patient #06 (Survivor)

value: Survival


title: nasopharyngeal gene expression of subject M101 at w2 [121143011012]


title: nasopharyngeal gene expression of subject M100 at w2 [121143011002]


title: 18294X1 4% Horse Serum Control

source_name: 18294X1 4% Horse Serum Control


title: 18294X3 4% Horse Serum Control

source_name: 18294X3 4% Horse Serum Control


title: 201533520048_R08C01

value: Control


title: nasopharyngeal gene expression of subject M096 at w2 [121143010962]


title: nasopharyngeal gene expression of subject M099 at w2 [121143010992]


title: CT1

description: scRNA-seq

value: embryos (8th somite pair to the tail end)

value: embryonic 9.5 day


title: Patient #04 (Survivor)

description: COVID-19 patient #04 (Survivor)


title: 201533520048_R02C01


title: Patient #02 (Survivor)

description: COVID-19 patient #02 (Survivor)


title: Patient #03 (Survivor)

description: COVID-19 patient #03 (Survivor)


title: Patient #01 (Survivor)

description: COVID-19 patient #01 (Survivor)


title: nasopharyngeal gene expression of subject M080 at w2 [121143010802]


title: Patient #05 (Survivor)

description: COVID-19 patient #05 (Survivor)


title: nasopharyngeal gene expression of subject M090 at w2 [121143010902]


title: HCT116 ABHD5 knock down, biological rep3

city: Chongqing

first: juan

last: Ou

address: gaotanyan

country: China

institute: Army Medical University

description: Gene expression data from ABHD5 knockdown HCT116 cell line

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Human Genome PrimeView Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: Human colorectal cancer line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

value: colon cancer

tag: genotype

value: ABHD5 knockdown


title: 201533520040_R04C01


title: 201533520040_R07C01


title: 201533520040_R05C01


title: nasopharyngeal gene expression of subject M078 at w2 [121143010782]


title: nasopharyngeal gene expression of subject M071 at w2 [121143010712]


title: HCT116 ABHD5 knock down, biological rep1


title: HCT116 control, biological rep3

description: Gene expression data from Human colon cancer cell lines HCT116


title: NRVMs siSlc39a2_3

city: Shenzhen

first: Zhihua

last: Wang

address: No. 12, Langshan Road, Xili Street, Nanshan District, Shenzhen

department: Shenzhen Key Laboratory of Cardiovascular Disease

institute: Fuwai Hospital Chinese Academy of Medical Sciences, Shenzhen

data_processing:
BGI used BGISEQ platform for RNA-Seq
The raw data include low quality, contamination of joints, and high levels of unknown base n reads, which need to be removed before analysis to ensure the reliability of the results
The clean reads were align to the reference genome sequnence using HISAT
The clean reads were align to the reference genome sequnence using Bowtie2
Genome_build: NCBI, Rattus_norvegicus , GCF_000001895.5_Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: Neonatal rat ventricular myocytes (NRVMs)

growth_protocol: NRVMs were maintained in DMEM supplemented with 1% Insulin-Transferrin-Selenium (ITS-G, BD Biosciences, CA, USA), 100 U/mL penicillin and 100 μg/ml streptomycin.

extract_protocol:
RNA of NRVMs extracted according to the manufacturer's instructions using Trizol reagent.
RNA libraries were prepared for sequencing according to manufacturer's instructions of Beijing Genomics Institution (BGI)

treatment_protocol: NRVMs were first transfected with siSlc39a2 or siNeg, then treated with PE for 36h after 12h.

value: Sprague-Dawley (SD) Rat

tag: transfection

value: untreated


title: NCCIT_SVA_RA_NO_DOXY_H3K9me3

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
ChIP-seq and ATAC-seq data were aligned to hg19 or panTro5 as appropriate using BWA-mem
RNA-seq data were analyzed with kallisto using hg19 or panTro5 as appropriate
ATAC-seq peaks were called with MACS2.
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Genome_build: hg19 for Homo sapiens samples and panTro5 for Pan troglodytes samples.
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for input of Chip-seq

source_name: NCCIT-dCas-KRAB-SVA-sgRNA

growth_protocol: The iPSC lines were expanded in feeder-free, serum-free mTeSR™1 medium (STEMCELL Technologies). Cells were passaged ~1:10 at 80% confluency using ReLeSR (STEMCELL Technologies) and small cell clusters (50–200 cells) were subsequently plated on tissue culture dishes coated overnight with Geltrex™ LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix (Fisher-Scientific).

extract_protocol: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NovaSeq6000, producing 100x100 PE reads or the NextSeq500 producing 80x80 PE reads

treatment_protocol: The stem cells were treated with a previously published media for differentiation into hippocampal intermediate progenitors (Yu et al 2014). This consists of 1:1 DMEM/F12 supplemented with N2, B27, Noggin, Cyclopamine, DKK-1 and SB43154 and PennStrep antibiotic. The cells were exposed to this media for five days prior to collection.

tag: antibodies

value: H3K9 Tri-methyl Abcam ab8898


title: NCCIT_SVA_RA_DOXY_H3K9me3


title: HCT116 ABHD5 knock down, biological rep2


title: nasopharyngeal gene expression of subject M138 at w1 [121142011382]


title: HCT116 control, biological rep2


title: HCT116 control, biological rep1


title: 201533520040_R02C01


title: 201533520040_R01C01


title: nasopharyngeal gene expression of subject M139 at w1 [121142011392]


title: nasopharyngeal gene expression of subject M135 at w1 [121142011352]


title: NCCIT_SVA_RA_input (Control for ChIP)


title: NRVMs siSlc39a2_1


title: nasopharyngeal gene expression of subject M134 at w1 [121142011342]


title: 201533520040_R03C01


title: NRVMs siSlc39a2_2


title: 201533520026_R08C01


title: NCCIT_SVA_RA_DOXY_RNA_rep1

extract_protocol:
Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library


title: 201533520026_R06C01


title: 201533520026_R04C01


title: NCCIT_SVA_RA_NO_DOXY_RNA_rep3


title: NCCIT_SVA_RA_DOXY_RNA_rep3


title: 201533520026_R07C01

value: SC/SRMS


title: NRVMs siSlc39a2.PE_1

value: treated with PE for 36 hours


title: NRVMs siSlc39a2.PE_2


title: 201533520026_R05C01


title: 201533520040_R06C01


title: 201533520026_R02C01


title: 201533520001_R06C01


title: 201533520026_R01C01


title: nasopharyngeal gene expression of subject M132 at w1 [121142011322]


title: HEK393_cells_40S-seq_eIF4A1_KD

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
The adaptor and low quality bases of all sequencing data were removed by Cutadapt.
For Ribo-seq, the adaptor CTGTAGGCACCATCAAT was used. The first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428. For 80S-seq, 40S-seq and eIF3-seq, the adaptor was set as AAAAAAAAAA. The trimmed reads were aligned to mouse (human) transcriptome, using STAR with default parameters.
Genome_build: GRCm38/GRCh38
Supplementary_files_format_and_content: For Ribo-seq, the processed data files are tab separated read count. The first column is gene name, and the second column is footprint count on mRNAs. For 80S-seq, 40S-seq and eIF3-seq,  the processed data files are read count at individual sites of gene, which were seperated by comma. The first column is chromosome name, the second column is strand of the gene, the third column is gene name. The others are read count at individual sites of the gene. The read count section was seperated by colon. The first value is the genomic coordinate, the second value is the length of footprint, the third value is the count of footprint.

source_name: HEK293 40S ribo-seq eIF4A1 knockdown

growth_protocol: MEF and HEK293 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
For cell lysates, at least four 10 cm dishes of cells were harvested in 400 µl ice-cold polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2). Cells were then disrupted by vortexing six times for 20s using lysing matrix D (Fisher), followed by a 40 s interval each time on ice, then centrifuged at 12,000g, 4 °C for 10 min. Samples were then subjected to sucrose gradient sedimentation. Sucrose solutions were prepared in polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2 and 2% Triton X-100). A 15%-45% (w/v) sucrose density gradients were freshly prepared in SW41 ultracentrifuge tubes (Backman) using a Gradient Master (BioComp Instruments). 500 µl of supernatant from cell lysates prepared as described above was loaded onto sucrose gradients followed by centrifugation for 2.5 hr at 32,000 rpm, 4 °C in a SW41 rotor. Separated samples were fractionated at 1.5 ml min-1 through an automated fractionation system (Isco) that continually monitors OD254 values. Ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4 °C for 1 hr. SUPERase•In (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol LS reagent.
Fragmented RNAs were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 20-70 nt (for 40S-seq and eIF3-seq) or 25-35 nt (for Ribo-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 µl RNA gel elution buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.1 U/µl SUPERase•In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
Purified RNA fragments were re-suspended in Nuclease-free water, then dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase•In and 20 U T4 polynucleotide kinase). Dephosphorylated RNA fragments were precipitated using ethanol and re-suspended in Nuclease-free water. 0.15 μg linker (rApp/NNNNCTGTAGGCACCATCAAT/3ddC) then was added to the RNA fragments, heated at 70 °C for 90 s and then cooled to room temperature, followed by ligation for 3 hr at at 22 °C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase•In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 45-95 nt (for 40S-seq and eIF3-seq) or 60-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA gel elution buffer. RNA fragments were purified from RNA gel elution buffer as described earlier and re-suspended in Nuclease-free water. For reverse transcription, the following oligos containing barcodes were used:
(Phos)CTANNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)AGCNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)ATTNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)CCGNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
where Phos represents phosphorylation, NNN represents random sequence, SpC18 represents Hexa-ethyleneglycol spacer.
The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75 ° C for 3 min, followed by incubation on ice for at least 1 min. The reaction master mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel. Corresponding region was excised, which was expected to be approximately 200 nt. The first-strand cDNA products were recovered in DNA gel elution buffer (300 mM NaCl, 1 mM EDTA), then purified and re-suspended in Nuclease-free water as described earlier.
cDNA products were circularized in 20 μl of reaction containing 1×CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr and the reaction was heat inactivated at 80 °C for 10 min.

tag: cell line/type

tag: genotype/treatment

value: eIF4A1 knockdown

tag: molecule subtype

value: Ribosome associated RNA


title: NCCIT_SVA_RA_NO_DOXY_RNA_rep2

tag: cell type


title: nasopharyngeal gene expression of subject M129 at w1 [121142011292]

source_name: nasopharyngeal cells

tag: subject

value: nasopharyngeal cells


title: NRVMs siNeg.PE_3

tag: strain

value: siNeg

tag: treatment


title: NRVMs siNeg.PE_2


title: nasopharyngeal gene expression of subject M127 at w1 [121142011272]

tag: time point

tag: age


title: nasopharyngeal gene expression of subject M130 at w1 [121142011302]


title: nasopharyngeal gene expression of subject M128 at w1 [121142011282]


title: 201533520026_R03C01

source_name: rhabdomyosarcoma

tag: molecular group

value: ERMS


title: nasopharyngeal gene expression of subject M126 at w1 [121142011262]


title: 201533520001_R08C01


title: HEK393_cells_eIF3-seq_eIF4A1_KD

source_name: HEK293 eIF3 associated ribo-seq Control


title: NRVMs siNeg_3


title: NRVMs siNeg_2


title: HEK393_cells_eIF3-seq_Control


title: 201533520001_R04C01


title: NCCIT_SVA_RA_NO_DOXY_RNA_rep1


title: nasopharyngeal gene expression of subject M133 at w1 [121142011332]


title: HEK393_cells_80S-seq_eIF4A1_KD

source_name: HEK293  80S ribosome-seq eIF4A1 knockdown


title: nasopharyngeal gene expression of subject M122 at w1 [121142011222]


title: 201533520001_R07C01


title: NRVMs siNeg_1


title: nasopharyngeal gene expression of subject M123 at w1 [121142011232]


title: NCCIT_SVA_RA_DOXY_RNA_rep2


title: 201533520001_R02C01


title: HEK393_cells_80S-seq_Control

source_name: HEK293 80S ribosome-seq Control


title: Mid-ABX #810 Day 90

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

data_processing:
Library strategy: 16s rRNA seq
demultiplex
quality control
taxonomic analysis
alpha diversity analysis
beta diversity analysis
microbiome taxonomy differential abundane analysis
microbiome functional prediction
Genome_build: mm19/Silva-V34-classifier.qza
Supplementary_files_format_and_content: OTU table csv file

source_name: Feces

extract_protocol:
Fecal pellets were collected aseptically and placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. DNA was harvested using genomic DNA extraction kit and PCR with 16S V3-V4 region primer
RNA libraries were prepared for sequencing using standard Illumina 16S Metagenomic Sequencing Library Preparation protocols

value: BALB/c

value: three cycles of AOM/DSS and treated with ABX at day 56-63, sacrifice at day 90


title: nasopharyngeal gene expression of subject M120 at w1 [121142011202]


title: Mid-ABX #810 Day 63

value: three cycles of AOM/DSS and treated with ABX at day 56-63, sacrifice at day 63


title: Ex2-RIF-50mL

city: New York

first: Kohta

last: Saito

state: NY

address: 413 E 69th St

institute: Weill Cornell Medicine

description: H37Rv Transposon Library

data_processing:
Library strategy: Tn-Seq
Samples were processed by Macrogen according to their HiSeq protocols, with return of the raw fastq files
Raw fastq files were processed using TPP software (https://transit.readthedocs.io/en/latest/tpp.html), which extracts counts of transposon insertions at individual TA sites in the H37RvMA genome from TnSeq experiments.
Resulting wig output files are suitable for further analysis using TRANSIT software (https://transit.readthedocs.io/en/latest/index.html)
Genome_build: NC_000962 (Specific sequenced strain for H37RvMA: http://www.ncbi.nlm.nih.gov/pubmed/20472797; available with TPP software: https://transit.readthedocs.io/en/latest/index.html)
Supplementary_files_format_and_content: wig file outputs from TPP software that mapped TA sites to the H37Rv genome and reduced to unique template counts for subsequent use in TRANSIT software

organism: Mycobacterium tuberculosis

source_name: Transposon Library cell culture

growth_protocol: See "Characteristics" field for sample-s[ecific details. The Mtb H37Rv transposon library was constructed by himar1 mutagenesis as described (J. E. Long, M. DeJesus, D. Ward, R. E. Baker, T. Ioerger, C. M. Sassetti, Identifying essential genes in Mycobacterium tuberculosis by global phenotypic profiling. Methods Mol Biol 1279, 79-95 (2015).)

extract_protocol:
After harvesting the cells, DNA was extracted using a published CTAB protocol (M. H. Larsen, K. Biermann, S. Tandberg, T. Hsu, W. R. Jacobs Jr, Genetic manipulation of Mycobacterium tuberculosis. Current protocols in microbiology 6, 10A. 12.11-10A. 12.21 (2007).)
DNA was sheared using a focused-ultrasonicator (Covaris) and purified using a QIAquick PCR purification kit (Qiagen). Sheared DNA underwent end repair and A-tailing using NEBNext Ultra End Repair/dA-Tailing Module (New England Biolabs). Products were again purified with the QIAquick.  PCR purification kit (Qiagen), and then underwent adaptor ligation with T4 ligase (NEB) overnight. DNA of >100 base pairs was subsequently purified with AMPure XP beads (Beckman Coulter) and a DynaMag-2 magnet (Thermo Fisher). DNA products were PCR amplified using Choice Taq polymerase (Denville Scientific), and purified with QIAquick PCR purification kit (Qiagen). Appropriate DNA size (300-400 BP) was selected using a Pippin Prep machine (Sage Science) and corresponding precast 2% agarose gel cassette (Sage Science) as per the manufacturer’s protocol. A second hemi-nested PCR amplification with indexing was performed, followed by another PCR purification and quantification using dsDNA Broad Range Qubit Kit (Life Technologies). Samples were shipped to Macrogen for quality control, further processing, and sequencing using HiSeq 2500 (Illumina).

tag: culture media

value: Phosphate buffered saline with 0.02% tyloxapol

value: Rifampin 100 microM

tag: library outgrowth conditions

value: 50mL 7H9 media with glycerol, OADC, tyloxapol, and 50 ug/mL of kanamycin

tag: growth protocol

value: Nutrient starved for 2 weeks, followed by 5 days of indicated treatment


title: Ex1-RIF-Agar

description: H37Rv Transposon Library

value: 7H10 agar plates with glycerol, OADC, tyloxapol, and 50 ug/mL of kanamycin


title: Mid-ABX #810 Day 56

value: three cycles of AOM/DSS and sacrifice at day 56


title: nasopharyngeal gene expression of subject M119 at w1 [121142011192]


title: nasopharyngeal gene expression of subject M118 at w1 [121142011182]


title: Ex1-RIF-50mL

description: H37Rv Transposon Library


title: nasopharyngeal gene expression of subject M117 at w1 [121142011172]


title: NRVMs siSlc39a2.PE_3

value: Sprague-Dawley (SD) Rat


title: 201533520001_R01C01


title: 201533520001_R03C01


title: Ex2-RIF-5mL

description: H37Rv Transposon Library

value: 5mL 7H9 media with glycerol, OADC, tyloxapol, and 50 ug/mL of kanamycin


title: Ex2-RIF-Agar

description: H37Rv Transposon Library


title: Mid-ABX #810 Day 0

value: No traetment and sacrifice at day 0


title: Mid-ABX #809 Day 90


title: nasopharyngeal gene expression of subject M115 at w1 [121142011152]


title: Ex1-RIF-5mL

description: H37Rv Transposon Library


title: nasopharyngeal gene expression of subject M116 at w1 [121142011162]


title: NRVMs siNeg.PE_1

value: treated with PE for 36 hours


title: Mid-ABX #809 Day 63


title: nasopharyngeal gene expression of subject M110 at w1 [121142011102]


title: HEK393_cells_40S-seq_Control

source_name: HEK293 40S ribo-seq Control

value: Control

value: Ribosome associated RNA


title: Mid-ABX #809 Day 56


title: Ex1-DMSO-Agar

description: H37Rv Transposon Library

value: 1% DMSO


title: nasopharyngeal gene expression of subject M109 at w1 [121142011092]

value: nasopharyngeal cells


title: 201492570224_R03C01

value: ARMS


title: Mid-ABX #809 Day 0

value: BALB/c


title: Ex2-DMSO-50mL

description: H37Rv Transposon Library


title: Ex2-DMSO-Agar

description: H37Rv Transposon Library


title: nasopharyngeal gene expression of subject M107 at w1 [121142011072]


title: 201492570224_R08C01


title: 201492570224_R05C01

value: ERMS


title: 201492570224_R07C01


title: Mid-ABX #808 Day 90

value: three cycles of AOM/DSS and treated with ABX at day 56-63, sacrifice at day 90


title: Ex1-DMSO-50mL

description: H37Rv Transposon Library

value: Phosphate buffered saline with 0.02% tyloxapol


title: 201492570224_R06C01


title: Mid-ABX #808 Day 63

value: three cycles of AOM/DSS and treated with ABX at day 56-63, sacrifice at day 63


title: nasopharyngeal gene expression of subject M106 at w1 [121142011062]


title: nasopharyngeal gene expression of subject M105 at w1 [121142011052]


title: Ex2-DMSO-5mL

description: H37Rv Transposon Library

value: Nutrient starved for 2 weeks, followed by 5 days of indicated treatment


title: Mid-ABX #808 Day 56


title: Mid-ABX #808 Day 0


title: Ex2-Starved-Agar

description: H37Rv Transposon Library

value: 7H10 agar plates with glycerol, OADC, tyloxapol, and 50 ug/mL of kanamycin

value: Nutrient starved for 2 weeks


title: Ex1-DMSO-5mL

description: H37Rv Transposon Library


title: Ex1-Starved-Agar

description: H37Rv Transposon Library


title: nasopharyngeal gene expression of subject M102 at w1 [121142011022]


title: nasopharyngeal gene expression of subject M101 at w1 [121142011012]


title: nasopharyngeal gene expression of subject M100 at w1 [121142011002]


title: Ctrl #813 Day 90

value: three cycles of AOM/DSS and sacrifice at day 90


title: nasopharyngeal gene expression of subject M099 at w1 [121142010992]


title: 201247490021_R05C01


title: 201247490021_R08C01


title: Ex1-Starved-50mL

description: H37Rv Transposon Library

value: 50mL 7H9 media with glycerol, OADC, tyloxapol, and 50 ug/mL of kanamycin


title: Ctrl #813 Day 0

value: No traetment and sacrifice at day 0


title: 201492570102_R02C01


title: Ex2-Starved-5mL

description: H37Rv Transposon Library

value: 5mL 7H9 media with glycerol, OADC, tyloxapol, and 50 ug/mL of kanamycin


title: nasopharyngeal gene expression of subject M097 at w1 [121142010972]


title: 201247490021_R06C01


title: Ctrl #813 Day 63

value: three cycles of AOM/DSS and sacrifice at day 63


title: 201492570224_R01C01


title: Ex1-Starved-5mL

description: H37Rv Transposon Library


title: 201247490021_R04C01


title: 201247490021_R07C01


title: Ctrl #812 Day 63


title: 201247490021_R03C01


title: Ex2-Inoculum-Agar

description: H37Rv Transposon Library

value: 7h9 with glycerol, OADC, tyloxapol, and 50 ug/mL of kanamycin

value: Cells grown in nutrient rich media


title: 201492570102_R04C01


title: 201492570224_R02C01


title: Ctrl #812 Day 56

value: three cycles of AOM/DSS and sacrifice at day 56


title: Ctrl #813 Day 56


title: Ex1-Inoculum-Agar

description: H37Rv Transposon Library


title: Ex2-Starved-50mL

description: H37Rv Transposon Library


title: Ctrl #812 Day 0


title: 201247470019_R05C01


title: Ex2-Inoculum-50mL

description: H37Rv Transposon Library


title: nasopharyngeal gene expression of subject M096 at w1 [121142010962]

value: nasopharyngeal cells


title: 201247470019_R04C01


title: Ctrl #811 Day 90

value: BALB/c


title: nasopharyngeal gene expression of subject M139 at d1 [121141011392]


title: 201247470019_R07C01

value: ERMS


title: nasopharyngeal gene expression of subject M078 at w1 [121142010782]


title: Ctrl #812 Day 90


title: Ex1-Inoculum-50mL

description: H37Rv Transposon Library


title: nasopharyngeal gene expression of subject M138 at d1 [121141011382]


title: 201247490021_R02C01


title: Ex1-Inoculum-5mL

description: H37Rv Transposon Library


title: nasopharyngeal gene expression of subject M135 at d1 [121141011352]


title: Ex2-Starved-C

description:
Nutrient starved for 2 weeks
DMSOvsDay0_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
day0-C

data_processing:
10-20 x 10^6 paired-end reads were obtained for each sample replicate on an Illumina HiSeq 2500.
Post-run de-multiplexing and adapter removal were performed and fastq files were inspected using fastqc
Trimmed fastq files were then aligned to the reference genome
Bam files were sorted and merged using SAMtools
Gene counts were obtained using featureCounts from the Bioconductor Rsubread package; differentially expressed genes were identified using the DESeq2 R package
Genome_build: NC_000962.3
Supplementary_files_format_and_content: text files for differentially expressed genes among conditions, with FPKM data

source_name: H37Rv Mtb

extract_protocol:
After incubation in RNAprotect, samples were lysed in TRIzol (Invitrogen) with bead beating, and RNA was extracted using RNeasy mini kit (Qiagen) as per manufacturer protocol.
Sample libraries were prepared for RNA-seq using the Ribo-Zero Magnetic Bacterial kit (Epicentre) in conjunction with TruSeq Stranded Total RNA kit (Illumina).


title: nasopharyngeal gene expression of subject M090 at w1 [121142010902]


title: Ctrl #811 Day 63


title: Late-ABX #888 Day73

tag: stain

value: three cycles of AOM/DSS and treated with ABX at day 66-73


title: nasopharyngeal gene expression of subject M098 at w1 [121142010982]


title: Ex2-Starved-B

description:
Nutrient starved for 2 weeks
DMSOvsDay0_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
day0-B

value: Phosphate buffered saline with 0.02% tyloxapol


title: Ctrl #811 Day 56


title: nasopharyngeal gene expression of subject M130 at d1 [121141011302]


title: Ex2-Inoculum-5mL

description: H37Rv Transposon Library


title: 201247470019_R03C01


title: nasopharyngeal gene expression of subject M133 at d1 [121141011332]


title: nasopharyngeal gene expression of subject M132 at d1 [121141011322]


title: 201247470019_R01C01


title: 201247470019_R06C01


title: Late-ABX #820 Day73


title: 201247470016_R02C01

value: ARMS


title: 201247470019_R02C01


title: Late-ABX #818 Day73


title: 201247470019_R08C01


title: nasopharyngeal gene expression of subject M122 at d1 [121141011222]


title: 201172580053_R08C01


title: Ex2-RIF100-A

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Rif100vsDMSO_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
DMSOvsDay0_DESeq2normalized.txt
Rif100-A

value: Rifampin 100 microM


title: Mid-ABX #885 Day63

value: three cycles of AOM/DSS and treated with ABX at day 56-63


title: nasopharyngeal gene expression of subject M117 at d1 [121141011172]


title: Ctrl #811 Day 0


title: 201247470016_R01C01


title: Ex2-RIF10-C

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
DMSOvsDay0_DESeq2normalized.txt
Rif10-C

value: Rifampin 10 microM


title: Mid-ABX #883 Day63


title: Ex2-Starved-A

description:
Nutrient starved for 2 weeks
DMSOvsDay0_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
day0-A


title: nasopharyngeal gene expression of subject M129 at d1 [121141011292]


title: nasopharyngeal gene expression of subject M116 at d1 [121141011162]


title: Mid-ABX #882 Day63


title: Ex2-RIF100-C

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Rif100vsDMSO_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
DMSOvsDay0_DESeq2normalized.txt
Rif100-C


title: nasopharyngeal gene expression of subject M119 at d1 [121141011192]


title: Late-ABX #817 Day73


title: Mid-ABX #810 Day63


title: Ex2-RIF10-A

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
DMSOvsDay0_DESeq2normalized.txt
Rif10-A


title: Ex2-RIF10-B

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
DMSOvsDay0_DESeq2normalized.txt
Rif10-B


title: Ex2-RIF100-B

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Rif100vsDMSO_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
DMSOvsDay0_DESeq2normalized.txt
Rif100-B


title: nasopharyngeal gene expression of subject M115 at d1 [121141011152]


title: Mid-ABX #808 Day63


title: Ex2-DMSO-C

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
DMSOvsDay0_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
DMSO-C

value: 1% DMSO


title: KO2

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
B2

hyb_protocol: Samples were processed on the NanoString nCounter Flex System per manufacturer instructions

scan_protocol: using the nCounter Mouse PanCancer Pathways panel

data_processing: Within nSolver (4.0) the nCounter Advanced Analysis (version 2.0.134) was run using the raw data in order to predict the best housekeeping genes to use (based on the gnorm program). 14 housekeeping genes were used (discarded Hprt, Eef1g, Polr2a, Alas1, G6pdx, Gusb). Differentially expressed genes were identified as genes with a p value of less than 0.05 versus the respective baseline control.

label: NanoString

source_name: CD45-tumor cells

label_protocol: 100 ng of purified RNA was added to 3 μL of Reporter CodeSet and 2 μL Capture ProbeSet using an nCounter master kit as recommended (NanoString Technologies)

extract_protocol: Total RNA was extracted using a QIAshredder kit (QIAGEN) and an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s protocol.

tag: genotype

value: Prdm1fl/flFoxP3YFP-Cre (KO)

tag: tissue

value: Tumor

tag: tumor stage

value: less than or equal to 1.5 cm3


title: KO1

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
B1


title: nasopharyngeal gene expression of subject M112 at d1 [121141011122]


title: nasopharyngeal gene expression of subject M111 at d1 [121141011112]


title: 201172580053_R07C01


title: 201172580053_R06C01

value: SC/SRMS


title: WT2

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
A2

value: FoxP3YFP-Cre (WT)


title: nasopharyngeal gene expression of subject M110 at d1 [121141011102]


title: Ex2-DMSO-B

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
DMSOvsDay0_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
DMSO-B


title: Early-ABX #804 Day53

value: three cycles of AOM/DSS and treated with ABX at day 46-53


title: Ex2-DMSO-A

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
DMSOvsDay0_DESeq2normalized.txt
Rif10vsDMSO_DESeq2normalized.txt
Rif100vsDMSO_DESeq2normalized.txt
DMSO-A


title: 201172580053_R03C01


title: 210111_Resolution_sir3-8-EcoGII_37C_m6A_DIP

city: Berkeley

first: Molly

last: Brothers

state: CA

address: UC Berkeley 440 Barker Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
FASTQ generation with Illumina Casava v2.2
Raw reads were mapped to SacCer3 genome modified to include  mat∆ using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA)
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: bedGraph (normalized to genome-wide median)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast were cultured at 30°C in YPD except for the following: Samples 21 and 22 were grown at 25°C in YPD. Samples 23 and 24 were grown at 37°C in YPD.

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin or DNA was fragmented using sonication. V5 immunoprecipitations were performed using anti-V5 antibody (Invitrogen R960-25). m6A immunoprecipitations were performed using anti-m6A antibody (Synaptic Systems 202-003). For ChIP-seq, DNA was purified with 1X v/v SPRI Select beads (Beckman-Coulter Beckman Coulter, B23317)
For ChIP-seq: NEB Ultra II library prep kit. For MeDIP-seq: Swift Biosciences Accel-NGS 1S Plus
ChIP-seq and MeDIP-seq

treatment_protocol: For ChIP-seq experiments (Samples 1 and 2), cells were fixed in 1% formaldehyde for 15 minutes at 30°C and then quenched with 300mM glycine for 10min at 30°C.

tag: ip antibody

value: anti-m6A antibody (Synaptic Systems 202-003, lot 2-109)

tag: condition

value: Cycling at 37C

value: mat-delta::KanMX, sir3-8-M.ECOGII-NatMX


title: Early-ABX #801 Day53

value: BALB/c


title: 210111_Resolution_sir3-8-EcoGII_37C_m6A_input


title: Early-ABX #879 Day53


title: WT1

description:
3 μL of Reporter CodeSet and 2 μL Capture ProbeSet
A1


title: 210111_Resolution_sir3-8-EcoGII_25C_m6A_DIP

value: Cycling at 25C


title: 201172580047_R07C01


title: nasopharyngeal gene expression of subject M104 at d1 [121141011042]

value: nasopharyngeal cells


title: nasopharyngeal gene expression of subject M099 at d1 [121141010992]


title: 201172580053_R01C01

value: ERMS


title: nasopharyngeal gene expression of subject M098 at d1 [121141010982]


title: Ex1-LogPhase-A

description:
Logarithmically growing cells in nutrient rich media
LogPhaseVSDay0.txt
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
LogPhase-A

value: 7h9 with glycerol, OADC, and tyloxapol


title: 210111_Resolution_sir3-8-EcoGII_25C_m6A_input


title: Early-ABX #802 Day53


title: nasopharyngeal gene expression of subject M106 at d1 [121141011062]


title: Ctrl #812 Day0

value: No treatment


title: 201172580053_R02C01

value: ARMS


title: 201172580053_R05C01


title: Ex1-Starved-B

description:
Nutrient starved for 2 weeks
LogPhaseVSDay0.txt
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
day0-B

value: Phosphate buffered saline with 0.02% tyloxapol


title: 210716_Solo_sir3-bahD-EcoGII_m6A_input

value: Cycling


title: nasopharyngeal gene expression of subject M136 at d0 [121140011362]


title: 210716_Solo_SIR3-EcoGII_m6A_DIP

value: mat-delta::HphMX, SIR3-M.ECOGII-NatMX


title: Ex1-Starved-A

description:
Nutrient starved for 2 weeks
LogPhaseVSDay0.txt
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
day0-A


title: Ex1-RIF100-C

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
LogPhaseVSDay0.txt
Rif100-C

value: Rifampin 100 microM


title: Ex1-Starved-C

description:
Nutrient starved for 2 weeks
LogPhaseVSDay0.txt
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
day0-C


title: Ex1-RIF100-B

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
LogPhaseVSDay0.txt
Rif100-B


title: 210716_Solo_sir3-bahD-EcoGII_m6A_DIP


title: nasopharyngeal gene expression of subject M135 at d0 [121140011352]


title: 210716_Solo_SIR3-EcoGII_m6A_input


title: Ctrl #808 Day0


title: 201172580047_R06C01


title: 201172580053_R04C01


title: nasopharyngeal gene expression of subject M134 at d0 [121140011342]


title: 201172580047_R08C01


title: Ex1-LogPhase-B

description:
Logarithmically growing cells in nutrient rich media
LogPhaseVSDay0.txt
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
LogPhase-B


title: PC3_siAZIN1_Rep3

city: Leuven

first: Thomas

last: Van den Broeck

state: Outside U.S./Canada

address: Herestraat, 49

country: Belgium

institute: KU Leuven

data_processing:
Final libraries were pooled and sequenced on the HISeq 2500 (Illumina), generating reads of 50 bp length
After removing adapter sequences, reads were mapped to the human reference genome (GRCh37 - Hg19) using TopHat with default settings.
Reads were aggregated with HT-Seq and DESeq was used to normalize and calculate differential expression between conditions.
Genome_build: GRCh37 - Hg19
Supplementary_files_format_and_content: Absolute counts
Supplementary_files_format_and_content: foldChange and log2FoldChange of siAZIN versus siScr (DESeq)

source_name: Prostate

growth_protocol: PC3 cells were plated on 6 cm plates (0.5 × 106 cells/well)

extract_protocol:
RNA was extracted according to the RNeasy protocol (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Day 1 after plating, cells were lipofected with siAZIN1 or siScr. Between 48 and 72 hours post lipofection, cells were harvested for RNA extraction.

value: KD AZIN1 (siAZIN1)


title: nasopharyngeal gene expression of subject M071 at d1 [121141010712]

extract_protocol: RNA was extracted by a TRIzol reagent (Invitrogen)/chlorform method, cleaned using the RNAeasy Micro Kit (Qiagen) (OpenWetWare contributors, 2015)


title: Ctrl #810 Day0


title: Ex1-LogPhase-C

description:
Logarithmically growing cells in nutrient rich media
LogPhaseVSDay0.txt
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
LogPhase-C


title: PC3_siAZIN1_Rep2


title: Ctrl #809 Day0


title: 201172580047_R01C01

extract_protocol: Data were generated from formalin-fixed paraffin-embedded (FFPE) tissue samples. DNA of 158 patients was extracted and hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays


title: Ex1-RIF10-C

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5Rif10VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif100VSDay5DMSO.txt
LogPhaseVSDay0.txt
Rif10-C

value: Rifampin 10 microM


title: 210716_Solo_sir3D-EcoGII_m6A_input


title: 201172580047_R03C01


title: 201172580047_R05C01


title: 201172580047_R04C01

value: PRMS


title: PC3_siScr_Rep3

value: Control (siScr)


title: Ex1-RIF10-A

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5Rif10VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif100VSDay5DMSO.txt
LogPhaseVSDay0.txt
Rif10-A


title: 210114_Birthday_SIR3-EcoGII_m6A_input

value: anti-m6A antibody (Synaptic Systems 202-003, lot 2-109)


title: 210114_Birthday_sir3D-EcoGII_m6A_DIP


title: Ex1-RIF10-B

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5Rif10VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif100VSDay5DMSO.txt
LogPhaseVSDay0.txt
Rif10-B


title: 201172580047_R02C01


title: 210114_Birthday_SIR3-EcoGII_m6A_DIP


title: nasopharyngeal gene expression of subject M130 at d0 [121140011302]


title: PC3_siAZIN1_Rep1


title: nasopharyngeal gene expression of subject M132 at d0 [121140011322]


title: Ex1-DMSO-C

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
Day5Rif100VSDay5DMSO.txt
LogPhaseVSDay0.txt
DMSO-C

value: 1% DMSO


title: PC3_siScr_Rep2


title: nasopharyngeal gene expression of subject M119 at d0 [121140011192]


title: nasopharyngeal gene expression of subject M126 at d0 [121140011262]


title: 210114_Birthday_sir3D-EcoGII_m6A_input


title: nasopharyngeal gene expression of subject M122 at d0 [121140011222]


title: PC3_siScr_Rep1


title: FW_P4_Donor3

city: Rotterdam

first: Derk

last: ten Berge

state: Zuid-Holland

address: Postbus 2040

department: Cell Biology

institute: Erasmus MC

data_processing:
Alignment: data was aligned with TopHat & Bowtie2 (paired-end read,  inner-mate distance 50 bp) to refseq human genome hg19
Gene Expression: Cufflinks was used to generate gene expression levels, reference data set used was the UCSC refseq annotation for hg19, transcripts and genes were counted.
Expression/counts are reported in FPKM
Genome_build: hg19
Supplementary_files_format_and_content: table with raw gene counts for every gene and every sample

source_name: in vitro cultured bone marrow multipotent stromal cells

growth_protocol: Bone marrow aspirates from three post-menopausal women (ages: 64, 64, 73) were isolated from femoral bone marrow aspirates of adults undergoing total hip replacement (given informed consent). Bone marrow aspirates were diluted with expansion medium to 20 ml and plated in 175cm2 culture flasks. MSCs expansion medium consisted of: MEM-α (Gibco brand, Thermo-Fisher), containing 10% heat-inactivated FCS (Gibco brand, Thermo-Fisher), 50 μg/mL gentamicin (Invitrogen Life Technologies brand, Thermo-Fisher), 1.5 μg/ml amphotericin B [Fungizone™] (Invitrogen Life Technologies brand, Thermo-Fisher), 10-4 M L-ascorbic acid 2-phosphate (Sigma-Aldrich) and 1 ng/mL basic Fibroblast Growth Factor 2 [FGF2] (R&D Systems, Minneapolis, USA ems). After 24 hours, the flasks were gently washed with PBS containing 1% FCS and adherent cells expanded in expansion medium, refreshed every three day for nine days.

extract_protocol:
Cells were transferred from incubator onto ice, medium aspirated and immediately 0.1 ml phenol/guanidine thiocyanate solution (TriPure Isolation Reagent; Sigma-Aldrich) per cm2 culture surface added to each cell culture well. The solution of lysed cells was then homogenized by pipetting, incubated for 15 minutes at RT, and RNA isolated using a chloroform-ethanol extraction according to the TriPure Isolation Reagent protocol.
RNA sequencing library was prepared using the Trueseq kit (Illumina, Eindhoven, the Netherlands). Average amount of paired reads per sample were 30 million and sequencing was performed with a Illumina HiSeq 2000 (Illumina). Data was aligned (paired-end read, inner-mate distance 50 bp) to refseq human genome hg19 using TopHat & Bowtie2. Cufflinks was used to generate gene expression levels, the UCSC refseq annotation for hg19 reference data was used as reference set and transcripts and genes were counted.

treatment_protocol: For each donor, the cells were passaged (after steps described in growth protocol) into expansion medium without additional components (10,000 cells/cm2), with vehicle CHAPS (2,300 cells/cm2) or with 250 ng/ml WNT3A (2,300 cells/cm2). WNT3A = recombinant mouse WNT3A, made in house by genetically modified Schneider Drosophila melanogaster S2 cells; CHAPS = 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate hydrate (CHAPS) (Sigma-Aldrich). After 24 hours, the flasks without additional components were switched to expansion medium: without FGF2 and with CHAPS, with FGF2 and with CHAPS, without FGF2 and with WNT3A, with FGF2 and with WNT3A. After six hours, these cells (passage 1 samples) were harvested as described under extraction protocol. Cells in the remaining two flasks, cultured with CHAPS or WNT3A from the beginning, were expanded with daily refreshing of the expansion medium with CHAPS or WNT3A respectively, until 80% confluence was reached and then passaged to 2,300 cells/cm2. MSCs were expanded in this way until expansion ceased. At passage four, WNT3A and CHAPS expanded cells were plated (10,000 cells/cm2) after 24 hours the medium was refreshed and six hours later the cells (passage 4 samples) harvested as described under extraction protocol.

tag: donor id

tag: donor sex

value: female

value: femoral bone marrow multipotent stromal cells

tag: passage

value: FGF2 + WNT3A


title: Ctrl #813 Day0

value: BALB/c


title: 210114_Birthday_no-EcoGII_m6A_input

tag: strain


title: Ex1-DMSO-B

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
Day5Rif100VSDay5DMSO.txt
LogPhaseVSDay0.txt
DMSO-B

tag: treatment


title: nasopharyngeal gene expression of subject M133 at d0 [121140011332]

data_processing: The data were analyzed using R/Rstudio. Outliers were identified using raw intensity data using the arrayQualityMetrics package and removed from the dataset. RMA was performed to reduce the data from 300304 probe-level features to 27189 genes. After removing non-annotated genes/control probes, 18526 genes remained, which were for the conclusions in the paper.

tag: subject

tag: time point

tag: cell type

value: nasopharyngeal cells


title: FW_P1_Donor3


title: VW_P1_Donor3

value: WNT3A only


title: FC_P1_Donor3

value: FGF2 + CHAPS


title: FC_P4_Donor3


title: 210716_Solo_sir3D-EcoGII_m6A_DIP


title: 200808_Chase_sir3D-EcoGII_m6A_DIP


title: nasopharyngeal gene expression of subject M117 at d0 [121140011172]

tag: age


title: nasopharyngeal gene expression of subject M116 at d0 [121140011162]


title: 200808_Chase_sir3D-EcoGII_m6A_input


title: Ex1-DMSO-A

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
Day5Rif100VSDay5DMSO.txt
LogPhaseVSDay0.txt
DMSO-A

tag: culture media

value: Phosphate buffered saline with 0.02% tyloxapol


title: 200808_Chase_SIR3-EcoGII_m6A_DIP

value: Cycling


title: nasopharyngeal gene expression of subject M115 at d0 [121140011152]


title: 210122_Crabby_Sir3-MEcoGII-3xV5_ChIP

value: anti-V5 antibody (Invitrogen R960-25 lot 2330339)


title: 200808_Chase_no-EcoGII_m6A_input


title: FW_P4_Donor2


title: 200808_Chase_no-EcoGII_m6A_DIP


title: nasopharyngeal gene expression of subject M106 at d0 [121140011062]


title: nasopharyngeal gene expression of subject M118 at d0 [121140011182]


title: FC_P4_Donor2


title: nasopharyngeal gene expression of subject M112 at d0 [121140011122]


title: FC_P1_Donor2


title: Ctrl #811 Day0

value: No treatment


title: nasopharyngeal gene expression of subject M110 at d0 [121140011102]


title: FW_P1_Donor2


title: nasopharyngeal gene expression of subject M099 at d0 [121140010992]


title: 210122_Crabby_Sir3-MEcoGII-3xV5_input


title: nasopharyngeal gene expression of subject M104 at d0 [121140011042]


title: nasopharyngeal gene expression of subject M097 at d0 [121140010972]


title: FW_P4_Donor1


title: Dbp siRNA-3 (RNA-seq)

city: Cambridge

first: Matthew

middle: R

last: Brown

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
Illumina's RTA version 2.7.7. for basecalling
RNA-sequencing reads were first mapped to the mm10 or rn6 build of the mouse and rat reference genome, respectively, using HISAT v2.1.0 with default settings. FeatureCounts v2.0.0 from the Subread package was used to count mapped gene-level reads. Gene count matrices were uploaded into the edgeR v3.28.1 package and normalized to counts per million (CPM) reads using the default Trimmed Mean of M-values (TMM) method.
Genome_build: mm10, rn6
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA was isolated from freshly picked mouse islets or transfected INS-1 832/13 cells using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA size and quality were assessed using the Tape Station Bionalyzer (Agilent, Santa Clara, CA), and concentration was determined by Qubit fluorometry. RNA libraries were prepared using 100 ng of total RNA.
RNA libraries were prepared using polyA selection method (Illumina, San Diego, CA) according to manufacturer's instructions.

tag: cell line

value: Pancreatic beta cell

value: Dbp siRNA


title: Dbp siRNA-1 (RNA-seq)


title: nasopharyngeal gene expression of subject M102 at d0 [121140011022]

city: Utrecht

first: Wouter

last: de Steenhuijsen Piters

address: Heidelberglaan 100

institute: UMC Utrecht


title: nasopharyngeal gene expression of subject M138 at d0 [121140011382]


title: VW_P1_Donor2


title: nasopharyngeal gene expression of subject M071 at d0 [121140010712]


title: Dbp siRNA-2 (RNA-seq)


title: VC_P1_Donor2

value: CHAPS only


title: FW_P1_Donor1


title: FC_P4_Donor1


title: 34C Late exponential phase R1

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: 34C vs 37C late exponential phase R1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of rokA mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F650 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown C+Y medium on different temperatures (34, 37 or 40C) and harvested at OD600 of 0.3 (mid exponential phase) and 0.70 (late exponential phase).

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: growth

value: Grown at 34C till late exponential phase

source_name: F550 Mean

value: Grown at 37C till late exponential phase


title: 34C Mid exponential phase R2

description: 34C vs 37C mid exponential phase R2

value: Grown at 34C till mid exponential phase

value: Grown at 37C till mid exponential phase


title: Scramble siRNA-3 (RNA-seq)

value: Scramble siRNA


title: 40C Mid exponential phase R2

description: 40C vs 37C mid exponential phase R2

value: Grown at 40C till mid exponential phase


title: FC_P1_Donor1

value: female

value: femoral bone marrow multipotent stromal cells


title: 34C Late exponential phase R2

description: 34C vs 37C late exponential phase R2


title: 40C Mid exponential phase R1

description: 40C vs 37C mid exponential phase R1


title: VC_P1_Donor1


title: Scramble siRNA-2 (RNA-seq)


title: 34C Mid exponential phase R1

description: 34C vs 37C mid exponential phase R1


title: 1h untreated relA- mutant [3C]

status: Public on Nov 23 2021

city: Omaha

first: Scot

middle: P

last: Ouellette

state: NE

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

description:
rRNA depleted
Processed RNAseq data for GAS
3C

data_processing:
original fastq format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns), and low quality 3’ regions (Phred score < 30)
trimmed fastq files were processed by FastQC
fastq files were mapped to Chlamydia trachomatis 434/Bu or Streptococcus pyogenes NZ131 by CLC Genomics Workbench 12 for RNAseq analyses
read counts were modeled using Generalized Linear Model (GLM), assuming a negative binomial distribution, and reported as transcripts per million (TPM)
Wald test was used for statistical analysis of two-group comparisons
Genome_build: http://bacteria.ensembl.org/Chlamydia_trachomatis_434_bu_gca_000068585/Info/Index or http://bacteria.ensembl.org/Streptococcus_pyogenes_nz131_gca_000018125/Info/Index
Supplementary_files_format_and_content: excel file showing fold changes and statistical significance between timepoints and treatment conditions

organism: Streptococcus pyogenes NZ131

source_name: Pure bacterial culture

growth_protocol: HEp2 cells were infected with C. trachomatis L2 and treated or not at 10hpi with inducers of amino acid starvation. Samples were collected at 10, 14, and 24hpi. S. pyogenes strains were cultured for 1h in the presence or absence of tryptophan.

extract_protocol:
Total RNA was collected from C. trachomatis infected cell cultures using Trizol. Total RNA was DNased then further purified to remove eukaryotic mRNA and both prokaryotic and eukaryotic rRNA using Oligotex, MicrobEnrich, MicrobExpress, and Ribozero. For S. pyogenes, total RNA was collected, DNased, and purified with Ribozero to remove rRNA.
TruSeq® Stranded Total RNA Library Prep

treatment_protocol: Indicated above in the the first characteristics column.

tag: protocol

value: Normal DMEM

tag: genotype/variation

value: relA- strain (stringent response null)


title: 1h trp-free relA- mutant [1D]

description:
rRNA depleted
Processed RNAseq data for GAS
1D

value: Trp-free DMEM


title: 1h trp-free relA- mutant [3D]

description:
rRNA depleted
Processed RNAseq data for GAS
3D


title: 1h trp-free wild-type [2B]

description:
rRNA depleted
Processed RNAseq data for GAS
2B

value: wild-type strain


title: 1h trp-free wild-type [3B]

description:
rRNA depleted
Processed RNAseq data for GAS
3B


title: 40C Late exponential phase R2

description: 40C vs 37C late exponential phase R2

value: Grown at 40C till late exponential phase


title: 1h trp-free relA- mutant [2D]

description:
rRNA depleted
Processed RNAseq data for GAS
2D


title: VW_P1_Donor1

value: WNT3A only


title: 40C Late exponential phase R1

description: 40C vs 37C late exponential phase R1


title: Scramble siRNA-1 (RNA-seq)

value: Pancreatic beta cell


title: 1h untreated relA- mutant [2C]

description:
rRNA depleted
Processed RNAseq data for GAS
2C


title: 1h untreated relA- mutant [1C]

description:
rRNA depleted
Processed RNAseq data for GAS
1C


title: Ex1-RIF100-A

description:
Nutrient starved for 2 weeks, followed by 5 days of indicated treatment
Day5Rif100VSDay5DMSO.txt
Day5DMSO_vs_Day0.txt
Day5Rif10VSDay5DMSO.txt
LogPhaseVSDay0.txt
Rif100-A

value: Phosphate buffered saline with 0.02% tyloxapol

value: Rifampin 100 microM


title: 1h untreated wild-type [3A]

description:
rRNA depleted
Processed RNAseq data for GAS
3A


title: 1h untreated wild-type [1A]

description:
rRNA depleted
Processed RNAseq data for GAS
1A


title: PHLC50

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

institute: University Health Network

description: DirectHyb

hyb_protocol: Standard Illumina protocol

data_processing: Data were normalised using quantile normalisation and log2 transformation,background correction with the lumi package in R

source_name: Xenograft

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit/DASL Assay kit for Illumina arrays

growth_protocol: Human primary lung tumors grown in the subcutaneous pocket at the flank of NOD SCID mice to form xenograft tumors

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatment was applied to the cells prior to extraction

tag: tissue

value: patient-derived xenograft (PDX)

tag: histology

value: LUSC


title: Hs4 bait_LPS+IL4 B cell-rep_B2

city: Chicago

first: Amy

last: Kenter

state: Illinois

address: 835 S Wolcott Ave

institute: University of Illinois at Chicago

data_processing:
Library strategy: 4C-seq
Reads were trimmed and aligned to an in silico library constructed based on the mouse (Mus musculus) genome (mm9)
The quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33 (known as Sanger scores) instead of the previous 64 offset
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated

source_name: LPS+IL4 activated splenic B cells

growth_protocol: Resting splenic B cells were sorted for CD43- resting B cells using anti-CD43 magnetic microbeads (MACS, Miltenyi) according to the manufacturer’s instructions. B cells cultured at a density of 5-8 x 105 cells/ml in RPMI, glutamine (4 mM), penicillin (100 U/ml)-streptomycin (100 mg/ml), b-mercaptoenthanol (50 mM), supplemented with FCS (20% vol/vol) with the activators, LPS (50 mg/ml) and IL4 (10 ng/ml).  Rag2-/- pro-B cells that were cultured with IL7 and expanded in ex vivo culture for 4-5 days.  Splenic T cells that were enriched using the mouse T cell enrichment column kit  (MTCC-5, R&D) and cultured with ConA  (5ng/ml) (15324505, MP Biomedical).

extract_protocol: * The library was quantitated by qPCR and sequenced on one lane for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3 and analyzed with Casava1.8.2.  PhiX library was spiked into the lane at approximately 10% to balance the imaging cycles for higher quality.

treatment_protocol: Cells were crosslinked using 1% formaldehyde. Hind III and DpnII were used as the primary and secondary restriction enzymes, respectively for each of two biological replicates.  Inverse PCR was performed using the Expand Long Template PCR System from two viewpoints with barcoded primers

value: LPS+IL4  B cells

value: LPS+IL4 activated


title: PHLC110

description: DirectHyb

value: LUAD


title: Hs4 bait_ConA splenic T cell-rep_T2

source_name: ConA activated splenic T cell

value: ConA activated splenic T cells

value: ConA activated


title: PHLC123

description: DirectHyb


title: Hs4 bait_LPS+IL4 B cell-rep_B1


title: PHLC207

description: DirectHyb


title: PHLC57

description: DirectHyb


title: 1h trp-free wild-type [1B]

description:
rRNA depleted
Processed RNAseq data for GAS
1B


title: Hs4 bait_ConA splenic T cell-rep_T1


title: PHLC152

description: DirectHyb


title: PHLC113

description: DirectHyb


title: PHLC162

description: DirectHyb


title: Patient ID: 67, sample ID: 103

city: UMEÅ

first: Pernilla

last: Wikström

address: Department of Medical biosciences, Buildning 6M, 2nd floor

department: Medical biosciences, Pathology

institute: Umeå University

hyb_protocol: Clariom D Human Arrays were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip TM Expression Wash, Stain and Scan Manual (PN 702731, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA) the arrays were then washed and stained using the GeneChip TM Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip TM Scanner 3000 7G.

data_processing: The dataset was Robust Multichip Average (RMA) normalized. Briefly, the raw intensity values were background corrected, log2 transformed and then quantile normalized.

label: Biotin

source_name: spine

label_protocol: 100 ng of RNA was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip TM WT PLUS Reagent Kit manual Target Preparation for GeneChip TM Whole Transcript (WT) Expression Arrays User Guide (P/N 703174, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA).

extract_protocol: Allprep RNA/DNA/Protein isolation protocol (Qiagen, Hilden, Germany)

tag: disease state

value: prostate cancer

value: metastasis tissue sample

tag: tissue source

value: spine

tag: treatment group

value: Castration resistant

tag: patient id


title: Hs4 bait_Resting splenic B cell-rep_U2

source_name: Resting splenic B cell

tag: strain

value: Resting splenic B cells

value: unstimulated


title: Patient ID: 62, sample ID: 98

value: Hormone-naïve


title: Hs4 bait_Resting splenic B cell-rep_U1

tag: treatment


title: Patient ID: 64, sample ID: 100


title: PHLC85

description: DirectHyb


title: Patient ID: 65, sample ID: 101


title: Patient ID: 66, sample ID: 102

value: Short-term castrated


title: Hs4 bait_Rag2-/- pro-B cells-rep_P2

source_name: BM Pro-B cells

value: BM derived Rag2-/- pro-B cells

value: ex vivo IL7 expansion


title: VC_P1_Donor3

tag: donor id

tag: donor sex

value: female

value: femoral bone marrow multipotent stromal cells

tag: passage

value: CHAPS only


title: 200808_Chase_SIR3-EcoGII_m6A_input

tag: ip antibody

value: anti-m6A antibody (Synaptic Systems 202-003, lot 2-109)

tag: condition

value: Cycling

tag: genotype


title: Patient ID: 61, sample ID: 97


title: Patient ID: 60, sample ID: 96


title: Hs4 bait_Rag2-/- pro-B cells-rep_P1

tag: cell type


title: Patient ID: 59, sample ID: 95


title: Em bait_Rag2-/- pro-B cells-rep_P2

description: Em-bait


title: PHLC55

description: DirectHyb

value: patient-derived xenograft (PDX)

value: LUSC


title: Em bait_Resting splenic B cell-rep_U2

description: Em-bait


title: Em bait_LPS+IL4 B cell-rep_B1

description: Em-bait

value: LPS+IL4  B cells

value: LPS+IL4 activated


title: Em bait_ConA splenic T cell-rep_T1

description: Em-bait

value: ConA activated splenic T cells

value: ConA activated


title: 210114_Birthday_no-EcoGII_m6A_DIP


title: Em bait_LPS+IL4 B cell-rep_B2

description: Em-bait


title: Em bait_ConA splenic T cell-rep_T2

description: Em-bait


title: Patient ID: 63, sample ID: 99

value: prostate cancer

value: metastasis tissue sample

value: spine


title: Em bait_Resting splenic B cell-rep_U1

description: Em-bait

value: Resting splenic B cells

value: unstimulated


title: Em bait_Rag2-/- pro-B cells-rep_P1

description: Em-bait

value: BM derived Rag2-/- pro-B cells

value: ex vivo IL7 expansion


title: Patient ID: 58, sample ID: 94

value: Hormone-naïve


title: Patient ID: 55, sample ID: 91

value: Castration resistant


title: FASTED-H3K27me3_S5_ChIP-seq

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and aligned to the mm9 reference genome using Bowtie version 1.1.2 with the following criteria: -m 1 --best --strata. Duplicate reads were marked using SAMBLASTER before compression to BAM files. To directly compare FED and FASTED ChIP-seq samples, uniquely mapped reads for each mark were normalized by total reads per condition, sorted and indexed using samtools version 1.9
Genome_build: mm9
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K9bhb, H4K12bhb and H3K27ac enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5.11 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Small Intestine

growth_protocol: Male and female mice (strains: Lgr5EGFP-IRES-CreERT2/+ Strain name: B6.129P2-Lgr5tm1(cre/ERT2)Cle/J, JAX, 008875) and C57BL/6J (JAX, 000664)) were purchased, bred in house, and maintained at 72°F +/- 2 °F on a 12h light/dark cycle. Six- to twelve-week-old aged matched males and females were randomly assigned to either fed or fasted groups. Fed animals were provided ad libitium access to food (PicoLab 5053, #0007688) and water for 24h, fasted animals were completely food deprived for 24h with ad libitium access to water. Experimental mice were singly housed on aspen bedding for the duration of experiments

extract_protocol:
Chromatin immunoprecipitations were performed using a previously published protocol with modifications for SI crypts. Briefly, whole isolated crypts from 4 animals were pooled per treatment per replicate and cross linked for 10 min at 37°C with 1% formaldehyde in supplemented media and quenched with 0.125M glycine for 5 min at 37°C. Crypts were washed with PBS with 1× protease inhibitor cocktail (Sigma-Aldrich) and stored at -80°C. Pellets were thawed and then lysed for 30 min on ice with I-ChIP buffer (12mM Tris–HCl pH 8.0, 6mM EDTA pH 8.0, 0.1x PBS, 0.5% SDS) plus cOmplete mini protease inhibitors. Sonication conditions were optimized for SI crypt cells using a Bioruptor (Diagnode) to achieve shear length of 250-500bp. 10% total chromatin was reserved as an input control. Chromatin was diluted 5 fold and immunoprecipitation was performed overnight by incubation of the sonicated cell lysate with 30ul of protein G magnetic dynabeads (Invitrogen) previously coupled to target antibody for a minimum of 1h at 4°C. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC). Elution and reverse cross linking was performed in 50ul direct elution buffer (10mM Tris–HCl, pH 8.0, 5mM EDTA, pH 8.0, 300mM NaCl and 0.5% SDS) with Proteinase K and RNaseA at 65°C overnight. Eluted DNA was cleaned up with solid-phase reversible immobilization (SPRI) beads (Beckman-Coulter).
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

treatment_protocol:
Crypt isolation followed previously published protocols with minor modifications [Guo, 2009 #5169;Tinkum, 2015 #4005]. Briefly fed or fasted mice were euthanized by CO2, the whole SI was collected, flushed with PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) to remove feces, and the mesentery was removed. The SI sample was cut longitudinally then cut transversely into 4 equal pieces. Each sample was placed on ice in PBS (Ca2+- and Mg2+-free, 100nM TSA) while the remaining samples were collected. After collection of all samples, SI were incubated in PBS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) for 10 min then transferred to HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA). Crypts were released through a series of vortex washes at 1,600rpm in HBSS (Ca2+- and Mg2+-free, 2mM EDTA, 100nM TSA) at 4°C. Supernatants from all vortex washes were filtered through 70-μm mesh and pooled into 50ml conical tubes to remove villus material and tissue fragments. Isolated crypts were pelleted at 1000rpm at 4°C. After this step, whole crypts were utilized for flow cytometry (detailed below), spheroid cell line establishment [de la Cruz Bonilla, 2018 #5161] and treatment (detailed below), or ChIP-seq (detailed below). For ChIP-seq, crypts were first suspended in ADMEM/F12 (D6421, Sigma) supplemented with 10 U/mL penicillin, 10μg/mL streptomycin, 2mM L-glutamine, 10mM HEPES, 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem), 10µM Y-27632 dihydrochloride (Sigma), 0.5mM N-acetylcysteine amide (Sigma), and 100nM TSA.
Whole crypt isolates were suspended in Matrigel™ and plated in a 24-well tissue culture dish (30 μl per well) as described [de la Cruz Bonilla, 2018 #5161]. Cultures were grown in 50% L-WRN conditioned media supplemented with 10µM TGF-β RI Kinase Inhibitor VI (SB431542, Calbiochem) and 10µM Y-27632 dihydrochloride (Sigma) added to each culture well. Media was changed every second day and spheroids were subcultured every third day. For experimental treatments of spheroid cultures, 50% L-WRN conditioned media was supplemented with either 5 or 10mM (R)-(–)-3-Hydroxybutyric acid (298360, Sigma) with 10µM TGF-β RI Kinase Inhibitor VI and 10µM Y-27632 dihydrochloride added to each treatment culture well. Standard media changes occurred for untreated control culture wells. All treatments were 24h prior to spheroid isolation from Matrigel™ for ChIP-qPCR or immunoblotting analyses.

value: crypt

value: wildtype

tag: Sex

value: pooled male and female

tag: chip-antibody

value: H3K27me3 Abcam ab6002


title: FASTED-H3K27me3_S2_ChIP-seq

tag: tissue


title: Patient ID: 56, sample ID: 92


title: FASTED-H3K4me3_S5_ChIP-seq

value: H3K4me3 Abcam ab8580


title: FASTED-H3K79me2_S5_ChIP-seq

value: H3K79me2 Abcam ab3594


title: Patient ID: 53, sample ID: 89


title: FASTED-Input_S5_ChIP-seq


title: Patient ID: 54, sample ID: 90


title: FASTED-H3K4me3_S2_ChIP-seq


title: Patient ID: 52, sample ID: 88


title: Patient ID: 48, sample ID: 82

source_name: crista

value: crista


title: Patient ID: 57, sample ID: 93


title: Patient ID: 49, sample ID: 84

source_name: dermis

value: dermis


title: Patient ID: 49, sample ID: 83

source_name: LN

value: prostate cancer

value: LN


title: FASTED-H3K27ac_S5_ChIP-seq

value: H3K27ac Abcam ab4729


title: Patient ID: 47, sample ID: 81

value: metastasis tissue sample


title: Patient ID: 51, sample ID: 87

value: spine


title: Patient ID: 50, sample ID: 86


title: Patient ID: 46, sample ID: 79


title: FASTED-H3K9me3_S5_ChIP-seq

value: H3K9me3 Abcam ab8898


title: FASTED-H3K4me1_S5_ChIP-seq

value: H3K4me1 Abcam ab8895


title: FASTED-H4K12bhb_S5_ChIP-seq


title: Patient ID: 50, sample ID: 85


title: FASTED-H3K9me3_S2_ChIP-seq


title: FASTED-H3K79me2_S2_ChIP-seq


title: FASTED-Input_S2_ChIP-seq


title: FASTED-H4K12bhb_S2_ChIP-seq


title: Patient ID: 46, sample ID: 80


title: Patient ID: 45, sample ID: 78


title: Patient ID: 43, sample ID: 74


title: Patient ID: 44, sample ID: 77


title: FASTED-H3K4me1_S2_ChIP-seq


title: Patient ID: 43, sample ID: 75


title: Patient ID: 44, sample ID: 76


title: FASTED-H3K9bhb_S5_ChIP-seq

value: H3K9bhb PTM-biolabs PTM-1250


title: FASTED-H3K9bhb_S2_ChIP-seq


title: FED-H3K27me3_F4_ChIP-seq


title: FED-Input_F1_ChIP-seq


title: FED-H3K4me3_F4_ChIP-seq


title: FED-Input_F4_ChIP-seq


title: FED-H3K27me3_F1_ChIP-seq


title: Patient ID: 41, sample ID: 71

value: Castration resistant


title: Patient ID: 40, sample ID: 69


title: Patient ID: 39, sample ID: 68


title: Patient ID: 37, sample ID: 66