title: PC3 1uM EPZ, Replicate 3

hyb_protocol: Biotinylated cRNA were hybridized to GeneChip® Human Transcriptome 2.0 arrays.

scan_protocol: not provided

data_processing:
Raw data (CEL files) were processed and normalized using Robust Multichip Average (RMA) by Bioconductor oligo package.
Differentially expressed genes (DEGs) were identified by the Bioconductor limma package

label: Biotin

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Cleanup was performed using RNeasy kit from Qiagen per manufacturer's instructions.

tag: cell line

tag: tissue

value: prostate cancer cell line


title: NegativeControl_2

status: Public on Aug 09 2019

type: SRA

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

country: USA

institute: University of Colorado Boulder

library_source: transcriptomic

data_processing:
Adapters trimmed using Trimmomatic.
Reads aligned with Tophat2, followed by remapping of unaligned reads with Bowtie2.
Repetitive element transcripts aligned using Repenrich algorithim.
Differential expression analyzed with Deseq2.
Genome_build: rn6
Supplementary_files_format_and_content: Raw gene and repetitive element counts for each sample.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Control (scrambled) siRNA-treated RNA-seq

growth_protocol: Primary astrocytes were harvested from neonatal pups and purified using standard protocols. Cells were grown in DMEM/F12, subcultured at 90% confluency, and transfected and/or treated at 70% confluency.

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns. IP lysates purified using J2 antibody-bound immunoprecipitation beads, and total RNA extracted with Trizol.
PolyA libraries were prepared according to Illumina's instructions using the TruSeq kit, and total RNA libraries for immunoprecipitated samples were prepared using the V2 Scriptseq kit (Epicenter).

treatment_protocol: siRNA treatments using Lipofectamine 3000 according to manufacturer's instructions.

tag: strain

value: Sprague-Dawley

tag: cell type

value: Primary rat astrocytes

tag: passages

tag: treatment

value: scrambled (control) siRNA

tag: ip antibody


title: PC3 1uM EPZ, Replicate 1

type: RNA

city: CHICAGO

first: Rajita

last: Vatapalli

state: IL

address: 303 E SUPERIOR, 6-250

institute: Northwestern University

description: PC3 treated with 1uM EPZ004777 for 8 days

molecule: total RNA

organism: Homo sapiens

growth_protocol: LNCaP and PC3 were routinely grown in RPMI media with 10% FBS and 1% Pen-strep.

treatment_protocol: Cells were treated with either DMSO vehicle or 1uM EPZ004777.


title: PC3 1uM EPZ, Replicate 2


title: NegativeControl_1


title: Control_J2ip3

source_name: IP control immunoprecipitated RNA-seq

value: J2 antibody


title: Control_J2ip2


title: Control_J2ip1


title: Control_input2

source_name: IP control input RNA-seq


title: Control_input3


title: MP-735-16

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, using Cutadapt-1.2.1 and low-quality (q < 25) sequence, then mapped to mm10 whole genome using TopHat2 (with Bowtie2 settings of 'sensitive') and quantified to RefSeq89 annotation, using strict paired-end compatibility, with requirement of junction reads to match introns, minimum feature overlap of 95%, and minimum reads of 1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include alignment counts per gene for each sample

organism: Mus musculus

growth_protocol: All the experiments were performed using age-matched, and when possible, littermate controls. The animals were fed with a regular chow diet ad libitum and were housed at an ambient temperature.

extract_protocol:
Total RNA was extracted from snap-frozen quadriceps muscles (n=4/sex/genotype) using RNeasy mini kit (Qiagen). The quality of total RNA was validated by Bioanalyzer (Agilent Technologies). Approximately 1 µg of RNA per sample was used to construct the cDNA library
RNA libraries were prepared for sequencing using standard Illumina protocols, using the TruSeq stranded mRNA library prep kit (Illumina). The cDNA libraries were quantitated using KAPA library quantification kit for Illumina platforms (Kapa Biosystems). The individual indexed libraries were diluted to 4 nM and pooled in equal quantity and denatured before loading onto the Illumina NextSeq 500. The sequencing was run as paired-end reads (2 × 75 bp per read) with a targeted depth of 60 million paired-end reads per sample.

tag: genotype/variation

tag: age

value: 6 months

tag: Sex

value: Female

value: Skeletal muscle (quadriceps)


title: Control_input1


title: PC3 DMSO, Replicate 3

description: PC3 treated with DMSO vehicle for 8 days

value: DMSO


title: MP-733-16

value: Male


title: PC3 DMSO, Replicate 2


title: PC3 DMSO, Replicate 1


title: MP-734-16

source_name: WT_Female_Skeletal muscle (quadriceps)

value: WT


title: MP-736-16

source_name: WT_Male_Skeletal muscle (quadriceps)


title: MP-737-16


title: LNCaP 1uM EPZ, Replicate 1

description: LNCaP treated with 1uM EPZ004777 for 8 days

source_name: LNCaP

value: LNCaP


title: Nxt1_totalRNA_R_rep2

city: Cardiff

first: Helen

last: White-Cooper

state: Wales

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

description:
processed data files:
Nxt1_CircRNA.txt

data_processing:
Raw reads were trimmed with trimmomatic v.0.36 (HEADCROP:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Sequence reads were aligned to the Drosophila genome (Dm6.23) using STAR v.2.5.3a with options: --outMultimapperOrder Random --outSAMmultNmax 1. Flybase r6.23 annotations were supplied to index the genome but annotations were not provided for mapping.
Read counts were generated using Subread package FeatureCounts v. 1.6.2 ; reads mapping to one location were assigned to exons (for mRNA) or introns (for pre-mRNA) and reported by gene_id. (metafeature). DESeq2  was used to normalise reads counts and calculate fpkm values
CircRNAs were identified using PTESFinder v.1 (parameters -s 65 -u)
Genome_build: Dm6.23 (FlyBase)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample. CircRNA abundance was meaured as a normalised number of backspliced reads for each structure (see methods for details). Bigwig files which can visualize strand specific read abundances in genome browsers

organism: Drosophila melanogaster

source_name: Larval carcass

growth_protocol: Larvae were maintained in standard food vials containing cornmeal, yeast, dextrose and plant agar. Proprionic acid and Nipagen (10% p-hydroxy benzoic acid methyl ester) were added as anti-microbial and anti-fungal, respectively.

extract_protocol:
3rd instar stationary larvae were dissected in a magnetic chamber and all internal tissues were removed. The larval carcasses were put in in lysis buffer and frozen. Total RNA was extracted with the RNAeasy Mini Kit (Qiagen). 1ug of RNA was treated with 20 units of RNAseR (Epicentre) in a 25uL reaction at 37oC for 30 minutes. Mock samples were treated with the same volume of water.  All samples were then cleaned up with 2 volumes of RNA Clean XP beads(Agencourt) and eluted with 13uL of water.
10uL of mock and RNAseR treated samples were used to make RNA libraries using the TruSeq Stranded total RNAseq with Ribozero gold LT kit (Illumina). Libraries were pooled in equimolar proportions and sequenced on a 2x75bp High-output NextSEq500 cartridge

treatment_protocol: Larvae were put in vial that contained 0.05% bromophenol blue added to the food. Stationary larvae were typically stationary and had white or light blue-ish guts.

value: Larval carcass

value: yw

tag: genotype

tag: developmental stage

value: 3rd instar stationary larvae


title: Nxt1_totalRNA_R_rep3

description:
processed data files:
Nxt1_CircRNA.txt


title: LNCaP DMSO, Replicate 3

description: LNCaP treated with DMSO vehicle for 8 days


title: MP-732-16


title: LNCaP 1uM EPZ, Replicate 2


title: LNCaP DMSO, Replicate 1


title: LNCaP 1uM EPZ, Replicate 3


title: Nxt1_totalRNA_R_rep1

description:
processed data files:
Nxt1_CircRNA.txt


title: LNCaP DMSO, Replicate 2


title: Zucker Fatty Rat - BT2 #3 [B7-BT2]

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
9264_5515_69798_HJY3CBGX5_AH15-B7-BT2_TACAGC
processed data file: DESeq_BT2_normalized_counts.csv

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm10 and rn6 for mouse and rat RNA-seq
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

source_name: Zucker Fatty Rat - BT2

extract_protocol: Libraries were prepared according to the Illumina TruSeq polyA+ Sample Prep Kit protocol

treatment_protocol: Zucker fatty rats that have mutation in leptin receptor gene treated with BT2

value: Zucker

tag: status

value: fatty, obese rat

value: liver


title: Zucker Fatty Rat - BT2 #4 [B10-BT2]

description:
9264_5515_69799_HJY3CBGX5_AH16-B10-BT2_TATAAT
processed data file: DESeq_BT2_normalized_counts.csv


title: WT_totalRNA_R_rep3

description:
processed data files:
WT_CircRNA.txt


title: Zucker Fatty Rat - Vehicle #4 [D6-Vehicle]

description:
9264_5515_69797_HJY3CBGX5_AH14-D6-Vehicle_TAATCG
processed data file: DESeq_BT2_normalized_counts.csv

source_name: Zucker Fatty Rat - Vehicle

treatment_protocol: Zucker fatty rats that have mutation in leptin receptor gene

value: Vehicle


title: MP-731-16


title: MP-730-16


title: Zucker Fatty Rat - Vehicle #3 [D5-Vehicle]

description:
9264_5515_69796_HJY3CBGX5_AH13-D5-Vehicle_GACGAC
processed data file: DESeq_BT2_normalized_counts.csv


title: Nxt1_totalRNA_M_rep3

description:
processed data files:
pre-mRNA_fpkm.txt
mRNA_fpkm.txt


title: MP-729-16


title: Nxt1_totalRNA_M_rep2


title: Nxt1_totalRNA_M_rep1


title: WT_totalRNA_R_rep2

description:
processed data files:
WT_CircRNA.txt


title: Zucker Fatty Rat - Obese #4 [L8-Obese]

description:
9264_5515_69795_HJY3CBGX5_AH12-L8-Obese_CCAACA
processed data file: DESeq_ZF_normalized_counts.csv

source_name: Zucker Fatty Rat - Obese


title: WT_totalRNA_R_rep1

description:
processed data files:
WT_CircRNA.txt


title: WT_totalRNA_M_rep3


title: MP-728-16


title: Zucker Fatty Rat - Obese #3 [L6-Obese]

description:
9264_5515_69794_HJY3CBGX5_AH11-L6-Obese_CATGGC
processed data file: DESeq_ZF_normalized_counts.csv


title: WT_totalRNA_M_rep1


title: WT_totalRNA_M_rep2


title: MP-727-16


title: Zucker Lean Rat - Control #4 [L42-Lean]

description:
9264_5515_69793_HJY3CBGX5_AH10-L42-Lean_CAGGCG
processed data file: DESeq_ZF_normalized_counts.csv

source_name: Zucker Lean Rat - Control

treatment_protocol: Zucker lean rats that are the control for the Zucker fatty

value: Lean control rat


title: Vol3.H3K27AC.UNTREATED

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Base-calling was performed with bcl2fastq (v2.2.0). Adaptors were trimmed and RNA-seq reads were aligned to hg19 using UCSC knownGene annotations with STAR using default settings (v2.5.3a).
Read quantification was performed with Salmon (v0.11.0) with the parameters –fldMean 50 –fldSD 1 –seqBias and UCSC knownGene annotations.
Genes with fewer than 100 total counts were removed, and normalized abundance measurements were determined with DESeq2 (v1.20.0).
ChIP-seq reads were aligned to hg19 with bowtie2 (v2.2.5). Reads in ENCODE blacklist regions were removed with samtools (v1.3).
Peaks were called with MACS2 (v2.1.0.20150420) using parameters –q 0.01 –m 10 50 --nomodel --shiftsize=150 and input controls.
The consensus peak set, normalized peak signal, and differential peak binding were determined with diffBind (v2.8.0). chipSeeker (v1.16.1) was used to annotate peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized gene-level abundance counts derived from DESeq2 are provided for each in RNAseq.NormalizedAbundance.txt. Normalized signal across consensus peak sets derived from DiffBind for both H3K9/14ac and H3K27ac are available in Resistant-v-Sensitive.H3AC.ConsensusPeaks.txt, Resistant-v-Sensitive.H3K27AC.ConsensusPeaks.txt, Romidepsin-v-Untreated.H3AC.ConsensusPeaks.txt, and Romidepsin-v-Untreated.H3K27AC.ConsensusPeaks.txt. Each row is a feature (gene or peak) and each column contains the normalized values for a given sample.

molecule: genomic DNA

source_name: Peripheral blood

growth_protocol: Cells were cultured in IMDM supplemented with 20% FBS and 1% penicillin/streptomycin in a 37°C incubator with 5% CO2.

extract_protocol:
0.05-0.5x106 cells were snap-frozen on dry ice for 15 minutes after 3 washes with PBS. Chromatin was prepared and ultra-low-input ChIP performed according to Brind'Amour et al., 2015 (Nature Communications).
ChIP DNA was end-repaired, A-tailed, and ligated to Illumina PE adapters. Ligated fragments were PCR amplified using Illumina indexed primers for 12 cycles. DNA was purified using Ampure XP DNA purification beads between each step. Full methodology is available in Brind'Amour et al., 2015 (Nature Communications).

treatment_protocol: Cells were immediately placed into culture after collection and sorting. Cells were collected for ChIP and sequencing after 24 hours in culture.

tag: cell markers

tag: disease

tag: hdaci group

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: Vol3.INPUT.ROMI

treatment_protocol: Cells were immediately placed into culture after collection and sorting. Cells were treated with 2.5 nM romidepsin for 4 hours before transfer to fresh media. Cells were collected for ChIP sequencing after 24 hours in culture.

value: 2.5 nM romidepsin


title: Zucker Lean Rat - Control #3 [L41-Lean]

description:
9264_5515_69792_HJY3CBGX5_AH9-L41-Lean_CACGAT
processed data file: DESeq_ZF_normalized_counts.csv


title: Vol3.H3K27AC.ROMI


title: Vol3.H3AC.UNTREATED

value: H3ac (EMD Millipore, 06-599)


title: Zucker Fatty Rat - BT2 #2 [B4-BT2]

description:
9263_5515_69791_HK2NYBGX5_AH8-B4-BT2_CCGTCC
processed data file: DESeq_BT2_normalized_counts.csv


title: MP-725-16

value: 6 months


title: MP-723-16

value: Female

value: Skeletal muscle (quadriceps)


title: MP-724-16

value: Male


title: MP-722-16

value: WT


title: MP-726-16


title: Vol3.H3AC.ROMI


title: Zucker Fatty Rat - Vehicle #1 [D1-Vehicle]

description:
9263_5515_69788_HK2NYBGX5_AH5-D1-Vehicle_TAGCTT
processed data file: DESeq_BT2_normalized_counts.csv


title: Zucker Fatty Rat - Vehicle #2 [D4-Vehicle]

description:
9263_5515_69789_HK2NYBGX5_AH6-D4-Vehicle_CTTGTA
processed data file: DESeq_BT2_normalized_counts.csv


title: Vol2.INPUT.UNTREATED


title: MS-1 endothelial cell line, biological rep2

city: Seoul

first: Jung-Kyu

last: Han

address: 101 Daehak-ro, Jongro-gu,

department: Internal Medicine

country: South Korea

institute: Seoul National University Hospital

description: MS-1 endothelial cell line

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Human Gene 1.0 ST Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were processed using Affymetrix GCOS software and normalized with RMA method. RMA files were imported into GeneSpring 7.3 software (Agilent Technologies) and further analyzed.

label: biotin

source_name: MS-1 cell line

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

growth_protocol: SFBs were maintained in DMEM supplemented with 10% FBS (Gibco), penicillin/streptomycin (Gibco), L-glutamine (Gibco) and sodium pyruvate (Gibco). Mock-SFBs, iECs, and primary ECs were maintained in EBM-2 (Lonza) containing 10% FBS (Gibco) and penicillin/streptomycin (Gibco). MS-1 cells were maintained in DMEM supplemented with 10% FBS,  penicillin/streptomycin.

extract_protocol: Total RNA was extracted using an RNeasy Mini Kit (Qiagen).

treatment_protocol: not applicable

tag: cell line

value: MS-1 endothelial cell line


title: induced endothelial cells, biological rep3

description: iECs derived by transduction of 5 key factors

source_name: Tie-2 GFP transgenic mouse

value: 8 weeks old

value: induced endothelial cells


title: primary endothelial cells from mouse lungs, biological rep2

description: Primary endothelial cells from adult mouse lungs


title: MS-1 endothelial cell line, biological rep1

description: MS-1 endothelial cell line


title: induced endothelial cells, biological rep2


title: primary endothelial cells from mouse lungs, biological rep1


title: Zucker Fatty Rat - Obese #1 [L2-Obese]

description:
9263_5515_69786_HK2NYBGX5_AH3-L2-Obese_CAGATC
processed data file: DESeq_ZF_normalized_counts.csv

tag: tissue


title: induced endothelial cells, biological rep1


title: Zucker Fatty Rat - BT2 #1 [B3-BT2]

description:
9263_5515_69790_HK2NYBGX5_AH7-B3-BT2_ATGTCA
processed data file: DESeq_BT2_normalized_counts.csv

tag: strain


title: Heart (ventricle), mNIA2

city: Pittsburgh

first: Niranjana

last: Natarajan

state: PA

address: 200 Lothrop street, BST1720

institute: University of Pittsburgh

data_processing:
Short reads were aligned to the mouse transcriptome using the Burrows-Wheeler aligner (BWA) mem algorithm with default parameters.
Gene expression levels were quantified using an expectation-maximization algorithm. Differential expression analyses were performed using DESeq2.
Genome_build: RefSeq Transcripts 87 (transcript annotations are with regard to Mus musculus genome build mm10)
Supplementary_files_format_and_content: genecount

source_name: heart - ventricles

extract_protocol:
Total RNA from the lower half of the mouse heart ventricles was isolated using Ribozol. Four biological replicates were used per diet, each replicate represents myocardium from a single animal. Quality control of RNA samples were performed by tape station, samples with RIN > 7.0 were processed for library preparation and qPCR. Single-end (75 base pairs) sequencing was performed using an Illumina NextSeq 1x75 high output flow cell. Quality control, poly-adenylated mRNA isolation, library preparation, qPCR and sequencing were performed by the Harvard FAS center for systems biology.
Libraries were generated from RNA using Kapa mRNA HyperPrep kit, to generate strand-specific, poly-A enriched libraries.

treatment_protocol: Six-week-old, male C57BL/6 mice were obtained from Charles Rivers Laboratory and housed at the Harvard BRI under a 12-hour light/dark cycle and given unrestricted access to food and water. The animals were randomly assigned to one of four diets – standard rodent chow (Prolabâ IsoProâ RMH 3000 5P75, LabDiet, St. Louis, MO), NIA primate diet (5L1F, LabDiet, St. Louis, MO), UW primate diet (Envigo TD.85387, Harlan Laboratories, Madison, WI), or modified NIA diet (NIA diet modified to have sucrose and fat content matching the UW diet, Table 2), for a period of six months. Animals were weighed and then euthanized by isoflurane overdose followed by exsanguination. Hearts were collected, weighed, and bisected – one used for histological analyses (paraformaldehyde preserved) and one for RNA-seq (liquid nitrogen frozen).

tag: diet

value: mNIA

value: heart - ventricles


title: Zucker Lean Rat - Control #2 [L37-Lean]

description:
9263_5515_69785_HK2NYBGX5_AH2-L37-Lean_TGACCA
processed data file: DESeq_ZF_normalized_counts.csv

value: Zucker


title: Heart (ventricle), mNIA4


title: Vol2.H3AC.UNTREATED


title: Heart (ventricle), UW4

value: UW


title: Heart (ventricle), mNIA1


title: Zucker Lean Rat - Control #1 [L32-Lean]

description:
9263_5515_69784_HK2NYBGX5_AH1-L32-Lean_CGATGT
processed data file: DESeq_ZF_normalized_counts.csv

value: liver


title: Vol2.H3AC.ROMI


title: Vol1.INPUT.ROMI


title: mock-infected skin fibroblast, biological rep2

description: mock-infected mouse adult SFBs

tag: cell type

value: mock-infected skin fibroblast


title: Heart (ventricle), UW3


title: mock-infected skin fibroblast, biological rep3

description: mock-infected mouse adult SFBs


title: Zucker Fatty Rat - Obese #2 [L5-Obese]

description:
9263_5515_69787_HK2NYBGX5_AH4-L5-Obese_GATCAG
processed data file: DESeq_ZF_normalized_counts.csv

value: fatty, obese rat


title: Heart (ventricle), mNIA3


title: Vol2.H3K27AC.UNTREATED

tag: treatment

value: H3K27ac (Abcam ab4729)


title: Vol2.H3K27AC.ROMI

value: 2.5 nM romidepsin


title: skin fibroblast, biological rep1

description: mouse adult SFBs

value: skin fibroblast


title: mock-infected skin fibroblast, biological rep1

description: mock-infected mouse adult SFBs


title: Vol1.H3K27AC.UNTREATED


title: Vol1.H3K27AC.ROMI


title: BMMs, JPRB19 (lane 05)

city: Oberlin

first: Jordan

last: Price

state: OH

address: 119 Woodland St

institute: Oberlin College

data_processing:
Transcript abundance (TPM) was generated using Kallisto as described in Bray et al, 2016 PMID: 27043002
Genome_build: UCSC Mus musculus  genome (mm10)
Supplementary_files_format_and_content: tab-separated values (.tsv) files; content: Kallisto output file format containing transcript ID and TPM values

source_name: Bone marrow-derived macrophages

growth_protocol: We derived bone marrow-derived macrophages (BMMs) in RPMI supplemented with 10.0% fetal bovine serum, 2.0 mM L-glutamine, 100 μM streptomycin (all from Life Technologies), and 5.0% supernatant from 3T3 cells expressing macrophage colony-stimulating factor (generated in-house).

extract_protocol:
Qiagen RNeasy total RNA extraction kit per manufacturer instructions
Wafergen's PrepX RNAseq kit; libraries were pooled and run on two lanes of an Illumina HiSeq 2000 (Lanes 4 and 5,  corresponding to "L004" & "L005" in the raw data file names, and "L4" & "5 in the processed file names)

treatment_protocol: The indicated treatments and infections were administered in the RPMI-based media noted above, with the addition of 0.41 mM thymidine (Sigma) and 25.0 μg/mL kanamycin sulfate (Sigma)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 25.0 nM thapsigargin for 18 hours prior to RNA harvest

value: bone marrow-derived macrophages (BMMs)

tag: cells/condition


title: BMMs, JPRV21 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 μM tunicamycin for 18 hours prior to RNA harvest


title: BMMs, JPRV17 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 10.0 μM tunicamycin + 200.0 nM ISRIB for 18 hours prior to RNA harvest


title: Heart (ventricle), UW1


title: Heart (ventricle), UW2


title: BMMs, JPRV15 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 10.0 μM tunicamycin for 18 hours prior to RNA harvest


title: Vol1.H3AC.UNTREATED

value: H3ac (EMD Millipore, 06-599)


title: Heart (ventricle), NIA3

value: NIA


title: BMMs, JPRV13 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 mM dithiothreitol for 18 hours prior to RNA harvest


title: Heart (ventricle), NIA4

value: heart - ventricles


title: Vol1.H3AC.ROMI


title: CTCL1181.INPUT.CD4P.VOR.POST

value: Mycosis fungoides

value: Resistant


title: skin fibroblast, biological rep2

description: mouse adult SFBs

value: 8 weeks old


title: BMMs, JPRV9 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 1.0 μg/mL brefeldin A for 18 hours prior to RNA harvest


title: CTCL1181.H3K27AC.CD4P.VOR.POST


title: Heart (ventricle), NIA1


title: BMMs, JPRV7 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 mM 2-deoxyglucose + 200.0 nM ISRIB for 18 hours prior to RNA harvest


title: Heart (ventricle), Chow4

value: chow


title: BMMs, JPRV5 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 mM 2-deoxyglucose for 18 hours prior to RNA harvest


title: Subject RV infected 6 [naive experiment]

city: cleveland

first: richard

last: silver

state: ohio

address: 2109 Adelbert Rd

institute: CWRU

description: normalized data to this group

hyb_protocol: mirVana protocol

scan_protocol: mirVana protocol

data_processing: 2011-2015; normalized using an Expression Console feature called Robust Multi-chip Analysis.

source_name: BAL

label_protocol: Batched frozen cell pellets were lysed with mirVana buffer (# AM1560, ThermoFisher Scientific, Waltham MA), mRNA isolated and cDNA synthesized according to mirVana protocols.  Samples were run on Affymetrix Human Genome U133 plus 2.0 arrays (ThermoFisher Scientific)

growth_protocol: Bronchalveolar lavage cells from LTBI and naïve humans

extract_protocol: Unsorted cells of Naïve subjects were incubated with H37RV or not for 24hrs, centrifuged, supernate collected and cell pellet fast frozen

tag: agent

value: H37RV infected

value: Naive


title: Heart (ventricle), Chow3


title: Subject RV infected 5 [naive experiment]

description: normalized data to this group

treatment_protocol: Unsorted cells of Naïve subjects were incubated with H37RV or not for 24hrs, centrifuged, supernate collected and cell pellet fast frozen


title: Subject RV infected 3 [naive experiment]

description: normalized data to this group


title: Subject RV infected 1 [naive experiment]

description: normalized data to this group


title: Subject RV infected 4 [naive experiment]

description: normalized data to this group


title: Heart (ventricle), Chow2


title: CTCL1145.INPUT.CD4P.VOR.POST

value: Sezary syndrome


title: CTCL1145.H3AC.CD4P.VOR.POST


title: Subject RV infected 2 [naive experiment]

description: normalized data to this group


title: CTCL1181.H3AC.CD4P.VOR.POST


title: Heart (ventricle), NIA2


title: BMMs, JPRV11 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 1.0 μg/mL brefeldin A + 200.0 nM ISRIB for 18 hours prior to RNA harvest

value: bone marrow-derived macrophages (BMMs)


title: CTCL1145.H3K27AC.CD4P.VOR.POST

value: H3K27ac (Abcam ab4729)


title: Heart (ventricle), Chow1


title: Subject MED 6 [naive experiment]

description: normalized data to this group

value: medium alone


title: TRF1_Control_rep2

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

data_processing:
ChIP-seq and ChIRT-seq:
ChIP-seq and ChIRT-seq sequenced reads were processed with the RUbioSeq pipeline, that performed read alignment to the mouse reference genome (NCBI37/mm9, https://ccb.jhu.edu/software/tophat/igenomes.shtml) with BWA 0.7.10, removed duplicated reads with the Picard tools v1.107 (https://broadinstitute.github.io/picard/) and converted the resulting alignment files to BED format with BEDTools 2.16.2. All ChIP and input samples were randomly normalized to the same number of reads. Peak calling was performed with MACS2 v2.0.10.20130712. Significant peaks were associated with nearby genes using Homer v4.10.1 and functional annotations for associated genes were obtained with Homer and Enrichr. Heatmaps with signal density over called peaks and gene TSS sites were calculated and plotted with Deeptools.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: BED files containing aligned reads for each sample, with duplicates removed and with a balanced number of reads, used as input for MACS2.

source_name: p53-/- iPS Infected by control shRNA

growth_protocol: p53-/- iPS cells were cultured in gelatin-coated plates with DMEM (high glucose) supplemented with serum replacement (KSR, Invitrogen), LIF 1000 u/ml, non-essential amino acids, glutamax and beta-mercaptoethanol (known as iPS medium). The medium was supplemented with MEK inhibitor PD0325901 (1mM) and GSK3 inhibitor CHR99021 (3mM), together known as 2i.

extract_protocol:
Reverse crosslinking was achieved by addition of 20 ml of 5M NaCl and incubation at 65ºC for 8 hours. DNA was recovered by RNase and proteinase K treatment, phenol/chloroform extraction and ethanol precipitation.
10 to 15ng of DNA per sample were used for the ChIP-seq experiment. Samples were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7645). Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 490 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 500 sequencer, by following the manufacturer's protocols.

tag: strain/background

tag: shRNA

value: control

value: TRF1 (custom)


title: BMMs, JPRV21 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 μM tunicamycin for 18 hours prior to RNA harvest


title: BMMs, JPRB19 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 25.0 nM thapsigargin for 18 hours prior to RNA harvest


title: CTCL992.PRE.INPUT.CD4P_CD7N

value: Mycosis fungoides

value: Sensitive


title: Subject MED 4 [naive experiment]

description: normalized data to this group


title: Subject MED 5 [naive experiment]

description: normalized data to this group


title: Suz12_INPUT_rep2

source_name: p53-/- iPS Infected by control shRNA and shRNA against TRF1

value: control, TRF1


title: BMMs, JPRV3 (lane 05)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma for 18 hours prior to RNA harvest


title: CTCL992.PRE.H3K27AC.CD4P_CD7N


title: BMMs, JPRV1 (lane 05)

value: 100.0 ng/mL Pam3CSK4 for 18 hours prior to RNA harvest


title: Subject MED 1 [naive experiment]

description: normalized data to this group


title: del_TRF1_Suz12_rep2

source_name: p53-/- iPS Infected by TRF1 shRNA

value: Suz12 (Abcam ab12073)


title: H3K27me3_and_TRF1control_INPUT_rep2


title: Subject MED 2 [naive experiment]

description: normalized data to this group


title: BMMs, JPRV13 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 mM dithiothreitol for 18 hours prior to RNA harvest


title: CTCL992.POST.H3K27AC.CD4P_CD7N


title: Subject MED 3 [naive experiment]

description: normalized data to this group

value: Naive


title: CTCL992.PRE.H3AC.CD4P_CD7N

value: H3ac (EMD Millipore, 06-599)


title: CTCL992.POST.H3AC.CD4P_CD7N


title: Control_Suz12_rep2


title: CTCL992.FU.H3K27AC.CD4P


title: Subject CD4 cells depleted then RV infected 11 [CD4 experiment]

description: normalized data to this group

growth_protocol: Bronchalveolar lavage cells from LTBI  humans

extract_protocol: BAL cells were prepared for infection as unsorted samples, and following depletion CD4+ T-cells.  For T-cell subset depletion, BAL cells were incubated with magnetized EasySep antibodies (CD4 #18052, CD8 #18053 StemCell Technologies, Cambridge MA) and collected following passage through EasySep magnet using EasySep human cell depletion protocols.   Following depletion, flow cytometry was used to confirm the efficacy of T-cell depletion; samples were not used in further studies unless removal of at least 90% of the targeted T-cell subset was achieved.  Due to limitations of cell numbers and significant cell loss during depletion procedures, CD4+ T cells could not always be depleted in parallel from the same samples.

treatment_protocol: Unsorted or CD4 depleted cells were incubated with H37RV or not for 24hrs, centrifuged, supernate collected and cell pellet fast frozen

value: CD4 cells depleted then H37RV infected

value: latent tuberculosis infection (LTBI)

value: BAL


title: BMMs, JPRV11 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 1.0 μg/mL brefeldin A + 200.0 nM ISRIB for 18 hours prior to RNA harvest

value: bone marrow-derived macrophages (BMMs)


title: BMMs, JPRV9 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 1.0 μg/mL brefeldin A for 18 hours prior to RNA harvest


title: Subject CD4 cells depleted then RV infected 10 [CD4 experiment]

description: normalized data to this group


title: CTCL992.FU.H3AC.CD4P


title: Control_H3K27me3_rep2

value: control

value: H3K27me3 (Millipore 07-449)


title: BMMs, JPRV17 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 10.0 μM tunicamycin + 200.0 nM ISRIB for 18 hours prior to RNA harvest


title: CTCL409.POST.INPUT.CD4P

value: Mycosis fungoides/Sezary syndrome

value: Resistant


title: BMMs, JPRV15 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 10.0 μM tunicamycin for 18 hours prior to RNA harvest


title: Subject CD4 cells depleted then RV infected 8 [CD4 experiment]

description: normalized data to this group


title: del220

description:
Isolation of poly A+ RNA from total RNA.
Unstranded RNA-seq
processed data file: RNAseq_Gene_FPKM.txt

data_processing:
ChIP-seq and CHIRT-seq: ChIP-seq and CHIRT-seq sequenced reads were processed with the RUbioSeq pipeline, that performed read alignment to the mouse reference genome (NCBI37/mm9, https://ccb.jhu.edu/software/tophat/igenomes.shtml) with BWA 0.7.10, removed duplicated reads with the Picard tools v1.107 (https://broadinstitute.github.io/picard/) and converted the resulting alignment files to BED format with BEDTools 2.16.2. All ChIP and input samples were randomly normalized to the same number of reads. Peak calling was performed with MACS2 v2.0.10.20130712. Significant peaks were associated with nearby genes using Homer v4.10.1 and functional annotations for associated genes were obtained with Homer and Enrichr. Heatmaps with signal density over called peaks and gene TSS sites were calculated and plotted with Deeptools.
RNA-seq: Single-end sequenced reads were analyzed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (NCBI37/mm9, https://ccb.jhu.edu/software/tophat/igenomes.shtml) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.1.9, allowing three mismatches and twenty multihits. Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1, using the mouse NCBI37/mm9 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml . GSEAPreranked was used to perform gene set enrichment analysis of the KEGG pathways collection on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were finally considered.
Genome_build: NCBI37/mm9 (GSCv37)
Supplementary_files_format_and_content: BED files containing aligned reads for each sample, with duplicates removed and with a balanced number of reads, used as input for MACS2.
Supplementary_files_format_and_content: RNAseq_Gene_FPKM.txt: Tabulated text file with gene FPKM values (Cuffnorm).

extract_protocol:
Total RNA was extracted with TRIzol reagent (ThermoFisher 15596026) and then purified and treated with DNase using RNeasy Kit (QIAGEN 74106), following manufacturer´s instructions.
Total RNA (1µg) was used for the RNA-seq experiment, and the obtained sample RNA Integrity Number was 10 (Agilent 2100 Bioanalyzer). The poly(A)+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB, Cat. No. E7760) as recommended by the manufacturer. This kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced. Adapter-ligated library was completed by PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 500 sequencer, by following manufacturer's protocols.


title: del223


title: del_TRF1_H3K27me3_rep2


title: BMMs, JPRV3 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma for 18 hours prior to RNA harvest


title: Ctrl223


title: CTCL409.POST.H3K27AC.CD4P

value: H3K27ac (Abcam ab4729)


title: BMMs, JPRV7 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 mM 2-deoxyglucose + 200.0 nM ISRIB for 18 hours prior to RNA harvest


title: Ctrl220


title: CTCL1235.POST.INPUT.CD4P

value: Mycosis fungoides


title: CTCL409.POST.H3AC.CD4P

value: H3ac (EMD Millipore, 06-599)


title: Subject CD4 cells depleted then RV infected 6 [CD4 experiment]

description: normalized data to this group

value: CD4 cells depleted then H37RV infected


title: CTCL1235.POST.H3AC.CD4P


title: BMMs, JPRV5 (lane 04)

value: 100.0 ng/mL Pam3CSK4  + 6.0 ng/mL recombinant mouse interferon gamma + 2.0 mM 2-deoxyglucose for 18 hours prior to RNA harvest


title: Subject CD4 cells depleted then RV infected 7 [CD4 experiment]

description: normalized data to this group

value: latent tuberculosis infection (LTBI)

value: BAL


title: Subject CD4 cells depleted then RV infected 5 [CD4 experiment]

description: normalized data to this group


title: Subject CD4 cells depleted then RV infected 9 [CD4 experiment]

description: normalized data to this group


title: Subject CD4 cells depleted then RV infected 4 [CD4 experiment]

description: normalized data to this group


title: ChIRTseq_TERRAwt

data_processing:
Library strategy: CHIRT-seq
ChIP-seq and CHIRT-seq: ChIP-seq and CHIRT-seq sequenced reads were processed with the RUbioSeq pipeline, that performed read alignment to the mouse reference genome (NCBI37/mm9, https://ccb.jhu.edu/software/tophat/igenomes.shtml) with BWA 0.7.10, removed duplicated reads with the Picard tools v1.107 (https://broadinstitute.github.io/picard/) and converted the resulting alignment files to BED format with BEDTools 2.16.2. All ChIP and input samples were randomly normalized to the same number of reads. Peak calling was performed with MACS2 v2.0.10.20130712. Significant peaks were associated with nearby genes using Homer v4.10.1 and functional annotations for associated genes were obtained with Homer and Enrichr. Heatmaps with signal density over called peaks and gene TSS sites were calculated and plotted with Deeptools.
RNA-seq: Single-end sequenced reads were analyzed with the nextpresso pipeline, as follows: Sequencing quality was checked with FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse reference genome (NCBI37/mm9, https://ccb.jhu.edu/software/tophat/igenomes.shtml) with TopHat-2.0.10 using Bowtie 1.0.0 and Samtools 0.1.1.9, allowing three mismatches and twenty multihits. Transcripts quantification and differential expression were calculated with Cufflinks 2.2.1, using the mouse NCBI37/mm9 transcript annotations from https://ccb.jhu.edu/software/tophat/igenomes.shtml . GSEAPreranked was used to perform gene set enrichment analysis of the KEGG pathways collection on a pre-ranked gene list, setting 1000 gene set permutations. Only those gene sets with significant enrichment levels (FDR q-value < 0.25) were finally considered.
Genome_build: NCBI37/mm9 (GSCv37)
Supplementary_files_format_and_content: BED files containing aligned reads for each sample, with duplicates removed and with a balanced number of reads, used as input for MACS2.
Supplementary_files_format_and_content: RNAseq_Gene_FPKM.txt: Tabulated text file with gene FPKM values (Cuffnorm).

extract_protocol:
Reverse crosslinking was achieved by addition of 20 ml of 5M NaCl and incubation at 65ºC for 8 hours. DNA was recovered by RNase and proteinase K treatment, phenol/chloroform extraction and ethanol precipitation.
0.5ng of DNA per sample were used for the CHIRT-seq experiment (5ng for the INPUT). An antisense TERRA RNA biotinylated transcript consisting of eight CCCTAA repeats was used as bait for TERRA capture. Samples were processed through subsequent enzymatic treatments for fragmentation (5 min), end-repair, dA-tailing, and ligation to adapters with "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" from New England BioLabs (catalog # E7805). Adapter-ligated libraries were completed by limited-cycle PCR and extracted with a [single] double-sided SPRI size selection. Resulting average fragment size is 400 bp from which 120 bp correspond to adaptor sequences. Libraries were applied to an Illumina flow cell for cluster generation and sequenced on an Illumina NextSeq 500 sequencer, by following manufacturer's protocols.

tag: capture oligo

value: TERRAwt


title: CTCL1200.PRE.H3K27AC.UNSORTED

value: PLL


title: BMMs, JPRV1 (lane 04)

value: 100.0 ng/mL Pam3CSK4 for 18 hours prior to RNA harvest

value: bone marrow-derived macrophages (BMMs)


title: Subject CD4 cells depleted then RV infected 3 [CD4 experiment]

description: normalized data to this group


title: Mettl14cKO mice-2

first: Zijie

last: Zhang

department: Chemistry

institute: University of Chicago

description:
Ribosome depleted RNA
sorted_beta_cell_count.txt

data_processing:
Seequencing reads were aligned to reference genome by Tophat2
For the m6A-seq analysis, read count of connected bins was quantified by R package RADAR. For RNA-seq analysis, read count at gene level was summarized by FeatureCounts of Rsubread package.
Differential methylation sites detection by QNB_1.1.11 package.
Differential gene expression was identified using DESeq2_1.18.1 package.
Genome_build: hg38
Supplementary_files_format_and_content: The peak file contains m6A peaks in BED12 format with additional columns of differential test statistics.  The corresponding read count files are read count matrix of input and m6A-IP where each row correspond to a peak in the peak files and each column corresponds to each sample. The gene read count files contain gene level quantification of reads from the Input library (RNA-seq), which is used for differential gene expression analysis.

source_name: Sorted beta cell

growth_protocol: The culture flask was coated with DMEM (glucose 4.5 g/L) containing penicillin-streptomycin (1%), fibronectin (2 μg/mL), and extracellular matrix (1% vol/vol) (Sigma-Aldrich) and incubated for at least 1 h in 5% CO2 at 37°C before the cells were seeded. EndoC-bH1 cells were grown on Matrigel/fibronectin coated culture flasks containing DMEM (glucose 1 g/L), BSA fraction V (2% wt/vol) (Roche Diagnostics, Mannheim, Germany), 2-mercaptoethanol (50 μM), nicotinamide (10 mM), transferrin (5.5 μg/mL), sodium selenite (6.7 ng/mL), penicillin-streptomycin (1%) (Sigma-Aldrich).

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) following manufacture instruction. mRNA was purified using polyT beads (Thermo Fisher). Ribosome depleted RNA was purified using RiboGone kit (Takara).
m6A-seq (Input and IP) libraries were prepared using SMARTer Stranded total RNA-seq V2 pico input Kit (Takara). RNA-seq libraries were prepared using SMARTer Stranded RNA-seq Kit (Takara).

treatment_protocol: Transient knock-downs were performed using RNAiMAX Reagent following manufacturer’s instruction.

tag: genotype/variation

value: Mettl14 beta cell specific knockout

value: beta cell


title: Mettl14cKO mice-3


title: ChIRTseq_input

value: control


title: Mettl14cKO mice-1


title: Subject CD4 cells depleted then RV infected 2 [CD4 experiment]

description: normalized data to this group


title: Pool_Inputs (ChIP-seq)

value: control and TRF1


title: Subject CD4 cells depleted then RV infected 1 [CD4 experiment]

description: normalized data to this group


title: CTCL1200.OW.H3K27AC.UNSORTED

value: Resistant


title: CTCL1200.OW.INPUT.UNSORTED


title: WT mice-2

value: wild type


title: TRF1_Control

value: TRF1 (custom)


title: CTCL1200.OW.H3AC.UNSORTED


title: WT mice-3


title: del_TRF1_H3K27me3


title: CTCL1137.PRE.INPUT.CD4P

value: Mycosis fungoides


title: CTCL1137.PRE.H3AC.CD4P

value: H3ac (EMD Millipore, 06-599)


title: RNAseq_W1118_rep2

city: Beijing

first: Ming

last: Wang

state: Beijing

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

country: China

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Basecalls were performed using bcl2fastq v1.8.4 for Illumina HiSeq 2500 and HiSeq X Ten output.
RNA-seq reads (single-end reads or read1 for paired-end reads) were processed using Cutadapt (v1.16) . The adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and low-quality bases were trimmed from the 3’ end of reads, and reads short than 20 bp were discarded.
RNA-seq reads were aligned to UCSC dm3 using STAR (v2.5.2a), only uniquely mapped reads were retained.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
note: read2 for Illumina HiSeq X Ten paired-end reads not supplied by submitter
Genome_build: dm3
Supplementary_files_format_and_content: bigWig files were generated using the deeptools (v2.5.7). Score represents the normalized coverage of RNA fragments at a given genomic coordinate. Count file was generated using featureCounts (v1.6.1) for each alignment files.

source_name: ovary

growth_protocol: All fly stocks were maintained at 25°C on standard diet.

extract_protocol:
Total RNA was prepared with Trizol reagent (Invitrogen), Transcriptome libraries were prepared according (Armour et al. 2009, Nat Methods) using not-so-random priming (NSR). 1 ug total RNA was revere transcribed using SuperScript III enzyme with first-strand NSR primer. RNA template was removed with RNase H (Invitrogen). Then cDNA was mixed with exo-Klenow fragment (NEB) second-strand NSR primer to synthesize the second strand. For PCR amplification, purified second-strand synthesis reaction were mixed with LA Taq Version 2.0 (Takara) and P5-SBS3T-NSR and P7-SBS8N-NSR primers. Products were run on a 2% low-melt agarose gel, and the 250–500 bp range were purified.
RNA-seq was performed as described (Vagin et al., 2013 RNA and Armour et al., 2009 Nat Methods). Samples were sequenced on Illumina platforms with HiSeq X Ten.

treatment_protocol: Flies were fed with yeast. Germline specific knockdowns were done as described (Czech et al., 2013 Mol Cell). CRISPR/Cas9 mediated generation of dNxf2 mutants and Panx mutants were done as described (Port et al., 2014 PNAS).

tag: age

value: 3-5 old

value: ovary

tag: genotype


title: RNAseq_W1118_rep1


title: BMMs, LG2

description: library barcode: CTTGTA

data_processing:
Filtering: barcode and sequencing linker trimmed; bad-quality reads removed using Illumina's CASAVA filtering pipeline
Alignment using TopHat to UCSC Mus musculus genome (mm10)
Generation of normalized abundance measurements using Cufflinks
Calculation of differential expression using CuffDiff
(Data analysis above as described in Trapnell et al, 2012 PMID:      22383036)
Genome_build: UCSC Mus musculus  genome (mm10)
Supplementary_files_format_and_content: "transcript_abundance.txt" is a tab-delimited text file (.txt) that contains FPKM transcript abundance information for all samples (BG, BG2, LA, L2, LG, LG2) and differential expression comparison information for each combination of samples, pairwise.

growth_protocol: We generated bone marrow-derived macrophages (BMMs) in RPMI supplemented with 10.0% fetal bovine serum, 2.0 mM L-glutamine, 100 μM streptomycin (all from Life Technologies), and 5.0% supernatant from 3T3 cells expressing macrophage colony-stimulating factor (generated in-house).

extract_protocol:
Qiagen RNeasy total RNA extraction kit per manufacturer instructions
Wafergen's PrepX RNAseq kit

value: Infected with LP02 ΔflaA lux L. pneumophila MOI 1.0 for 6 hours, then stimulated with 2.0 ng/mL recombinant mouse interferon gamma + 1.5 mM 2-deoxyglucose prior to RNA harvest

tag: number of cells per condition


title: CTCL1137.OW.H3AC.CD4P

tag: cell markers

tag: disease

tag: hdaci group


title: CTCL1137.OW.H3K27AC.CD4P

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: Control_Suz12


title: RNAseq_dNxf2_mut_rep1

tag: tissue


title: CTCL1135.POST.H3K27AC.CD4P

value: Sezary syndrome


title: BMMs, LG

description: library barcode: GCCAAT

tag: strain

value: Infected with LP02 ΔflaA lux L. pneumophila MOI 1.0 for 6 hours, then stimulated with 2.0 ng/mL recombinant mouse interferon gamma for 12 hours prior to RNA harvest


title: BMMs, L2

description: library barcode: CAGATC

value: Infected with LP02 ΔflaA lux L. pneumophila MOI 1.0 for 6 hours, then stimulated with 1.5 mM 2-deoxyglucose prior to RNA harvest

tag: cell type


title: CTCL1135.POST.INPUT.CD4P

tag: treatment


title: CTCL1135.POST.H3AC.CD4P


title: Control_H3K27me3


title: Subject RV infected 9 [CD4 experiment]

description: normalized data to this group

value: H37RV infected

value: latent tuberculosis infection (LTBI)

value: BAL


title: Subject RV infected 10 [CD4 experiment]

description: normalized data to this group


title: RNAseq_dNxf2_mut_rep2


title: VBP rep3

city: Madison

first: Ziyue

state: WI

address: 425 Henry Mall

institute: UW Madison

data_processing:
bcl2fastq 1.8.4 software was used for basecalling
Sequencing reads were mapped to the hg19 genome using the short-read aligner Bowtie v1.0.0 (Langmead et al., 2009)
The transcript expected countx were estimated using RSEM v1.2.7 (Li et al., 2011) with parameters -p 5 and then normalized by the size of the library using EBSeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include expected count values for each sample

source_name: hiPSC-derived VBP

growth_protocol: Cells were maintained in airway epithelial cell medium (human primary cells) and VBP diifferentiation medium (hiPSC-derived VBP)

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini and Micro Kit following manufacturer’s protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were dissociated with 0.05% TE Trypsin-EDTA

value: induced pluripotent stem cell derived vocal fold basal progenitors


title: BMMs, BG2

description: library barcode: TGACCA

value: Stimulated with 50.0 ng/mL Pam3CSK4 for 6.0 hours, then 50.0 ng/mL Pam3CSK4 + 2.0 ng/mL recombinant mouse interferon gamma + 1.5 mM 2-deoxyglucose for 12 hours prior to RNA harvest

value: bone marrow-derived macrophages (BMMs)


title: VBP rep2


title: WT mice-1

value: wild type

value: beta cell


title: VBP rep4


title: Subject RV infected 8 [CD4 experiment]

description: normalized data to this group


title: VBP rep1


title: Subject RV infected 4 [CD4 experiment]

description: normalized data to this group


title: Subject RV infected 11 [CD4 experiment]

description: normalized data to this group


title: Subject RV infected 5 [CD4 experiment]

description: normalized data to this group


title: Subject RV infected 3 [CD4 experiment]

description: normalized data to this group


title: CTCL1126.POST.H3K27AC.CD4P

value: Resistant


title: BMMs, BG

description: library barcode: CGATGT

value: Stimulated with 50.0 ng/mL Pam3CSK4 for 6.0 hours, then 50.0 ng/mL Pam3CSK4 + 2.0 ng/mL recombinant mouse interferon gamma for 12 hours prior to RNA harvest


title: Subject RV infected 6 [CD4 experiment]

description: normalized data to this group


title: Subject RV infected 7 [CD4 experiment]

description: normalized data to this group


title: Subject RV infected 2 [CD4 experiment]

description: normalized data to this group


title: Subject RV infected 1 [CD4 experiment]

description: normalized data to this group


title: BMMs, LA

description: library barcode: ACAGTG

value: Infected with LP02 ΔflaA lux L. pneumophila MOI 1.0 for 18 hours prior to RNA harvest


title: VF rep4

source_name: primary vocal fold epithelial

value: normal vocal fold cells


title: CTCL1126.POST.H3AC.CD4P

value: H3ac (EMD Millipore, 06-599)


title: HepG2_Con

city: guangzhou

first: Feng

last: Lu

address: 601 huangpu avenue west

institute: Jinan university

data_processing:
Illumina HiSeq 1000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary_files_format_and_content: abundance measurements

source_name: hepatocellular carcinoma cells

growth_protocol: HepG2i cells were grown in DMEM medium containing 10% FBS,50 units/mL penicillin and supplemented with 100 µg/mL streptomycin

extract_protocol:
extraction protocol not provided.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2i cells cultured with DMEM containing 10% FBS medium and incubated at 37°C in 5% CO2 grown to 80-90% confluence before treated w/o DOX (1µg/mL) for 48 hours.

value: liver

tag: cell line

value: hepatocellular carcinoma


title: VF rep2


title: HepG2_Dox


title: CTCL1084.PRE.INPUT.CD4P_CD7N

value: Sezary syndrome

value: Sensitive


title: VF rep1


title: VF rep3


title: CTCL1084.OW.H3AC.CD4P_CD7N


title: siMETTL14-3-IP

description:
m6A enriched RNA
M14KD_Ctl_IP_count.txt

data_processing:
Library strategy: MeRIP-seq
Seequencing reads were aligned to reference genome by Tophat2
For the m6A-seq analysis, read count of connected bins was quantified by R package RADAR. For RNA-seq analysis, read count at gene level was summarized by FeatureCounts of Rsubread package.
Differential methylation sites detection by QNB_1.1.11 package.
Differential gene expression was identified using DESeq2_1.18.1 package.
Genome_build: hg38
Supplementary_files_format_and_content: The peak file contains m6A peaks in BED12 format with additional columns of differential test statistics.  The corresponding read count files are read count matrix of input and m6A-IP where each row correspond to a peak in the peak files and each column corresponds to each sample. The gene read count files contain gene level quantification of reads from the Input library (RNA-seq), which is used for differential gene expression analysis.

value: METTL14 knock down

value: EndoC-bH1 cell line


title: CTCL1084.PRE.H3AC.CD4P_CD7N


title: siMETTL14-2-IP

description:
m6A enriched RNA
M14KD_Ctl_IP_count.txt


title: Subject MED 10 [CD4 experiment]

description: normalized data to this group

tag: agent

value: medium alone

value: latent tuberculosis infection (LTBI)

value: BAL


title: CTCL1043.PRE.INPUT.CD4P_CD7N

value: Mycosis fungoides


title: CTCL1043.PRE.H3K27AC.CD4P_CD7N.REP2

value: H3K27ac (Abcam ab4729)


title: Subject MED 7 [CD4 experiment]

description: normalized data to this group


title: Subject MED 9 [CD4 experiment]

description: normalized data to this group


title: siMETTL14-1-IP

description:
m6A enriched RNA
M14KD_Ctl_IP_count.txt


title: Subject MED 11 [CD4 experiment]

description: normalized data to this group


title: Subject MED 8 [CD4 experiment]

description: normalized data to this group


title: CTCL1043.PRE.H3AC.CD4P_CD7N.REP2


title: siMETTL3-3-IP

description:
m6A enriched RNA
M3KD_Ctl_IP_count.txt

value: METTL3 knock down


title: T2

city: Chongqing

first: Hongming

last: Miao

state: Chongqing

address: Gaotanyan Street NO.30

department: Department of Biochemistry and Molecular Biology

institute: Third Military Medical University (Army Medical University)

description: Gene expression after 24hr-coculture with CT-26 cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: Macrophages marked by CD45+F4/80+ were isolated with FACS. RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Murine peritoneal macrophages were treated with regular culture medium (Ctrl) or co-cultured with CRC cells CT-26 (T) for 24 h. The migratory macrophages co-cultured with CT-26 cells from upper chamber of the Transwell were marked as group M.

value: migratory macrophages

value: co-cultured with CT-26 cells in lower chamber of Transwell

tag: gender

value: male


title: siMETTL3-2-IP

description:
m6A enriched RNA
M3KD_Ctl_IP_count.txt


title: Subject MED 5 [CD4 experiment]

description: normalized data to this group


title: M2

description: Gene expression of migrating macrophages-coculture with CT-26 cells

value: peritoneal macropahges

value: co-cultured with CT-26 cells from upper chamber of the Transwell


title: Subject MED 4 [CD4 experiment]

description: normalized data to this group


title: T1


title: M3


title: T3


title: M1


title: siMETTL3-1-IP

description:
m6A enriched RNA
M3KD_Ctl_IP_count.txt


title: Subject MED 3 [CD4 experiment]

description: normalized data to this group


title: CTCL1126.POST.INPUT.CD4P

value: Resistant


title: CTCL079.PRE.INPUT.CD26N


title: siControl-3-IP

description:
m6A enriched RNA
M3KD_Ctl_IP_count.txt;M14KD_Ctl_IP_count.txt;M14KD_Ctl_Gene_count.txt

value: control


title: CTCL1043.POST.H3AC.CD4P_CD7N

value: H3ac (EMD Millipore, 06-599)


title: siControl-2-IP


title: CTCL079.POST.H3K27AC.CD26N


title: CTCL079.POST.H3AC.CD26N


title: siControl-1-IP


title: CTCL1043.POST.H3K27AC.CD4P_CD7N

value: Sensitive


title: SUDHL6 1.5uM Compound 1 4 days EZH2 ChIP-seq

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

description: Compound 1 in Konze et al, ACS Chem Bio, 2013.

data_processing:
50-nucleotide sequence reads were aligned to the combined human (hg19) - drosophila (dm3) genome using Bowtie 2 version 2.2.5 with default settings. Samtools version 1.2 was used to compress, sort and index the aligned read files. Duplicate reads were removed using the MarkDupliates function in picard-tools with lenient validation stringency. Mapped reads were separated into reads mapped to human or fly chromosomes. BamToBed from Bedtools 2.24 converted the BAM files to intervals; bedtools' slop function along with chromosome sizes obtained from UCSC was used to extend th ereads to the 200bp fragment size.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq coverage files normalized against each DMSO control in BigWig format

source_name: Diffuse large B cell lymphoma

growth_protocol: KARPAS-422 cell line was grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen). SUDHL6 cell lines were grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
For ChIP-seq, cells were pelleted, fixed in 1% formaldehyde for 10 mins, lysed and sonicated. Chromatin samples were precleared with Protein A Dynabeads (Life Technologies), and incubated overnight at 40C with anti-EZH2 (Millipore 07-689), anti-H3K27me3 (Cell Signaling Techonology 9730), anti-SUZ12 (Active Motif 39357), and anti-H3K4me3 (Abcam ab8580). Chromatin-antibody complexes were precipitated using Protein A Dynabeads followed by washes in RIPA buffer and Tris/ EDTA. Samples were digested with RNAase A, treated with Proteinase K and 10% SDS, followed by cross-link reversal at 650C. DNA was purified using MinElute PCR purification kits (Qiagen).
DNA libraries for ChIP-seq were prepared using Ovation Ultralow DR Multiplex System kits (0330-32, NuGEN) followed by Illumina sequencing.

treatment_protocol: KARPAS-422 cells were treated for 4 and 8 days with 1.5 μM of CPI-360. SUDHL6 cells were treated for 4 days with 1.5uM of Compound 1. KMS28BM and KMS28PE cells were treated for 4 days with 1.5uM of CPI360. RL cells were treated for 10 days with 5uM of CPI169.

value: 1.5uM Compound 1 4 days

tag: chip antibody target

value: Millipore 07-689


title: Ctrl2

description: Gene expression after 24hr in regular medium

value: cultured alone


title: SUDHL6 1.5uM Compound 1 4 days Input ChIP-seq

value: Input


title: Ctrl1


title: Subject MED 2 [CD4 experiment]

description: normalized data to this group

value: medium alone

value: latent tuberculosis infection (LTBI)

value: BAL


title: siMETTL14-3-input

description:
Ribosome depleted RNA
M14KD_Ctl_input_count.txt

data_processing:
Library strategy: RNA-seq
Seequencing reads were aligned to reference genome by Tophat2
For the m6A-seq analysis, read count of connected bins was quantified by R package RADAR. For RNA-seq analysis, read count at gene level was summarized by FeatureCounts of Rsubread package.
Differential methylation sites detection by QNB_1.1.11 package.
Differential gene expression was identified using DESeq2_1.18.1 package.
Genome_build: hg38
Supplementary_files_format_and_content: The peak file contains m6A peaks in BED12 format with additional columns of differential test statistics.  The corresponding read count files are read count matrix of input and m6A-IP where each row correspond to a peak in the peak files and each column corresponds to each sample. The gene read count files contain gene level quantification of reads from the Input library (RNA-seq), which is used for differential gene expression analysis.

value: METTL14 knock down

value: EndoC-bH1 cell line


title: Subject MED 1 [CD4 experiment]

description: normalized data to this group


title: Ctrl3


title: SUDHL6 1.5uM Compound 1 4 days H3K27me3 ChIP-seq

value: Cell Signaling Technolgy 9730


title: Subject CD8 cells depleted then RV infected 8 [CD8 experiment]

description: normalized data to this group

extract_protocol: BAL cells were prepared for infection as unsorted samples, and following depletion CD8+ T-cells.  For T-cell subset depletion, BAL cells were incubated with magnetized EasySep antibodies (CD4 #18052, CD8 #18053 StemCell Technologies, Cambridge MA) and collected following passage through EasySep magnet using EasySep human cell depletion protocols.   Following depletion, flow cytometry was used to confirm the efficacy of T-cell depletion; samples were not used in further studies unless removal of at least 90% of the targeted T-cell subset was achieved.  Due to limitations of cell numbers and significant cell loss during depletion procedures, CD8+ T cells could not always be depleted in parallel from the same samples.

treatment_protocol: Unsorted or CD8 depleted cells were incubated with H37RV or not for 24hrs, centrifuged, supernate collected and cell pellet fast frozen

value: CD8 cells depleted then H37RV infected


title: siMETTL14-2-input


title: Vol3.CD4P.Untreated.RNA

data_processing:
Base-calling was performed with bcl2fastq (v2.2.0). Adaptors were trimmed and RNA-seq reads were aligned to hg19 using UCSC knownGene annotations with STAR using default settings (v2.5.3a).
Read quantification was performed with Salmon (v0.11.0) with the parameters –fldMean 50 –fldSD 1 –seqBias and UCSC knownGene annotations.
Genes with fewer than 100 total counts were removed, and normalized abundance measurements were determined with DESeq2 (v1.20.0).
ChIP-seq reads were aligned to hg19 with bowtie2 (v2.2.5). Reads in ENCODE blacklist regions were removed with samtools (v1.3).
Peaks were called with MACS2 (v2.1.0.20150420) using parameters –q 0.01 –m 10 50 --nomodel --shiftsize=150 and input controls.
The consensus peak set, normalized peak signal, and differential peak binding were determined with diffBind (v2.8.0). chipSeeker (v1.16.1) was used to annotate peaks.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized gene-level abundance counts derived from DESeq2 are provided for each in RNAseq.NormalizedAbundance.txt. Normalized signal across consensus peak sets derived from DiffBind for both H3K9/14ac and H3K27ac are available in Resistant-v-Sensitive.H3AC.ConsensusPeaks.txt, Resistant-v-Sensitive.H3K27AC.ConsensusPeaks.txt, Romidepsin-v-Untreated.H3AC.ConsensusPeaks.txt, and Romidepsin-v-Untreated.H3K27AC.ConsensusPeaks.txt. Each row is a feature (gene or peak) and each column contains the normalized values for a given sample.

extract_protocol:
RNA was isolated from 0.5-2x106 cells stored in TRIzol reagent following manufacturer's instruction.
cDNA from total RNA was synthesized with a Clontech SMARTer low input RNA kit. An Illumina TruSeq preparation kit was used for library constructon per manufacturer's instructions.

treatment_protocol: Cells were immediately placed into culture after collection and sorting. Cells were collected for RNA isolation and sequencing after 24 hours in culture.


title: SUDHL6 DMSO  4 days H3K27me3 ChIP-seq

value: DMSO  4 days


title: SUDHL6 DMSO  days EZH2 ChIP-seq

value: DMSO  days


title: Subject CD8 cells depleted then RV infected 9 [CD8 experiment]

description: normalized data to this group

value: CD8 cells depleted then V infected


title: siMETTL3-3-input

description:
Ribosome depleted RNA
M3KD_Ctl_input_count.txt

value: METTL3 knock down


title: siMETTL14-1-input


title: Subject CD8 cells depleted then RV infected 7 [CD8 experiment]

description: normalized data to this group


title: siMETTL3-2-input


title: Vol3.CD4P.Romi.RNA

treatment_protocol: Cells were immediately placed into culture after collection and sorting. Cells were treated with 2.5 nM romidepsin for 4 hours before transfer to fresh media. Cells were collected for RNA isolation and sequencing after 24 hours in culture.

value: 2.5 nM romidepsin


title: SUDHL6 DMSO 4 days Input ChIP-seq

value: DMSO 4 days


title: CTCL079.OW.H3K27AC.CD26N

extract_protocol:
0.05-0.5x106 cells were snap-frozen on dry ice for 15 minutes after 3 washes with PBS. Chromatin was prepared and ultra-low-input ChIP performed according to Brind'Amour et al., 2015 (Nature Communications).
ChIP DNA was end-repaired, A-tailed, and ligated to Illumina PE adapters. Ligated fragments were PCR amplified using Illumina indexed primers for 12 cycles. DNA was purified using Ampure XP DNA purification beads between each step. Full methodology is available in Brind'Amour et al., 2015 (Nature Communications).

value: Mycosis fungoides

value: Resistant

value: H3K27ac (Abcam ab4729)


title: Subject CD8 cells depleted then RV infected 6 [CD8 experiment]

description: normalized data to this group


title: RPMI8226 1.5uM CPI360 4 days Input ChIP-seq

source_name: Multiple Myeloma

value: 1.5uM CPI360 4 days

value: Input


title: Vol2.CD4P.Romi.RNA


title: Subject CD8 cells depleted then RV infected 4 [CD8 experiment]

description: normalized data to this group

value: latent tuberculosis infection (LTBI)


title: Subject CD8 cells depleted then RV infected 5 [CD8 experiment]

description: normalized data to this group

value: BAL


title: RPMI8226 1.5uM CPI360 4 days EZH2 ChIP-seq

value: Millipore 07-689


title: siMETTL3-1-input

value: EndoC-bH1 cell line


title: Subject CD8 cells depleted then RV infected 3 [CD8 experiment]

description: normalized data to this group


title: Vol1.CD4P.Untreated.RNA


title: siControl-3-input

description:
Ribosome depleted RNA
M3KD_Ctl_input_count.txt;M14KD_Ctl_input_count.txt;M3KD_Ctl_Gene_count.txt

value: control


title: RPMI8226 1.5uM CPI360 4 days H3K27me3 ChIP-seq

value: Cell Signaling Technolgy 9730


title: Vol1.CD4P.Romi.RNA


title: siControl-2-input


title: Vol2.CD4P.Untreated.RNA


title: CTCL992.CD4P_CD7N.PRE.RNA

value: Sensitive


title: siControl-1-input


title: T2D12 IP

data_processing:
Seequencing reads were aligned to reference genome byTophat2
Read count of connected bins was quantified by R package RADAR.
Differential methylation sites detection by RADAR
Genome_build: hg38
Supplementary_files_format_and_content: differential methylation sites in BED12 file. Read count matrix of consecutive bins.

source_name: T2D12, m6A enriched RNA (IP)

extract_protocol:
Total RNA was extracted from the tissue by TRIzol. mRNA was enriched by polyT beads followed by fragmentation with Bioruptor ultrasonicator. m6A-immunoprecipitation were performed using EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S). Kapa RNA hyper kit for Illumina was used to construct library from  mRNA for input RNA and eluted RNA from the  m6A-IP. The libraries were sequenced by the Hiseq4000 platform at SE50 mode.
Kapa RNA hyperPrep kit for Illumina

tag: group

value: type II diabetes

value: F

value: islets

tag: rip antibody

tag: batch

value: C


title: CTCL992.CD4P_CD7N.OW.RNA

source_name: Peripheral blood


title: RPMI8226 DMSO 4 days Input ChIP-seq

value: DMSO 4 days


title: RPMI8226 DMSO 4 days EZH2 ChIP-seq


title: RPMI8226 DMSO 4 days H3K27me3 ChIP-seq


title: CTCL992.CD4P.FU.RNA

value: Mycosis fungoides


title: T2D11 IP

source_name: T2D11, m6A enriched RNA (IP)

value: M

value: EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S)

value: A


title: CTCL409.CD4P.POST.RNA

value: Mycosis fungoides/Sezary syndrome

value: Resistant


title: RL 5uM CPI169 10 days EZH2 ChIP-seq

value: RL

value: 5uM CPI169 10 days


title: T2D9 IP

source_name: T2D9, m6A enriched RNA (IP)

value: B


title: RL 5uM CPI169 10 days H3K27me3 ChIP-seq


title: CTCL1235.CD4P.POST.RNA


title: Subject RV infected 9 [CD8 experiment]

description: normalized data to this group

value: H37RV infected

value: latent tuberculosis infection (LTBI)

value: BAL


title: RL 5uM CPI169 10 days Input ChIP-seq

value: Input


title: CTCL1234.SKIN.CD4P.POST.RNA

source_name: Skin


title: T2D6 IP

source_name: T2D6, m6A enriched RNA (IP)

value: type II diabetes


title: T2D4 IP

source_name: T2D4, m6A enriched RNA (IP)

value: islets


title: T2D5 IP

source_name: T2D5, m6A enriched RNA (IP)

value: F


title: RL DMSO 10 days EZH2 ChIP-seq

value: DMSO 10 days

value: Millipore 07-689


title: CTCL1200.UNSORTED.OW.RNA

value: PLL


title: CTCL1160.CD4P.OW.RNA

value: Mycosis fungoides


title: Subject CD8 cells depleted then RV infected 1 [CD8 experiment]

description: normalized data to this group

source_name: BAL

value: CD8 cells depleted then H37RV infected


title: RL DMSO 10 days Input ChIP-seq


title: T2D7 IP

source_name: T2D7, m6A enriched RNA (IP)

value: M

value: EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S)


title: T2D1 IP

source_name: T2D1, m6A enriched RNA (IP)

value: A


title: Subject CD8 cells depleted then RV infected 2 [CD8 experiment]

description: normalized data to this group


title: del_TRF1_Suz12

source_name: p53-/- iPS Infected by TRF1 shRNA

tag: strain/background

tag: shRNA


title: Subject RV infected 7 [CD8 experiment]

description: normalized data to this group


title: Subject RV infected 8 [CD8 experiment]

description: normalized data to this group


title: Subject RV infected 4 [CD8 experiment]

description: normalized data to this group


title: Ctl20 IP

source_name: Ctl20, m6A enriched RNA (IP)

value: control

value: C


title: CTCL1159.CD4P.VOR_POST.RNA

tag: cell markers

value: Resistant


title: KMS28PE 1.5uM CPI360 4 days EZH2 ChIP-seq

value: 1.5uM CPI360 4 days


title: Subject RV infected 2 [CD8 experiment]

description: normalized data to this group

value: H37RV infected

tag: disease

value: latent tuberculosis infection (LTBI)

value: BAL


title: Subject RV infected 6 [CD8 experiment]

description: normalized data to this group


title: Subject RV infected 5 [CD8 experiment]

description: normalized data to this group


title: KMS28PE 1.5uM CPI360 4 days H3K27me3 ChIP-seq

value: Cell Signaling Technolgy 9730


title: Subject RV infected 3 [CD8 experiment]

description: normalized data to this group


title: Subject MED 9 [CD8 experiment]

description: normalized data to this group

value: medium alone


title: Subject RV infected 1 [CD8 experiment]

description: normalized data to this group


title: CTCL1200.UNSORTED.PRE.RNA

tag: hdaci group


title: Subject MED 8 [CD8 experiment]

description: normalized data to this group


title: Subject MED 6 [CD4 experiment]

description: normalized data to this group


title: CTCL1145.CD4P.VOR_POST.RNA

value: Sezary syndrome

tag: chip antibody


title: Ctl18 IP

source_name: Ctl18, m6A enriched RNA (IP)

value: F

tag: tissue

value: islets


title: Ctl17 IP

source_name: Ctl17, m6A enriched RNA (IP)

value: B


title: CTCL1137.CD4P.PRE.RNA

value: Mycosis fungoides


title: KMS28PE DMSO 4 days EZH2 ChIP-seq

value: DMSO 4 days

value: Millipore 07-689


title: KMS28PE DMSO 4 days H3K27me3 ChIP-seq


title: CTCL1137.CD4P.OW.RNA


title: Ctl16 IP

source_name: Ctl16, m6A enriched RNA (IP)

value: M

value: EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S)


title: CTCL1135.CD4P.POST.RNA


title: KMS28PE None 4 days Input ChIP-seq

source_name: Multiple Myeloma

value: None 4 days

value: Input


title: Ctl8 IP

source_name: Ctl8, m6A enriched RNA (IP)

value: control

value: A


title: KMS28BM 1.5um CPI360 4 days EZH2 ChIP-seq

value: 1.5um CPI360 4 days


title: CTCL1125.CD4P.VOR_OT.RNA

source_name: Peripheral blood

value: Sensitive


title: KMS28BM 1.5uM CPI360 4 days H3K27me3 ChIP-seq

value: 1.5uM CPI360 4 days

value: Cell Signaling Technolgy 9730


title: CTCL1126.CD4P.POST.RNA

value: Sezary syndrome

value: Resistant


title: WT/floxed - LNA29 #8 [477_floxed_LNA]

description:
8901_5515_63427_HMYC7BGX3_AH22-477_TAATCG
processed data file: DESeq_wtflox_normalized_counts.csv

data_processing:
RNA-seq samples were aligned using STAR, quantified using Salmon, and normalized counts were determined using DESeq2
Genome_build: mm10 and rn6 for mouse and rat RNA-seq
Supplementary_files_format_and_content: Normalized counts files are comma separated value matrices containing the DESeq2 normalized counts for each of the samples.

source_name: WT/floxed - LNA29

extract_protocol: Libraries were prepared according to the Illumina TruSeq polyA+ Sample Prep Kit protocol

treatment_protocol: WT or floxed mouse treated with LNA29

tag: strain

tag: genotype/variation

value: WT/floxed

value: liver


title: KMS28BM DMSO 4 days H3K27me3 ChIP-seq

tag: treatment


title: CTCL1084.CD4P_CD7N.OW.RNA


title: Subject MED 6 [CD8 experiment]

description: normalized data to this group

value: medium alone

value: latent tuberculosis infection (LTBI)

tag: cell type

value: BAL


title: KMS28BM DMSO 4 days EZH2 ChIP-seq

tag: cell line

value: DMSO 4 days

value: Millipore 07-689


title: Ctl4 IP

source_name: Ctl4, m6A enriched RNA (IP)

tag: gender

value: F

value: islets

value: EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S)


title: Subject MED 5 [CD8 experiment]

description: normalized data to this group

tag: agent


title: Subject MED 7 [CD8 experiment]

description: normalized data to this group


title: CTCL1084.CD4P_CD7N.PRE.RNA


title: Ctl1 IP

source_name: Ctl1, m6A enriched RNA (IP)

tag: group

value: control

value: M

value: A


title: SIRT1KO - saline #4 [476_KO_saline]

description:
8901_5515_63426_HMYC7BGX3_AH21-476_CCAACA
processed data file: DESeq_SIRT1KO_normalized_counts.csv

source_name: SIRT1KO - saline

treatment_protocol: SIRT1KO mouse treated with saline (control)

value: saline


title: T2D12 input

source_name: T2D12, mRNA (input)

value: type II diabetes

tag: rip antibody

value: C


title: Subject MED 3 [CD8 experiment]

description: normalized data to this group


title: CTCL1043.CD4P_CD7N.PRE.RNA

value: Mycosis fungoides

value: Sensitive


title: SIRT1KO - saline #3 [473_KO_saline]

description:
8901_5515_63425_HMYC7BGX3_AH20-473_CACGAT
processed data file: DESeq_SIRT1KO_normalized_counts.csv

value: liver


title: Subject MED 4 [CD8 experiment]

description: normalized data to this group

value: medium alone


title: KMS28BM DMSO 4 days Input ChIP-seq

tag: chip antibody target

value: Input


title: CTCL079.OW.H3AC.CD26N

value: Resistant

value: H3ac (EMD Millipore, 06-599)


title: CTCL1043.CD4P_CD7N.POST.RNA


title: T2D11 input

source_name: T2D11, mRNA (input)

tag: batch


title: WT/floxed - saline #5 [467_floxed_saline]

description:
8901_5515_63424_HMYC7BGX3_AH19-467_CAACTA
processed data file: DESeq_wtflox_normalized_counts.csv

source_name: WT/floxed - saline

treatment_protocol: WT or floxed mouse treated with saline (control)

value: WT/floxed


title: Subject MED 2 [CD8 experiment]

description: normalized data to this group

source_name: BAL

value: latent tuberculosis infection (LTBI)

value: BAL


title: CTCL079.CD4P_CD26N.PRE.RNA


title: KARPAS-422 1.5uM CPI360 4 days H3K4me3 ChIP-seq

source_name: Diffuse large B cell lymphoma

value: 1.5uM CPI360 4 days

value: Abcam ab8580


title: T2D6 input

source_name: T2D6, mRNA (input)

value: M

value: islets


title: Subject MED 1 [CD8 experiment]

description: normalized data to this group


title: SIRT1KO - LNA29 #4 [466_KO_LNA]

description:
8901_5515_63423_HMYC7BGX3_AH18-466_ATTCCT
processed data file: DESeq_SIRT1KO_normalized_counts.csv

source_name: SIRT1KO - LNA29

treatment_protocol: SIRT1KO mouse treated with LNA29


title: CTCL079.CD4P_CD26N.OW.RNA


title: WT/floxed - LNA29 #7 [WT8_LNA]

description:
8901_5515_63422_HMYC7BGX3_AH17-WT8_ATGAGC
processed data file: DESeq_wtflox_normalized_counts.csv


title: KARPAS-422 1.5uM CPI360 4 days H3K27me3 ChIP-seq

value: Cell Signaling Technolgy 9730


title: KARPAS-422 1.5uM CPI360 4 days H3K27ac ChIP-seq

value: Active Motif 39133


title: WT/floxed - saline #4 [WT7_saline]

description:
8901_5515_63421_HMYC7BGX3_AH16-WT7_GAGTGG
processed data file: DESeq_wtflox_normalized_counts.csv

value: saline


title: T2D1 input

source_name: T2D1, mRNA (input)

value: type II diabetes

value: A


title: KARPAS-422 1.5uM CPI360 4 days Suz12 ChIP-seq

value: Active Motif 39357


title: T2D5 input

source_name: T2D5, mRNA (input)

value: F

value: B


title: KARPAS-422 1.5uM CPI360 4 days EZH2 ChIP-seq

value: Millipore 07-689


title: WT/floxed - LNA29 #5 [459_floxed_LNA]

description:
8900_5515_63419_HML3JBGX3_AH14-459_GTAGAG
processed data file: DESeq_wtflox_normalized_counts.csv

value: liver


title: KARPAS-422 1.5uM CPI360 8 days H3K4me3 ChIP-seq

value: 1.5uM CPI360 8 days


title: T2D7 input

source_name: T2D7, mRNA (input)


title: WT/floxed - LNA29 #6 [474_floxed_LNA]

description:
8900_5515_63420_HML3JBGX3_AH15-474_GTCCGC
processed data file: DESeq_wtflox_normalized_counts.csv

value: WT/floxed


title: Ctl20 input

source_name: Ctl20, mRNA (input)

value: control

value: C


title: Ctl18 input

source_name: Ctl18, mRNA (input)


title: IL4.eGFP_04: M2 macrophage treated with eGFP-NPs

city: Seattle

first: Matthias

last: Stephan

state: WA

address: 1100 Fairview Ave. N., Thomas Research Buildin

institute: Fred Hutchinson Cancer Research Institute

hyb_protocol: The ligated RNA were co-incubated with miRNA capture probeset, miRNA reporter codeset in hybridization buffer following the protocol provided by NanoString. The hybridation happened in 65 °C for at least 12 hours.

scan_protocol: All samples were read on nCounter Analysis System (NanoString Technologies).

data_processing: Raw data was processed and checked for quality using the R/Bioconductor package NanoStringQCPro (Nickles D, Sandmann T, Ziman R and Bourgon R (2017). NanoStringQCPro: Quality metrics and data processing methods for NanoString mRNA gene expression data. R package version 1.10.0.). Expression values were normalized to the geometric mean of housekeeping genes and log2-transformed using nSolver 4.0 software (NanoString Technologies). FDR for ratio data was calculated from the p-values returned by the t-test using the Benjamini-Yekutieli method.

source_name: Bone Marrow Derrived Macrophages

label_protocol: Ligation master mix (provided by NanoString) was added to the mRNA solution and incubated under 48 °C for 5min to allow ligation, followed with purification to remove unligated molecules.

growth_protocol: To prepare BMDMs, bone marrow progenitor cells were harvested from mouse bone marrow cavity of femur following established protocol [Curr Protoc Immunol. 2008 Nov;Chapter 14:Unit 14.1.]. These cells were then seeded in 100 mm culture dishes in complete media (DMEM supplemented with 4.5 g/L D-glucose, L-glutamine, 10% heat-inactivated fetal bovine serum (FBS), 100 U/mL penicillin and 100 μg/mL, Glutamax 50 mL/500 mL, supplemented with 20 ng/mL M-CSF (Peprotech, cat#315-02) at a seeding density of 0.5 – 1.0 e6/ml. Cells were allowed to grow ex vivo under 37 °C, 5% CO2 for 7 days to fully derive into BMDMs.

extract_protocol: RNA was extracted using RNeasy Plus Universal Mini kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Sample RNA was quantified using a NanoDrop Microvolume Spectrophotometer (Thermo Fisher, Waltham, MA) and quality checked and RINe scores determined by TapeStation (Agilent, Santa Clara, CA).

treatment_protocol: At day 7 ex vivo, culture media was replaced with macrophage conditioned media (macrophage complete medium supplemented with 20 ng/mL MPLA (Sigma, cat#L6895) or 20 ng/mL IL4 (eBioscience, cat# 34-8041)). BMDMs were used between 7 - 21 days ex vivo for all experiments. For nanoparticle treatment, 1 microgram of either IRF5-NPs or eGFP-NPs were co-incubated with BMDMs for 1 hours, followed with completly removal of nanoparticles and 2X wash with culture medium.

value: Bone Marrow Derrived Macrophages

tag: cytokine exposure

tag: time of cytokine exposure

value: 4 days

tag: nanoparticle treatment

value: eGFP-NPs for 1 hour


title: Ctl17 input

source_name: Ctl17, mRNA (input)

value: M

value: islets


title: KARPAS-422 1.5uM CPI360 8 days Suz12 ChIP-seq


title: SIRT1KO - LNA29 #3 [454_KO_LNA]

description:
8900_5515_63417_HML3JBGX3_AH12-454_AGTTCC
processed data file: DESeq_SIRT1KO_normalized_counts.csv


title: KARPAS-422 1.5uM CPI360 8 days EZH2 ChIP-seq


title: IL4.eGFP_03: M2 macrophage treated with eGFP-NPs


title: IL4.eGFP_02: M2 macrophage treated with eGFP-NPs


title: T2D4 input

source_name: T2D4, mRNA (input)


title: IL4.IRF5_04: M2 macrophage treated with IRF5-NPs

value: IRF5-NPs for 1 hour


title: IL4.eGFP_01: M2 macrophage treated with eGFP-NPs


title: KARPAS-422 1.5uM CPI360 8 days H3K27me3 ChIP-seq

value: Cell Signaling Technolgy 9730


title: KARPAS-422 1.5uM CPI360 8 days H3K27ac ChIP-seq

value: Active Motif 39133


title: IL4.IRF5_02: M2 macrophage treated with IRF5-NPs


title: Ctl16 input

source_name: Ctl16, mRNA (input)


title: SIRT1KO - saline #2 [457_KO_saline]

description:
8900_5515_63418_HML3JBGX3_AH13-457_CCGTCC
processed data file: DESeq_SIRT1KO_normalized_counts.csv

source_name: SIRT1KO - saline

value: saline


title: RL DMSO 10 days H3K27me3 ChIP-seq

value: RL

value: DMSO 10 days


title: Ctl4 input

source_name: Ctl4, mRNA (input)

value: F

value: A


title: Ctl8 input

source_name: Ctl8, mRNA (input)


title: KARPAS-422 DMSO 8 days H3K4me3 ChIP-seq

value: DMSO 8 days

value: Abcam ab8580


title: Ctl1 input

source_name: Ctl1, mRNA (input)

value: control


title: WT/floxed - LNA29 #3 [458_floxed_LNA]

description:
8899_5515_63412_HMLJ2BGX3_AH7-458_CAGATC
processed data file: DESeq_wtflox_normalized_counts.csv

source_name: WT/floxed - LNA29

value: WT/floxed

value: liver


title: SIRT1KO - LNA29 #2 [475_KO_LNA]

description:
8899_5515_63413_HMLJ2BGX3_AH8-475_GATCAG
processed data file: DESeq_SIRT1KO_normalized_counts.csv


title: IL4.IRF5_01: M2 macrophage treated with IRF5-NPs

value: Bone Marrow Derrived Macrophages

value: 4 days


title: WT/floxed - saline #3 [WT5_saline]

description:
8900_5515_63414_HML3JBGX3_AH9-WT5_TAGCTT
processed data file: DESeq_wtflox_normalized_counts.csv

source_name: WT/floxed - saline


title: IL4_3: BMDM_treated with IL4 as M2 standards


title: SIRT1KO - LNA29 #1 [453_KO_LNA]

description:
8899_5515_63411_HMLJ2BGX3_AH6-453_GCCAAT
processed data file: DESeq_SIRT1KO_normalized_counts.csv


title: KARPAS-422 DMSO 8 days Suz12 ChIP-seq

source_name: Diffuse large B cell lymphoma

value: Active Motif 39357


title: GoldCLIP_dNxf2Halo_mael_KD_CLIP_rep2

data_processing:
Basecalls were performed using bcl2fastq v1.8.4 for Illumina HiSeq X Ten output.
CLIP-seq reads (read1 for paired-end reads) were processed using Cutadapt (v1.16) . The adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and low-quality bases were trimmed from the 3’ end of reads, and reads short than 15 nt were discarded. After adapter removal, reads were collapsed, the first 10 bases were trimmed (the 5' end linkers contains 10 random nucleotides).
The processed CLIP-seq reads were aligned to fruitfly dm3 and spike-in genome (hg19, UCSC) using Bowtie v1.1.2, only uniquely mapped reads were retained for futther analysis.
Genome_build: dm3
Supplementary_files_format_and_content: bigWig files

molecule: other

source_name: OSC

growth_protocol: OSC cells were maintained at 25 °C in Shields and Sang M3 Insect media (Sigma) supplemented with 10% fetal bovine serum (PAN-Seratech, Eden Bach, DE), 10 mg/ml insulin, 0.6 mg/ml glutathione and 5% fly extract.

extract_protocol:
Lysates were lysed in PBS supplemented with 0.2% Triton, dounced 30 times, clarified from debri, and HaloTag-protein-RNA complexes were isolated using HaloTag Beads.
Briefly, RNA in the Halo-RBP-RNA complex was released and reverse transcribed. Then cDNAs were gel purified and amplified by PCR to add Illumina adaptors. The final libraries were purified and sequenced on Illumina X Ten platform.

treatment_protocol: The DNA templates containing T7 promoters were in vitro transcribed as described (Chamberlin M et al.,1970 Nature). The purified Maelstrom and LacZ dsRNAs were  co-transfected with plasmids overexpressing RFP-Dicer2 into dNxf2-Halo OSCs using FuGeneHD for 3 days. CLIP was performed as descried (Gu et al., 2018 GPB, Nostrand et al., 2016, Nature Methods).

value: OSC

tag: genotype

value: mael KD

tag: clip antibody

value: Halo-ligand


title: SIRT1KO - saline #1 [451_KO_saline]

description:
8899_5515_63410_HMLJ2BGX3_AH5-451_ACAGTG
processed data file: DESeq_SIRT1KO_normalized_counts.csv

tag: tissue


title: WT/floxed - LNA29 #4 [WT6_LNA]

description:
8900_5515_63415_HML3JBGX3_AH10-WT6_CTTGTA
processed data file: DESeq_wtflox_normalized_counts.csv

tag: strain


title: KARPAS-422 DMSO 8 days H3K27ac ChIP-seq

tag: chip antibody

value: Active Motif 39133


title: IL4_2: BMDM_treated with IL4 as M2 standards


title: GoldCLIP_dNxf2Halo_Lacz_KD_CLIP_rep2

value: Lacz KD


title: KARPAS-422 DMSO 8 days H3K27me3 ChIP-seq

tag: treatment

value: Cell Signaling Technolgy 9730


title: KARPAS-422 DMSO 8 days Input ChIP-seq

value: Input


title: GoldCLIP_dNxf2Halo_Lacz_KD_CLIP_rep1


title: WT/floxed - saline #2 [442_floxed_saline]

description:
8899_5515_63409_HMLJ2BGX3_AH4-442_TGACCA
processed data file: DESeq_wtflox_normalized_counts.csv

tag: genotype/variation

value: saline


title: IL4_4: BMDM_treated with IL4 as M2 standards

tag: cell type


title: MPLA_4: BMDM_treated with MPLA as M1 standards

value: MPLA


title: WT/floxed - LNA29 #2 [WT4_LNA]

description:
8899_5515_63408_HMLJ2BGX3_AH3-WT4_TTAGGC
processed data file: DESeq_wtflox_normalized_counts.csv


title: MPLA_3: BMDM_treated with MPLA as M1 standards


title: RNAseq_dNxf2_mut_Panx_FL10B_rep2

data_processing:
Basecalls were performed using bcl2fastq v1.8.4 for Illumina HiSeq 2500 and HiSeq X Ten output.
RNA-seq reads (single-end reads or read1 for paired-end reads) were processed using Cutadapt (v1.16) . The adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and low-quality bases were trimmed from the 3’ end of reads, and reads short than 20 bp were discarded.
RNA-seq reads were aligned to UCSC dm3 using STAR (v2.5.2a), only uniquely mapped reads were retained.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: dm3
Supplementary_files_format_and_content: bigWig files

source_name: ovary

tag: age

value: 3-5 old

value: ovary

value: nxf2 -/-, panx FL10B tethered


title: KARPAS-422 DMSO 8 days EZH2 ChIP-seq

tag: cell line

value: DMSO 8 days

value: Millipore 07-689


title: RNAseq_dNxf2_mut_Panx_FL10B_rep1


title: MPLA_1: BMDM_treated with MPLA as M1 standards

value: Bone Marrow Derrived Macrophages


title: WT/floxed - LNA29 #1 [WT2_LNA]

description:
8899_5515_63406_HMLJ2BGX3_AH1-WT2_ATCACG
processed data file: DESeq_wtflox_normalized_counts.csv

value: WT/floxed

value: liver


title: WT/floxed - saline #1 [WT3_saline]

description:
8899_5515_63407_HMLJ2BGX3_AH2-WT3_CGATGT
processed data file: DESeq_wtflox_normalized_counts.csv


title: KMC36

city: Stellenbosch

first: Stephanie

last: Rollero

address: Victoria Street

department: DVO

country: South Africa

institute: Stellenbosch University

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina HiSeq2500 reads were trimmed and clipped for quality control in TrimGalore! (Galaxy Version 0.4.3.1).
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into TopHat v2.0.8 for alignment on the reference genome GCA_001417885 and paired-end into BAM files.
BAM files were imported into Cufflinks v.2.2.1.2, the transcripts were assembled and FPKM counts were calculated.
The differential expression was testing in Cuffdiff v2.2.1.5
Genome_build: GCA_001417885
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Kluyveromyces marxianus

source_name: KM 36h rep3

growth_protocol: The cells were growing in a medium containing 230 g/l of sugars, 200 mg/l of assimilable nitrogen (amino acids and ammonium) and 10 mg/l of phytosterolsat 25°C.

extract_protocol:
Total RNA extraction were perform with acid phenol and chloroform and purified by isopropanol precipitation.
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: 109 cells were harvested by centrifugation at 2000 g for 5 min at 4°C and the cell pellets were washed with distilled water and then flash-frozen with liquid nitrogen and stored at -80°C.

tag: strains

value: IWBT Y855

tag: fermentation time (h)


title: GoldCLIP_dNxf2Halo_mael_KD_CLIP_rep1

value: OSC

value: mael KD


title: SCD20

data_processing:
Illumina Casava1.7 software used for basecalling.
Illumina HiSeq2500 reads were trimmed and clipped for quality control in TrimGalore! (Galaxy Version 0.4.3.1).
Read quality was checked for each sample using FastQC v0.10.1.
High-quality reads were then imported into TopHat v2.0.8 for alignment on the reference genome GCA_000218975 and paired-end into BAM files.
BAM files were imported into Cufflinks v.2.2.1.2, the transcripts were assembled and FPKM counts were calculated.
The differential expression was testing in Cuffdiff v2.2.1.5
Genome_build: GCA_000218975
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: SC 20h rep3


title: IL4_1: BMDM_treated with IL4 as M2 standards

value: 4 days


title: Mettl14 knock-out2

type: protein

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: The antibodies used on the Kinex™ KAM-1325 antibody microarrays consist of polyclonal and monoclonal antibodies that are specific for proteins or phosphosites.

hyb_protocol: After blocking non-specific binding sites on the array, an incubation chamber is mounted onto the microarray to permit the loading of 2 samples side by side on the same chip and prevent mixing of the samples. Following sample incubation, unbound proteins are washed away and the array is then probed with anti-biotin antibody that is labelled with a proprietary fluorescent dye combination.

scan_protocol: Each array produces a pair of 16-bit images, which are captured with a Perkin-Elmer ScanArray Reader laser array scanner (Waltham, MA).

data_processing: Signal quantification is performed with ImaGene 9.0 from BioDiscovery (El Segundo, CA) with predetermined settings for spot segmentation and background correction. The background-corrected raw intensity data are logarithmically transformed with base 2.

molecule: protein

label_protocol: Proteins were covalently labeled with biotin. Free biotin molecules are then removed at the completion of labeling reactions by gel filtration.

extract_protocol: Total proteins were harvested from islets lysates using M-PER protein extraction reagent (Thermo Fisher, USA) supplemented with proteinase and phosphatase inhibitors  (Sigma, USA) according to standard protocol.

tag: strain background

value: KO; Mettl14 knock-out

value: islets

value: B


title: RNAseq_dNxf2_het_Panx_FL10B_rep1

value: nxf2 +/-, panx FL10B tethered


title: SCC20

source_name: SC 20h rep2


title: KMA36

source_name: KM 36h rep1


title: SCB20

source_name: SC 20h rep1


title: RNAseq_dNxf2_KD_rep2

data_processing:
Basecalls were performed using bcl2fastq v1.8.4 for Illumina HiSeq 2500 and HiSeq X Ten output.
RNA-seq reads (single-end reads or read1 for paired-end reads) were processed using Cutadapt (v1.16) . The adapter sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and low-quality bases were trimmed from the 3’ end of reads, and reads short than 20 bp were discarded.
RNA-seq reads were aligned to UCSC dm3 using STAR (v2.5.2a), only uniquely mapped reads were retained.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
note: read2 for Illumina HiSeq X Ten paired-end reads not supplied by submitter
Genome_build: dm3
Supplementary_files_format_and_content: bigWig files were generated using the deeptools (v2.5.7). Score represents the normalized coverage of RNA fragments at a given genomic coordinate. Count file was generated using featureCounts (v1.6.1) for each alignment files.

value: nxf2 knockdown


title: Control4

value: control

tag: batch

value: C


title: MPLA_2: BMDM_treated with MPLA as M1 standards

source_name: Bone Marrow Derrived Macrophages

tag: cytokine exposure

value: MPLA


title: Tg_ow

city: Fukuoka

first: Takehito

last: Uruno

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

description: low IL-31 level

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: DRG neurons, Dock8+/– (tcr)AND Tg

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from DRG neurons using Isogen (Nippon Gene) according to the manufacturer's instructions.

value: Dock8+/– (tcr)AND

value: DRG neurons


title: KMB36

source_name: KM 36h rep2


title: RNAseq_dNxf2_KD_rep1

value: 3-5 old

value: ovary


title: KMC6

source_name: KM 6h rep3


title: Tg_oo

description: high IL-31 level

source_name: DRG neurons, Dock8–/– (tcr)AND Tg

value: Dock8–/– (tcr)AND


title: SCD6

source_name: SC 6h rep3


title: Mettl14 knock-out1

value: A


title: Control3


title: RNAseq_dNxf2_het_Panx_FL10B_rep2


title: SCC6

source_name: SC 6h rep2


title: RNAseq_attp2_rep1

value: wild type


title: KMB6

source_name: KM 6h rep2

value: IWBT Y855


title: Control2


title: KMA6

source_name: KM 6h rep1


title: RNAseq_attp2_rep2


title: Control1