title: Can_SD_male_Cerebellum, biological rep6

status: Public on Mar 31 2019

type: RNA

city: Seewiesen

first: Meng-Ching

last: Ko

state: Bayern

address: Eberhard-Gwinner-Str. 6a

department: Behavioral Neurobiology

country: Germany

institute: Max Planck Institute for Ornithology

description: Molecular layer of the cerebellum was dissected from cryosections

hyb_protocol: The resulting cDNA was hybridized to the Custom Affymetrix Gene Chip® MPIO-ZF1s520811 Exon Array. The hybridization was carried out during 16 hours at 45°C and 60 rpm in the GeneChip Hybridization Oven 640.

scan_protocol: The arrays were washed, stained and scanned using the Affymetrix GeneChip Fluidics Station 450 and Affymetrix GeneChip scanner 3000 7G.

data_processing: The CEL files were generated by the Affymetrix® GeneChip® Command Console® Software (AGCC) and the quality control for evaluating the success of individual hybridizations was assessed by the Affymetrix® Expression Console™ software. Affymetrix CEL files were imported into ChipInspector software, version 21 (El Dorado Database version: vE28R1306 Genomatix GmbH (http://www.genomatix.de)

label: biotin

molecule: total RNA

organism: Serinus canaria

source_name: Cerebellum, molecular layer

label_protocol: RNA was processed for hybridization on the microarray by using the Ambion WT Expression Kit and the Affymetrix WT Terminal Labeling and Controls Kit.

growth_protocol: Adult animals housed in long or short light cycles in aviaries. Water and food were available ad libidum.

extract_protocol: For RNA preparation, brains were cut into four 40 µm para-sagittal sections mounted each on one slide . The areas were dissected with very fine forceps (a different one for each brain area to avoid contamination) under a stereo-microscope, transferred into 340μl RLT buffer mixture (containing DTT, Qiagen) and stored at -80 C till RNA purification (RNeasy® Micro Kit, Qiagen).

treatment_protocol: No treatment

tag: age

value: adult

tag: Sex

value: male

tag: light cycle

value: short day

tag: breeding

value: No

tag: treatment

value: No treatment

tag: song behavior

value: Absent


title: Can_SD_male_Cerebellum, biological rep5


title: Can_SD_female_Cerebellum, biological rep4

value: female


title: Can_SD_male_Cerebellum, biological rep4


title: Can_SD_female_Cerebellum, biological rep6


title: Can_SD_male_Cerebellum, biological rep3


title: Can_SD_male_Cerebellum, biological rep1


title: Can_SD_female_Cerebellum, biological rep2


title: Can_LD_male_Cerebellum, biological rep6

value: long day

value: Yes

value: Present


title: Can_LD_male_Cerebellum, biological rep5


title: Can_SD_female_Cerebellum, biological rep5


title: Can_SD_female_Cerebellum, biological rep3


title: Can_SD_male_Cerebellum, biological rep2


title: Can_SD_female_Cerebellum, biological rep1


title: Can_LD_male_Cerebellum, biological rep1


title: Can_LD_male_Cerebellum, biological rep3


title: Can_LD_female_Cerebellum, biological rep3


title: Can_LD_male_Cerebellum, biological rep4


title: Can_LD_female_Cerebellum, biological rep5


title: Can_LD_male_Cerebellum, biological rep2


title: Can_SDfT_HVC_6 HVC, biological rep5

description: HVC was dissected from cryosections

source_name: HVC

value: testosterone


title: Can_LD_female_Cerebellum, biological rep4


title: Can_LD_female_Cerebellum, biological rep6


title: Can_SDfT_HVC_8 HVC, biological rep6

description: HVC was dissected from cryosections


title: Can_LD_female_Cerebellum, biological rep2


title: Can_LD_female_Cerebellum, biological rep1


title: Can_SDfT_HVC_5 HVC, biological rep4

description: HVC was dissected from cryosections


title: Can_SDfT_HVC_4 HVC, biological rep3

description: HVC was dissected from cryosections


title: Can_SDfT_ENT_8 Entopallium, biological rep6

description: Entopallium was dissected from cryosections

source_name: Entopallium


title: Can_SDmT_HVC_7 HVC, biological rep6

description: HVC was dissected from cryosections


title: Can_SDfT_ENT_7 Entopallium, biological rep5


title: Can_SDfT_HVC_2 HVC, biological rep2

description: HVC was dissected from cryosections


title: Can_SDfT_ENT_1 Entopallium, biological rep1


title: Can_SDfT_HVC_1 HVC, biological rep1

description: HVC was dissected from cryosections


title: Can_SDfT_ENT_6 Entopallium, biological rep4


title: Can_SDfT_ENT_5 Entopallium, biological rep3


title: Can_SDfT_ENT_4 Entopallium, biological rep2


title: Can_SDmT_ENT_5 Entopallium, biological rep4


title: Can_SDmT_ENT_7 Entopallium, biological rep6


title: Can_SDmT_ENT_6 Entopallium, biological rep5


title: Can_SD_female_NatSing_HVC_960R HVC, biological rep3

description: HVC was dissected from cryosections


title: Can_SDmT_ENT_4 Entopallium, biological rep3


title: Can_SDmT_ENT_3 Entopallium, biological rep2


title: Can_SD_female_NatSing_ENT_963L Entopallium, biological rep6


title: Can_SD_female_NatSing_HVC_961R HVC, biological rep4

description: HVC was dissected from cryosections


title: Can_SDmT_ENT_2 Entopallium, biological rep1


title: Can_SD_female_NatSing_HVC_963L HVC, biological rep6

description: HVC was dissected from cryosections


title: Can_SD_female_NatSing_HVC_962R HVC, biological rep5

description: HVC was dissected from cryosections


title: Can_SD_female_NatSing_HVC_959R HVC, biological rep2

description: HVC was dissected from cryosections


title: Can_SD_female_NatSing_HVC_958R HVC, biological rep1

description: HVC was dissected from cryosections


title: Can_SD_female_NatSing_ENT_962R Entopallium, biological rep5


title: Can_SD_female_NatSing_ENT_960R Entopallium, biological rep3


title: Can_SD_female_NatSing_ENT_959R Entopallium, biological rep2


title: Can_SD_female_NatSing_ENT_961R Entopallium, biological rep4


title: Can_SDmT_HVC_2 HVC, biological rep1

description: HVC was dissected from cryosections


title: Can_SDmT_HVC_6 HVC, biological rep5

description: HVC was dissected from cryosections


title: Can_SDmT_HVC_4 HVC, biological rep3

description: HVC was dissected from cryosections


title: Can_SD_female_NatSing_ENT_958R Entopallium, biological rep1


title: Can_SD_female_HVC_10 HVc, biological rep6

description: HVC was dissected from cryosections


title: Can_SD_female_HVC_3 HVc, biological rep3

description: HVC was dissected from cryosections


title: Can_SD_female_HVC_6 HVc, biological rep5

description: HVC was dissected from cryosections


title: Can_SDmT_HVC_3 HVC, biological rep2

description: HVC was dissected from cryosections


title: Can_SD_female_ENT_10 Entopallium, biological rep5


title: Can_SD_female_HVC_2 HVc, biological rep2

description: HVC was dissected from cryosections


title: Can_SDmT_HVC_5 HVC, biological rep4

description: HVC was dissected from cryosections


title: Can_SD_female_HVC_1 HVc, biological rep1

description: HVC was dissected from cryosections


title: Can_SD_female_ENT_6 Entopallium, biological rep4


title: Can_SD_female_HVC_5 HVc, biological rep4

description: HVC was dissected from cryosections


title: Can_SD_female_ENT_5 Entopallium, biological rep3


title: Can_SD_male_HVC_6 HVC, biological rep6

description: HVC was dissected from cryosections


title: Can_SD_male_HVC_4 HVC, biological rep4

description: HVC was dissected from cryosections


title: Can_SD_female_ENT_1 Entopallium, biological rep1


title: Can_SD_female_ENT_3 Entopallium, biological rep2


title: Can_SD_male_HVC_3 HVC, biological rep3

description: HVC was dissected from cryosections


title: Can_SD_male_ENT_4 Entopallium, biological rep4


title: Can_SD_male_HVC_5 HVC, biological rep5

description: HVC was dissected from cryosections


title: Can_SD_male_HVC_2 HVC, biological rep2

description: HVC was dissected from cryosections


title: Can_SD_male_ENT_6 Entopallium, biological rep6


title: Can_SD_male_ENT_3 Entopallium, biological rep3


title: Can_SD_male_ENT_2 Entopallium, biological rep2


title: Can_SD_male_ENT_1 Entopallium, biological rep1


title: Can_SD_male_ENT_5 Entopallium, biological rep5


title: Can_SD_male_HVC_1 HVC, biological rep1

description: HVC was dissected from cryosections


title: Can_LD_female_HVC_725 HVC, biological rep4

description: HVC was dissected from cryosections


title: Can_LD_female_HVC_735 HVC, biological rep6

description: HVC was dissected from cryosections


title: Can_LD_female_HVC_730 HVC, biological rep5

description: HVC was dissected from cryosections


title: Can_LD_female_HVC_724 HVC, biological rep3

description: HVC was dissected from cryosections


title: Can_LD_female_HVC_697 HVC, biological rep2

description: HVC was dissected from cryosections


title: Can_LD_female_ENT_735 Entopallium, biological rep6


title: Can_LD_female_HVC_689 HVC, biological rep1

description: HVC was dissected from cryosections


title: Can_LD_male_HVC_4 HVC, biological rep3

description: HVC was dissected from cryosections


title: Can_LD_female_ENT_730 Entopallium, biological rep5


title: Can_LD_female_ENT_725 Entopallium, biological rep4


title: Can_LD_male_HVC_1 HVC, biological rep1

description: HVC was dissected from cryosections


title: Can_LD_female_ENT_697 Entopallium, biological rep2


title: Can_LD_male_HVC_22 HVC, biological rep5

description: HVC was dissected from cryosections


title: Can_LD_female_ENT_724 Entopallium, biological rep3


title: Can_LD_male_HVC_3 HVC, biological rep2

description: HVC was dissected from cryosections


title: CB_female_HVC_92 HVC, biological rep5

description: HVC was dissected from cryosections

organism: Uraeginthus cyanocephalus


title: Can_LD_male_ENT_36 Entopallium, biological rep4


title: Can_LD_male_ENT_34 Entopallium, biological rep2


title: Can_LD_male_ENT_37 Entopallium, biological rep5


title: Can_LD_male_ENT_32 Entopallium, biological rep1


title: Can_LD_female_ENT_689 Entopallium, biological rep1


title: CB_female_HVC_93 HVC, biological rep6

description: HVC was dissected from cryosections


title: Can_LD_male_HVC_172 HVC, biological rep6

description: HVC was dissected from cryosections


title: Can_LD_male_HVC_5 HVC, biological rep4

description: HVC was dissected from cryosections


title: CB_female_HVC_89 HVC, biological rep3

description: HVC was dissected from cryosections


title: Can_LD_male_ENT_38 Entopallium, biological rep6


title: CB_female_HVC_91 HVC, biological rep4

description: HVC was dissected from cryosections


title: CB_female_ENT_89 Entopallium, biological rep5


title: CB_female_HVC_83 HVC, biological rep2

description: HVC was dissected from cryosections


title: CB_female_ENT_87 Entopallium, biological rep4


title: CB_female_HVC_80 HVC, biological rep1

description: HVC was dissected from cryosections


title: CB_female_ENT_83 Entopallium, biological rep2


title: CB_male_HVC_88 HVC, biological rep5

description: HVC was dissected from cryosections


title: CB_male_ENT_88 Entopallium, biological rep5


title: CB_male_HVC_90 HVC, biological rep6

description: HVC was dissected from cryosections


title: CB_female_ENT_85 Entopallium, biological rep3


title: CB_female_ENT_91 Entopallium, biological rep6


title: CB_male_ENT_82 Entopallium, biological rep2


title: CB_male_HVC_81 HVC, biological rep1

description: HVC was dissected from cryosections


title: CB_male_HVC_84 HVC, biological rep3

description: HVC was dissected from cryosections


title: CB_male_HVC_86 HVC, biological rep4

description: HVC was dissected from cryosections


title: CB_female_ENT_80 Entopallium, biological rep1


title: CB_male_HVC_82 HVC, biological rep2

description: HVC was dissected from cryosections


title: CB_male_ENT_81 Entopallium, biological rep1


title: CB_male_ENT_86 Entopallium, biological rep4


title: FW_female_HVC_17-2 HVC, biological rep6

description: HVC was dissected from cryosections

organism: Ploceus bicolor


title: FW_female_HVC_8-2 HVC, biological rep4

description: HVC was dissected from cryosections


title: FW_female_HVC_5-2 HVC, biological rep3

description: HVC was dissected from cryosections


title: CB_male_ENT_84 Entopallium, biological rep3


title: FW_female_ENT_17 Entopallium, biological rep6


title: FW_male_HVC_18 HVC, biological rep6

description: HVC was dissected from cryosections


title: FW_female_ENT_13 Entopallium, biological rep5


title: FW_female_ENT_8 Entopallium, biological rep3


title: FW_female_HVC_4 HVC, biological rep2

description: HVC was dissected from cryosections


title: FW_male_HVC_12 HVC, biological rep4

description: HVC was dissected from cryosections


title: FW_female_ENT_12-9 Entopallium, biological rep4


title: FW_female_HVC_2 HVC, biological rep1

description: HVC was dissected from cryosections


title: FW_female_HVC_13 HVC, biological rep5

description: HVC was dissected from cryosections


title: FW_male_HVC_7 HVC, biological rep3

description: HVC was dissected from cryosections


title: FW_female_ENT_5 Entopallium, biological rep2


title: FW_female_ENT_2 Entopallium, biological rep1


title: circSLC45A4_siRNA_3_Rep_1

type: SRA

city: Berlin

first: Nikolaus

last: Rajewsky

state: Berlin

address: Robert-Rössle-Str. 10

department: Systems Biology of Gene Regulatory Elements

institute: Max-Delbrück Center for Molecular Medicine / Berlin Institute for Medical Systems Biology

library_source: transcriptomic

data_processing:
demultiplexing and conversion to FASTQ with bcl2fastq v2.17.1.14 --barcode-mismatches 1 -r 1 -d 1 -p 1-w 1
mapping to hg38 with STAR 2.5.0a; default parameters
counting with htseq-count v0.8.0, gene model gencode v23; -f bam -m union -r pos -i gene_name -a 10
differential expression analysis with DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: Htseq count file, raw counts and genomic feature accession number

molecule: polyA RNA

organism: Homo sapiens

source_name: Neuroblastoma cells

growth_protocol: DMEM/F12 with 10 % FBS and 1xGlutaMax; media change every two days; passage every 4 days

extract_protocol:
Trizol extraction
Illumina TruSeq; polyA selected

treatment_protocol: siRNA transfection with Lipofectamine RNAiMax, 25 pmol siRNA per 6-well

tag: cell line

tag: sirna


title: FW_male_ENT_6 Entopallium, biological rep2


title: scramble_siRNA_Rep_2


title: scramble_siRNA_Rep_1


title: FW_male_ENT_18 Entopallium, biological rep6


title: circSLC45A4_siRNA_2_Rep_1


title: FW_male_HVC_14 HVC, biological rep5

description: HVC was dissected from cryosections


title: FW_male_ENT_3 Entopallium, biological rep1


title: Can_LD_male_ENT_35 Entopallium, biological rep3


title: circSLC45A4_siRNA_1_Rep_1


title: FW_male_HVC_6 HVC, biological rep2

description: HVC was dissected from cryosections


title: FW_male_ENT_10 Entopallium, biological rep4


title: FW_male_ENT_7 Entopallium, biological rep3


title: FW_male_ENT_14 Entopallium, biological rep5


title: circSLC45A4_siRNA_2_Rep_2


title: HEK293T-SCREEN-Variant6

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

country: USA

institute: Memorial Sloan Kettering

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7.
No samples were excluded from bioinformatics analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene expression counts per gene estimated by STAR

growth_protocol: HEK293T cells (CRL-3216, obtained from ATCC) were grown in culture using media consisting of DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). HEK293T was used until passage 20. Cells were passaged at ~80% confluency every 2-4 days to maintain an actively growing population and avoid anoxic conditions. Cells  were tested for mycoplasma bi-weekly.

extract_protocol:
RNA was extracted with Macherey-Nagel’s  NucleoSpin RNA Plus kit.
Illumina TruSeq Stranded Total RNA Gold, IDT-ILM unique dual indices for barcoding.

treatment_protocol: Transfections were performed using 50ug of transfection quality plasmid DNA (Qiagen Maxiprep) encoding desired BE3-P2A-EGFP, variants thereof or nCas9-UGI-NLS-P2A-EGFP and gRNAs (nuclease-to-gRNA ratio 75:25%). 6x10E6 HEK293T or 15x10E6 HepG2 were seeded into TC-treated 150mm plates 18-24h prior to transfection to yield  ~60-80 % confluency on the day of transfection. Cells were transfected using 150uL TransIT-293 (HEK293T, Mirus) or 150uL transfeX (HepG2, ATCC) reagents per plate, according to the manufacturers’ protocols (mixing DNA and reagent in 5mL Optimem, 30min incubation). Cells were sorted 36-40h after transfection, for either top 5% or all-GFP after doublet-exlusion and gating for the cell population on a BD FACSARIA II.

tag: guide

value: RNF2 site 1:GTCATCTTAGTCATTACCTG(AGG)

tag: gfp

value: Top 5%

tag: design


title: HEK293T-SCREEN-Variant5


title: HEK293T-SCREEN-Variant3


title: HEK293T-SCREEN-CATINACTIVE

value: CATINACTIVE


title: HEK293T-SCREEN-NEGATIVECONTROL

value: NEGATIVECONTROL


title: HEK293T-SCREEN-POSITIVECONTROL

value: POSITIVECONTROL


title: circSLC45A4_siRNA_1_Rep_2


title: HEK293T-SCREEN-Variant2


title: HEK293T-SCREEN-Variant1


title: mRNA_Slc45a4_shRNA_Rep_3

data_processing:
demultiplexing and conversion to FASTQ with bcl2fastq v2.17.1.14 --barcode-mismatches 1 -r 1 -d 1 -p 1-w 1
mapping to mm10 with STAR 2.4.2a; default parameters
counting with GenomicAlignments/summarizeOverlaps with gencode.vM16; mode Union, single End True, ignore.strand False preprocess.reads=invertStrand
differential expression analysis with DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: counts file, raw counts and genomic feature accession number (ENSEMBL)

organism: Mus musculus

source_name: embryonic mouse cortex, GFP+ cells

growth_protocol: standard procedures

extract_protocol:
isolation of electroporated GFP+ cells by FACS, Trizol extraction
Illumina TruSeq; polyA selected

treatment_protocol: in utero electroporation at E13.5; animals were sacrificed at E15.5

tag: strain

tag: shRNA

tag: tissue

value: cortex

tag: time point

tag: fluorescent label

value: GFP


title: scramble_shRNA_Rep3


title: HEK293T-SCREEN-Variant4


title: mRNA_Slc45a4_shRNA_Rep_1


title: scramble_shRNA_Rep2


title: scramble_shRNA_Rep1


title: circSLC45A4_siRNA_3_Rep_2


title: mRNA_Slc45a4_shRNA_Rep_2


title: circSlc45a4_shRNA_Rep_3


title: circSlc45a4_shRNA_Rep_2


title: circSlc45a4_shRNA_Rep_1


title: Dkk+/+ replicate 2 [Dkk1C2P]

city: WESTMEAD

first: PIERRE

last: OSTEIL

state: NSW

address: 214 Hawkesbury Road

department: Embryology

country: Australia

institute: CMRI

description:
Dkk1C2P
Control posterior replicate 2

hyb_protocol: Hybridization carried out at Australian Genome Research Facility using standard Illumina protocols.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Idat files were analysed using GenomeStudio. Further analysis was performed in R using BeadArray and illuminaMousev2.db libraries. Probes annotated as bad quality according to illuminaMousev2PROBEQUALITY were removed.

source_name: Posterior epiblast, control

label_protocol: Labelling carried out at Australian Genome Research Facility using standard Illumina protocols.

growth_protocol: Mouse embryos collected at E7.75.

extract_protocol: RNA extracted using QIAGEN RNA microcolumns.

treatment_protocol: Embryos of four genotypes were collected: Dkk+/+ and Dkk-/-.

tag: embryo genotype

value: Dkk+/+

value: Posterior epiblast

tag: developmental stage


title: Mettl3-deficient HSC 3 m6A-tagged

first: Heather

last: Lee

state: NY

institute: Columbia University

description:
Mettl3Deficient_meRIPSeq.txt
EluteM3

data_processing:
Analysis of meRIP-seq data was performed using the Quantas pipeline (https://zhanglab.c2b2.columbia.edu/index.php/Quantas) with minor modifications.  In brief, raw reads were mapped to the mouse genome and an exon-junction database using OLego. Due to the low input during library preparation, potential PCR duplicates were removed using Picard (http://broadinstitute.github.io/picard). Exonic and junction reads were then counted to estimate transcript abundance (read per kilobase per million reads, or RPKM) and perform differential expression analysis using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene names and RPKM values for input, m6A-antibody-tagged and antibody-unbound fractions from HSC meRIP-Seq.

source_name: HSC

extract_protocol:
Bone marrow cells were flushed from adult hindlimbs and stained for Lineage- Sca1+ cKit+ CD150+ CD48- HSCs. poly(A)+RNA was isolated from 3,000 sorted HSCs using Dynabeads Oligo-(dT)25 magnetic beads (ThermoFisher Scientific) according to manufacturer’s instructions. 1.25 μg of anti-m6A antibody (Synaptic Systems) was pre-bound to Protein A/G magnetic beads (Millipore) in IP buffer (20-mM Tris pH 7.5, 140-mM NaCl, 1% NP-40, 2-mM EDTA) for 1 h. Sample RNA was incubated with antibody-bound Protein A/G beads for 2 hours at 4 ºC. Samples were washed twice in low-salt-wash buffer (10-mM Tris pH 7.5, 5 mM EDTA), twice with high-salt-wash buffer (20-mM Tris pH 7.5, 1-M NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1-mM EDTA) and twice with RIPA buffer (20-mM Tris pH 7.5, 150-mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, 1-mM EDTA). All wash solutions for each sample were collected as the “unbound” fraction. RNA was eluted from the beads by incubating with 50μl 20mM N6-methyladenosine 5-monophosphate sodium salt (Sigma) for 1hr at 4 ºC.
RNA from input, m6A-antibody unbound, and m6A-antibody eluted fractions was reverse transcribed, amplified, tagmented and index according to the Smart-seq2 protocol. Samples were seuqneced on Illumina NextSeq 500 with paired-end 150-bp read lengths.

treatment_protocol: Mice were given 10ug pIpC by intraperitoneal injection every other day for 5 doses. Mice were sacrificed 10 days after the last injection.

value: bone marrow

tag: cell type

value: HSC

tag: genotype

value: Mx1-cre; Mettl3fl/fl 10 days after pIpC

tag: rip antibody

value: anti-m6A antibody (Synaptic Systems)

tag: fraction

value: m6A-tagged fraction


title: Dkk-/- replicate 3 [Dkk1M3A]

description:
Dkk1M3A
KO anterior replicate 3

source_name: Anterior epiblast, Dkk knockout

value: Dkk-/-

value: Anterior epiblast


title: Mettl3-deficient HSC 3 Unbound

description:
Mettl3Deficient_meRIPSeq.txt
FlowM3

value: Unbound fraction


title: Dkk-/- replicate 1 [Dkk1M1P]

description:
Dkk1M1P
KO posterior replicate 1

source_name: Posterior epiblast, Dkk knockout


title: Dkk-/- replicate 2 [Dkk1M2P]

description:
Dkk1M2P
KO posterior replicate 2


title: Dkk+/+ replicate 3 [Dkk1C3P]

description:
Dkk1C3P
Control posterior replicate 3


title: Dkk-/- replicate 3 [Dkk1M3P]

description:
Dkk1M3P
KO posterior replicate 3


title: Dkk-/- replicate 2 [Dkk1M2A]

description:
Dkk1M2A
KO anterior replicate 2


title: WT HSC 3 Unbound

description:
WT_meRIPSeq.txt
Flowthrough 3

value: Wild-type


title: Mettl3-deficient HSC 1 Unbound

description:
Mettl3Deficient_meRIPSeq.txt
FlowM1


title: Mettl3-deficient HSC 1 Input

description:
Mettl3Deficient_meRIPSeq.txt
InputM1

value: Input fraction


title: WT HSC 2 m6A-tagged

description:
WT_meRIPSeq.txt
Elution 2


title: Mettl3-deficient HSC 1 m6A-tagged

description:
Mettl3Deficient_meRIPSeq.txt
EluteM1


title: Dkk+/+ replicate 1 [Dkk1C1P]

description:
Dkk1C1P
Control posterior replicate 1


title: Dkk+/+ replicate 1 [Dkk1C1A]

description:
Dkk1C1A
Control anterior replicate 1

source_name: Anterior epiblast, control


title: WT HSC 3 m6A-tagged

description:
WT_meRIPSeq.txt
Elution 3


title: Mettl3-deficient HSC 2 m6A-tagged

description:
Mettl3Deficient_meRIPSeq.txt
EluteM2


title: Dkk+/+ replicate 3 [Dkk1C3A]

description:
Dkk1C3A
Control anterior replicate 3


title: Mettl3-deficient HSC 2 Unbound

description:
Mettl3Deficient_meRIPSeq.txt
FlowM2


title: Dkk+/+ replicate 2 [Dkk1C2A]

description:
Dkk1C2A
Control anterior replicate 2


title: WT HSC 3 Input

description:
WT_meRIPSeq.txt
Input 3


title: Mettl3-deficient HSC 2 Input

description:
Mettl3Deficient_meRIPSeq.txt
InputM2


title: Dkk-/- replicate 1 [Dkk1M1A]

description:
Dkk1M1A
KO anterior replicate 1


title: WT HSC 2 Unbound

description:
WT_meRIPSeq.txt
Flowthrough 2


title: FW_male_HVC_1 HVC, biological rep1

description: HVC was dissected from cryosections

tag: age

value: adult

tag: Sex

value: male

tag: light cycle

value: long day

tag: breeding

value: Yes

tag: treatment

value: No treatment

tag: song behavior

value: Present


title: CaCO-2et KRAS WT treated with MS-275 for 72 hrs replicate N3

first: Florian

last: Uhlitz

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

description:
WT_72HR_E5_N3
AS-170964-LR-26498

data_processing:
Quality control was performed using FastQC
Reads were mapped using STAR aligner v2.5.0c
Mapped reads were counted using subread featureCounts
Read counts were normalised using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimeted file of DESeq2 normalised read counts

source_name: CaCO-2et KRAS WT_MS-275 for 72 hrs

growth_protocol: CaCO-2et KRAS G12V and CaCO-2et KRAS WT were cultured in DMEM supplemented with 10% FCS, 1% Pen/strep and 1% Ultraglutamine.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: Cells were cultured 72hours prior to the experiment and further maintained for the duration of the experiment in the presence of doxycycline (2µg/ml) (Applichem) to induce an ectopic expression of KRAS G12V and WT respectively. Cells were also treated with either DMSO (0.1%v/v) (PanReac AppliChem) or MS-275 (5µM) (CAS No.: 209783-80-2) (Selleckchem) for the specified duration (1, 6, 24 and 72hrs).

tag: cell line

value: CaCO-2et KRAS WT

tag: treatment duration

value: 72 hrs


title: WT HSC 1 Input

description:
WT_meRIPSeq.txt
Input 1

tag: strain

tag: tissue

value: bone marrow

value: HSC


title: CaCO-2et KRAS WT treated with MS-275 for 72 hrs replicate N1

description:
WT_72HR_E5_N1
AS-170168-LR-26494


title: CaCO-2et KRAS WT treated with MS-275 for 72 hrs replicate N2

description:
WT_72HR_E5_N2
AS-170438-LR-26496


title: WT HSC 2 Input

description:
WT_meRIPSeq.txt
Input 2


title: WT HSC 1 m6A-tagged

description:
WT_meRIPSeq.txt
Elution 1

value: anti-m6A antibody (Synaptic Systems)


title: CaCO-2et KRAS WT treated with DMSO for 72 hrs replicate N1

description:
WT_72HR_DMSO_N1
AS-170167-LR-26494

source_name: CaCO-2et KRAS WT_DMSO for 72 hrs

value: DMSO


title: P6_KRAS_FIRE

data_processing:
RAW data was processed with BD Precise Whole Transcriptome Assay Analysis Pipeline v2.0
edgeR TMM read count normalisation
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Tab-delimeted files of edgeR TMM normalised read counts. The file plate_anno.tsv contains cell ID, transgene and barcode information.

source_name: Organoid-derived single cells expressing KRAS or control transgene FLUC and FIRE reporter

growth_protocol: Organoid were cultured in 48-well plates with 15µl droplets of Matrigel (BD) per well overlaid with 300µl crypt culture medium containing EGF (50ng/ml), Noggin (100ng/ml) and R-Spondin1 (functionally tested from R-Spondin-conditioned medium; CCM-REN)

extract_protocol:
Total RNA extraction with Precise WTA Kit (BD)
Pre-dispensed library chemistry with Precise WTA Kit (BD)

treatment_protocol: Transgenes were induced by addition of 2µg/ml doxycycline to the medium.

value: Transgenic B6

value: intestinal organoids

tag: transgenes

value: FLUC;KRAS (mixed sample, non-demultiplexed)

tag: reporter

value: FIRE


title: P8_KRAS_FIRE


title: P5_KRAS_FIRE


title: CaCO-2et KRAS WT treated with MS-275 for 24 hrs replicate N2

description:
WT_24HR_E5_N2
AS-170436-LR-26496

source_name: CaCO-2et KRAS WT_MS-275 for 24 hrs

value: 24 hrs


title: CaCO-2et KRAS WT treated with MS-275 for 24 hrs replicate N3

description:
WT_24HR_E5_N3
AS-170963-LR-26498


title: P2_KRAS

source_name: Organoid-derived single cells expressing KRAS or control transgene FLUC

value: No reporter


title: P3_KRAS_CTNNB1

source_name: Organoid-derived single cells expressing KRAS, CTNNB1 or control transgene FLUC

value: FLUC;KRAS;CTNNB1 (mixed sample, non-demultiplexed)


title: CaCO-2et KRAS WT treated with DMSO for 72 hrs replicate N2

description:
WT_72HR_DMSO_N2
AS-170437-LR-26496


title: WT HSC 1 Unbound

description:
WT_meRIPSeq.txt
Flowthrough 1

value: Wild-type

value: Unbound fraction


title: P7_KRAS_FIRE


title: CaCO-2et KRAS WT treated with DMSO for 24 hrs replicate N2

description:
WT_24HR_DMSO_N2
AS-170435-LR-26496

source_name: CaCO-2et KRAS WT_DMSO for 24 hrs


title: P1_KRAS_BRAF

source_name: Organoid-derived single cells expressing KRAS, BRAF or control transgene FLUC

value: FLUC;KRAS;BRAF (mixed sample, non-demultiplexed)


title: P4_KRAS_CTNNB1


title: CaCO-2et KRAS WT treated with MS-275 for 24 hrs replicate N1

description:
WT_24HR_E5_N1
AS-170166-LR-26494


title: CaCO-2et KRAS WT treated with MS-275 for 6 hrs replicate N3

description:
WT_6HR_E5_N3
AS-170962-LR-26498

source_name: CaCO-2et KRAS WT_MS-275 for 6 hrs

value: 6 hrs


title: CaCO-2et KRAS WT treated with MS-275 for 6 hrs replicate N2

description:
WT_6HR_E5_N2
AS-170434-LR-26496

value: CaCO-2et KRAS WT


title: CaCO-2et KRAS WT treated with MS-275 for 6 hrs replicate N1

description:
WT_6HR_E5_N1
AS-170164-LR-26494


title: CaCO-2et KRAS WT treated with DMSO for 6 hrs replicate N2

description:
WT_6HR_DMSO_N2
AS-170433-LR-26496

source_name: CaCO-2et KRAS WT_DMSO for 6 hrs


title: CaCO-2et KRAS WT treated with DMSO for 24 hrs replicate N1

description:
WT_24HR_DMSO_N1
AS-170165-LR-26494


title: CaCO-2et KRAS WT treated with DMSO for 6 hrs replicate N1

description:
WT_6HR_DMSO_N1
AS-170961-LR-26498


title: CaCO-2et KRAS WT treated with MS-275 for 1 hrs replicate N3

description:
WT_1HR_E5_N3
AS-170163-LR-26494

source_name: CaCO-2et KRAS WT_MS-275 for 1 hrs

value: 1 hrs


title: Mettl3-deficient HSC 3 Input

description:
Mettl3Deficient_meRIPSeq.txt
InputM3

value: bone marrow

value: Mx1-cre; Mettl3fl/fl 10 days after pIpC

value: Input fraction


title: CaCO-2et KRAS WT treated with MS-275 for 1 hrs replicate N1

description:
WT_1HR_E5_N1
AS-170162-LR-26494


title: CaCO-2et KRAS WT treated with MS-275 for 1 hrs replicate N2

description:
WT_1HR_E5_N2
AS-170432-LR-26496


title: CaCO-2et KRAS G12V treated with MS-275 for 72 hrs replicate N2

description:
G12V_72HR_E5_N2
AS-170960-LR-26497

source_name: CaCO-2et KRAS G12V_MS-275 for 72 hrs

value: CaCO-2et KRAS G12V

value: 72 hrs


title: CaCO-2et KRAS G12V treated with MS-275 for 72 hrs replicate N3

description:
G12V_72HR_E5_N3
AS-170968-LR-26498


title: CaCO-2et KRAS WT treated with DMSO for 1 hrs replicate N1

description:
WT_1HR_DMSO_N1
AS-170161-LR-26494

source_name: CaCO-2et KRAS WT_DMSO for 1 hrs

value: DMSO


title: CaCO-2et KRAS WT treated with DMSO for 1 hrs replicate N2

description:
WT_1HR_DMSO_N2
AS-170431-LR-26496


title: CaCO-2et KRAS G12V treated with DMSO for 72 hrs replicate N2

description:
G12V_72HR_DMSO_N2
AS-170959-LR-26497

source_name: CaCO-2et KRAS G12V_DMSO for 72 hrs


title: CaCO-2et KRAS G12V treated with DMSO for 24 hrs replicate N1

description:
G12V_24HR_DMSO_N1
AS-170427-LR-26495

source_name: CaCO-2et KRAS G12V_DMSO for 24 hrs


title: CaCO-2et KRAS G12V treated with MS-275 for 24 hrs replicate N3

description:
G12V_24HR_E5_N3
AS-170967-LR-26498

source_name: CaCO-2et KRAS G12V_MS-275 for 24 hrs


title: CaCO-2et KRAS G12V treated with DMSO for 72 hrs replicate N1

description:
G12V_72HR_DMSO_N1
AS-170429-LR-26495


title: CaCO-2et KRAS G12V treated with MS-275 for 6 hrs replicate N2

description:
G12V_6HR_E5_N2
AS-170956-LR-26497

source_name: CaCO-2et KRAS G12V_MS-275 for 6 hrs


title: CaCO-2et KRAS G12V treated with MS-275 for 24 hrs replicate N1

description:
G12V_24HR_E5_N1
AS-170428-LR-26495


title: CaCO-2et KRAS G12V treated with MS-275 for 72 hrs replicate N1

description:
G12V_72HR_E5_N1
AS-170430-LR-26495


title: CaCO-2et KRAS G12V treated with MS-275 for 24 hrs replicate N2

description:
G12V_24HR_E5_N2
AS-170958-LR-26497


title: DN3(IK)-input-3d-2

city: Hershey

first: Sinisa

last: Dovat

state: PA

address: 500 University Dr

institute: Penn State University

description: input for DN3(IK) day 3

library_source: genomic

data_processing:
qc of fastq data,FastQC,version 0.11.4, cutoff 28
mapping,BWA,version 0.7.13, bwa aln -q 5 -l 32 -k 2
qc of mapped data, samtools,version 1.2, MAPQ > 30
qc of mapped data, PICARD, version 2.0.1
peak call, MACS2, version 2.1.1, q < 0.05
Genome_build: mm9
Supplementary_files_format_and_content: processed chip-seq files are in .bed format for peaks information and bigwig file for signal information

molecule: genomic DNA

source_name: JE131 cell line (DN3 cells)

growth_protocol: cells were cultured in RPMI1640 with 10% FBS at 37℃ with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions for KAPA HyperPrep kit.

treatment_protocol: DN3 cells were transduced with retrovirus that contains HA-tagged wild-type murine Ikaros for 1 day, 2 days and 3 days.

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

tag: cell treatment

value: DN3 cells transduced with Ikaros for 3 days

tag: chip antibody


title: CaCO-2et KRAS G12V treated with MS-275 for 6 hrs replicate N3

description:
G12V_6HR_E5_N3
AS-170966-LR-26498


title: DN3(IK)-input-3d-1

description: input for DN3(IK) day 3

tag: cell type


title: CaCO-2et KRAS G12V treated with MS-275 for 6 hrs replicate N1

description:
G12V_6HR_E5_N1
AS-170426-LR-26495


title: CaCO-2et KRAS G12V treated with DMSO for 24 hrs replicate N2

description:
G12V_24HR_DMSO_N2
AS-170957-LR-26497

value: 24 hrs


title: DN3(IK)-input-2d-1

description: input for DN3(IK) day 2

value: DN3 cells transduced with Ikaros for 2 days


title: DN3(IK)-input-1d-1

description: input for DN3(IK) day 1

value: DN3 cells transduced with Ikaros for 1 day


title: DN3-input-2

description: input for DN3 wt

value: DN3 cells without transduction


title: CaCO-2et KRAS G12V treated with DMSO for 6 hrs replicate N2

description:
G12V_6HR_DMSO_N2
AS-170955-LR-26497

source_name: CaCO-2et KRAS G12V_DMSO for 6 hrs


title: CaCO-2et KRAS G12V treated with DMSO for 6 hrs replicate N1

description:
G12V_6HR_DMSO_N1
AS-170425-LR-26495


title: CaCO-2et KRAS G12V treated with MS-275 for 1 hrs replicate N3

description:
G12V_1HR_E5_N3
AS-170423-LR-26495

source_name: CaCO-2et KRAS G12V_MS-275 for 1 hrs


title: DN3-input-1

description: input for DN3 wt


title: CaCO-2et KRAS G12V treated with MS-275 for 1 hrs replicate N2

description:
G12V_1HR_E5_N2
AS-170954-LR-26497


title: CaCO-2et KRAS G12V treated with MS-275 for 1 hrs replicate N1

description:
G12V_1HR_E5_N1
AS-170424-LR-26495


title: CaCO-2et KRAS G12V treated with DMSO for 1 hrs replicate N1

description:
G12V_1HR_DMSO_N1
AS-170965-LR-26498

source_name: CaCO-2et KRAS G12V_DMSO for 1 hrs


title: CaCO-2et KRAS G12V treated with DMSO for 1 hrs replicate N2

description:
G12V_1HR_DMSO_N2
AS-170953-LR-26497


title: CB_male_ENT_90 Entopallium, biological rep6

source_name: Entopallium

value: adult

value: male

value: long day

value: Yes

value: No treatment

value: Present


title: simDia2#3

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

description: processed data file: GeneCount.tsv

data_processing:
Base calling was performed with the Illumina bcl2fastq.
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/).
The paired-end reads were aligned by TopHat 2.0.6.
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: GeneCount.tsv: Tab-delimited text file includes raw counts and RPKM values for each gene per sample.

extract_protocol:
RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: Bone marrow-derived mesenchymal stem cells

tag: sirna


title: simDia2#1

description: processed data file: GeneCount.tsv


title: siCTL#3

description: processed data file: GeneCount.tsv

value: Non-targeting control


title: siCTL#1

description: processed data file: GeneCount.tsv


title: simDia2#2

description: processed data file: GeneCount.tsv


title: siCTL#2

description: processed data file: GeneCount.tsv


title: ExVivoColon_Ripk2-/-_d0_rep_6

city: Saint-Malo

first: Phuong

middle: Hang

last: PHAM

address: 7 allée Métis

department: Data science

country: France

institute: Parean Biotechnologies

hyb_protocol: Samples were hybridized to SurePrint G3 mouse 8x60K (G4858A-028005) and SurePrint G3 mouse v2 8x60K (G4852B-074809) arrays and scanned by G2565CA Scanner System (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Image analyses and raw signal intensities were quantified by Feature Extraction Software v10.7.3.1 (Agilent Technologies) according to the GE1_107_Sep09 protocol.

source_name: Endothelial cell_RIP2KO_d0

label_protocol: Labelling of total RNA (100ng) was performed with the One-Color Low Input Quick Amp Labelling kit (Agilent Technologies).

growth_protocol: To get insights how Ripk2 signaling can specifically contribute to the eradication of C. rodentium, we next performed microarray analysis by using total RNA from caecal tissue of infected Ripk2-/- and wild-type mice that were sacrificed on days 0, 4, and 12 p.i., which further reflects the peak of infection.

extract_protocol: Total RNA was prepared from total tissue of caecum tip by using the column-based RNeasy® Micro Kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and RNA quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Samples with RNA integrity number (RIN) ranging from 8.5-10 were selected for further analysis.

treatment_protocol: Age- and sex-matched mice were inoculated with wild-type C. rodentium strain DBS100 (1x 109 CFU) by oral gavage.

tag: strain background

tag: genotype/variation

tag: age

value: 6-8 weeks

tag: gender

value: Colon

tag: time

value: at d0 after fecal transplant


title: ExVivoColon_Nod2-/-_d20_rep_6

source_name: Endothelial cell_NOD2KO_d20

tag: time point

value: at d20 after fecal transplant


title: ExVivoColon_Nod2-/-_d04_rep_5

source_name: Endothelial cell_NOD2KO_d04

value: at d04 after fecal transplant


title: EpISC-Iw_REP1

data_processing:
Extraction and alignment: Raw reads from published dataset and from newly generated data were extracted and aligned using Salmon program (Patro et al 2017) using reference transcriptome M17 (05/04/2018) from Gencode (Website) which converts the raw reads into Transcripts Per Million (TPM).
Filtering: Transcripts which had a count value of 0 across all conditions were removed from the analysis.
Normalisation: We performed normalisation of the TPM across the different samples by using DESEq2 and negative binomial transformation of the data per sample was performed by using the EdgeR package.
Genome_build: Gencode M17

source_name: Epiblast Stem Cell

growth_protocol: Dissected epiblast were maintained on gelatin 0.1%  inactivated mouse embryonic fibroblasts (MEF) in EpiSC culture medium consisting of Knockout-DMEM , Knockout Serum Replacement (20%), Non-Essential Amino Acid , GlutaMAX-TM , Penicillin-Streptomycinand β-Mercaptoethanol .

extract_protocol:
RNA was extracted from cell samples with the ISOLATE II RNA Mini Kit (Bioline, Cat# BIO-52075)
TruSeq Stranded mRNA Sample preparation protocol

treatment_protocol: Media were supplemented with recombinant human Fgf2 (10ng/mL) and recombinant Human/Mouse/Rat Activin A (20ng/mL), IWP2 (5µM) and SB431542 (2 µM).

value: Epiblast Stem Cell

value: Wnt inhibited

tag: growth factor

value: Activin A + FGF2

tag: inhibitor


title: EpiSC-IwAF_REP2

value: IWP2 removed after derivation


title: ExVivoColon_Ripk2-/-_d20_rep_5

source_name: Endothelial cell_RIP2KO_d20


title: EpISC-Iw_REP2


title: EpiSC-IwAF_REP1


title: EpiSC-AFDKKnull_REP3

value: DKK1 KO line


title: ExVivoColon_WT_d12_rep_6

source_name: Endothelial cell_WT_d12

value: WT

value: male

value: at d12 after fecal transplant


title: ExVivoColon_Ripk2-/-_d0_rep_5


title: EpiSC-AFDKKnull_REP2


title: ExVivoColon_Ripk2-/-_d0_rep_4


title: ExVivoColon_Nod2-/-_d04_rep_4


title: ExVivoColon_WT_d20_rep_5

source_name: Endothelial cell_WT_d20


title: ExVivoColon_WT_d12_rep_5


title: ExVivoColon_WT_d0_rep_5

source_name: Endothelial cell_WT_d0


title: ExVivoColon_Nod2-/-_d12_rep_5

source_name: Endothelial cell_NOD2KO_d12


title: ExVivoColon_Nod2-/-_d0_rep_5

source_name: Endothelial cell_NOD2KO_d0


title: ExVivoColon_WT_d12_rep_4


title: ExVivoColon_Ripk2-/-_d20_rep_4


title: ExVivoColon_Ripk2-/-_d12_rep_5

source_name: Endothelial cell_RIP2KO_d12


title: ExVivoColon_Nod2-/-_d04_rep_3


title: ExVivoColon_Nod2-/-_d12_rep_4


title: EpiSC-AFDKKnull_REP1


title: ExVivoColon_WT_d0_rep_4


title: EpiSC-AF_REP2

value: Control line


title: EpiSC-AF_REP1


title: 44As3ex1

city: Chuo-ku

first: Yutaka

last: Naito

state: Tokyo

address: 5-1-1, Tsukiji

country: Japan

institute: National cancer center research institute

description: Total RNA extracted form fibroblasts, and 100 ng of RNA for analysis

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Pack (Agilent)

scan_protocol: Agilent SureScan G4900DA

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Extracellular vesicles treated immortalized stomach fibroblast

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies)

growth_protocol: Human GC cell lines were established by Dr. Kazuyoshi Yanagihara (National Cancer Center Hospital East, Tokyo, Japan). Human stomach fibroblast was established by Dr. Masakazu Yashiro (Osaka City University, Osaka, Japan), Dr. Kosei Hirakawa (Osaka City University, Osaka, Japan), and Dr. Tohru Kiyono (National Cancer Center, Tokyo, Japan). GC cell lines were cultured in RPMI-1640 (Nissui Pharmaceutical, Tokyo, Japan) supplemented with 10% heat-inactivated FBS and 1% AA at 37 °C in 5% CO2. Fibroblast lines were cultured in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, CA, USA) with 10% fetal bovine serum and 100 μg/ml penicillin/streptomycin and 0.5 mM sodium pyruvate (Sigma-Aldrich, MO, USA).

extract_protocol: Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and a Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif.).

treatment_protocol: EVs derived from DGC cell lined (10 μg/mL) or PBS (-) were treated to the immortalized stomach fibroblast and cultured for 5 days. The fibroblast without EV and PBS treatment (No treat) was also prepared as a control.

tag: cell

value: Immortalized stomach fibroblast


title: HSC-44PEex1


title: ExVivoColon_Ripk2-/-_d12_rep_4

tag: tissue


title: ExVivoColon_WT_d04_rep_5

source_name: Endothelial cell_WT_d04


title: ExVivoColon_WT_d12_rep_3


title: ExVivoColon_Nod2-/-_d12_rep_3


title: ExVivoColon_WT_d0_rep_3


title: No_treat1

source_name: No treat immortalized stomach fibroblast


title: ExVivoColon_Nod2-/-_d20_rep_5


title: No_treat2


title: ExVivoColon_Nod2-/-_d04_rep_2


title: PBS1

source_name: PBS (-) treated immortalized stomach fibroblast


title: ExVivoColon_WT_d20_rep_4


title: NF60_As32

description: Total RNA extracted form cells, and 100 ng of RNA for analysis

source_name: Cellular RNA of NF60 cultured with 44As3

growth_protocol: DGC cell lines (44As3 and HSC-44PE) were previously established by Dr. Kazuyoshi Yanagihara (National Cancer Center Hospital East, Tokyo, Japan). Human stomach fibroblasts were established by Dr. Masakazu Yashiro and Dr. Kosei Hirakawa (Osaka City University, Osaka, Japan). Immortalization of the stomach fibroblasts was performed by Dr. Tohru Kiyono (National Cancer Center, Tokyo, Japan). DGC cell lines were cultured in RPMI-1640 (Nissui Pharmaceutical, Tokyo, Japan) supplemented with 10% heat-inactivated FBS and 1% AA at 37 °C in 5% CO2. Fibroblast lines were cultured in Dulbecco’s modified Eagle medium (DMEM; Invitrogen, CA, USA) with 10% fetal bovine serum and 100 μg/ml penicillin/streptomycin and 0.5 mM sodium pyruvate (Sigma-Aldrich, MO, USA).

treatment_protocol: The immortalized stomach fibroblasts were co-cultured with DGC cell lines or were mono-cultured. Co-culture of the fibroblasts and DGC cells were performed by using trans-well cultures.

value: NF60 cultured with 44As3

tag: dose


title: ExVivoColon_Ripk2-/-_d20_rep_3


title: ExVivoColon_Nod2-/-_d0_rep_4


title: ExVivoColon_WT_d04_rep_4


title: NF58_As32

source_name: Cellular RNA of NF58 cultured with 44As3

value: NF58 cultured with 44As3


title: ExVivoColon_Ripk2-/-_d04_rep_5

source_name: Endothelial cell_RIP2KO_d04

value: 6-8 weeks


title: ExVivoColon_Ripk2-/-_d0_rep_2

source_name: Endothelial cell_RIP2KO_d0

value: Colon


title: NF60_As31


title: NF60_PE2

source_name: Cellular RNA of NF60 cultured with HSC-44PE

value: NF60 cultured with HSC-44PE


title: HSC-44PEex2


title: ExVivoColon_Ripk2-/-_d04_rep_4


title: PBS2


title: NF60_PE1


title: 44As3ex2


title: ExVivoColon_WT_d20_rep_3

value: at d20 after fecal transplant


title: ExVivoColon_Ripk2-/-_d04_rep_3

value: at d04 after fecal transplant


title: ExVivoColon_Nod2-/-_d20_rep_3

source_name: Endothelial cell_NOD2KO_d20


title: ExVivoColon_WT_d04_rep_3


title: ExVivoColon_Ripk2-/-_d12_rep_3


title: NF58_As31


title: ExVivoColon_WT_d0_rep_1

value: at d0 after fecal transplant


title: ExVivoColon_Ripk2-/-_d04_rep_2


title: NF58_PE1

source_name: Cellular RNA of NF58 cultured with HSC-44PE

value: NF58 cultured with HSC-44PE


title: ExVivoColon_Ripk2-/-_d20_rep_1

source_name: Endothelial cell_RIP2KO_d20


title: 44PE_N602

source_name: Cellular RNA of HSC-44PE cultured with NF60

value: HSC-44PE cultured with NF60


title: ExVivoColon_Nod2-/-_d04_rep_1

source_name: Endothelial cell_NOD2KO_d04


title: ExVivoColon_Nod2-/-_d12_rep_2

source_name: Endothelial cell_NOD2KO_d12


title: ExVivoColon_Nod2-/-_d20_rep_2


title: 44As3_N582

source_name: Cellular RNA of 44As3 cultured with NF58

value: 44As3 cultured with NF58


title: NF58_PE2


title: ExVivoColon_WT_d0_rep_2

source_name: Endothelial cell_WT_d0


title: 44PE_N582

source_name: Cellular RNA of HSC-44PE cultured with NF58

value: HSC-44PE cultured with NF58


title: 44As3_N581


title: ExVivoColon_WT_d04_rep_2

source_name: Endothelial cell_WT_d04

value: WT


title: ExVivoColon_WT_d20_rep_2

source_name: Endothelial cell_WT_d20

value: male


title: 44PE_N601


title: ExVivoColon_Nod2-/-_d0_rep_2

source_name: Endothelial cell_NOD2KO_d0


title: ExVivoColon_Ripk2-/-_d20_rep_2


title: 44As3_N601

source_name: Cellular RNA of 44As3 cultured with NF60

value: 44As3 cultured with NF60


title: 44PE_N581


title: NF60_1

source_name: Cellular RNA of NF-60


title: ExVivoColon_Nod2-/-_d12_rep_1

value: at d12 after fecal transplant


title: ExVivoColon_Nod2-/-_d0_rep_3


title: NF60_2


title: 30kPa_HDF_miRNA_1

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

data_processing:
After sequencing, reads were filtered base on qc and the Illumina adapter was removed
Alignment against total human genome (GRCh38, GTF= GENECODE v 27) was performed using Salmon
Total number of reads for each individual human microRNA were counted by STAR software
Genome_build: GRCh38
Supplementary_files_format_and_content: tab files containing:   column 1 – gene ID   column 2 - lenght  column 3 – counts for unstranded RNA-seq  column 4 – counts for the 1st read strand aligned with RNA   column 5 – counts for the 2nd read strand aligned with RNA

source_name: HDF

growth_protocol: HDF cells were growth in EGM Bullet Kit mededium in culture. PDMS matrix with a 3 or 30 kPa module were made, and 4 dishes for each condition were coated overnight with 1% fibronectin

extract_protocol:
Cells were lysated using TRIzol follow the company protocols. Total RNA were run in a 15% denaturating gel with 7 M urea (0.8 ml 10x TBE, 1.4 ml water, 3.8 g urea, 3 ml acrylamide, 64 ul 10% APS, 4 ul TEMED). The region between 15 an 31 nt was cut and small RNA fraction was extracted from the gel using 0.3 M NaCl-TE overnight and purified using isopropanol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No cell treatment

tag: growth protocol

value: Growth at 30 kPa

value: Human Dermal fibroblast cells


title: 30kPa_HDF_miRNA_3


title: NF58_1

source_name: Cellular RNA of NF-58


title: ExVivoColon_Nod2-/-_d0_rep_1


title: 44As3cell2

source_name: Cellular RNA of 44As3


title: NF58_2


title: HSC-44PEcell2

source_name: Cellular RNA of HSC-44PE


title: ExVivoColon_Ripk2-/-_d12_rep_2

source_name: Endothelial cell_RIP2KO_d12


title: ExVivoColon_Ripk2-/-_d12_rep_1


title: ExVivoColon_WT_d04_rep_1


title: HUES7_3

city: Manchester

first: Adam

last: Stevens

address: Oxford Road

department: Medicine

country: United Kingdom

institute: University of Manchester

description: Gene expression data from HUES7 human embryonic stem cell line

hyb_protocol: Labelled PolyAcRNA was hybridised to the Human Genome U133 Plus 2.0 Array (hgu133plus2.0, Affymetrix, SantaClara, CA, USA)

scan_protocol: Data initially visualised using MIAMIVICE software.

data_processing:
Data were processed using frozen robust multiarray averaging  (fRMA)(McCall, Bolstad et al., 2010)
An expression barcode and a z-score of gene expression in comparison to 63331 examples of hgu133plus2.0 was defined for each tissue (McCall et al., 2014, Zilliox & Irizarry, 2007) and used for unsupervised analysis. For analysis of gene expression specific to each tissue a z-score of 5 was used to call a gene present and a barcode was assigned scoring 1 for presence and 0 for absence of gene expression (McCall, 2015, McCall et al., 2010, McCall et al., 2014).

source_name: HUES7 human embryonic cell line

label_protocol: biotin-16-dUTP was labelled using EpiLabel™ (Epistem)

growth_protocol: ICM and trophectoderm from 6 day old human embryos. Human embryonic stem cell lines from fibronectin-coated (Millipore) tissue culture flasks with Stem Pro feeder free medium.

extract_protocol: cDNA was prepared by polyAPCR amplification(Brady & Iscove, 1993) which amplifies all polyadenylated RNA in a given sample, preserving the relative abundance` in the original sample

treatment_protocol: Donated embryos were cultured in ISM-1/2 sequential media (Medicult, Jyllinge, Denmark) until blastocyst formation. At embryonic day 6 the zona pellucida of the embryos were removed by brief treatment with acid Tyrode’s solution pH 5.0. After 3 passages 100 hESC cells were isolated from each line (assessed separately as > 85% Oct4 positive)

value: HUES7cell line


title: 3kPa_HDF_miRNA_2

value: Growth at 3 kPa


title: 3kPa_HDF_miRNA_1


title: HUES3_3

description: Gene expression data from HUES3 human embryonic stem cell line

source_name: HUES3 human embryonic cell line

value: HUES3cell line


title: HSC-44PEcell1


title: HUES7_2


title: ExVivoColon_Ripk2-/-_d0_rep_1

source_name: Endothelial cell_RIP2KO_d0

value: 6-8 weeks

value: Colon


title: 30kPa_HDF_miRNA_2


title: HUES3_4


title: 3kPa_HDF_miRNA_3


title: MS57-D071717 MAIT aCD3-P1

city: Cincinnati

first: Shouxiong

last: Huang

state: OH

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati College of Medicine

data_processing:
Sequence reads aligned to the genome and converted to intensity counts
edgeR to identify differentially expressed genes between CD69+CD26++ and CD69-CD26+/- subsets with defined fold change (>2 folds) and p-values (<0.05).
Supplementary_files_format_and_content: intensity count in excel

source_name: Human MAIT cells aCD3-stimulated

extract_protocol:
mirVana kit (ThermoFisher)
NEBNext Ultra Directional RNA Library Prep 185 kit (New England BioLabs)


title: HUES7_1


title: A375,DMSO,repl2

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

description:
smallRNAseq
a375_II

data_processing:
Raw sequences were de-multiplexed using the Illumina pipeline CASAVA v1.8.
Cutadapt v.1.2.1 was used for trimming adapter sequences off the raw reads. Reads with N calls were discarded using FASTX_Toolkit v 0.0.13.1 and only reads with all base calls showing a Phred score higher than 30 were retained for further analysis.
miRExpress v2.1.3 was exploited to identify pre-miRNA sequences (miRBase v.21) allowing at least 95% of sequence identity and a length tolerance range of 4bp for mapping.
Expression values were normalized to reads per million (rpm).
Genome_build: miRBase v.21
Supplementary_files_format_and_content: Tab-delimited text file including normalized read count per sample.

source_name: A375 cells

growth_protocol: 10^06 cells of A375 cell line were seeded in 10cm dishes in DMEM HG complete medium.

extract_protocol:
RNA was extracted using miRNeasy MINI Kit (Qiagen), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 24h, A375 cells were treated with DMSO for 48h. At the end of the treatment, cells were harvested.

tag: cell line

value: melanoma cell line

tag: treatment

value: DMSO


title: 44As3_N602


title: MAN1_3

description: Gene expression data from MAN1 human embryonic stem cell line

source_name: MAN1 human embryonic stem cell line

tag: cell type

value: MAN1 stem cell line


title: MS41-D062217 MAIT BCG-P1

source_name: Human MAIT cells BCG-stimulated


title: ExVivoColon_WT_d20_rep_1

value: at d20 after fecal transplant


title: A375,DMSO,repl1

description:
smallRNAseq
a375_I


title: MS30-D062317 MAIT BCG-P2


title: MS31-D062317 MAIT aCD3-P1


title: HUES3_2


title: HUES3_1


title: ExVivoColon_Nod2-/-_d20_rep_1

source_name: Endothelial cell_NOD2KO_d20


title: MS56-D071717 MAIT BCG-P2


title: MS55-D071717 MAIT BCG-P1


title: MS29-D062317 MAIT BCG-P1


title: MS43-D062217 MAIT aCD3-P1


title: MAN1_2


title: MS42-D062217 MAIT BCG-P2


title: TE7

description: Gene expression data from human trophectoderm

source_name: Trophectoderm from human blastocyst

value: Trophectoderm


title: MAN1_1


title: ICM8

description: Gene expression data from human Inner Cell Mass

source_name: Inner Cell Mass from human blastocyst

value: inner cell mass


title: HEK293T-HEKs2-ABE-treated-rep1

tag: guide

value: HEK site 2:GAACACAAAGCATAGACTGC

tag: gfp

value: Top 5%


title: HEK293T-HEKs2-control-rep2


title: HEK293T-HEKs2-ABE-treated-rep2


title: HEK293T-HEKs2-control-rep3


title: TE8


title: HEK293T-HEKs2-ABE-treated-rep3


title: HEK293T-HEKs2-control-rep1


title: TE4


title: TE2


title: 44As3cell1


title: ICM4


title: ICM2


title: ICM7


title: Adriamycin Set 2

city: Charleston

first: Deepak

last: Nihalani

state: SC

address: 70 President St.

department: Medicine/Nephrology

institute: Medical University of South Carolina

description: Immortalized Human Podocytes Cell Lines

data_processing:
Downstream bioinformatics analyses was performed by using a combination of programs including Bowtie2, Tophat2, HTseq and Cufflink .
Reference genome and gene model annotation files were acquired from NCBI/UCSC/Ensemble genome browser.
Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Gene expression level quantification was done using HTSeq v0.6.1 and for each gene read numbers counts were mapped, whereas, Reads Per Kilobase of exon model (RPKM) of each gene was calculated based on the length of the gene and expression levels were analyzed
DESeq2 R package (2_1.6.3) database was used for the differential expression (DE) analyses. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach and adjusted P-value <0.05 found by DESeq2 were assigned as DE. Analyses of DE of two conditions was performed using the DEGSeq R package (1.12.0). The P-values were also adjusted using Benjamini & Hochberg method. Corrected P-value of 0.005 and log2 (Fold change) of 1 were set as threshold for significantly differential expression.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Adriamycin

growth_protocol: RPMI 1640-based medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen), 2 g/liter of sodium bicarbonate (NaHCO3), insulin-transferrin-selenium (ITS) supplement (Sigma-Aldrich), and 200 units/ml penicillin and streptomycin (Roche Applied Science)

extract_protocol:
RNA was isolated using the qiagen RNeasy Mini Kit (Cat. No # 74104) and  1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Podocytes were incubated 4hours in the serum free RPMI medium and injury was given using PAN (100μg/ml) and Adriamycin (0.25μg/ml) for 48 hours.

tag: differentiation status

value: Differentiated

value: Podocytes (Glomerulus cells)

tag: differentiation duration

value: 14 day differentiation


title: Adriamycin Set 1

description: Immortalized Human Podocytes Cell Lines


title: Adriamycin Set 3

description: Immortalized Human Podocytes Cell Lines


title: PAN-set 2

description: Immortalized Human Podocytes Cell Lines

source_name: puromycin aminonucleoside


title: #P6 B2KO red-pulpMF

city: Sendai

first: Kazuhiko

last: Igarashi

address: Seiryo 2-1

institute: Tohoku University

description: Gene expression red-pulp macropahge from Bach2 knock out  mouse

hyb_protocol: Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (Agilent-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1_107_Sep9 and Grid: 028005_D_F_20101029) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: #P6 B2KO red-pulpMF

label_protocol: Total RNA was amplified with an Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and was labeled with indocarbocyanine through the use of a CyDye post-labeling Reactive Dye Pack (Amersham).

extract_protocol: RNA  was isolated with an RNeasy micro kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: Red-pulp macrophage cells was collected from spleen and were sorted by fow cytometer.

tag: strain

value: male

tag: age

tag: genotype/variation

value: Bach2 knock out


title: #952 WT red-pulpMF

description: Gene expression red-pulp macropahge from WT mouse

source_name: #952 WT red-pulpMF

tag: gender

value: wild type


title: #965 B2KO red-pulpMF

source_name: #965 B2KO red-pulpMF


title: #P6 WT red-pulpMF

source_name: #P6 WT red-pulpMF

value: female


title: 2C_L5.D709_1

city: San Francisco

first: Anubhav

middle: N.

last: Mathur

state: California

address: 513 Parnassus Ave, HSW12

institute: University of California, San Francisco

description: processed data file: ResultsDESeq.csv

data_processing:
Using an Illumina RNASeq, cDNA was sequenced to a 25M read depth.
Reads were aligned to Ensembl mg GRCm38.p4 reference genome using TopHat (v. 2. 0. 12).
After alignment, SAM files were generated using SAMtools.
Htseq-count (0. 6. 1p1, with union option) was used to obtain read counts.
Differentially expressed genes between paired samples was determined using the R/Bioconducter package DESeq2.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: ResultsDESeq.csv: Comma separated value file contains raw counts for each sample.

source_name: Lgr5-traced cells

extract_protocol:
Sorted cells were pelleted flash frozen in liquid nitrogen. RNA was sent overnight on dry ice to Expression analysis, Quintiles to perform all subsequent processing and sequencing. RNA was isolated using QIAGEN RNeasy Spin Columns and quality was checked using an Agilent Bioanalyzer Pico Chip.
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit.

value: Lgr5 hair follicle stem cells

value: skin injury

tag: condition

value: Treg-depleted

tag: experiment number


title: 2B_L5.D708_1

description: processed data file: ResultsDESeq.csv


title: Untreated Set 3

description: Immortalized Human Podocytes Cell Lines

source_name: Control/Untreated


title: Untreated Set 2

description: Immortalized Human Podocytes Cell Lines


title: #979 B2KO red-pulpMF

source_name: #979 B2KO red-pulpMF


title: #981 WT red-pulpMF

source_name: #981 WT red-pulpMF


title: 1C_L5.D705_1

description: processed data file: ResultsDESeq.csv

value: Treg-sufficient


title: 2D_L5.D710_1

description: processed data file: ResultsDESeq.csv


title: 1B_L5.D704_1

description: processed data file: ResultsDESeq.csv


title: HepG2-RNF2-R33A_K34A-rep3

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7 and downstream custom pipelines
No samples were excluded from bioinformatics analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene expression counts per gene estimated by STAR

growth_protocol: HEK293T cells (CRL-3216, obtained from ATCC) were grown in culture using media consisting of DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco). HepG2 cells (HB80-65, obtained from ATCC) were grown in EMEM (ATCC) supplemented with 10% FBS and 0.5% penicillin-streptomycin (Gibco).  Both cell lines were used for experiments until passage 20 for HEK293T and passage 12 for HepG2. Cells were passaged at ~80% confluency every 2-4 days to maintain an actively growing population and avoid anoxic conditions. Cells  were tested for mycoplasma bi-weekly.

extract_protocol:
RNA was extracted with Macherey-Nagel’s  NucleoSpin RNA Plus kit.
Illumina TruSeq Stranded Total RNA Gold, IDT-ILM unique dual indices for barcoding.

value: RNF2 site 1:GTCATCTTAGTCATTACCTG(AGG)


title: CD4 Sample 2

first: Gregory

last: Putzel

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Sorted CD4 positive T cells

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols


title: 2A_L5.D707_1

description: processed data file: ResultsDESeq.csv


title: CD4 Sample 1


title: HepG2-RNF2-BE3-rep3


title: 1A_L5.D703_1

description: processed data file: ResultsDESeq.csv


title: HepG2-RNF2-R33A_K34A-rep2


title: HUES7_4

source_name: HUES7 human embryonic cell line

value: HUES7cell line


title: HepG2-RNF2-control-rep3


title: ILC3 Sample 2

description:
LZ_05
CD45+CD3-RORγtGFP+CD127+

source_name: Sorted ILC3s


title: ILC3 Sample 3

description:
LZ_06
CD45+CD3-RORγtGFP+CD127+


title: ILC3 Sample 1

description:
LZ_04
CD45+CD3-RORγtGFP+CD127+


title: PAN-Treated 1

description: Immortalized Human Podocytes Cell Lines


title: Untreated Set 1

description: Immortalized Human Podocytes Cell Lines


title: 1D_L5.D706_1

description: processed data file: ResultsDESeq.csv


title: HepG2-RNF2-control-rep2


title: HepG2-RNF2-BE3-rep2


title: PAN-set 3

description: Immortalized Human Podocytes Cell Lines


title: HepG2-RNF2-R33A_K34A-rep1


title: HepG2-RNF2-control-rep1.


title: HEK293T-RNF2-R33A_K34A-rep2


title: HEK293T-RNF2-R33A_K34A-rep3


title: HEK293T-RNF2-BE3-rep3


title: HEK293T-RNF2-BE3-rep2


title: HEK293T-RNF2-R33A_K34A-rep1


title: HepG2-RNF2-BE3-rep1


title: ExVivoColon_Ripk2-/-_d04_rep_1

source_name: Endothelial cell_RIP2KO_d04

tag: strain background

value: 6-8 weeks

value: Colon

tag: time

value: at d04 after fecal transplant


title: HEK293T-RNF2-BE3-rep1

value: Top 5%


title: HEK293T-RNF2_CI-treated-rep2


title: HEK293T-RNF2_CI-control-rep1


title: HEK293T-RNF2_CI-treated-rep1


title: HEK293T-RNF2_CI-control-rep2


title: AllGFP-HEK293T-EMX1-treated-rep3

data_processing:
RNA sequencing data was aligned to the human reference genome (GRCh38/hg38) using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Variants associated with BE treatment were called using the GATK best practices pipeline using GATK 3.8.1 and Picard 2.7.
No samples were excluded from bioinformatics analyses.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene expression counts per gene estimated by STAR

value: EMX1 site 1:GAGTCCGAGCAGAAGAAGAA (GGG)

value: All GFP


title: DN3(IK)-input-2d-2

description: input for DN3(IK) day 2

source_name: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

tag: cell treatment

value: DN3 cells transduced with Ikaros for 2 days

tag: chip antibody


title: DN3(IK)-input-1d-2

description: input for DN3(IK) day 1

tag: cell line

value: DN3 cells transduced with Ikaros for 1 day


title: AllGFP-HEK293T-EMX1-treated-rep2

tag: treatment


title: Mutant HSC rep 4

description:
RNASeq.txt
M8

data_processing:
Analysis of RNA-seq data was performed using the Quantas pipeline (https://zhanglab.c2b2.columbia.edu/index.php/Quantas) with minor modifications.  In brief, raw reads were mapped to the mouse genome and an exon-junction database using OLego. Due to the low input during library preparation, potential PCR duplicates were removed using Picard (http://broadinstitute.github.io/picard). Exonic and junction reads were then counted to estimate transcript abundance (read per kilobase per million reads, or RPKM) and perform differential expression analysis using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene names and RPKM values for control and Mettl3-deleted HSCs.

source_name: HSC

extract_protocol:
Bone marrow cells were flushed from adult hindlimbs and stained for Lineage- Sca1+ cKit+ CD150+ CD48- HSCs. 150 HSCs were FACS sorted into 0.2% Triton X-100 and then proceeded to library preparation.
RNA libraries were prepared for sequencing using the Smart-seq2 method. Samples were seuqneced on Illumina HiSeq 2500 with paired-end 100-bp read lengths.

tag: tissue

value: bone marrow

tag: cell type

value: HSC

tag: genotype

value: Mx1-cre; Mettl3fl/fl 10 days after pIpC


title: Mutant HSC rep 3

description:
RNASeq.txt
M7


title: Mutant HSC rep 2

description:
RNASeq.txt
M6


title: AllGFP-HEK293T-EMX1-treated-rep1

tag: guide

tag: gfp


title: AllGFP-HEK293T-EMX1-control-rep1


title: HEK293T-NT-treated-rep2


title: Mutant HSC rep 1

description:
RNASeq.txt
M4

tag: strain


title: HEK293T-NT-control-rep2


title: HEK293T-EMX1-treated-rep2


title: HEK293T-NT-treated-rep1


title: HEK293T-NT-control-rep1


title: Control HSC rep3

description:
RNASeq.txt
C8

value: Cre-negative 10 days after pIpC


title: BLM_3

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

country: Spain

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

data_processing:
Pre-processing: Sequences were pre-processed with Trimmomatic v0.36
Alignment: Pre-processed sequences were algined to mouse genome assembly mm10 using HISAT2 v2.1.0
Counts per gene were obtained with featureCounts v1.6.1 using the in-built RefSeq annotation for mm10 genome assembly
The raw counts were merged with those obtained in the previous study (GSE115503) and analyzed with DESeq2 v1.20.0 excluding those genes with less than 15 counts across all samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file "raw_counts_newsamples.txt" include raw counts obtained from featureCounts for the samples included in this entry
Supplementary_files_format_and_content: Tab-delimited text file "raw_counts_merged.txt" include raw counts obtained from merging the counts of the samples from this entry with the counts of the samples from the GSE115503 entry

extract_protocol:
Total RNA was isolated from mice frozen skin tissue using QIAzol lysis reagent (Qiagen, Hilden, Germany) and purified with RNeasy mini kit (Qiagen).
Transcriptome libraries were constructed with TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero Human/Mouse/Rat, #RS-122-2201). In brief, 300 ng of total RNA from each Sample was used to construct a cDNA library, followed by sequencing on the Illumina Hiseq 2500 with single end 50 bp reads and ~30 millions of reads per sample.

value: BALB/c

tag: age

value: Six-eight weeks

value: skin

tag: group

value: bleomycin


title: Control HSC rep2

description:
RNASeq.txt
C7


title: HEK293T-EMX1-control-rep2

first: Caleb

last: Lareau

institute: Memorial Sloan Kettering


title: Control HSC rep1

description:
RNASeq.txt
C6


title: Control_3

value: control


title: BLM_EHP_3


title: BLM_AJA_2

value: bleomycin+AJA


title: ExSed 2

city: Boston

first: Vanessa

last: Frodermann

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Massachusetts General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using BWA with the default configurations
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file was generated using bedtools over 1Kb genomic bin

extract_protocol:
Sorted LSKs underwent ATAC-seq. 20.000 sorted LSK cells were initially resuspended in lysis buffer and centrifuged. The nuclei pellets were then subjected to transposition reaction using the Nextera Tn5 transposase enzyme (Illumina). Tagmented DNA was purified with the MinElute PCR Purification Kit and eluted in 10L of elution buffer (Qiagen).
Barcoded libraries were prepared and PCR amplified. Double-sided bead purification was performed using AMPure XP beads to remove primer dimers and large >1,000 bp fragments. Libraries were sequenced 50 bp paired end on an Illumina HiSeq 2500.

treatment_protocol: To purify LSK, a PE-lineage depletion was performed with MACS columns (130-042-401, Miltenyi Biotec), according to the manufacturer’s protocol. Briefly, single cell suspensions were stained with a lineage cocktail of PE-conjugated antibodies: CD3 (100206), CD4 (130310), CD8 (100708), CD49b (108908), CD90.2 (140308), CD19 (115508), B220 (103208), NK1.1 (108708), TER119 (116208), CD11b (101208), CD11c (117308), Gr1 (108408; all 1:150, BioLegend), followed by incubation with anti-PE microbeads (130-048-801, Miltenyi Biotec). Lineage-depleted bone marrow cells were then stained with CD48-AF700 (103426), CD150-PerCP/Cy5.5 (115922), c-kit-PE/Cy7 (105814), Sca-1-BV605 (108133; all 1:150, BioLegend) and FAC-sorted using a FACSAria II cell sorter (BD Biosciences).

value: 7-8 weeks

tag: sample group

value: access to exercise wheels for 6 wks followed by a 3 wks wheel withdrawal (ExSed).

value: all long bones including pelvic bone

value: sorted LSK cells

tag: markers


title: BLM_AJA_1


title: AllGFP-HEK293T-EMX1-control-rep3

address: 417 E 68th St, Zuckerman - ZRC 1132

treatment_protocol: Transfections were performed using 50ug of transfection quality plasmid DNA (Qiagen Maxiprep) encoding desired BE3-P2A-EGFP, variants thereof or nCas9-UGI-NLS-P2A-EGFP and gRNAs (nuclease-to-gRNA ratio 75:25%). 6x10E6 HEK293T or 15x10E6 HepG2 were seeded into TC-treated 150mm plates 18-24h prior to transfection to yield  ~60-80 % confluency on the day of transfection. Cells were transfected using 150uL TransIT-293 (HEK293T, Mirus) or 150uL transfeX (HepG2, ATCC) reagents per plate, according to the manufacturers’ protocols (mixing DNA and reagent in 5mL Optimem, 30min incubation). Cells were sorted 36-40h after transfection, for either top 5% or all-GFP after doublet-exlusion and gating for the cell population on a BD FACSARIA II.

value: EMX1 site 1:GAGTCCGAGCAGAAGAAGAA (GGG)

value: All GFP


title: AllGFP-HEK293T-EMX1-control-rep2


title: BLM_AJA_3


title: HEK293T-EMX1-treated-rep1

value: Top 5%


title: ExSed 1


title: HepG2-RNF2-control-rep1

value: RNF2 site 1:GTCATCTTAGTCATTACCTG(AGG)


title: Ex 2

value: access to exercise wheels for 6 wks (Ex)


title: HepG2-RNF2-treated-rep1


title: PTL_9_Monocyte_miRNA

city: Seattle

first: alison

middle: g

last: paquette

state: WA

address: 401 Terry Avenue N

institute: Institute of Systems Biology

data_processing:
miRNAs were aligned to homo sapien miRNA transcripts with 0 mismatches catalouged by miRbase (V 21) using miRNA pipeline SRNAnalyzer (Wu et al, Nucleic Acids Research, 2017)
miRNA abudances were called calculated using single assignment miRNA mapping using SRNAnalyzer (Wu et al, Nucleic Acids Research, 2017)
Transcripts were filtered so that low expressing samples (mean read count <20), or mostly unexpressed (>50% of samples NA) transcripts were removed prior to preprocessing
Data was normalized using Read Counts Per Million (RPKM)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data matrix reflects RPKM values of final dataset

source_name: Monocytes

extract_protocol:
RNA was isolated from from peripheral monocytes (separated by Monocyte RosetteSep cocktail) using TRIsol LS (Invitrogen) following manufacturer’s instructions.
RNA library preparation was performed following the NEB NEBNext Multiplex Small RNA Library Preparation protocol. Briefly, 400 ng of total RNA was used as the input material. The 3’ SR Adapter was ligated to the small RNA, followed by RT primer hybridization to the 3’ SR adapter and then the 5’ SR Adapter was ligated to the opposite end (this strategy prevents formation of adapter-dimers). First stranded synthesis was then performed off the RT primer and the library was enriched by PCR using the following conditions: initial denaturation at 94oC for 30 seconds, followed by 15 cycles of 94oC for 15 seconds, 62oC for 30 seconds and 70oC for 15 seconds, and finally an extension step for 5 minutes at 70oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final Small RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size and libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).
Libraries were pooled in equimolar quantities and sequenced on a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate single-end reads of 50-bases in length.

tag: conditon

value: Preterm Delivery


title: PTL_6_Monocyte_miRNA


title: Sed 2

value: housed with igloos (Sed)


title: PTL_5_Monocyte_miRNA


title: Sed 1


title: HEK293T-EMX1-control-rep1


title: PTL_4_Monocyte_miRNA


title: PTL_3_Monocyte_miRNA


title: PTL_20_Monocyte_miRNA


title: PTL_19_Monocyte_miRNA


title: PTL_18_Monocyte_miRNA


title: V15

city: Wilrijk

first: Veerle

last: Van Hoeck

state: Antwerp

address: Campus Drie Eiken, Universiteitsplein 1

department: Department of Veterinary Sciences

country: Belgium

institute: University of Antwerp

description: AA - V15_S65_L006_R1_001 (paired) (GE) - Normalized expression values

data_processing:
All libraries were filtered using FASTX-Toolkit and cut adapt. Low quality reads, which contained more than 20 nucleotides with less than a 15 quality value were further filtered.
Reads were mapped using the local alignment with Bowtie2 against the masked Bos taurus genome assembly (Bos taurus UMD3.1).
Read counts were obtained using HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
Genome_build: Bos taurus UMD3.1
Supplementary_files_format_and_content: counts

organism: Bos taurus

source_name: Bovine Endometrial Epithelial Cells

growth_protocol: Cells were retrieved from three bovine uteri at early luteal stage. Endometrial cells were mechanically isolated by slightly scraping the luminal surface of the endometrium with a sterile glass slide. Erythrocytes were subsequently lysed by incubation with hyper-osmotic Lysis buffer. BEEC were maintained in DMEM medium supplemented with 2.5% Peniciline/Streptomycin, 2% Fungizone and 10% fetal bovine serum and incubated in controlled atmosphere of 5% CO2 at 38.5 °C and maximum humidity. After the adhesion process started, culture medium was renewed every 48 h. Cells were subcultured when primary monolayers reached 90% of confluence. BEEC monolayers at passage 1 were cultured until reach 90% of confluence, when cells were trypsinised and cryopreserved.

extract_protocol:
BEEC samples were harvested using TrypLE Express and pooled per three wells. Samples were snap frozen and stored at -80 °C until further processing. Total RNA was extracted using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. RNA purity and concentration were determined by spectrophotometry and RNA integrity was assessed using the Qiaxcel Bioanalyzer (Qiagen). Transcriptomes of BEEC exposed to the distinct groups of embryos were sequenced (NGS) on the Illumina HiSeq2000 platform using the TruseqTMRNA sample prep kit (version 2–single read–50 bp) according to the manufacturer’s recommendation.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: BEEC at passage 1 were thawed and seeded at a density of 3 × 104 cells/mL in 384-well dishes (Nunclon™; Thermo Scientific). BEEC were maintained in DMEM medium as described above and in controlled atmosphere of 5% CO2 at 38.5 °C and maximum humidity. Medium was renewed every 48 h. On Day 4 post fertilization, groups of 5 (pre-conditioned) morulas were transfered to sub-confluent BEEC monolayers. Embryos were cocultured with BEEC until Day 8, when endometrial cells were recovered for transcriptome analysis.

value: Endometrial Epithelial Cells

tag: passages

value: Endometrium

value: LOWAA


title: V12

description: AA - V12_S62_L006_R1_001 (paired) (GE) - Normalized expression values


title: PTL_13_Monocyte_miRNA


title: PTL_15_Monocyte_miRNA


title: PTL_17_Monocyte_miRNA


title: PTL_12_Monocyte_miRNA


title: PTL_14_Monocyte_miRNA


title: V8

description: AA - V8_S59_L006_R1_001 (paired) (GE) - Normalized expression values


title: Ex 1


title: 44As3exo 3

description: Total RNA extracted form extracellular vesicles, and 20 ng of RNA for analysis

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

source_name: Extracellular vesicles collected from 44As3 cells

label_protocol: The miRNA Complete Labeling and Hyb Kit (Agilent Technologies)

treatment_protocol: The 44As3 cell line and HSC-44PE cell line were washed with phosphate-buffered saline (PBS), and the culture medium was replaced with serum-free RPMI 1640 medium contained antibiotic and antifungal drugs. After incubation for 48 h, the conditioned medium (CM) was collected and centrifuged at 2,000 x g for 10 min at 4°C. To thoroughly remove cellular debris, the supernatant was filtered through a 0.22-mm filter (Millipore). The CM was then used for EV isolation. To prepare EVs, CM was ultracentrifuged at 35,000 rpm using a SW41Ti rotor for 70 min at 4°C. The pellets were washed with PBS, ultracentrifuged at 35,000 rpm using the SW41Ti rotor for 70 min at 4°C and resuspended in PBS.

tag: phenotype

value: high-metastatic


title: PTL_11_Monocyte_miRNA


title: V10

description: Gluc - V10_S61_L006_R1_001 (paired) (GE) - Normalized expression values

value: HIGHGLUC


title: V14

description: Gluc - V14_S64_L006_R1_001 (paired) (GE) - Normalized expression values


title: HSC-44PEexo 3

source_name: Extracellular vesicles collected from HSC-44PE cells

value: low-metastatic


title: V9

description: Control - V9_S60_L006_R1_001 (paired) (GE) - Normalized expression values

value: control


title: V13

description: Control - V13_S63_L006_R1_001 (paired) (GE) - Normalized expression values


title: 44As3exo 1


title: V6

description: Gluc - V6_S58_L006_R1_001 (paired) (GE) - Normalized expression values


title: 44As3exo 2


title: HSC-44PEexo 2


title: HSC-44PEexo 1


title: V5

description: Control - V5_S57_L006_R1_001 (paired) (GE) - Normalized expression values


title: PTL_10_Monocyte_miRNA


title: CON_47_Monocyte_miRNA

value: Term Delivery


title: CON_9_Monocyte_miRNA


title: CON_8_Monocyte_miRNA


title: CON_46_Monocyte_miRNA


title: AB1Lysates_phage-20min_rep3

city: Chongqing

first: zichen

last: yang

address: Gaotanyan

country: China

institute: Army Medical University (Third Military Medical University)

data_processing:
The sequenced libraries were mapped against predicted  transcripts from the Acinetobacter baumannii ATCC  17978 genome using TopHat v2.0.4
The transcript  abundance (FPKM, Fragments Per Kilobase of exon per  Million fragments mapped) and significant changes in  transcript expression were estimated using Cufflinks  v2.0.2
Transcripts with p-values less than 0.05,  determined using CuffDiff
Genome_build: NC_021316.1 and NZ_CP018664.1 were used as the reference genomes

organism: Acinetobacter phage Abp1

source_name: AB1 and Abp1 lysates, 20min, replicate 3

growth_protocol: AB1with or wihout phage infection was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol:
Total RNA was isolated using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions and   checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer   2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further   purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and   RNase-Free DNase Set    (Cat#79254, QIAGEN, GmBH, Germany).
Barcoded sequencing libraries
Pooled libraries were enriched for the exome using hybridization (TruSeq Exome Enrichment Kit, Illumina), quantified using quantitative PCR and pooled in 1:1 ratio for pairedend sequencing on a HiSeq2500 (Illumina)

treatment_protocol: Bacterial culture were infected with phage Abp1 at MOI of 10 for 5min, 10min, 20min.The uninfected samples served as reference.

value: after phage infection of 20min


title: AB1Lysates_phage-10min_rep3

source_name: AB1 and Abp1 lysates, 10min, replicate 3

value: after phage infection of 10min


title: AB1Lysates_phage-20min_rep2

source_name: AB1 and Abp1 lysates, 20min, replicate 2


title: AB1Lysates_phage-20min_rep1

source_name: AB1 and Abp1 lysates, 20min, replicate 1


title: CON_41_Monocyte_miRNA


title: CON_35_Monocyte_miRNA


title: CON_34_Monocyte_miRNA


title: CON_44_Monocyte_miRNA


title: CON_45_Monocyte_miRNA


title: AB1Lysates_phage-10min_rep1

source_name: AB1 and Abp1 lysates, 10min, replicate 1


title: CON_38_Monocyte_miRNA


title: CON_33_Monocyte_miRNA


title: AB1Lysates_phage-10min_rep2

source_name: AB1 and Abp1 lysates, 10min, replicate 2


title: Healthy PBMC (Ex Vivo) (CD4_NT_1)

city: Cambridge

first: Paul

last: Blainey

address: 415 Main St

institute: Broad Institute

description: Ex Vivo.matrix

data_processing:
Bcls were demultiplexed using Illumina bcl2fastq (v2.20.0.422)
Fastqs were aligned to hg19 using STAR
Gene expression matrices were generated using Bowtie2
Genome_build: hg19
Supplementary_files_format_and_content: Matrices are provided as samples (columns) vs. genes (rows)

source_name: Healthy PBMC

extract_protocol:
Cells were resuspended in TCL buffer, supplemented with 1 mg/mL proteinase K, and processed through the Smart-seq2 protocol (on a microfluidic device)
Libraries were constructed using the Nextera XT (Illumina) library preparation kit

tag: disease state

value: Healthy

value: PBMC

tag: cell subset

value: CD4 T cells


title: CON_39_Monocyte_miRNA


title: AB1Lysates_phage-5min_rep1

source_name: AB1 and Abp1 lysates, 5min, replicate 1

value: after phage infection of 5min


title: Healthy PBMC (Ex Vivo) (CD4_NT_2)

description: Ex Vivo.matrix


title: AB1Lysates_phage-5min_rep2

source_name: AB1 and Abp1 lysates, 5min, replicate 2


title: Healthy PBMC (Ex Vivo) (CD4_LPS_2)

description: Ex Vivo.matrix


title: AB1Lysates_phage-5min_rep3

source_name: AB1  and Abp1 lysates, 5min, replicate 3


title: CON_40_Monocyte_miRNA


title: CON_31_Monocyte_miRNA


title: CON_32_Monocyte_miRNA


title: W83 Surface translocation rep3

city: Gainesville

first: Fata

last: Moradali

state: FL

address: 1395 Center Drive

institute: University of Florida

data_processing:
The cleaned and initially processed data files were downloaded from the Illumina website.
Files were analyzed using Rockhopper version 100.0 on the default setting.
All functional RNA messages were eliminated. Of the remaining transcripts, only genes with changes to expression (in RPKM) with  q-value <0.01 were retained.
Genome_build: GCF_001314265.1_ASM131426v1 (NCBI Reference Sequence: NZ_CP012889.1 for Porphyromonas gingivalis strain 381); GCF_000010505.1 (NCBI Reference Sequence: NC_010729.1 for Porphyromonas gingivalis ATCC 33277); GCF_000007585.1 (NCBI Reference Sequence: NC_002950.2 for Porphyromonas gingivalis strain 381)
Supplementary_files_format_and_content: counts

organism: Porphyromonas gingivalis

source_name: bacterial culture stabbed in soft agar medium

growth_protocol: Cultures of P. gingivalis 381 or W83 were grown by stabing in soft agar media and inuculating on surface of solid agar media and incubated anaerobically for 24 hours.

extract_protocol:
The Direct-zol RNA MiniPrep Kit (Zymo Research) kit was used for RNA extraction. Samples were next treated in two separate rounds with DNase I to digest gDNA. After washing the column, total RNA was eluted using nuclease free water. This elution was repeated a second time to concentrate samples.
Only samples with an RNA integrity number (RIN) of 7.0 or greater were processed. The Illumina Ribo-Zero magnetic kit for bacterial RNA was used to reduce ribosomal RNA. 5 μL of samples were fragmented and used to perform first strand synthesis with random priming. The NEBNext Ultra RNA library prep kit for Illumina (New England Biolabs) was used to prepare libraries. Samples were enriched by rounds of PCR and purified using the Agencourt AMPure XP system.

treatment_protocol: We tested the impact of the conditions that promote surfac translocation and biofilm modes on gene experssion profile.

tag: growth medium

value: Surface translocation


title: W83 Surface translocation rep2


title: CON_29_Monocyte_miRNA


title: Healthy PBMC (Ex Vivo) (CD4_LPS_1)

description: Ex Vivo.matrix


title: CON_26_Monocyte_miRNA


title: 381 Surface translocation rep3


title: W83 Surface translocation rep1


title: 381 Surface translocation rep2


title: W83 Biofilm rep3

source_name: bacteria grown on surface of solid agar medium

value: Biofilm


title: Healthy PBMC (Ex Vivo) (CD4_IFN_2)

description: Ex Vivo.matrix


title: 381 Surface translocation rep1


title: W83 Biofilm rep1


title: Healthy PBMC (Ex Vivo) (CD4_IFN_1)

description: Ex Vivo.matrix


title: CON_24_Monocyte_miRNA


title: 381 Biofilm rep3


title: W83 Biofilm rep2


title: CON_22_Monocyte_miRNA


title: CON_19_Monocyte_miRNA


title: Healthy PBMC (Ex Vivo) (CD4_DEX_2)

description: Ex Vivo.matrix


title: wild type CD8SP spleen cells rep2

city: Yokohama

first: kiyokazu

last: kakugawa

state: Kanagawa

address: 1-7-22 Suehiro-cho

department: IMS

institute: Riken

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were alingned to the mm10 genome assembly using Hisat2 with default option
data were processed with Cufflinks ver2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking of each gene

source_name: CD4-CD8+ Spleen T cell

extract_protocol:
total RNA was isolated using Trizol(ThermoFisher sientific) reagent
SureSelect Strand Specific RNA-Seq LibraryPreparation kit (Agilent Technologies) was used according to the manufacturer’s protocol.

treatment_protocol: thymocyte and spleen cells were sorted based on CD4, CD8 and TCR beta expression pattern.

value: spleen cells

value: 4-8 weeks

tag: cell markers

value: CD4- and CD8+


title: CON_20_Monocyte_miRNA

source_name: Monocytes


title: Healthy PBMC (Ex Vivo) (CD19_NT_2)

description: Ex Vivo.matrix

value: B cells


title: Healthy PBMC (Ex Vivo) (CD4_DEX_1)

description: Ex Vivo.matrix


title: 381 Biofilm rep1


title: wild type CD4SP spleen cells rep2

source_name: CD4+CD8- Spleen T cell

value: CD4+ and CD8-


title: CON_18_Monocyte_miRNA


title: 381 Biofilm rep2


title: wild type CD8SP spleen cells rep1


title: wild type DP thymocyte rep 2

source_name: CD4+CD8+ thymocyte

value: thymocyte

value: CD4+ and CD8+


title: Healthy PBMC (Ex Vivo) (CD19_NT_1)

description: Ex Vivo.matrix


title: Healthy PBMC (Ex Vivo) (CD19_LPS_1)

description: Ex Vivo.matrix


title: Healthy PBMC (Ex Vivo) (CD19_LPS_2)

description: Ex Vivo.matrix


title: wild type CD4SP spleen cells rep1


title: CON_17_Monocyte_miRNA


title: wild type DP thymocyte rep 1


title: CON_16_Monocyte_miRNA


title: Healthy PBMC (Ex Vivo) (CD19_IFN_2)

description: Ex Vivo.matrix


title: CON_14_Monocyte_miRNA


title: CON_13_Monocyte_miRNA


title: CON_10_Monocyte_miRNA


title: Healthy PBMC (Ex Vivo) (CD19_IFN_1)

description: Ex Vivo.matrix


title: CON_1_Monocyte_miRNA


title: Healthy PBMC (Ex Vivo) (CD19_DEX_2)

description: Ex Vivo.matrix


title: Healthy PBMC (Ex Vivo) (CD19_DEX_1)

description: Ex Vivo.matrix


title: PTL_9_Pax_miRNA

source_name: Whole Blood

extract_protocol:
Whole blood RNA was isolated from PAXgene tubes using microRNA isolation kit (Qiagen) using TRIsol LS (Invitrogen) following manufacturer’s instructions.
RNA library preparation was performed following the NEB NEBNext Multiplex Small RNA Library Preparation protocol. Briefly, 400 ng of total RNA was used as the input material. The 3’ SR Adapter was ligated to the small RNA, followed by RT primer hybridization to the 3’ SR adapter and then the 5’ SR Adapter was ligated to the opposite end (this strategy prevents formation of adapter-dimers). First stranded synthesis was then performed off the RT primer and the library was enriched by PCR using the following conditions: initial denaturation at 94oC for 30 seconds, followed by 15 cycles of 94oC for 15 seconds, 62oC for 30 seconds and 70oC for 15 seconds, and finally an extension step for 5 minutes at 70oC; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. One ul of the final Small RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size and libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).
Libraries were pooled in equimolar quantities and sequenced on a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate single-end reads of 50-bases in length.

tag: condition


title: Healthy PBMC (Ex Vivo) (CD14_IFN_2)

description: Ex Vivo.matrix

tag: cell type

value: CD14 monocytes


title: Healthy PBMC (Ex Vivo) (CD14_IFN_1)

description: Ex Vivo.matrix


title: PTL_6_Pax_miRNA

value: Term Delivery


title: Healthy PBMC (Ex Vivo) (CD14_NT_1)

description: Ex Vivo.matrix


title: PTL_5_Pax_miRNA


title: Healthy PBMC (Ex Vivo) (CD14_LPS_2)

description: Ex Vivo.matrix


title: Healthy PBMC (Ex Vivo) (CD14_LPS_1)

description: Ex Vivo.matrix


title: PTL_3_Pax_miRNA


title: PTL_4_Pax_miRNA


title: PTL_20_Pax_miRNA


title: Healthy PBMC (Validation) (CHIP_CD8_3)

description: Technical Validation - RNA-seq.matrix

value: CD8 T cells


title: PTL_19_Pax_miRNA


title: PTL_18_Pax_miRNA


title: Healthy PBMC (Ex Vivo) (CD14_DEX_1)

description: Ex Vivo.matrix


title: Healthy PBMC (Validation) (CHIP_CD8_2)

description: Technical Validation - RNA-seq.matrix


title: PTL_15_Pax_miRNA


title: SAMPLE 12: THP1_Echinaforce_rep6

type: genomic

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

description: THP1 cells treated with 1% Echinaforce for 48h, replicate6

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: CpG-probes were filtered before normalization based on following criteria: probes containing a SNP within 3 bp of the analyzed CpG site, bad quality probes based on an iterative greedycut algorithm with a detection p-value threshold of 0.01, and probes with missing values in at least one sample. After filtering these CpG-probes, methylation values were within-array normalized using the beta mixture quantile dilation (BMIQ) method. Another filtering step was performed after normalization based on following criteria: probes measuring methylation not at CpG sites (CC, CAG, CAH, …) and probes on sex chromosomes.

label: Cy5 and Cy3

source_name: THP1, Echinaforce, 48h, replicate6

label_protocol: Standard Illumina Protocol

growth_protocol: THP-1 cells were grown in RPMI-1640 medium supplemented with glutamine, 10 % heat inactivated Fetal Bovine Serum, 50 IU/mL Penicillin, 50 µg/mL Streptomycin, 10 mM HEPES and 0.05 mM β-mercaptoethanol.

extract_protocol: DNeasy Blood & Tissue kit (Qiagen) according to manufacturer’s instructions

treatment_protocol: Cells were treated with 1% Echinaforce® tincture versus ethanol solvent control. Each treatment condition consisted of six biological replicates.

tag: cell line

value: monocyte


title: SAMPLE 9: THP1_Echinaforce_rep3

description: THP1 cells treated with 1% Echinaforce for 48h, replicate3

source_name: THP1, Echinaforce, 48h, replicate3


title: SAMPLE 11: THP1_Echinaforce_rep5

description: THP1 cells treated with 1% Echinaforce for 48h, replicate5

source_name: THP1, Echinaforce, 48h, replicate5


title: SAMPLE 7: THP1_Echinaforce_rep1

description: THP1 cells treated with 1% Echinaforce for 48h, replicate1

source_name: THP1, Echinaforce, 48h, replicate1


title: SAMPLE 10: THP1_Echinaforce_rep4

description: THP1 cells treated with 1% Echinaforce for 48h, replicate4

source_name: THP1, Echinaforce, 48h, replicate4


title: PTL_17_Pax_miRNA


title: Healthy PBMC (Validation) (CHIP_CD8_1)

description: Technical Validation - RNA-seq.matrix

value: Healthy


title: Healthy PBMC (Validation) (CHIP_CD4_3)

description: Technical Validation - RNA-seq.matrix

value: PBMC


title: SAMPLE 8: THP1_Echinaforce_rep2

description: THP1 cells treated with 1% Echinaforce for 48h, replicate2

source_name: THP1, Echinaforce, 48h, replicate2


title: PTL_13_Pax_miRNA


title: PTL_14_Pax_miRNA


title: Healthy PBMC (Ex Vivo) (CD14_NT_2)

description: Ex Vivo.matrix

source_name: Healthy PBMC


title: Healthy PBMC (Validation) (CHIP_CD4_2)

description: Technical Validation - RNA-seq.matrix

value: CD4 T cells


title: PTL_11_Pax_miRNA


title: SAMPLE 4: THP1_EtOH_rep4

description: THP1 cells treated with ethanol for 48h, replicate4

source_name: THP1, EtOH, 48h, replicate4


title: Healthy PBMC (Validation) (CHIP_CD4_1)

description: Technical Validation - RNA-seq.matrix


title: SAMPLE 3: THP1_EtOH_rep3

description: THP1 cells treated with ethanol for 48h, replicate3

source_name: THP1, EtOH, 48h, replicate3


title: SAMPLE 6: THP1_EtOH_rep6

description: THP1 cells treated with ethanol for 48h, replicate6

source_name: THP1, EtOH, 48h, replicate6


title: PTL_10_Pax_miRNA


title: Healthy PBMC (Validation) (CHIP_CD19_3)

description: Technical Validation - RNA-seq.matrix


title: PTL_12_Pax_miRNA


title: SAMPLE 5: THP1_EtOH_rep5

description: THP1 cells treated with ethanol for 48h, replicate5

source_name: THP1, EtOH, 48h, replicate5


title: CON_9_Pax_miRNA


title: Healthy PBMC (Validation) (CHIP_CD19_2)

description: Technical Validation - RNA-seq.matrix


title: SAMPLE 2: THP1_EtOH_rep2

description: THP1 cells treated with ethanol for 48h, replicate2

source_name: THP1, EtOH, 48h, replicate2


title: SAMPLE 1: THP1_EtOH_rep1

description: THP1 cells treated with ethanol for 48h, replicate1

source_name: THP1, EtOH, 48h, replicate1


title: Healthy PBMC (Validation) (CHIP_CD19_1)

description: Technical Validation - RNA-seq.matrix


title: Healthy PBMC (Validation) (CHIP_CD14_3)

description: Technical Validation - RNA-seq.matrix


title: CON_47_Pax_miRNA


title: CON_49_Pax_miRNA