title: Cattle_BrainCortex_M1

source_name: BrainCortex

value: BrainCortex


title: Sk-BR-3_WR_3

status: Public on Mar 24 2022

type: SRA

city: Xiamen

first: Xing

last: Xu

state: Fujian

address: 422 Road, Siming District, Xiamen, China

country: China

institute: Xiamen University

description:
cell_line_RNA_expr_count.txt
cell_line_RNA_expr_fpkm.txt
cell_line_sample_annotation.txt

library_source: transcriptomic

data_processing:
DNA sequence reads were first trimmed by Cutadapt v2.10to remove the polyA/polyT/polyG (over 30bp), index primers and low-quality bases. The trimmed reads with less than 20bp were excluded at this stage. Clean reads were then aligned to the hg19 human genome using BWA (version 0.7.17)
CNVs across bins with variable length (500kb) were called using Ginkgo
RNA sequence reads were initially trimmed by Cutadapt v2.10 to remove the polyA/polyT/polyG (over 30bp), index primers and low-quality sequences. The trimmed reads containing fewer than 20bp were directly discarded. Filtered reads were then aligned to the hg19 human genome using STAR v2.6.0
Using the same reference and annotation, gene expression was quantified by HTSeq v0.13.5 and converted to fragments per kilobase transcript per million mapped reads (FPKM value)
Assembly: hg19
Supplementary files format and content: CNV matix and gene expression matix in text file

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer cells

growth_protocol: Cells are all cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
The RNAs of cells were released by using 0.2% Triton for 10 min while remaining DNAs within nucleus, and then the DNAs were released by using the alkaline lysis buffer (Vazyme Biotech, N603).
DNA libraries were constructed according to MDA (Multiple Displacement Amplification) method by using random primers and φ29 DNA polymerase to amplify DNAs, and RNA libraries were constructed according to Smart-seq2.

tag: cell type

value: breast cancer cells

tag: strain


title: RNA-seq: H1299-WT (+)Dox-xenograft-2

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

institute: Peking University

description:
XENO_H1299.csv
RNA_seq_XENO_H1299_WT_2

data_processing:
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the human genome (hg38, UCSC) and the mouse genome (mm10, UCSC) based on the origin of the cell lines. Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate reads per million (RPM).
Perl and python scripts were used to analyze small RNA-seq data. Adapters of sequences were trimmed and sequences with a length of 19-25nt were retained. To build the index of miRNA, we downloaded the mature miRNA sequences from miRBase, 3nt upstream and 3nt downstream of mature miRNA were added to the references. Each sequence was aligned to the reference using Bowtie software using the following parameters: -a -v 1 -3 3.In order to compare the miRNA expression in the line, the count of miRNAs was normalized. In RDR1 expression group, two ways were used to normalize miRNA data. Fly miRNA was added as spike-in in some samples. In non-spike-in method (including A549, HeLa, HepG2, HCT116 and NIH/3T3), the numbers of miRNAs were normalized to the numbers of total reads of the corresponding library to calculate RPM. In spike-in method (including H1299, Jurkat and RPE-1), the number of miRNAs was multiplied by a factor to make the count of fly miRNAs equal in all samples in a cell line. We used the top-10 highest expressed miRNAs as reference, which did not contain identical miRNAs in fly and human/mouse. Each of these 10 miRNAs was used to calculate a factor and the mean of these 10 factors was used as the factor for this sample for normalization. After normalization between samples within cell lines, the normalized reads of the sample with higher miRNA expression level was set at one million. In cell cycle inhibition, AGO2-CLIP and AGO2 knockdown experiments, miRNA expression was normalized with non-spike-in method. Some cell lines of RDR1 expression group were used in this analysis (A549, HeLa, HepG2). In order to be consistent with the previous analysis in RDR1 expression group, the normalized reads of the sample with higher miRNA expression level of RDR1 expression group was set at one million. In the miR-34c transfection assay, miRNA expression was normalized to the expression of endogenous miRNA, which was set at one million.
Assembly: hg38
Supplementary files format and content: Gene expression matrix; miRNA expression matrix

source_name: H1299 xenografts

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina), VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) and VAHTS Ribo-off Globin & rRNA Depletion Kits(Vazyme). Small RNA-seq libraries preparation using the NEBNext® Small RNA Library Prep Set for Illumina kits. Single-cell RNA-seq libraries preparation using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).

tag: cell type and treatment

value: WT with Dox induction

tag: genotype

value: WT

tag: cell line

tag: fraction

value: total RNA


title: Sk-BR-3_Bulk RNA_3


title: Sk-BR-3_WR_1


title: L_CON_S2

city: Auburn

first: Wellison

middle: J. S.

last: Diniz

state: Alabama

address: CASIC Building 559 Devall Drive Auburn University, 205

department: Animal Sciences

country: USA

institute: Auburn University

description:
Low_CON_2
RRBS (reduced represented bisulfite sequencing)

data_processing:
Illumina Casava software.
Sequencing adaptors and reads containing low quality bases were removed in an initial data-filtering step using Cutadapt. Reads with a PhredScore lower than 20 were filtered out. Quality control (QC) and read statistics were estimated with FastQC v0.11.8 and MultiQC v1.9 software.
NuGEN’s diversity trimming was carried out to remove diversity adaptors.
Trimmed reads were mapped to the bovine reference genome (UCSC - bosTau8, Illumina IGenome) using the Nextflow methylseq pipeline v1.5, which uses Bismark v0.22.3. Only cytosines in a CpG context were analyzed.
Genome_build: UCSC - bosTau8, Illumina IGenome
Supplementary_files_format_and_content: Normalized_Cytosinelevel.csv: Matrix table with normalized counts for every cytosine.

organism: Bos taurus

source_name: EBTr Cell culture

growth_protocol: The EBTr cells were cultured in Eagle’s Minimum Essential Medium, supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin and 0.11 g/L Na pyruvate (Sigma).

extract_protocol:
The DNA was extracted from the cell pellets with the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) and quantified using the PicoGreen DNA Quantification Kit (Invitrogen).
Libraries were bisulfite converted and PCR amplified prior to sequencing with NovaSeq S Prime in the 150 paired-end reads mode (Illumina, San Diego, CA).

treatment_protocol: Treatments were arranged as a completely randomized design with a two glucose levels [1 g/L (low) or 4.5 g/L (high)] × 3 OCM levels [control, 2.5X, and 5X]. Control medium contained basal concentrations of folate (0.001g/L), choline (0.001 g/L), vitamin B12 (4 µg/L), and methionine (0.015 g/L). One-carbon metabolites (folic acid, choline chloride, vitamin B12, and L-methionine) were supplemented to the media to achieve 2.5 or 5 times.

value: EBTr

tag: glucose treatment

value: Low (1 g/L )

tag: ocm treatment

value: CON


title: Cattle_Cecum_M2

city: Fort Collins

first: Michelle

middle: M

last: Halstead

state: CO

address: 200 West Lake Street

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Basecalling and demultiplexing were performed using ont-guppy-for-minknow (v3.0.5 for cattle data; v3.2.6 for pig and chicken data), and reads with quality score below 7 were discarded to obtain fastq files.
Demultiplexed fastq files were grouped together for each sample, and processed with Pychopper (v2.4.0) to identify and orient full-length reads.
Full-length strand-oriented reads for each sample were mapped to the respective genome assemblies (ARS-UCD1.2 for cattle; Sscrofa11.1 for pig; GRCg6a for chicken) with minimap2 (v2.16r922) with options “-ax splice -uf -k14” and modifying the maximum allowable intron size by species with option "-G 1000000" for pig and cattle, and "-G 400000" for chicken.
Uniquely mapped reads with a minimum quality score of 10 were extracted with Samtools (v1.7).
Uniquely mapped reads were used to obtain raw gene expression counts, based on the Ensembl v101 annotations for each species, using HTSeq (v0.11.2) with options "-i gene_id --type=exon --stranded=yes --mode=intersection-nonempty."
Genome_build: ARS-UCD1.2 (cattle), Sscrofa11.1 (pig), GRCg6a (chicken)
Supplementary_files_format_and_content: Raw gene counts, based on the Ensembl (v101) annotation for each species

molecule: polyA RNA

source_name: Cecum

extract_protocol:
Frozen tissues kept at -80°C were homogenized with a mortar and pestle in liquid nitrogen. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) followed by a column clean-up using the Direct-zol RNA Mini Prep Plus kit (Zymo Research, Irvine, CA) and performing an in-column DNA digestion. Integrity of the DNase-treated RNA was verified on the Experion electrophoresis system (Bio-Rad, Hercules, CA).
For each sample, 50 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9µl with nuclease free water.  Reactions were prepared (9 μl total RNA, 1 μl 10 µM VNP primer , 1 μl 10mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. One μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, and held at 4°C. A round of PCR was used to introduce barcodes to the cDNAs using Oxford Nanopore PCR barcoding expansion 1-96 kit (Cat. No.EXP-PBC096). Barcoding PCR reactions were set up for each cDNA (1 μl PCR barcode, 19 μl first-strand cDNA, 20μl LongAmp Taq 2x master mix), and cycled for [3 min at 95°C]x1, [15 sec at 95°C, 15 sec at 62°C, 7 min at 65°C] x13 cycles, [15 min at 65°C]x1, then held at 4°C. Each barcoded cDNA was purified in 1x Ampure XP Beads, eluted in 20µl of nuclease free water and quantified in the Qubit. Barcoded cDNAs were pooled in a final volume of 47µl and the pool was taken to the DNA Technologies Core and Expression Analysis Laboratory at the University of California Davis where they performed the adapter ligation on the cDNA pool using SQK-DCS109 kit following manufacturer's guidelines. 50 fmol of adapter ligated library was loaded onto PromethION flow cell vR9.4.1.
Long-read Nanopore cDNA sequencing

tag: Sex

value: Male

tag: tissue

value: Cecum


title: Cattle_BrainCortex_F1

value: Female


title: Patient3_cell2_DNA

library_source: genomic

data_processing:
Library strategy: MDA
DNA sequence reads were first trimmed by Cutadapt v2.10to remove the polyA/polyT/polyG (over 30bp), index primers and low-quality bases. The trimmed reads with less than 20bp were excluded at this stage. Clean reads were then aligned to the hg19 human genome using BWA (version 0.7.17)
CNVs across bins with variable length (500kb) were called using Ginkgo
RNA sequence reads were initially trimmed by Cutadapt v2.10 to remove the polyA/polyT/polyG (over 30bp), index primers and low-quality sequences. The trimmed reads containing fewer than 20bp were directly discarded. Filtered reads were then aligned to the hg19 human genome using STAR v2.6.0
Using the same reference and annotation, gene expression was quantified by HTSeq v0.13.5 and converted to fragments per kilobase transcript per million mapped reads (FPKM value)
Assembly: hg19
Supplementary files format and content: CNV matix and gene expression matix in text file

molecule: genomic DNA

source_name: multiple myeloma patients

value: multiple myeloma cells


title: RNA-seq: A549-AtRDR1 (+)Dox-xenograft

description:
XENO_A549.csv
RNA_seq_XENO_A549_At

source_name: A549-AtRDR1 xenografts

value: A549-AtRDR1 with Dox induction

value: A549-AtRDR1 stable cell line


title: Cattle_BoneMarrow_M2

source_name: BoneMarrow

value: BoneMarrow


title: L_5X_S9

description:
Low_5X_3
RRBS (reduced represented bisulfite sequencing)


title: Cattle_Cecum_F2


title: Cattle_BoneMarrow_M1


title: L_5X_S8

description:
Low_5X_2
RRBS (reduced represented bisulfite sequencing)


title: RNA-seq: A549-RDR1-Mut (+)Dox-xenograft

description:
XENO_A549.csv
RNA_seq_XENO_A549_Mut

source_name: A549-RDR1-Mut xenografts

value: A549-RDR1-Mut with Dox induction

value: A549-RDR1-Mut stable cell line


title: Cattle_BoneMarrow_F1


title: Patient3_cell4_DNA


title: Cattle_BrainCortex_F2

value: BrainCortex


title: L_CON_S1

description:
Low_CON_1
RRBS (reduced represented bisulfite sequencing)


title: Patient1_cell4_DNA


title: Cattle_Bladder_F1

source_name: Bladder

value: Bladder


title: L_2.5X_S4

description:
Low_2.5X_1
RRBS (reduced represented bisulfite sequencing)


title: Sk-BR-3_WR_2

value: breast cancer cells


title: Patient1_cell3_DNA


title: Cattle_BoneMarrow_F2


title: Cattle_Adipose_M2

source_name: Adipose

value: Adipose


title: Patient1_cell2_DNA


title: RNA-seq: H1299-WT (+)Dox-xenograft-1

description:
XENO_H1299.csv
RNA_seq_XENO_H1299_WT_1

value: WT with Dox induction

value: WT

value: total RNA


title: Patient3_cell3_DNA


title: Cattle_Adipose_M1


title: Patient3_cell1_DNA


title: L_5X_S7

description:
Low_5X_1
RRBS (reduced represented bisulfite sequencing)

value: EBTr

value: Low (1 g/L )


title: RNA-seq: H1299-RDR1-Mut (+)Dox-xenograft-1

description:
XENO_H1299.csv
RNA_seq_XENO_H1299_Mut_1

source_name: H1299-RDR1-Mut xenografts

value: H1299-RDR1-Mut with Dox induction

value: H1299-RDR1-Mut stable cell line


title: H_CON_S14

description:
High_CON_2
RRBS (reduced represented bisulfite sequencing)

value: High (4.5 g/L)

value: CON


title: Patient1_cell1_DNA

value: multiple myeloma cells


title: Patient2_cell3_DNA


title: Patient2_cell2_DNA


title: Cattle_Bladder_M2

value: Male


title: Patient2_cell1_DNA


title: H_CON_S15

description:
High_CON_3
RRBS (reduced represented bisulfite sequencing)


title: HCT-116_FD_4

description: Cell line DNA CNV.txt

source_name: colorectal cancer cells

value: colorectal cancer cells


title: H_5.0X_S21

description:
High_5.0X_3
RRBS (reduced represented bisulfite sequencing)


title: Cattle_Adipose_F2

value: Female


title: L_CON_S3

description:
Low_CON_3
RRBS (reduced represented bisulfite sequencing)


title: H_CON_S13

description:
High_CON_1
RRBS (reduced represented bisulfite sequencing)


title: H_5.0X_S20

description:
High_5.0X_2
RRBS (reduced represented bisulfite sequencing)


title: L_2.5X_S6

description:
Low_2.5X_3
RRBS (reduced represented bisulfite sequencing)


title: HCT-116_FD_5

description: Cell line DNA CNV.txt


title: H_5.0X_S19

description:
High_5.0X_1
RRBS (reduced represented bisulfite sequencing)


title: HCT-116_FD_3

description: Cell line DNA CNV.txt


title: Cattle_Adipose_F1


title: HCT-116_FD_2

description: Cell line DNA CNV.txt


title: Cattle_Abomasum_M1

source_name: Abomasum

value: Abomasum


title: Cattle_Abomasum_F1


title: HCT-116_FD_1

description: Cell line DNA CNV.txt


title: H_2.5X_S17

description:
High_2.5X_2
RRBS (reduced represented bisulfite sequencing)


title: H_2.5X_S18

description:
High_2.5X_3
RRBS (reduced represented bisulfite sequencing)


title: L_2.5X_S5

description:
Low_2.5X_2
RRBS (reduced represented bisulfite sequencing)


title: HCT-116_WD_3

description: Cell line DNA CNV.txt


title: H_2.5X_S16

description:
High_2.5X_1
RRBS (reduced represented bisulfite sequencing)


title: HCT-116_WD_2

description: Cell line DNA CNV.txt


title: HCT-116_Bulk DNA_2

description: Cell line DNA CNV.txt


title: HCT-116_Bulk DNA_1

description: Cell line DNA CNV.txt


title: Cord blood-CD34+ cells-MA9-ZNF521 transduced-at 58 days-replicate 2

type: RNA

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G

data_processing: All the following analyses were performed in R Bioconductor (version 3.5.1). Robust Multichip Average (RMA) processing was applied on raw data, based on the platform design (pd.clariom.d.human), allowing background subtraction, quantile normalization and median-polish summarization on core probe sets, by using oligo package.Global expression levels of 138.745 total transcripts were extracted from the ExpressionSet. Following Affymetrix Human Clariom D annotation (clariomdhumantranscriptcluster.db, version 8.7.0, org.Hs.eg.db, version 3.7.0 ) and filtering based on Entrez Gene Identifier and the exclusion of non-coding or uncharacterized protein transcripts (by subtracting microRNA, long non-coding RNA, long intergenic non-coding RNA, small nucleolar RNA, antisense, intronic, uncharachterized protein transcripts), 20.558 total features were further considered.

label: biotin

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA)

growth_protocol: Cord blood (CB)-CD34+ cells were purchased from Lonza and cultured as 0.5-1.0x105 cells/ml in xeno-free StemMACS™ HSC Expansion Media (Miltenyi Biotec) in presence of Thrombopoietin (TPO), FLT3-Ligand (FLT3-L) and Stem Cell Factor (SCF) (100 ng/ml).

extract_protocol: Total RNA was purified from duplicate samples by resuspending in TRI Reagent (Sigma-Aldrich) and freezing at –80°C before processing.

treatment_protocol: Lentiviral transformed cells were cultured in MyeloCult™ H5100 (STEMCELL Technologies) supplemented with 1 μM of Hydrocortisone (HC), 10 ng/ml of SCF, FLT3-L and Interleukin 3 (IL3).

value: Cord blood-CD34+ cells

tag: transduction

value: MA9-ZNF521 transduced

tag: time point

value: 58 days


title: Cord blood-CD34+ cells-MA9-ZNF521 transduced-at 23 days-replicate 1

value: 23 days


title: MCF-7_FD_2

description: Cell line DNA CNV.txt

value: breast cancer cells


title: MCF-7_FD_3

description: Cell line DNA CNV.txt


title: Cord blood-CD34+ cells-MA9-ZNF521 transduced-at 58 days-replicate 1


title: AspFum, single, 3

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

description:
Data from Aspergillus fumigatus single culture; replicate 3
Asp_AspKle_counts.xlsx

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v1.18 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1)
The reads were then mapped to the concatenated genome of Aspergillus fumigatus (Af293, genome version s03-m05-r06) and Klebsiella pneumoniae (NCBI_Assembly GCF_001596075.2, sequence-region NZ_CP014696.2 1 5284734 )  using NextGenMap (Sedlazeck et al., 2013), settings: -b -Q 30.
Reads mapping to rRNA loci were removed.  Read counting was done using HTseq (Anders et al., 2014) in the union mode using the above mentioned annotations.
Assembly: Pairwise comparison of differential expression analysis of single cultures with co-cultures was performed using edgeR v3.8.6 (Robinson et al., 2009)
Supplementary files format and content: tab delimited .txt files containing the output of the HTSeq analysis (read counts):
normalized (cpm; edgeR) read counts mapped to the indicated Aspergillus gene ID
normalized (cpm; edgeR) read counts mapped to the indicated Klebsiella gene ID

organism: Aspergillus fumigatus

source_name: fungal cells

growth_protocol: Cells were cultured statically for 24 hours at 37 °C in YPD medium. For mixed cultures, Aspergillus fumigatus spores were inoculated and allowed to germinate for 12 hours prior addition of Klebsiella pneumoniae.

extract_protocol:
Total RNA was purified using the Trizol reagent.
15μg of RNA was DNase-treated, cleaned up using the RNAeasy kit fron Qiagen and total RNA was subjected to rRNA depletion. Further library construction was done at the Next Generation Sequencing core facility (VBCF) at the Vienna BioCenter.

tag: strain id

tag: culture

value: single culture


title: MCF-7_WD_1

description: Cell line DNA CNV.txt


title: AspFum, single, 1

description:
Data from Aspergillus fumigatus single culture; replicate 1
Asp_AspKle_counts.xlsx


title: Cord blood-CD34+ cells-MA9-ZNF521 transduced-at 23 days-replicate 2


title: MCF-7_WD_3

description: Cell line DNA CNV.txt


title: MCF-7_Bulk DNA_3

description: Cell line DNA CNV.txt


title: MCF-7_Bulk DNA_2

description: Cell line DNA CNV.txt


title: AGA10: Macrophages differentiated in the presence of GW3965 and GSK2033 #1

city: Madrid

first: Miguel

middle: A

last: Vega

address: Ramiro de Maeztu 9

country: Spain

institute: CIB (CSIC)

data_processing:
BGISEQ-500 platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh37 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: At the beginning of the differentiaton prtocol, monocytes were treated with LXR agonist GW3965 (1 μM, Tocris), LXR antagonist GSK2033 (1 μM, Tocris), GW3965 and GSK2033, or dimethyl sulfoxide (DMSO) as vehicle.

value: Monocyte-derived M-CSF macrophages

tag: agent

value: GW3965 and GSK2033


title: MCF-7_WD_4

description: Cell line DNA CNV.txt


title: Cattle_Abomasum_M2


title: AGA11: Macrophages differentiated in the presence of GW3965 and GSK2033 #2


title: Cord blood-CD34+ cells-ZNF521 transduced-at 23 days-replicate 2

value: ZNF521 transduced


title: MCF-7_Bulk DNA_1

description: Cell line DNA CNV.txt


title: MCF-7_FD_1

description: Cell line DNA CNV.txt


title: MCF-7_WD_2

description: Cell line DNA CNV.txt


title: AGA12: Macrophages differentiated in the presence of GW3965 and GSK2033 #3


title: AGA8: Macrophages differentiated in the presence of GSK2033 #3


title: Cord blood-CD34+ cells-ZNF521 transduced-at 23 days-replicate 1


title: Cord blood-CD34+ cells-untreated-replicate 2

value: untreated


title: Sk-BR-3_FD_4

description: Cell line DNA CNV.txt


title: HCT-116_WD_1

description: Cell line DNA CNV.txt


title: AspFum, single, 2

description:
Data from Aspergillus fumigatus single culture; replicate 2
Asp_AspKle_counts.xlsx


title: AGA7: Macrophages differentiated in the presence of GSK2033 #1


title: AGA6: Macrophages differentiated in the presence of GW3965 #3


title: M31_iDKO_1M

city: Cleveland

first: Evan

last: Deneris

state: Ohio

address: 2210 Circle Dr., Robbins E640

department: Neurosciences

institute: Case Western Reserve University

data_processing:
Illumina Casava 2.20 software used for basecalling.
RNA-seq reads were filtered for low-quality sequence, then mapped to mm10 whole genome using hisat2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks and control samples were compared to iPKO, iLKO, and iDKO samples using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files for the RNA-seq contain all replicate RPKM expression values. Excel files contain all differential expression comparisons.

organism: Mus musculus

source_name: 5-HT neuron

growth_protocol: Brain tissue was taken from transgenic mice (age 3-5 months) maintained under standard housing conditions.

extract_protocol:
Dissected tissue encompassing the dorsal raphe and median raphe nucleus of 10 day and 1 month post-tamoxifen adult hindbrains from Tph2::CreER; Rosa-TdTomato,  Pet1 fl/fl; Tph2::CreER; Rosa-TdTomato, Lmx1b fl/fl; Tph2::CreER; Rosa-TdTomato, and Pet1 fl/fl; Lmx1b fl/fl; Tph2::CreER; Rosa-TdTomato animals. TdTomato+ 5-HT  neurons were sorted using a BD FACSAria SORP into Trizol LS.
Purified total RNA was amplified with the TRIO RNA-seq kit (Nugen)

treatment_protocol: Adult animals aged 2-3 months were treated with tamoxifen (250mg/kg) disolved in corn oil by oral gavage once per day for 5 days. Animals were housed for 10 days or 1 month post-tamoxifen treatment until brain tissue was dissected for cell sorting.

value: 5-HT neuron

tag: age

value: adult


title: Sk-BR-3_FD_1

description: Cell line DNA CNV.txt


title: AGA5: Macrophages differentiated in the presence of GW3965 #2


title: M29_iDKO_1M

description: Purified total RNA was amplified with the TRIO RNA-seq kit (Nugen)

value: Pet1 fl/fl; Lmx1b fl/fl; Tph2::CreER; Rosa-TdTomato


title: Cord blood-CD34+ cells-MA9 transduced-at 23 days-replicate 2

value: MA9 transduced


title: MCF-7_FD_4

description: Cell line DNA CNV.txt


title: M28_iDKO_1M


title: M30_iDKO_1M


title: iPCKO_1M_19

value: Pet1 fl/fl; Tph2::CreER; Rosa-TdTomato


title: AGA4: Macrophages differentiated in the presence of GW3965 #1


title: Sk-BR-3_FD_2

description: Cell line DNA CNV.txt


title: Sk-BR-3_WD_4

description: Cell line DNA CNV.txt


title: iPCKO_1M_18


title: Sk-BR-3_WD_3

description: Cell line DNA CNV.txt


title: Cord blood-CD34+ cells-MA9 transduced-at 23 days-replicate 1


title: Sk-BR-3_WD_6

description: Cell line DNA CNV.txt


title: AGA3: Macrophages differentiated in the presence of DMSO #3

value: DMSO


title: M32_iPKO_10d


title: lncRNAs HBO treatment3

first: Xuehua

last: Liu

address: 8 Gongti South Road, Chaoyang District Beijing

department: Department of Hyperbaric Oxygen

institute: Beijing Chaoyang Hospital, Capital Medical University

data_processing:
illumina Hiseq 2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using Hisat2（version:2.0.4）
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi A et al., Nat Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: spinal cord

extract_protocol:
Spinal cord tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TransZol Up Plus RNA Kit（Cat#ER501-01，Trans）was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spinal cord

value: 7-9 weeks

value: wild type

tag: treatment

value: HBO treatment


title: AGA2: Macrophages differentiated in the presence of DMSO #2

tag: cell type


title: Sk-BR-3_WD_5

description: Cell line DNA CNV.txt

source_name: breast cancer cells

tag: strain


title: iPCKO_10d_6


title: AGA8: Macrophages differentiated in the presence of GSK2033 #2


title: Sk-BR-3_WD_1

description: Cell line DNA CNV.txt


title: iPCKO_10d_5


title: Sk-BR-3_WD_2

description: Cell line DNA CNV.txt


title: Sk-BR-3_FD_3

description: Cell line DNA CNV.txt


title: lncRNAs HBO treatment2


title: iLCKO_1M_23

value: Lmx1b fl/fl; Tph2::CreER; Rosa-TdTomato


title: Sk-BR-3_Bulk DNA_3

description: Cell line DNA CNV.txt

value: breast cancer cells


title: iLCKO_1M_22


title: Cord blood-CD34+ cells-untreated-replicate 1

value: Cord blood-CD34+ cells


title: lncRNAs Spinal cord injury3

value: injury


title: iLCKO_1M_21


title: lncRNAs Spinal cord injury1


title: lncRNAs Spinal cord injury2


title: Caecum2 after gavage with STL solution

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

description: Gene expression after 30 days of gavage (D30)

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mus musculus Sure Print GE 4x44 v2 microarrays with oligonucleotide 45,220 probes (G2519F) 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 8x15K were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) 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: Mus musculus male force-fed with STL solution individual 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Standard chow and water ad libitum (Diet A04C-10, Scientific Animal Food and Engineering, Augy, France)

extract_protocol: Total RNA was extracted from hepatic tissues, ileum cells and caecum using RNAspin columns (Macherey-Nagel). For ileum cells the NucleoZOL (Macherey-Nagel) kit was used. RNA quality was observed with Nanodrop and absorbance ratios A260/280 and A260/230 were found between 2.0 and 2.2. RNA quality was also examined by RNA ScreenTape Analysis (Agilent) and a minimal RNA integrity number (RIN) of 0.8 was required for all samples.

treatment_protocol: Mice were fed for 30 days with an aqueous decoction of the roots flour, with fructose, CGA and STL solutions. The mice gavages consisted in a daily force-feeding of 500 µl of stemming solution decoctions of chicory flour, fructose, CGA or STL solution besides the standard chow. For the chicory flour, the decoction corresponded to 30 mg root powder/mouse/day. The administrated dose of fructose, CGA and STL was calculated to correspond to the concentration of the inulin in the chicory roots at the daily consumption. Controls will undergo an equivalent force-feeding with water.

value: Caecum

tag: gender

value: female

value: 8 weeks of age at D0


title: Sk-BR-3_Bulk DNA_1

description: Cell line DNA CNV.txt


title: Sk-BR-3_FD_5

description: Cell line DNA CNV.txt


title: AGA1: Macrophages differentiated in the presence of DMSO #1

value: Monocyte-derived M-CSF macrophages


title: SMC_ATLL_skin_TCR

city: Seoul

first: EUN-HYE

last: JOO

address: 81, Irwon-ro, Gangnam-gu

department: Samsung Genome Institute

country: South Korea

institute: Samsung Medical Center

data_processing:
Genome alignment, UMI counting and calling cell barcode: Cellranger 4.0.0
T cell receptor VDJ annotation: CellRanger 4.0.0
Genome_build: hg38
Supplementary_files_format_and_content: MTX: Sparse matrix for gene quantification.
Supplementary_files_format_and_content: TSV: Metadata describing the gene and feature names of the sparse matrix.
Supplementary_files_format_and_content: CSV: TCR clonetype annotation.

source_name: Skin

extract_protocol:
Specimens were placed in phosphate-buffered saline (PBS) on ice. Biopsy samples were cryopreserved in optimal cutting temperature (OCT) compound and stored at -80ºC. The cells were collected through a 70-μm cell strainer (#352340, Corning) and followed by dissociation in Trypsin solution (350 μL PBS, 50 μL 0.25% Trypsin). Cells were washed once and re-suspended in 100 μL of freshly prepared PBS-bovine serum albumin (BSA; 1 x PBS and 0.04% BSA) and processed on the 10x Genomics platform.
Single cell dissociates were loaded into the Chromium system (10x Genomics, USA) targeting 25,000 cells. The Chromium Single Cell 5’ Kit (10x Genomics, USA) was used to generate scRNA-seq and TCR libraries, according to the manufacturer’s instructions. Each library was loaded on a NovaSeq 6000 platform (Illumina, USA) with pair-end reads of 150 bp.

tag: disease

value: Adult T-cell Leukemia/Lymphoma

value: Skin

value: Male


title: iLCKO_1M_20

value: 5-HT neuron

value: adult

tag: genotype


title: Caecum2 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 2


title: iLCKO_10d_9


title: SMC_ATLL_skin_scRNA


title: iPCKO_1M_17

value: Pet1 fl/fl; Tph2::CreER; Rosa-TdTomato


title: lncRNAs Control2

value: spinal cord

value: 7-9 weeks

value: no injury


title: iLCKO_10d_11

value: Lmx1b fl/fl; Tph2::CreER; Rosa-TdTomato


title: Caecum1 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 1


title: lncRNAs Control1

value: wild type


title: Caecum3 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 3


title: iCon_1M_16

value: Tph2::CreER; Rosa-TdTomato


title: lncRNAs HBO treatment1

value: HBO treatment


title: iCon_1M_15


title: Ago2&1_2 [ChIP-seq input]

city: Zurich

first: Constance

last: Ciaudo

email: cciaudo@ethz.ch, ciaudobeyer@gmail.com

address: Otto-Stern-Weg 7

department: D-BIOL

country: Switzerland

institute: ETH

data_processing:
Reads were trimmed using trimmomatic and parameters ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20
Bowtie2 read mapping to M. musculus and D. melanogaster genomes
Filtering of PCR duplicates using samtools
deeptools coverage using number of mapped D. melanogaster reads as scaling factors
Genome_build: GENCODE vM23/mm10, D. melanogaster genome dm6
Supplementary_files_format_and_content: bw

source_name: Ago2&1 KO mESCs

growth_protocol: mESCs have been grown in medium supplemented with Serum+LIF

extract_protocol:
ChIP-seq protocol using an H3K27me3 antibody was performed as described in the publication’s methods section. D. melanogaster genomic DNA was spiked in to allow sequencing normalization.
Library was constructed by the Functional Genomics Center Zürich (FGCZ) using the NEBNext Ultra II DNA Library Prep Kit from NEB with 1ng starting material.

treatment_protocol: Per sample, 2x 5 Mio. Cells were fixed with formaldehyde before chromatin extraction

value: Embryonic stem cells

tag: strain background

value: 129/Ola background

value: Blastocyst

value: Ago2&1 KO

tag: chip antibody

value: Input


title: Ago2&1_1 [ChIP-seq input]


title: iCon_1M_13


title: Caecum3 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 3

value: Caecum

value: female

value: 8 weeks of age at D0


title: WT_2 [ChIP-seq input]

source_name: WT mESCs

value: WT mESCs


title: Sk-BR-3_Bulk DNA_2

description: Cell line DNA CNV.txt

value: breast cancer cells


title: iCon_10d_4

value: 5-HT neuron

value: adult


title: Caecum1 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 1

value: male


title: WT_1 [ChIP-seq input]


title: Caecum2 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 2


title: Caecum3 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 3


title: iCon_10d_2


title: Ago2&1_2 [ChIP-seq]

value: H3K27me3, abcam, ab6002


title: Caecum1 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 1


title: Caecum3 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 3


title: Caecum1 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 1


title: Ago2&1_1 [ChIP-seq]


title: Caecum2 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 2


title: iCon_10d_1

source_name: 5-HT neuron


title: conditional KO brain EC rep 3

city: Daejeon

first: JUNGMO

last: KIM

state: -- None selected --

address: 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

institute: Institute for Basic Science

data_processing:
The quality assessment of raw sequence data was performed using FastQC (Version: FastQC 0.11.3)
Sequenced reads were aligned to the mm10 mouse genome assembly (GRCm38, the mouse genome was downloaded from the iGenome portal) reference genome with STAR (version 2.7.3a)
the aligned reads were used to quantify mRNA expression by using HTSeq-count (version 0.6.1)
Differentially expressed genes were presented using hypergeometric calculation implemented in the DESeq2 Bioconductor package in R statistical language.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all Samples

source_name: conditional KO brain EC

extract_protocol:
RNA from FACS-sorted cells was isolated using the RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer's instructions.
RNA library construction was performed with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: brain

value: EC

value: Cdh5CreERT2-nf2 floxed

value: post natal day 9


title: lncRNAs Control3

source_name: spinal cord

value: spinal cord

value: 7-9 weeks

value: wild type

value: no injury


title: Caecum 2 Control corresponding to CGA and STL intake

source_name: Mus musculus male control2 individual 2

value: Caecum


title: WT_2 [ChIP-seq]

value: Embryonic stem cells

value: 129/Ola background

value: Blastocyst


title: MYC RS4

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

description: CHIP-seq

data_processing:
Sequencing reads were processed using the AQUAS pipeline (https://github.com/kundajelab/chipseq_pipeline) with minor modifications and according to the ENCODE3 guidelines. Reads were aligned to the hg38 genome build using BWA-ALN and peaks were called using MACS2.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files

source_name: Peripheral blood

growth_protocol: Not applicable

extract_protocol:
ChIP-seq was performed as previously described and in accordance with the Encode guidelines (Chapuy et al., 2013; Landt et al., 2012). The following antibodies were used for ChIP: MYC (CellSignaling 13987T)
ChIPseq libraries were prepared using Swift S2 Acel reagents (Swift 21096) on a Beckman Coulter Biomek i7 liquid handling platform from approximately 1 ng of DNA according to manufacturer’s protocol and using 14 cycles of PCR amplification. Sequencing libraries were quantified by Qubit fluorometer and Agilent TapeStation 2200. Library pooling and indexing was evaluated by shallow sequencing on Illumina NovaSeq 6000. Subsequently, libraries were sequenced on NovaSeq targeting 40 million 100 bp read pairs by the Molecular Biology Core facilities at the Dana-Farber Cancer Institute.

treatment_protocol: Not applicable

tag: antibody

value: MYC


title: WT_1 [ChIP-seq]

value: WT mESCs


title: conditional KO brain EC rep 2


title: conditional KO brain EC rep 1


title: MYC MV411

description: CHIP-seq


title: Caecum 1 Control corresponding to CGA and STL intake

source_name: Mus musculus male control2 individual 1

value: 8 weeks of age at D0


title: Caecum 2 Control corresponding to chicory and fructose intake

source_name: Mus musculus male control1 individual 2

value: male


title: Infection_MK

city: Guangzhou

first: Jiayi

last: Xie

state: Guangdong

address: North Campus, Sun Yat-sen University

institute: Sun Yat-sen University

data_processing:
The scRNA-seq reads were aligned to the mm10 reference genomes, and unique molecular identifier (UMI) counts were obtained by CellRanger 3.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz with barcode sequences corresponding to column indices
Supplementary_files_format_and_content: features.tsv.gz with feature sequences corresponding to row indices
Supplementary_files_format_and_content: matrix.mtx.gz with filtered feature-barcode matrices

source_name: bone marrow

extract_protocol:
Bone marrow cells were flushed from mouse femora and tibiae, cells then underwent red blood cell lysis using 0.16 M ammonium chloride solution. Sorted FSC high CD41+ single cells then underwent library construction.
Sorted  FSC high CD41+ single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library and Gel Bead Kit v3 (10X Genomics, PN-1000075) and the Chromium Single Cell B Chip Kit (10X Genomics, PN-1000074) as the manufacturer’s protocol.

value: megakaryocytes

value: bone marrow

value: 6-8 weeks


title: Caecum 1 Control corresponding to chicory and fructose intake

source_name: Mus musculus male control1 individual 1


title: control brain EC rep 3

source_name: control brain EC

value: brain

value: EC

value: nf2 floxed


title: RS4 Input

description: CHIP-seq


title: Control_MK


title: MV411 Input

description: CHIP-seq


title: Cardiac KO-6

city: Xi'an

first: Zhihui

last: Feng

address: 28# West Xianning Road

institute: Xi'an Jiaotong University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Heart

extract_protocol:
Fresh ventricular wall tissue samples were chopped in Trizol (Invitrogen, 15596018),  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: post natal month 2


title: Ileum3 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 3

value: Ileum

value: female


title: control brain EC rep 2

value: post natal day 9


title: Cardiac KO-5


title: control brain EC rep 1


title: Cardiac KO-4


title: GM-MØ macrophage donor3

first: Amaya

middle: Rocío

last: Puig Kröger

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

institute: Hospital General Universitario Gregorio Marañón

description:
GMMO_C
Monocyte-derived GM-CSF macrophages

data_processing:
HiSeq 4000 platform.
Low quality reads (more than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using STAR with the following additional parameters: --sdjbOverhang 150 --OutSAMType BAM
Gene expression levels were determined in R with the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.rpkm.txt: Tab-delimited text files include Entrez Gene ID and RPKM values for each Sample.

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 10^6 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ) or in the presence of 1000 U/ml GM-CSF to generate GM-CSF-polarized macrophages (GM-MØ).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a Bioanalyzer Agilent 2100.
RNA libraries were prepared for sequencing using Takara Bio SMARTer Stranded Total RNA-Seq - Pico Input Mammalian.

treatment_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FBS containing M-CSF or GM-CSF for 7 days.

value: Monocyte-derived macrophages

tag: condition

value: GM-CSF


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 3 - Technical Replicate 4

city: Bogota

first: Juan

middle: Manuel

last: Anzola

state: Bogota

department: Bioinformatics

country: Colombia

institute: CorpoGen

data_processing:
1. Quality control using  MULTIQC
2. Adapters and low quality sequence were trimmed with TRIMMOMATIC
3. The mapping was done against the genome reference sequences using SMALT
4. A first mapping process was done against a mouse reference genome (Mus musculus assembly GRC m38.p6). Reads mapping to mouse were removed
5. The rest of the reads were subsequently mapped against MTB H37Rv and to the available BL-323 and BC-391 genomes
6. obtention of  differentially expressed genes was done using SUBREAD package
7. Differentially expressed genes were determined using the tool edgeR.
Assembly: CP010873 (strain 323) and CP017596 (strain 391)
Supplementary files format and content: EdgeR counts of reads mapping to genes in CP010873 and CP017596

organism: Mycobacterium tuberculosis

source_name: Mus musculus

growth_protocol: Clinical isolates were cultured in Middlebrook 7H10 supplemented with 5% glycerol. For the infection of mice, an isolated colony was grown in 60 ml of Middlebrook 7H9 medium supplemented with 5% glycerol, 10% OADC, and 0.02% of Tyloxapol Premium (SIGMA / T8761) without the addition of antibiotics. When bacteria reached the mid-logarithmic growth phase (0.013 for BL-323 and 0.0325 for BC-391 at OD 680), the bacteria were centrifuged at 3,500 rpm, and aliquots of 1-ml were stored at -80ºC until use. For mice infection, each aliquot was evaluated for bacterial concentration by UFCs. For mice infection, 250,000 UFCs/mL in sterile saline solution were used.

extract_protocol:
Lungs stored at -80°C were removed and maintained in liquid nitrogen until processing. All the procedures were handled at 4ºC to avoid RNA degradation. Both mouse lungs were pulverized with liquid nitrogen, and aliquots of lung powder were stored to -80°C until used. To release the bacterial cells, mild-lysis buffer RLT Plus (Cat No: 1053393 Qiagen) supplemented with 10% β-mercaptoethanol was added. After centrifugation at 14,000 rpm/4ºC for 5 min, the bacterial enriched pellet was used for RNA extraction using the Quick-RNA Miniprep Kit (Zymo Research), following the manufacturer's instructions
Depletion of eukaryotic ribosomal subunits was carried out with the Ribo-Zero Kit (llumina® Ribo-Zero Plus rRNA Depletion Kit Cat: 20037135) following the manufacturer's instructions. Depleted RNA (500 ng of each sample) was used to construct libraries using the TruSeq® Stranded mRNA llumina® kit. The fragmentation time was adjusted to 14 min to obtain ~ 200-400 bp inserts, and the PCR enrichment was set to 15 cycles. To ensure good quality and quantity for the libraries, the concentration was verified by Qubit™ dsDNA HS (ThermoFisher Cat: Q32852), and the size of the libraries was verified using Agilent 2100 bioanalyzer System High Sensitivity DNA Kit (Cat: 5067-4626). The libraries with the correct insert size were subjected to bacterial ribosomal subunits depletion with an in-house subtractive hybridization
TruSeq® Stranded mRNA llumina®

treatment_protocol: The progressive pulmonary TB model [20, 21] was used for the transcriptomic assay of Beijing isolates. The bacterial aliquots were thawed and sonicated for 30 seconds at 20kHz to disaggregate the bacterial clumps and held at 4°C until inoculation. Male BALB/c mice, between 6-8 weeks old with ~22 gr weight were used. Mice were anaesthetized with 100% of Sevofluorane in a gas chamber and infected with both Beijing isolates by trachea exposure using a total of 250,000 bacteria

tag: tissue

value: Lungs

value: Balb/c


title: GM-MØ macrophage donor2

description:
GMMO_B
Monocyte-derived GM-CSF macrophages


title: Cardiac KO-3


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 3 - Technical Replicate 2


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 3 - Technical Replicate 3


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 3 - Technical Replicate 1


title: Ileum2 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 2

value: 8 weeks of age at D0


title: Cardiac KO-2


title: GM-MØ macrophage donor1

description:
GMMO_A
Monocyte-derived GM-CSF macrophages


title: Ileum1 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 1


title: Ileum2 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 2


title: Ileum1 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 1


title: Ileum3 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 3


title: Cardiac KO-1


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 2 - Technical Replicate 4


title: M-MØ macrophage donor3

description:
MMO_C
Monocyte-derived M-CSF macrophages

value: M-CSF


title: Cardiac WT-6

value: wild type


title: Ileum3 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 3


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 2 - Technical Replicate 3


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 2 - Technical Replicate 2


title: M-MØ macrophage donor2

description:
MMO_B
Monocyte-derived M-CSF macrophages


title: Ileum1 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 1

value: male


title: Cardiac WT-5


title: Ileum2 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 2


title: M-MØ macrophage donor1

description:
MMO_A
Monocyte-derived M-CSF macrophages


title: Cardiac WT-4


title: CD14+ monocytes donor3

source_name: monocytes

value: CD14+ Monocytes


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 2 - Technical Replicate 1


title: Cardiac WT-3


title: Ileum2 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 2


title: Ileum3 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 3


title: CD14+ monocytes donor2


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 1 - Technical Replicate 3


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 1 - Technical Replicate 4


title: CD14+ monocytes donor1


title: mRNA-seq: GSC2 NS

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

data_processing:
RNA-seq were mapped to the human genome (hg19) using tophat2 (version 2.1.0) with a transcript annotation file from Gencode (Release 19)
The reads count per gene were obtained with the HTseq-count script on properly paired reads and Genecode V19 transcript annotation file
Differential expression analysis between groups was based on reads count using DESeq2 and edgeR R packages
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample …

source_name: glioblastoma stem cell

growth_protocol: Glioblastoma stem cells were cultured in Neurobasal Medium supplemented with B27 1%; N2 0.5%; bFGF 0.05% and EGF 0.005% at 37°C in 5% CO2 humidified incubator. Culture medium was replaced twice a week and when spheres became large and numerous, they were enzymatically dissociated with accutase. Glioblastoma stem cell cultures were characterized by assessing self renewal, differentiation and tumorigenic ability as well as their expression of stemness markers (CD133, SOX2). Finally, all cultures were also classified according to Verhaak's classification of glioblastomas using the method of classification to nearest centroids (ClaNC) with a 840 gene signature.

extract_protocol:
The total RNA were extracted using the RNeasy Mini Kit (Qiagen, 74104) following the manufacturer's protocol. RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).
TruSeq Stranded mRNA library preparation and sequencing on illumina  HiSeq4000 were performed by Integragen, SA (Evry, France), according to the manufacturer's protocol.

treatment_protocol: SMART vector non targeting PGK-TurboGFP (VSC11713) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and processed 120 h later for RNA-seq analysis

value: Glioblastoma stem cells:GSC2

value: non targeting shRNA


title: Cardiac WT-2


title: Cardiac WT-1


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 1 - Technical Replicate 2


title: Ileum 2 Control corresponding to CGA and STL intake

source_name: Mus musculus male control2 individual 2


title: Ileum1 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 1


title: M. tuberculosis Classical Beijing  391 Day 60 Post Infection Biological Replicate 1 - Technical Replicate 1


title: Con-rep3 RNAseq

city: Suzhou

first: xiaolu

last: xie

address: No. 1055, Sanxiang Road, Gusu District,

institute: Second Affiliated Hospital of Soochow University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
Genome_build: Hg19
Supplementary_files_format_and_content: excel format: FPKM

source_name: THP-1 cells

growth_protocol: THP-1 cells were cultured in RPMI1640 culture medium mixed with 10% fetal bovine serum in an incubator with 37℃ and 5% CO2.

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

treatment_protocol: THP-1 cells were seeded in six-well plates with 800,000 cells per well. PMA was then added at a concentration of 25 ng/mL per well.THP-1 cells were infected with S. aureus at a ratio of 1:20 or mock infected for 2h at 37℃. Extracellular bacteria were removed by Gentamicin at a concentration of 200µg/mL.

tag: cell line

value: mock control cells


title: Ileum 1 Control corresponding to CGA and STL intake

source_name: Mus musculus male control2 individual 1


title: Con-rep2 RNAseq


title: Ileum 2 Control corresponding to chicory and fructose intake

source_name: Mus musculus male control1 individual 2


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 4

source_name: Mus musculus


title: Con-rep1 RNAseq


title: Sample-rep3 RNAseq

value: infected with intracellular Staphylococcus aureus


title: Ileum 1 Control corresponding to chicory and fructose intake

source_name: Mus musculus male control1 individual 1


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 2


title: Bam RNAi; Aramis RNAi RNA-seq 2

city: Albany

first: Prashanth

last: Rangan

state: NY

address: 1400 Washington

department: Biological Sciences

institute: RNA Institute

description: Sample 2B

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
For RNA-seq samples differential gene expression was assayed by DEseq2 (version 1.24.0), using a false discovery rate of (FDR) of 0.05, and genes with >|1.5| log2(foldchange)  were considered significant.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: count table

organism: Drosophila melanogaster

source_name: Ovaries

growth_protocol: Flies were fattened on yeast prior to dissection, ovaries were dissected in 1x PBS.

extract_protocol:
RNA was isolated using TRIzol (Invitrogen, 15596026), treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907).  mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08)
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

value: Ovaries

tag: disection

value: dissected 1-3 days post-eclosion

tag: experiment

value: mRNA-seq

value: UAS-Dicer2;NosGAL4 > bam RNAi; aramis RNAi


title: Bam (ii) RNA-seq 2

description: Sample 4B

value: UAS-Dicer2;NosGAL4 > bam RNAi


title: Bam (ii) RNA-seq 1

description: Sample 3B


title: Sample-rep2 RNAseq


title: Bam RNAi; Aramis RNAi RNA-seq 1

description: Sample 1B


title: Liver3 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 3

value: liver

value: female


title: Liver2 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 2


title: aramis_mRNA_ip3

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
Genes were considered enriched if they exceeded 2 fold enrichment in IP or IgG samples compared to Input samples with and had a FDR < 0.05. Genes were considered Aramis targets if they were enriched in the IP sample, but not the IgG sample.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: count table

growth_protocol: Ovaries dissected in 1x PBS.

treatment_protocol: Samples with the characteristic Immunoprecipitiation source "IP" were subected to IP with an antibody against FLAG conjugated to the protein indicated those with the characteristic Immunoprecipitiation source "IgG" were subjected to IP using control mouse IgG, and those with the characteristic Immunoprecipitiation source "Input" consisted of 10% of the total lysate reserved for RNA extraction using Trizol.

value: mRNA IP seq

value: IP


title: Liver1 after gavage with STL solution

source_name: Mus musculus male force-fed with STL solution individual 1

value: 8 weeks of age at D0


title: Sample-rep1 RNAseq


title: aramis_mRNA_igg3

value: IgG


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 2

value: Lungs

value: Balb/c


title: Liver3 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 3


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 3


title: Ddit3 DNT 42647R

city: Bar Harbor

first: Gareth

last: Howell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
NGSQCToolkit v2.3 for the removal of adapters and trimming low quality bases (Phred < 30)
Bowtie2 v2.2.0 to align reads
RSEM v1.2.12 to quantify gene expression as counts per million (cpm), TPM or FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expected raw counts, TPM and FPKM values for each sample, but only raw counts were used for downstream analysis

source_name: Retina

extract_protocol:
Retinas were removed, kept at room temperature for 24hrs and then stored in RNA-later at -80 °C.  RNA was harvested using Trizol reagent and QIAGEN miRNeasy mini extraction kit.
RNA libraries was prepared using TruSeq RNA Sample preparation kit v2 (Illumina, San Diego, CA)

treatment_protocol: Mice of 2-6 months of age were used for controlled optic nerve crush (CONC) or sham treatment (DNT- did not touch)

tag: Sex

value: M

value: DNT


title: Ddit3 CONC 42647L

value: CONC


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 1


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 4


title: Liver2 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 2


title: aramis_mRNA_igg2


title: Ddit3 DNT 42645R


title: Liver1 after gavage with CGA solution

source_name: Mus musculus male force-fed with CGA solution individual 1


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 3


title: aramis_mRNA_in2

value: Input


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 3


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 4


title: Liver3 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 3


title: Jun DNT 42604R

value: F

value: Jun


title: Liver2 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 2


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 2


title: aramis_mRNA_ip1

value: Ovaries

value: dissected 1-3 days post-eclosion


title: Jun CONC 42604L


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 1


title: M. tuberculosis Classical Beijing  391 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 1


title: aramis_mRNA_igg1


title: Liver1 after gavage with fructose solution

source_name: Mus musculus male force-fed with fructose solution individual 1

value: male


title: Liver3 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 3

value: liver


title: Control DNT 42603R

value: Control


title: aramis_mRNA_in1

value: mRNA IP seq


title: Control CONC 42603L


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 3


title: bamRNAi_polysome_1

data_processing:
Library strategy: Polysome-Seq
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
Translation efficiancy was calculated as the counts per million for each gene in the polysome library divided by the input library, targets were defined as genes 2 standard deviations below the median TE in the aramisRNAi samples but not in the UAS-TKV or bamRNAi control samples,  additionally upregulated targets were required to have a higher TE in aramis RNAi compared to the bam RNAi or UAS-tkv controls and downregulated targets were required to have a lower TE in aramis RNAi compared to the bam RNAi or UAS-tkv Controls.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: tabular file (count table)

extract_protocol:
RNA was isolated using TRIzol for input samples (Invitrogen, 15596026) or acid phenol-chloroform treatment for polysome samples, treated with DNase (TURBO DNA-free Kit, Life Technologies, AM1907).  mRNA-enriched libraries were obtained by treating total RNA with poly(A)tail selection beads following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08)
Following the manufacturer's instructions of the NEXTflex Rapid Directional RNAseq Kit (Bioo Scientific Corp, NOVA-5138-08), except RNA was fragmented for 13 minutes

treatment_protocol: For samples characteristic polysome fraction "polysome" samples were loaded onto polysome gradients, spun at 35,000g and fractionated prior to RNA isolation. For samples with the Experiment characteristic "polysome-seq" and the Characteristic polysome fraction "input" 20% of polysome lysate was reserved and later extracted using Trizol.

tag: dissection

value: polysome-seq

tag: fraction

value: polysome

value: UAS-Dicer2;NosGAL4 > bam RNAi


title: Control DNT 42601R

tag: age

tag: treatment


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 4

value: Lungs

tag: strain


title: aramis_mRNA_in3


title: bamRNAi_polysome_2


title: aramis_mRNA_ip2

value: IP


title: Liver2 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 2

tag: gender

value: 8 weeks of age at D0


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 2

value: Balb/c


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 1


title: bamRNAi_input_2

value: input


title: Control CONC 42601L

value: CONC


title: Liver1 after gavage with chicory flour decoction

source_name: Mus musculus male force-fed with chicory flour decoction individual 1


title: Ddit3 CONC 42645L

value: M


title: Liver 1 Control corresponding to CGA and STL intake

source_name: Mus musculus male control2 individual 1


title: Liver 2 Control corresponding to CGA and STL intake

source_name: Mus musculus male control2 individual 2


title: Jun DNT 42379R

value: F

value: Jun

value: DNT


title: bamRNAi_input_1

value: dissected 1-3 days post-eclosion

value: Ovaries


title: aramisRNAi_polysome_2

value: UAS-Dicer2;NosGAL4 > aramis RNAi


title: Liver 2 Control corresponding to chicory and fructose intake

source_name: Mus musculus male control1 individual 2

value: liver

value: male


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 3

source_name: Mus musculus


title: aramisRNAi_polysome_1

source_name: Ovaries

value: polysome-seq

value: polysome


title: Liver 1 Control corresponding to chicory and fructose intake

source_name: Mus musculus male control1 individual 1


title: Jun DNT 42376R


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 2

value: Lungs


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 1


title: aramisRNAi_input_2


title: aramisRNAi_input_1


title: Control DNT 42366R

value: Control


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 4


title: Control CONC 42366L


title: JK312 treated SNU601

city: Incheon

first: Seungyoon

last: Nam

state: Incheon

address: Namdong-gu, Namdongdae-ro 774-21

institute: Gachon University Colleage of Medicine

description: JK312 treated SNU601

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human  2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix). Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC).

source_name: stomach cancer cell line

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: grown in RPMI-1640 (Invitrogen) and 10% fetal calf serum (Hyclone), under a 37°C, 5% CO2, and 95% atmosphere. Cells line identities were validated by short tandem repeat profiling (ATCC).

extract_protocol: total cellular mRNA was isolated using RNeasy kits (Qiagen)

treatment_protocol: treated with DMSO, 5-, or 10-µM JK206, or JK312 for 48 hours

tag: cell type

value: stomach cancer cell line


title: UAS-TKV_polysome_2

tag: genotype

value: NosGAL4 > UAS-tkv


title: JK312 treated MKN1

description: JK312 treated MKN1


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 3

value: Balb/c


title: JK312 treated AGS

description: JK312 treated AGS

value: AGS


title: UAS-TKV_polysome_1


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 2


title: UAS-TKV_input_2

value: input


title: JK206 treated SNU601

description: JK206 treated SNU601


title: Control CONC 42302L

value: F

value: CONC


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 1


title: UAS-TKV_input_1


title: Jun DNT 42288R

value: Jun

value: DNT


title: JK206 treated MKN1

description: JK206 treated MKN1


title: JK206 treated AGS

description: JK206 treated AGS


title: M. tuberculosis Classical Beijing  391 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 4


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 4


title: Jun CONC 42379L


title: W11_S_NGC

city: Paris

first: Olivia

last: Bonduelle

address: 91 bd de l'Hopital

institute: INSERM U1135

data_processing:
FastQC version 0.11.8
Cell Ranger version 3.1.0
Change-O version 0.4.6
Assembly: mm10

source_name: draining lymph node B cells

extract_protocol:
RNA of single-B cells were prepared according to the Chromium single-cell V(D)J enrichment kit, mouse B cells.
Libraries were prepared according to the Chromium single-cell V(D)J enrichment kit, mouse B cells.

treatment_protocol: W614A-3S-specific GC and NGC B cells were sorted by Facs Aria (BD Biosciences). Single-B cell were isolated and  by 10X Genomics technology.

value: W614A-3S-specific B cells

tag: localisation

value: NGC:non-germinal center

tag: adjuvant immunization

value: SQE condition

value: Balb/C


title: Larp_ip3

data_processing:
Sequenced reads were aligned to the D. melanogaster genome (UCSC dm6) using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
Genes were considered enriched if they exceeded 2 fold enrichment in IP or IgG samples compared to Input samples with and had a FDR < 0.05. Genes were considered Larp targets if they were enriched in the IP sample, but not the IgG sample.
Genome_build: UCSC dm6
Supplementary_files_format_and_content: tabular file (count table)

treatment_protocol: Samples in the characteristics "RIP antibody" field: those with "IP" were subected to IP with an antibody against FLAG conjugated to the protein indicated, those with "IgG" were subjected to IP using control mouse IgG, and those with "Input" consisted of 10% of the total lysate reserved for RNA extraction using Trizol.

tag: group

value: Larp

value: dissected 1-3 days post-eclosion

value: mRNA IP seq

tag: rip antibody

value: IP

value: Ovaries


title: Jun CONC 42288L

source_name: Retina


title: W11_S_GC

value: GC:germinal center


title: Jun CONC 42376L

value: M


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 3

tag: tissue

value: Lungs

value: Balb/c


title: Larp_ip2


title: Jun DNT 42244R


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 2


title: Jun CONC 42244L


title: Larp_in3

value: none (Input)


title: Control DNT 42242R

value: Control


title: Larp_ip1


title: W11_A_GC

value: Alum condition


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 3 - Technical Replicate 1


title: WTA10.Pos2-1

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: WTA10 cells cultured in the presence of Doxycycline, replicate 2, sample1

data_processing:
bcl2fastq 2.17.1.14 were used for basecalling.
Sequenced reads were mapped to hg38 using STAR v2.4.2a with default parameters settings
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were computed using RSEM v1.2.25 and Gencode v24 annotation.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: WTA10 cells cultured in the presence of Doxycycline.

growth_protocol: cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS), 10mM HEPES, 0.1mM non-essential amino acid, 1mM sodium pyruvate, 2 mM L-glutamine, G418 (0.5mg/ml), Hygromycin B (0.1mg/ml) and Doxycycline (1μg/ml).

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries, using Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201).
Illumina TruSeq Stranded Total RNA Library Preparation Kit (Cat no: RS-122-2201) was used with 1 ug of total RNA for the construction of sequencing libraries according to manufacturer's protocol.

treatment_protocol: For induction of CagA, cells were washed thrice with PBS and cultured in the medium devoid of Doxycycline for 72 hours. Cells were harvested and subjected to RNA sequencing

tag: cell line

value: modified MKN-28 cells where CagA is induced

tag: cultured condition

value: with Doxycycline


title: WTA10.Pos2-2

description: WTA10 cells cultured in the presence of Doxycycline, replicate 2, sample 2


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 4


title: Control CONC 42242L

value: CONC


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 3


title: Ddit3_Jun DNT 42238R

value: F

value: DNT


title: Control DNT 42302R


title: WTA10.Pos1-1

description: WTA10 cells cultured in the presence of Doxycycline, replicate 1, sample1


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 1


title: Larp_igg3

value: Larp

tag: experiment

value: IgG


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 2 - Technical Replicate 2


title: Larp_in1

value: dissected 1-3 days post-eclosion

value: mRNA IP seq


title: WTA10.Pos1-2

description: WTA10 cells cultured in the presence of Doxycycline, replicate 1, sample 2


title: Ddit3_Jun CONC 42238L

tag: Sex


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 4


title: Ddit3 DNT 42229R


title: WTA10.Neg2-2

description: WTA10 cells cultured in the absence of Doxycycline, replicate 2, sample 2

source_name: WTA10 cells cultured in the absence of Doxycycline.

value: without Doxycycline


title: Ddit3 CONC 42229L


title: WTA10.Neg2-1

description: WTA10 cells cultured in the absence of Doxycycline, replicate 2, sample 1


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 3


title: Ddit3 DNT 42142R


title: Porthos_ip3

data_processing:
Sequenced reads were aligned to the M21017.1 NCBI Drosophila rRNA sequence record using HISAT2 (version 2.1.0)
Raw counts were generated using featureCounts (version 1.4.6.p5)
For total RNA IP experiments, expression was normalized to the matched inputs and a luciferase spike-in. Enrichment was assesed compared to the IgG control.
Genome_build: M21017.1 NCBI Drosophila rRNA sequence
Supplementary_files_format_and_content: tabular file (count table)

treatment_protocol: Samples in the characteristics "RIP antibody" field:  those with "IP" were subected to IP with an antibody against FLAG conjugated to the protein indicated, those with "IgG" were subjected to IP using control mouse IgG, and those with "Input" consisted of 10% of the total lysate reserved for RNA extraction using Trizol.

value: Porthos

tag: dissection

value: rRNA IP seq

value: IP

value: traffic jam > UAS-porthos::HA::FLAG

value: Ovaries


title: WTA10.Neg1-2

description: WTA10 cells cultured in the absence of Doxycycline, replicate 1, sample 2


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 2

value: Lungs

value: Balb/c


title: W11_A_NGC

value: W614A-3S-specific B cells

value: NGC:non-germinal center

value: Alum condition

value: Balb/C


title: Porthos_ip2


title: M. tuberculosis Classical Beijing  391 Day 3 Post Infection Biological Replicate 1 - Technical Replicate 1


title: WTA10.Neg1-1

description: WTA10 cells cultured in the absence of Doxycycline, replicate 1, sample 1

value: modified MKN-28 cells where CagA is induced


title: Porthos_ip1


title: Ddit3_Jun CONC 42014L

value: F

value: CONC


title: siCtrl_NT_2

city: Montréal

first: Alexandre

last: Orthwein

state: QC

address: 3755 Chemin de la Côte-Sainte-Catherine

department: Lady Davis Institute

country: Canada

institute: McGill University

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.7.1a
Readcounts were computed by STAR during sequence alignment based on annotations from Gencode version 37
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 37 transcript annotations
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

source_name: HeLa cells

growth_protocol: DMEM + 10% FBS + Pen/Strep

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using the KAPA RNA Hyperprep Ribo Erase Kit and were further amplified for sequencing.

treatment_protocol: Cisplatin 10microM;siRNA treatment against SNRNP200

value: epithelial cells

value: cervix

value: scramble siRNA


title: Porthos_in3

value: Porthos

value: dissected 1-3 days post-eclosion

value: none (Input)


title: siCtrl_NT_1


title: Larp_in2

value: Larp

value: mRNA IP seq


title: Ddit3 DNT 42013R

value: DNT


title: Porthos_in2

value: rRNA IP seq

value: traffic jam > UAS-porthos::HA::FLAG

value: Ovaries


title: Ddit3_Jun DNT 42014R


title: Ddit3 CONC 42013L


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 2

value: Lungs

value: Balb/c


title: Porthos_in1


title: Larp_igg2

value: IgG


title: siCtrl_CIS_6hrs_2

value: scramble siRNA, Cisplatin 6hrs


title: siCtrl_CIS_6hrs_1


title: Porthos_igg3


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 1


title: Larp_igg1


title: Ddit3_Jun DNT 42011R

value: F


title: siCtrl_CIS_24hrs_2

value: epithelial cells

value: scramble siRNA, Cisplatin 24hrs


title: Porthos_igg2


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 4


title: siCtrl_CIS_24hrs_1

value: cervix


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 3


title: Ddit3_Jun DNT 41891R


title: Porthos_igg1

value: Porthos


title: Ddit3 CONC 42142L

value: M

value: CONC


title: 200-2_NT_2

value: SNRNP200-2 KD


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 2


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 4


title: Ddit3_Jun CONC 41891L


title: 200-2_NT_1


title: Athos_ip3

value: Athos

value: dissected 1-3 days post-eclosion

value: IP


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 2 - Technical Replicate 1


title: small RNA-seq: HeLa-WT-Palb

city: Beijing

first: Li

last: Ding

address: No.5, Yiheyuan Road

institute: Peking University

description:
smallRNA_cell_cycle_block.csv
small_RNA_seq_HeLa_48h_Palb

data_processing:
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the human genome (hg38, UCSC) and the mouse genome (mm10, UCSC) based on the origin of the cell lines. Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate reads per million (RPM).
Perl and python scripts were used to analyze small RNA-seq data. Adapters of sequences were trimmed and sequences with a length of 19-25nt were retained. To build the index of miRNA, we downloaded the mature miRNA sequences from miRBase, 3nt upstream and 3nt downstream of mature miRNA were added to the references. Each sequence was aligned to the reference using Bowtie software using the following parameters: -a -v 1 -3 3.In order to compare the miRNA expression in the line, the count of miRNAs was normalized. In RDR1 expression group, two ways were used to normalize miRNA data. Fly miRNA was added as spike-in in some samples. In non-spike-in method (including A549, HeLa, HepG2, HCT116 and NIH/3T3), the numbers of miRNAs were normalized to the numbers of total reads of the corresponding library to calculate RPM. In spike-in method (including H1299, Jurkat and RPE-1), the number of miRNAs was multiplied by a factor to make the count of fly miRNAs equal in all samples in a cell line. We used the top-10 highest expressed miRNAs as reference, which did not contain identical miRNAs in fly and human/mouse. Each of these 10 miRNAs was used to calculate a factor and the mean of these 10 factors was used as the factor for this sample for normalization. After normalization between samples within cell lines, the normalized reads of the sample with higher miRNA expression level was set at one million. In cell cycle inhibition, AGO2-CLIP and AGO2 knockdown experiments, miRNA expression was normalized with non-spike-in method. Some cell lines of RDR1 expression group were used in this analysis (A549, HeLa, HepG2). In order to be consistent with the previous analysis in RDR1 expression group, the normalized reads of the sample with higher miRNA expression level of RDR1 expression group was set at one million. In the miR-34c transfection assay, miRNA expression was normalized to the expression of endogenous miRNA, which was set at one million.
Assembly: hg38
Supplementary files format and content: Gene expression matrix; miRNA expression matrix

source_name: HeLa

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina), VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) and VAHTS Ribo-off Globin & rRNA Depletion Kits(Vazyme). Small RNA-seq libraries preparation using the NEBNext® Small RNA Library Prep Set for Illumina kits. Single-cell RNA-seq libraries preparation using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).

tag: cell type and treatment

value: Hela cells treated with 0.5 uM palbociclib for 48h

value: WT

value: HeLa

tag: fraction

value: Gel-purified 15-50nt small RNAs


title: Athos_ip2

value: rRNA IP seq

value: Ovaries


title: 200-2_CIS_6hrs_2

tag: treatment

value: SNRNP200-2 KD, Cisplatin 6hrs


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 4

value: Lungs

tag: strain

value: Balb/c


title: Athos_ip1


title: small RNA-seq: HeLa-WT-DMSO

description:
smallRNA_cell_cycle_block.csv
small_RNA_seq_HeLa_48h_DMSO

value: Hela cells treated with DMSO for 48h


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 3 - Technical Replicate 3


title: Athos_in3

value: none (Input)


title: 200-2_CIS_24hrs_2

value: epithelial cells

value: cervix

value: SNRNP200-2 KD, Cisplatin 24hrs


title: 200-2_CIS_6hrs_1


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 2


title: Athos_in2

value: Athos


title: 200-2_CIS_24hrs_1


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 1


title: small RNA-seq: HepG2-AtRDR1 (+)Dox-2nt-ds-miR-34c-IP

description:
smallRNA_34c.csv
small_RNA_seq_IP_HepG2_At_plus_Dox_2nt_ds

source_name: HepG2-AtRDR1 stable cell line

value: HepG2-AtRDR1 with Dox induction for 3 days and transfected with annealed 2nt-overhang miR-34c for next 2 days

value: HepG2-AtRDR1 stable cell line

value: AGO2-IP RNAs


title: Athos_in1

value: dissected 1-3 days post-eclosion


title: Ddit3_Jun CONC 42011L

tag: age

value: F

value: CONC


title: small RNA-seq: HepG2-AtRDR1 (-)Dox-2nt-ds-miR-34c-IP

description:
smallRNA_34c.csv
small_RNA_seq_IP_HepG2_At_no_Dox_2nt_ds

value: HepG2-AtRDR1 without Dox induction for 3 days and transfected with annealed 2nt-overhang miR-34c for next 2 days


title: 200-1_NT_2

tag: cell type

value: SNRNP200-1 KD


title: Athos_igg3

value: rRNA IP seq

value: IgG

tag: genotype

value: Ovaries


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 3

value: Lungs

value: Balb/c


title: 200-1_NT_1

value: epithelial cells


title: small RNA-seq: HepG2-AtRDR1 (+)Dox-1nt-ds-miR-34c-IP

description:
smallRNA_34c.csv
small_RNA_seq_IP_HepG2_At_plus_Dox_1nt_ds

value: HepG2-AtRDR1 with Dox induction for 3 days and transfected with annealed 1nt-overhang miR-34c for next 2 days


title: 200-1_CIS_6hrs_2

value: cervix

value: SNRNP200-1 KD, Cisplatin 6hrs


title: 200-1_CIS_6hrs_1


title: Athos_igg2

value: Athos


title: Athos_igg1


title: small RNA-seq: HepG2-AtRDR1 (-)Dox-1nt-ds-miR-34c-IP

description:
smallRNA_34c.csv
small_RNA_seq_IP_HepG2_At_no_Dox_1nt_ds

value: HepG2-AtRDR1 without Dox induction for 3 days and transfected with annealed 1nt-overhang miR-34c for next 2 days

value: HepG2-AtRDR1 stable cell line


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 1


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 2


title: 200-1_CIS_24hrs_2

value: SNRNP200-1 KD, Cisplatin 24hrs


title: Aramis_ip3

value: Aramis

value: dissected 1-3 days post-eclosion

value: IP


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 4


title: Aramis_ip2


title: M. tuberculosis Beijing-Like 323 Day 28 Post Infection Biological Replicate 1 - Technical Replicate 3


title: small RNA-seq: HepG2-AtRDR1 (+)Dox-ss-miR-34c-IP

description:
smallRNA_34c.csv
small_RNA_seq_IP_HepG2_At_plus_Dox_ss

value: HepG2-AtRDR1 with Dox induction for 3 days and transfected with 1nt-shorter miR-34c-5p for next 2 days

value: AGO2-IP RNAs


title: 200-1_CIS_24hrs_1


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 2 - Technical Replicate 3


title: Aramis_ip1

value: rRNA IP seq


title: MLL-r B-ALL protein

description: CITE-seq data of MLL-r B-ALL infant leukemia

data_processing:
Raw sequencing files were processed using a DropEst pipeline
Quality control, normalization, graph-based clustering, gene signatures were performed using CellRouter
The project yaml file to be used with the indrops pipeline available at https://github.com/indrops/indrops can be provided upon request
Quality control, normalization, graph-based clustering and identification of gene signatures were performed using CellRouter (https://github.com/edroaldo/cellrouter)
Prediction of multipotent cells was performed using StemID (https://github.com/dgrun/StemID).
We used scImpute to account for drop-out rates in single-cell RNA-seq data (https://github.com/Vivianstats/scImpute)
Genome_build: GRCh38
Supplementary_files_format_and_content: .rds files containing gene expression counts

molecule: protein

source_name: Peripheral blood

extract_protocol:
RNA was purified and proccessed for indrop according to the protocol from Klein et al (Cell, 2015, doi:10.1016/j.cell.2015.04.044)
RNA libraries were prepared for sequencing by the indrop core facility at Harvard Medical School. We used library version v3 where R1 is the biological read. R2 carries the first half of the gel barcode, R3 carries the library index and R4 the second half of the gel barcode, the UMI and a fraction of the polyA tail.

value: MLL-r B-ALL infant leukemia


title: small RNA-seq: HepG2-AtRDR1 (-)Dox-ss-miR-34c-IP

description:
smallRNA_34c.csv
small_RNA_seq_IP_HepG2_At_no_Dox_ss

value: HepG2-AtRDR1 without Dox induction for 3 days and transfected with 1nt-shorter miR-34c-5p for next 2 days


title: small RNA-seq: HepG2-AtRDR1 (-)Dox (AGO2-IP)

description:
smallRNA_AGO2_IP_HepG2.csv
small_RNA_seq_IP_HepG2_no_Dox

value: HepG2-AtRDR1 without Dox induction followed by AGO2 IP

value: WT


title: small RNA-seq: HepG2-AtRDR1 (+)Dox (AGO2-IP)

description:
smallRNA_AGO2_IP_HepG2.csv
small_RNA_seq_IP_HepG2_plus_Dox

value: HepG2-AtRDR1 with Dox induction for 6 days followed by AGO2 IP


title: MLL-r B-ALL Replicate 2

tag: replicate

value: Replicate 2

tag: library index

value: TTACCTCC


title: Aramis_in3

tag: group

value: none (Input)

value: Ovaries


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 3 - Technical Replicate 4

value: Lungs

value: Balb/c


title: Aramis_in2

value: Aramis

tag: rip antibody


title: small RNA-seq: A549-AtRDR1 (+)Dox (AGO2-IP)

description:
smallRNA_AGO2_IP_A549.csv
small_RNA_seq_IP_A549_plus_Dox

source_name: A549-AtRDR1 stable cell line

value: A549-AtRDR1 with Dox induction for 6 days followed by AGO2 IP

value: A549-AtRDR1 stable cell line


title: small RNA-seq: A549-AtRDR1 (-)Dox (AGO2-IP)

description:
smallRNA_AGO2_IP_A549.csv
small_RNA_seq_IP_A549_no_Dox

value: A549-AtRDR1 without Dox induction followed by AGO2 IP


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 4

tag: tissue


title: Aramis_in1

value: dissected 1-3 days post-eclosion


title: Aramis_igg3

value: rRNA IP seq

value: IgG


title: M. tuberculosis Beijing-Like 323 Day 14 Post Infection Biological Replicate 1 - Technical Replicate 2


title: Array3

description:
Early passage Single-cell RNA-seq data of human MLL-r B-ALL PDX model.
processed data file: reads.Array3_R1.fastq_bq10_star_corrected.umi.dge.txt.gz
processed data file: scimpute_count_Leukemia.csv

data_processing:
Reads were first aligned to hg19, and individual reads were tagged according to the 12-bp barcode sequence and the 8-bp UMI contained in read 1 of each fragment. Following alignment, reads were binned and collapsed onto 12-bp cell barcodes that corresponded to individual beads using Drop-seq tools (http://mccarrolllab.com/dropseq). Barcodes were collapsed with a single-base error tolerance (Hamming distance = 1), with additional provisions for single insertions or deletions. An identical collapsing scheme (Hamming distance = 1) was then applied to UMIs to obtain quantitative counts of individual mRNA molecules.
Quality control, normalization, graph-based clustering and identification of gene signatures were performed using CellRouter (https://github.com/edroaldo/cellrouter).
Prediction of multipotent cells was performed using StemID (https://github.com/dgrun/StemID). Cluster classification was performed using SingleCellNet (https://github.com/pcahan1/singleCellNet/).
We used scImpute to account for drop-out rates in single-cell RNA-seq data (https://github.com/Vivianstats/scImpute).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt, *.csv: Tab- or comma-delimited text files containing gene expression counts.

source_name: Human MLL-r B-ALL purified from mouse spleen (PDX) by FACS, replicate 1

extract_protocol: RNA was prepared following the Seq-Well protocol (Gierahn et al., Nature Methods, 2018).

value: MLL-r B-ALL PDX model


title: ZJX-2018051605-1

city: Wuhan

first: Dong

last: Li

state: Hubei

address: No.1095 Jie Fang Avenue

institute: Tongji Hospital, Tongji Medical College,Huazhong University of Science and Technology

data_processing:
The raw reads were manufactured by removing containing adapter, poly‘N’, low quality and <17nt reads using FASTQC to acquire clean reads.
Mapping reads were got by mapping clean reads to reference genome of BWA
The miRDeep2 was used to recognize known mature miRNAs according to miRBase21 (www.miRBase.org) and to predict novel miRNAs.
The miRNA expression were counted by Reads Per Million (RPM) values
Assembly: hg19
Supplementary files format and content: text files include all detected miRNAs

source_name: Exosome

extract_protocol:
Blood were obtained from healthy volunteers or patients with SV who have not received any treatments for at least three months.Plasma exosomes and exosomal RNA of 15 samples were extracted and purified by exoRNeasy Maxi Kit.Appropriately 50ng exosomal RNA of each samples was used to establish small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age(years)

tag: gender

value: Male

tag: disease state

value: segmental vitiligo (SV) patient

value: Exosome