title: Mus domesticus e17.5 placenta [DOM_M8_P3]

city: Riverside

first: Polly

last: Campbell

state: CA

address: 3401 Watkins Drive

department: Evolution, Ecology, and Organismal Biology

institute: University of California Riverside

data_processing:
QC of raw sequencing reads and trimming were performed in Trim Galore! 0.4.5 (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), using a phred score cutoff of 20 and minimum sequence length of 20 after trimming.
A pseudo-hybrid (Mus domesticus X Mus spretus) genome using was generated based on the mouse genome (GRCm38.89) using  the genome preparation tool of the program SNPsplit (Brabraham Bioinformatics). All placenta samples were mapped to the pseudo-hybrid genome.
The RRBS reads were mapped to the converted pseudo-hybrid genome using the Bismark Bisulfite Aligner (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/bismark/).
We filtered the resulting alignment files using SAMtools 0.1.19 (Li et al. 2009), retaining only high quality (MAPQ score 40), uniquely mapped, paired reads for analysis.
We randomly downsampled all alignment files to the same number of reads (~10 million reads) using SAMtools 0.1.19 (Li et al. 2009).
To analyze allele specific methylation (ASM) in hybrids we split the hybrid alignment files with SNPsplit as described above for RNAseq alignments, but using the bisulfite option of the program.
CpG methylation information was extracted from the alignment files using the Bismark-methylation-extractor tool (Babraham Bioinformatics).
Differential methylation (DM) and ASM were analyzed in SeqMonk (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: All samples were mapped to the pseudo-hybrid genome (Mus domesticus X Mus spretus) based on the mouse genome (GRCm38.89)
Supplementary_files_format_and_content: tab-delimited supplementary text files include bismark methylation counts (e.g.: DOM_RRBS_M15_P1_meth.txt.gz) and differential methylation analysis (e.g.: DMR_DOMvsSPRET_female.txt) and allele specific methylation analysis outputs (e.g.: ASM_males) for each comparison

organism: Mus musculus domesticus

source_name: Mus domesticus e17.5 placenta

extract_protocol:
Pregnant females (n=5/type of pregnancy) were euthanized by cervical dislocation between 10:00 and 11:00 AM on embryonic day 17-18 (e17.5) and the maternal brain was extracted. Embryos were separated from placentas and placentas were weighed, and the maternally-derived decidual layer was removed as previously described (Qu et al. 2014) and discarded.  Only fetally-derived placental tissue was used in this study. All tissues were transferred immediately to RNAlater (Thermo Fisher, USA), kept at 4°C overnight to allow RNAlater perfusion, and stored at -20°C until DNA and RNA extraction.
library preparation and sequencing were performed by the sequencing facility (NXT-Dx, Ghent, Belgium).
Sequencing was performed on the Illumina HiSeq 4000 platform, producing >13 million 50bp paired-end reads per sample.

tag: pregnancy type code

value: DOM

tag: placenta weight (g)

tag: embryo weight (g)

tag: placenta (percent embryo weight)

tag: embryo sex

value: f

tag: # males in litter

tag: # females in litter

tag: litter size

tag: proportion males in litter

value: placenta

tag: molecule subtype

value: bisulfite converted DNA


title: Mouse Islet 18 [exon-level]

status: Public on Nov 09 2020

type: RNA

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

country: USA

institute: University of Wisconsin-Madisin

hyb_protocol: Sample set 01 hybridized to Mouse Exon 1.0 ST arrays at 45°C for 16 hrs O/N following all procedures outlined in the GeneChip WT Terminal Labeling and Hybridization User Manual ( P/N 702808 Rev.6)  for Mouse Exon 1.0 ST Arrays

scan_protocol: GeneChips post processed on the AFX Fluidics 450 Station according to all AFX protocols  and procedures defined for the Mouse Exon 1.0 ST Array (FS450 _0001) as outlined  GeneChip Expression Wash,Stain and Scan user Manual (P/N 702731 rev.3)  GC scanned on the GC3000 G7 Scanner (S/N 50205130).

data_processing:
Raw probe cell intesity data was analyzed at both the gene- and exon-level using the Robust Multichip Analysis (RMA) algorithm within the Affymetrix Expression Console 1.3 software package. Data extracted and processed using Affymetrix Command Console version 3.2.4.1515W.
affymetrix-algorithm-name = rma-exon-full : dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.0.20

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: KO High Fat Diet

label_protocol: Ambion GeneChip WT Expression kit ( Lot#4440536) used for labeling. Targeted 200ng RNA in-put for each sample. All protocols and procedures followed as outlined in the Ambion WT Expression Kit manual (Manual P/N 4425209 Rev. D ). All samples carried through to 16 hour IVT O/N reaction. Upon completion of IVT reactions, samples cleaned up according to the protocol and procedures outlined in the Ambion WT Expression manual and quantified on the NanoDrop  Ten ug cRNA used for template input for round 2 of ss cDNA synthesis  Round two ss cDNA samples purified according to the protocol and procedures outlined in the Ambion WT manual and quantified on the NanoDrop. Samples set up for fragmentation with a 5.5ug template in-put.  Samples fragmented with a 5.5ug template in-put, upon completion of fragmentation 45ul transferred to new 0.2ml tube for end-terminus labeling, the remaining vol. to be used for Agilent  Fragmented cDNA samples stored at -20°C  1ul used for analysis on the Agilent RNA Nano chip – tested samples look similar and within the recommended nt range  All samples end-terminus labeled.

growth_protocol: Pancreatic islets were isolated from 37-40-week-old experimental mice (WT or GazKO; control-or HFD-fed;  N=5 per  group)  using  a  collagenase  digestion  procedure  previously  described4.  A  stereomicroscope was  used  to  hand-pick  islets  from  contaminating  acinar  tissue  into  a  microfuge  tubecontaining  1  ml phosphate-buffered saline (PBS) and washed one additional time in PBS, with pulse centrifugation used to pellet the islets.

extract_protocol: The PBS was aspirated, and 200 μl RLT buffer (Qiagen) added. Islets were lysed using a plastic micropestle homogenizer and RNA purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s directions. RNA quality was assessed by electrophoresis using a Eukaryote Total RNA Pico cartridge and Bioanalyzer 2100 instrument (Agilent). The minimum RNA Integrity Score (RIN) of samples subject to microarray analysis was 7.40, with most samples having RIN scores of 8.0 or above.

tag: age

value: 6 months

tag: Sex

value: male

tag: genotype

value: Gaz KO

tag: diet

value: High Fat

tag: cell type

value: Pancreatic islets


title: Mus domesticus e17.5 placenta [DOM_M21_P2]

type: SRA

library_source: genomic

molecule: genomic DNA

value: m

tag: tissue


title: Mus domesticus e17.5 placenta [DOM_M18_P3]


title: Mouse Islet 15 [exon-level]

source_name: WT Control Diet

value: WT

value: Control


title: Mus domesticus e17.5 placenta [DOM_M8_P1]


title: T70

city: Beijing

first: Chen

last: Wu

address: 17 Panjiayuan Nanli, Chaoyang District

country: China

institute: Cancer Hospital, Chinese Academy of Medical Sciences

description:
S114
ACGEJ123pairs_gene_expression_hg19.txt

library_source: transcriptomic

data_processing:
We used HISAT2 (v2.1.0) to align RNA sequence reads to the UCSC hg19 human genome and then used StringTie (v1.3.3b) to re-assemble transcriptome and quantify the expression level of each gene in each sample. The assembly process was guided by the reference annotations from GENCODE (v19). Gene expression levels were quantified by Transcript per Million (TPM).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ACGEJ123pairs_gene_expression_hg19.txt: Tab-delimited text file containing the expression abundance (TPM) of each gene in each sample.

organism: Homo sapiens

source_name: Tumor tissue sample

extract_protocol:
Total RNA were extracted from tissue samples using the AllPrep DNA/RNA Kit (Qiagen).
RNA degradation and contamination were monitored on 1% agarose gels. RNA concentration was measured by Qubit® RNA Assay Kit in Qubit® 2.0. RNA library preparation used NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina and 3 nanograms RNA per sample as the initial materials. Ribosomal RNA was removed using Epicentre Ribo-ZeroTM Gold Kits. Library fragments were purified using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China).

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

tag: patient

tag: population

value: Chinese


title: T72

description:
S115
ACGEJ123pairs_gene_expression_hg19.txt


title: Mus domesticus e17.5 placenta [DOM_M21_P4]

tag: pregnancy type code

tag: placenta weight (g)


title: Mouse Islet 14 [exon-level]


title: Mus domesticus e17.5 placenta [DOM_M16_P2]

tag: embryo weight (g)

tag: placenta (percent embryo weight)


title: P7_Ctx__Qk_KO.rep3

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

data_processing:
Basecalls performed using Torrent Suite version 4.0.2
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d
Genome_build: mm10
Supplementary_files_format_and_content: Expression values for refseq gene models (GRCm38.p4) were calcurated with RSEM (ver. 1.3.0).

molecule: polyA RNA

source_name: P7 mouse cerebral cortex

extract_protocol:
Total RNA from cerebral cortical regions of brains or neuronal stem cells were extracted using Rneasy Plus Midi kit (Qiagen) according to the manufacturer’s instructions.
Libraries were prepared according to Life Techonology's instructions accompanying the Ion AB Library Builder™ System and Library Builder. Briefly, total RNA was treated with Dynabeads® mRNA DIRECT™ Microkit to prepare PolyA-selected messenger RNA. RNA libraries were then prepared using the Life Techonology Ion Total RNA-Seq Kit for the AB Library Builder™ System and Library Builder. High-throughput sequencing was performed using the Ion Proton System. Sfpq mRNA level was down-regulated less than 10% in Neuro-2a treated with Sfpq-siRNA comparing those of Luc-siRNA.

tag: strain

value: cerebral cortex of brain

value: postnatal day 7


title: Mus domesticus e17.5 placenta [DOM_M18_P4]

tag: embryo sex

tag: # males in litter

tag: # females in litter


title: T68

description:
S112
ACGEJ123pairs_gene_expression_hg19.txt


title: Mouse Islet 13 [exon-level]

source_name: KO Control Diet


title: Mus domesticus e17.5 placenta [DOM_M16_P1]

tag: litter size

tag: proportion males in litter

tag: molecule subtype


title: Mus domesticus e17.5 placenta [DOM_M15_P2]


title: T67

description:
S111
ACGEJ123pairs_gene_expression_hg19.txt


title: T65

description:
S110
ACGEJ123pairs_gene_expression_hg19.txt


title: Mus domesticus e17.5 placenta [DOM_M15_P1]


title: Mouse Islet 12 [exon-level]

tag: age

tag: Sex

tag: genotype


title: Mouse Islet 11 [exon-level]

tag: diet

tag: cell type


title: T63

description:
S109
ACGEJ123pairs_gene_expression_hg19.txt

tag: tissue

tag: patient

tag: population


title: Ck127: genomic DNA from normal colon mucosa

type: genomic

city: Basel

first: Faiza

last: Noreen

address: Mattenstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised toIllumina Infinium HumanMethylation850 Beadchip using standard Illumina protocol

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

data_processing: Average Beta, normalized using minfi

label: cy3 and cy5

source_name: colon

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

value: colon

tag: time point

tag: gender

value: female

tag: polyp

value: no

tag: clonic location

value: distal

tag: disease state

value: normal

tag: age (years)

tag: aspirin

value: longterm

tag: bmi

tag: batch


title: pCk127: genomic DNA from normal colon mucosa


title: Ak127: genomic DNA from normal colon mucosa

value: proximal


title: T7

description:
S113
ACGEJ123pairs_gene_expression_hg19.txt


title: pAk127: genomic DNA from normal colon mucosa


title: T59

description:
S108
ACGEJ123pairs_gene_expression_hg19.txt


title: T58

description:
S107
ACGEJ123pairs_gene_expression_hg19.txt


title: pCk113: genomic DNA from normal colon mucosa

value: high


title: pAk113: genomic DNA from normal colon mucosa


title: Mouse Islet 10 [exon-level]

tag: age

value: 6 months

value: male

value: Gaz KO

value: High Fat


title: pCk101: genomic DNA from normal colon mucosa


title: Mouse Islet 8 [exon-level]

source_name: WT High Fat Diet

tag: Sex

value: WT

value: Pancreatic islets


title: Ck113: genomic DNA from normal colon mucosa


title: Mouse Islet 7 [exon-level]

tag: genotype


title: Ck101: genomic DNA from normal colon mucosa

value: nonuser


title: T57

description:
S106
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

value: Chinese


title: Mouse Islet 9 [exon-level]

tag: diet


title: pAk101: genomic DNA from normal colon mucosa

value: colon


title: T55

description:
S105
ACGEJ123pairs_gene_expression_hg19.txt


title: Ak113: genomic DNA from normal colon mucosa

value: female


title: pCk097: genomic DNA from normal colon mucosa

value: yes


title: pAk097: genomic DNA from normal colon mucosa


title: Ak101: genomic DNA from normal colon mucosa

value: no


title: Ck097: genomic DNA from normal colon mucosa

value: distal

value: normal


title: T51

description:
S103
ACGEJ123pairs_gene_expression_hg19.txt


title: Mouse Islet 5 [exon-level]

value: Control

tag: cell type


title: inv(16):KitD816Y L-GMP 1

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

country: Denmark

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

description: Granulocyte-Monocyte Progenitor (GMP)

hyb_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin using the Affymetrix/ThermoFisher Fluidics Station 450, and the arrays were scanned in the Affymetrix GeneArray 3000 7G scanner to generate fluorescent images

scan_protocol: Cell intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC; Affymetrix).

data_processing: For normalization and batch correction of murine microarray data, microarray CEL files of our own sorted inv(16)/KITD816Y AML GMP replicates were normalized together with 21 public available microarray CEL files of normal murine BM populations (GSE15907). Briefly, we applied the Robust Multichip Average (RMA) method for normalization of all microarray CEL files partitioned by origins, and applied the empirical Bayes method ?Combat? in an R package to eliminate potential lab batch effects. Batches were defined as the study number, while the covariate was defined as the type of cell population.

source_name: Bone marrow

label_protocol: Purified RNA was analyzed on expression arrays. RNA was processed using Mouse Gene 1.0 ST Reagent Kit. RNA was reverse transcribed and used for cRNA synthesis, labelling and hybridization with Mouse Gene 1.0 ST Array (ThermoFisher) according to the manufacturer’s protocol.

growth_protocol: Untreated fresh BM of sorted GMPs

extract_protocol: RNA was extracted from 200000 sorted GMPs using miRNeasy KIT (Qiagen) according to the manufacturer's instructions

value: granulocyte macrophage progenitor (GMP) cells

tag: cell markers

value: Lin- Sca1- ckit+ CD41- FcgR+ CD150-


title: Mouse Islet 6 [exon-level]

value: 6 months

value: male


title: Ak097: genomic DNA from normal colon mucosa

tag: tissue

value: proximal

value: longterm

value: high


title: pCk016: genomic DNA from normal colon mucosa

value: nonuser


title: Mouse Islet 4 [exon-level]

value: WT

value: Pancreatic islets


title: pAk016: genomic DNA from normal colon mucosa

value: colon


title: Ck016: genomic DNA from normal colon mucosa

value: female


title: Mouse Islet 3 [exon-level]

value: Gaz KO


title: Ck015: genomic DNA from normal colon mucosa

value: no


title: Ak015: genomic DNA from normal colon mucosa


title: T40

description:
S99
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

tag: patient

tag: population

value: Chinese


title: Mouse Islet 1 [exon-level]

value: Control


title: T41

description:
S100
ACGEJ123pairs_gene_expression_hg19.txt


title: pCk015: genomic DNA from normal colon mucosa

tag: time point

tag: gender

value: yes

value: distal

value: normal


title: T39

description:
S98
ACGEJ123pairs_gene_expression_hg19.txt


title: pAk013: genomic DNA from normal colon mucosa

tag: polyp

tag: clonic location


title: T52

description:
S104
ACGEJ123pairs_gene_expression_hg19.txt


title: pCk013: genomic DNA from normal colon mucosa

tag: disease state

tag: age (years)


title: Ck013C: genomic DNA from normal colon mucosa

tag: aspirin

tag: bmi


title: T35

description:
S97
ACGEJ123pairs_gene_expression_hg19.txt


title: Ak013: genomic DNA from normal colon mucosa

tag: batch


title: pC603: genomic DNA from normal colon mucosa


title: T49

description:
S102
ACGEJ123pairs_gene_expression_hg19.txt


title: T346

description:
S96
ACGEJ123pairs_gene_expression_hg19.txt


title: pA603: genomic DNA from normal colon mucosa


title: Mouse Islet 2 [exon-level]

tag: age

value: 6 months

tag: Sex

value: male


title: Ak016: genomic DNA from normal colon mucosa

value: proximal


title: C603: genomic DNA from normal colon mucosa


title: T339

description:
S95
ACGEJ123pairs_gene_expression_hg19.txt


title: A603: genomic DNA from normal colon mucosa


title: pC601: genomic DNA from normal colon mucosa

value: longterm


title: T43

description:
S101
ACGEJ123pairs_gene_expression_hg19.txt


title: 110_GMP

description: Granulocyte-Monocyte Progenitor (GMP)

hyb_protocol: Affymetrix EukGE-WS2v4_450 Hybridization protocol

scan_protocol: Arrays were scanned in the Affymetrix Genearray 2500 scanner to generate flourescent images, as described in Affymetrix GeneChip protocol.

data_processing:
Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA). Each of the newly generated microarray CEL files of our own 5 inv(16) AML patient GMPs were normalized and batch corrected together with our previously published microarray CEL files of 40 normal BM populations essentially as described for the murine microarray data. Each of the 5 AML patient microarray CEL files was normalized individually together with all 40 microarray CEL files of the normal BM populations.
data processing as described in Rapin et al. Blood (2014)

label_protocol: 2.5ug amplified cDNA was fragmentated and labeled using Encore Biotin Module V2 according to manufactures instructions. www.nugeninc.com/nugen/index.cfm/products/pl/target-preparation/encore-biotin-module/

extract_protocol: RNeasy from Qiagen. According to manufaturer protocol.  Followed by amplification with NuGEN's WT Ovation Pico kit. Again according to manufacturer protocol.

tag: diagnosis

value: AML

value: Bone marrow

value: granulocyte macrophage progenitor (GMP)

tag: genotype


title: pA601: genomic DNA from normal colon mucosa

value: colon


title: T337

description:
S94
ACGEJ123pairs_gene_expression_hg19.txt


title: T335

description:
S93
ACGEJ123pairs_gene_expression_hg19.txt


title: C601: genomic DNA from normal colon mucosa

value: female


title: HIF-KD_sorted_3

city: Zurich

first: Lubor

last: Borsig

address: Winterthurerstrasse 190

department: Physiology

institute: University of Zurich

data_processing:
Reads were aligned with the STAR (Dolbin A. et al., 2012) aligner with the additional options (--outFilterMatchNmin 30 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.05 --outFilterMultimapNmax 50)
Expression counts were computed using the Bioconductor package GenomicRanges (Lawrence M., 2013.).
Differential expression was computed using the Edger package (Robinson M. D. et al., 2010).
Genome_build: The mouse genome build and annotation from Ensembl (GRCm38) were used as the reference.
Supplementary_files_format_and_content: raw counts of sequencing reads for the annotated features. formatted as a matrix table, saved as a plain tab-delimited text file

source_name: MC-38 cell line, orthotopic mouse tumor

extract_protocol:
RNA was isolated using RNeasy Plus Mini kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transduction

value: yes, pLKO.1-puro

tag: in vivo passaging

value: MC-38 cell line derived orthotopic tumor

tag: knockdown

value: HIF-1 alpha


title: 92_GMP

description: Granulocyte-Monocyte Progenitor (GMP)

tag: tissue

tag: cell type

tag: cell markers


title: A601: genomic DNA from normal colon mucosa

tag: time point

tag: gender

tag: polyp

value: no


title: T333

description:
S92
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

tag: patient

tag: population

value: Chinese


title: pC580: genomic DNA from normal colon mucosa

tag: clonic location

value: distal

tag: disease state

tag: age (years)

tag: aspirin

tag: bmi

value: high


title: pA580: genomic DNA from normal colon mucosa

value: normal

tag: batch


title: C580C: genomic DNA from normal colon mucosa

value: yes

value: nonuser


title: 60_GMP

description: Granulocyte-Monocyte Progenitor (GMP)

tag: diagnosis

tag: genotype


title: 163_CMP

description: Common myeloid Progenitor (CMP)

data_processing:
Cell intesity files (CEL files) were generated in the Genechip Command Console Software (AGCC), (Affymetrix, Santa Clara, CA, USA). Each of the newly generated microarray CEL files of our own 5 inv(16) AML patient GMPs were normalized and batch corrected together with our previously published microarray CEL files of 40 normal BM populations essentially as described for the murine microarray data. Each of the 5 AML patient microarray CEL files was normalized individually together with all 40 microarray CEL files of the normal BM populations.
Data processing as described in Rapin et al. Blood (2014)

growth_protocol: Untreated fresh BM of sorted CMPs

value: Common myeloid Progenitor (CMP)


title: 159_GMP

description: Granulocyte-Monocyte Progenitor (GMP)

value: AML


title: pC392: genomic DNA from normal colon mucosa


title: Mock_sorted_3

tag: transduction

tag: in vivo passaging

tag: knockdown

value: mock


title: pA392: genomic DNA from normal colon mucosa

tag: tissue

value: proximal


title: A580: genomic DNA from normal colon mucosa

value: colon

tag: time point


title: C392: genomic DNA from normal colon mucosa

tag: gender

value: female


title: T332

description:
S91
ACGEJ123pairs_gene_expression_hg19.txt


title: A392: genomic DNA from normal colon mucosa

tag: polyp


title: Mock_sorted_1

value: yes, pLKO.1-puro


title: T329

description:
S88
ACGEJ123pairs_gene_expression_hg19.txt

tag: patient


title: pC271: genomic DNA from normal colon mucosa


title: T330

description:
S89
ACGEJ123pairs_gene_expression_hg19.txt

tag: population


title: HIF-KD_sorted_2

value: MC-38 cell line derived orthotopic tumor


title: pA271: genomic DNA from normal colon mucosa

tag: clonic location


title: A271: genomic DNA from normal colon mucosa

tag: disease state


title: T328

description:
S87
ACGEJ123pairs_gene_expression_hg19.txt


title: pC254: genomic DNA from normal colon mucosa

tag: age (years)

value: longterm


title: HIF-KD_sorted_1

value: no

value: HIF-1 alpha


title: T327

description:
S86
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

value: Chinese


title: pA254: genomic DNA from normal colon mucosa

tag: aspirin


title: T331

description:
S90
ACGEJ123pairs_gene_expression_hg19.txt


title: C254: genomic DNA from normal colon mucosa

value: distal

tag: bmi


title: Mock_sorted_2


title: pC249: genomic DNA from normal colon mucosa

value: normal

tag: batch


title: T323

description:
S84
ACGEJ123pairs_gene_expression_hg19.txt


title: C249: genomic DNA from normal colon mucosa

value: yes


title: T321

description:
S83
ACGEJ123pairs_gene_expression_hg19.txt


title: A249: genomic DNA from normal colon mucosa


title: C271: genomic DNA from normal colon mucosa

value: nonuser

value: high


title: T319

description:
S82
ACGEJ123pairs_gene_expression_hg19.txt


title: pC245: genomic DNA from normal colon mucosa


title: T318

description:
S81
ACGEJ123pairs_gene_expression_hg19.txt


title: A245: genomic DNA from normal colon mucosa


title: C245: genomic DNA from normal colon mucosa


title: pA245: genomic DNA from normal colon mucosa


title: T317

description:
S80
ACGEJ123pairs_gene_expression_hg19.txt


title: pC238: genomic DNA from normal colon mucosa


title: pA238: genomic DNA from normal colon mucosa


title: A254: genomic DNA from normal colon mucosa


title: C238: genomic DNA from normal colon mucosa


title: T316

description:
S79
ACGEJ123pairs_gene_expression_hg19.txt


title: A238: genomic DNA from normal colon mucosa


title: pA249: genomic DNA from normal colon mucosa


title: T325

description:
S85
ACGEJ123pairs_gene_expression_hg19.txt


title: C237: genomic DNA from normal colon mucosa


title: pA237: genomic DNA from normal colon mucosa


title: T313

description:
S76
ACGEJ123pairs_gene_expression_hg19.txt


title: T315

description:
S78
ACGEJ123pairs_gene_expression_hg19.txt


title: T314

description:
S77
ACGEJ123pairs_gene_expression_hg19.txt


title: pC237: genomic DNA from normal colon mucosa


title: HSD2OB-tg 3m 3

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene ST 2.1 were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Wild-type and HSD2^OB-tg mice were housed under standard laboratory conditions at 24°C on a 12:12 h light–dark cycle with free access to standard chow and water. Mice were sacrificed at 3, 6, 12 and 18 m of age for females

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

treatment_protocol: Total RNA was extracted from was extracted from the tibiae and femur of 3, 6, 12 and 18 months old WT and HSD2OB-tg mice. Bone marrow was flushed from the tibia prior to isolation

tag: age

value: 3 months

tag: Sex

value: Female

tag: genotype/variation

value: transgenic


title: WT 3m 2

value: wild-type


title: pA223: genomic DNA from normal colon mucosa

value: colon

value: female

value: proximal


title: HSD2OB-tg 3m 2


title: WT 3m 1


title: WT 3m 3


title: HSD2OB-tg 6m 3

value: 6 months


title: WT 6m 3


title: T312

description:
S75
ACGEJ123pairs_gene_expression_hg19.txt


title: T310

description:
S74
ACGEJ123pairs_gene_expression_hg19.txt


title: A237: genomic DNA from normal colon mucosa

value: no

value: longterm


title: pA191: genomic DNA from normal colon mucosa


title: pC223: genomic DNA from normal colon mucosa


title: C191: genomic DNA from normal colon mucosa


title: HSD2OB-tg 3m 1


title: pC191: genomic DNA from normal colon mucosa


title: WT 6m 1


title: A191: genomic DNA from normal colon mucosa


title: T308

description:
S73
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue


title: pC149: genomic DNA from normal colon mucosa


title: pA149: genomic DNA from normal colon mucosa


title: A223: genomic DNA from normal colon mucosa


title: HSD2OB-tg 6m 2


title: HSD2OB-tg 6m 1


title: WT 12m 3

value: 12 months


title: T306

description:
S72
ACGEJ123pairs_gene_expression_hg19.txt

value: Chinese


title: C149: genomic DNA from normal colon mucosa

value: distal

value: normal


title: T305

description:
S71
ACGEJ123pairs_gene_expression_hg19.txt


title: HSD2OB-tg 12m 3


title: A149: genomic DNA from normal colon mucosa

value: yes

value: nonuser


title: T304

description:
S70
ACGEJ123pairs_gene_expression_hg19.txt


title: pA137: genomic DNA from normal colon mucosa

value: high


title: T301

description:
S69
ACGEJ123pairs_gene_expression_hg19.txt


title: A137: genomic DNA from normal colon mucosa


title: C137: genomic DNA from normal colon mucosa


title: T300

description:
S68
ACGEJ123pairs_gene_expression_hg19.txt


title: HSD2OB-tg 12m 1

value: Female


title: WT 12m 2


title: A136: genomic DNA from normal colon mucosa


title: pC136: genomic DNA from normal colon mucosa


title: pA136: genomic DNA from normal colon mucosa


title: HSD2OB-tg 12m 2

value: transgenic


title: C136: genomic DNA from normal colon mucosa


title: WT 12m 1

value: wild-type


title: T295

description:
S66
ACGEJ123pairs_gene_expression_hg19.txt


title: T297

description:
S67
ACGEJ123pairs_gene_expression_hg19.txt


title: C135: genomic DNA from normal colon mucosa

value: colon


title: pA135: genomic DNA from normal colon mucosa

value: female


title: A135: genomic DNA from normal colon mucosa

value: proximal


title: pC062: genomic DNA from normal colon mucosa


title: pC137: genomic DNA from normal colon mucosa


title: T294

description:
S65
ACGEJ123pairs_gene_expression_hg19.txt


title: HSD2OB-tg 18m 3

value: 18 months


title: T292

description:
S64
ACGEJ123pairs_gene_expression_hg19.txt


title: HSD2OB-tg 18m 2


title: pA062: genomic DNA from normal colon mucosa

value: no


title: C062: genomic DNA from normal colon mucosa

value: longterm


title: WT 18m 2


title: GSC-CW468-Sphere-batch2-1

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

description: Bioprinting_RNAseq_Batch2_Processed_Data.xlsx

data_processing:
Paired-end FASTQ sequencing reads were trimmed using Trim Galore version 0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using cutadapt version 2.3. Transcript quantification was performed using Salmon version 0.13.1 in the quasi-mapping mode from transcripts derived from human Gencode release 30 (GRCh38.12). Salmon “quant” files were converted using Tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) and differential expression analysis was performed using DESeq2 in the R programming language.
Genome_build: human Gencode release 30 (GRCh38.12).
Supplementary_files_format_and_content: Salmon Quant Text file, Excel File containing gene expression (Transcripts per Million) and differential expression analysis

source_name: Patient Derived Glioblastoma Stem Cell

growth_protocol: Xenografted tumors were dissociated using a papain dissociation system according to the manufacturer’s instructions. GSCs were then cultured in Neurobasal medium supplemented with 2% B27, 1% L-glutamine, 1% sodium pyruvate, 1% penicillin/streptomycin, 10 ng/mL basic human fibroblast growth factor (bFGF), and 10 ng/mL human epidermal growth factor (EGF) for at least 6 hours to recover expression of surface antigens. GSC phenotypes were validated by expression of stem cell markers (SOX2 and OLIG2) functional assays of self-renewal (serial neurosphere passage), and tumor propagation using in vivo limiting dilution. THP-1 monocytes were cultured in RPMI 1640 (Gibco) medium supplemented with 10% heat-inactivated fetal bovine serum (FBS, Invitrogen) and 1% penicillin/streptomycin. To obtain monocyte-derived M2 macrophage, THP-1 monocytes were first seeded in 6-well plates at a density of 5 x 105 cells/mL (3 mL/well). Polarization to M2 macrophage was induced by (1) incubating cells in 200 ng/mL phorbol 12-myristate 13-acetate (PMA, Sigma Aldrich) for 48 hours, (2) replacing with THP1 complete medium for 24 hours, and then (3) incubating in 20 ng/mL interleukin 4 (IL4, Peprotech) and 20 ng/mL interleukin 13 (IL13, Peprotech) for 48 hours. hNP1 neural progenitor cells (Neuromics) were cultured on Matrigel coated plates using the complete NBM medium for GSCs. Human astrocytes (ThermoFisher) were cultured with astrocyte medium (ScienCell) supplemented with 1% penicillin/streptomycin. Before printing, GSCs, hNP1s, and astrocytes were digested by Accutase (Stemcell Technology), and macrophages were digested with TrypLE (ThermoFisher). For the 3D tetra-culture samples, the cell suspension solution for the tumor core consisted of 25 x 106 cells/mL GSCs and 12.5 x 10e6 cells/mL macrophages (GSCs:M2=2:1). For the 3D tri-culture samples, the core cell suspension solution consisted of 25 x 10e6 cells/mL GSCs only. The cell suspension solution for the peripheral region for both models consisted of 10 x 106 cells/mL hNP1s and 10 x 10e6 cells/mL astrocytes. All cell suspensions were aliquoted into 0.5ml Eppendorf tubes and stored on ice before use. The prepolymer solution for bioprinting was prepared with 8% (w/v) GelMA, 0.5% (w/v) GMHA, and 0.6% (w/v) lithium phenyl(2,4,6-trimethylbenzoyl)phosphinate (LAP) (Tokyo Chemical Industry). Prepolymer solution was kept at 37 °C in dark before use. Cell suspension was mixed with prepolymer solution at 1:1 ratio immediately before printing to maximize viability.  The two-step bioprinting process utilized a customized light-based 3D printing system. Components of the system included a digital micromirror device (DMD) chip (Texas Instruments), a motion controller (Newport), a light source (Hamamatsu), a printing stage, and a computer with software to coordinate all the other components. The thickness of the printed samples was precisely controlled by the motion controller and the stage. Cell-material mixture was loaded onto the printing stage, and the corresponding digital mask was input onto the DMD chip. Light was turned on for an optimized amount of exposure time (20 seconds for the core and 15 seconds for the periphery). The bioprinted 3D tri-culture/tetra-culture samples were then rinsed with DPBS and cultured in maintenance medium at 37 °C with 5% CO2. Maintenance medium was made of 50% of complete NBM medium, 25% of THP1 medium, and 25% of astrocyte medium.

extract_protocol: Total RNA of each sample was extracted using Direct-zol RNA MiniPrep Kit (Zymo) and immediately stored at −80 °C.

treatment_protocol: EGFP labeled GSCs and mCherry labeled THP1s were isolated from 3D printed tri-culture and tetra-culture samples using flow cytometry (BD FACSAria II). Cells isolated from 3D and sphere cultured cells were treated with TRIzol reagent (Life Technologies) before RNA extraction.

tag: cell type

value: Patient Derived Glioblastoma Stem Cell

tag: growth protocol

value: Patient Derived GSCs grown in traditional sphere cell culture


title: WT 6m 2

value: 6 months


title: WT 18m 3


title: A062: genomic DNA from normal colon mucosa

tag: tissue


title: HSD2OB-tg 18m 1


title: C056: genomic DNA from normal colon mucosa

tag: time point

value: distal


title: T288

description:
S61
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

value: Chinese


title: Macrophage-THP1-3D-2

description: Bioprinting_RNAseq_Batch1_Processed_Data.xlsx

source_name: THP1-derived macrophage

value: THP1-derived macrophage

value: Macrophages derived from THP1 cells and  grown in a 3D bioprinted tetra-culture model


title: WT 18m 1

value: Female


title: pC056: genomic DNA from normal colon mucosa

tag: gender

value: normal

value: nonuser

value: high


title: T287

description:
S60
ACGEJ123pairs_gene_expression_hg19.txt


title: T285

description:
S59
ACGEJ123pairs_gene_expression_hg19.txt


title: pC049: genomic DNA from normal colon mucosa

value: colon

value: female

tag: polyp


title: C049: genomic DNA from normal colon mucosa


title: A049: genomic DNA from normal colon mucosa

value: proximal


title: Macrophage-THP1-2D-1

value: Macrophages derived from THP1 cells and grown in traditional cell culture


title: pA049: genomic DNA from normal colon mucosa

value: no

value: longterm


title: T291

description:
S63
ACGEJ123pairs_gene_expression_hg19.txt

tag: patient


title: GSC-CW468-Tetraculture-2

value: Patient Derived Glioblastoma Stem Cell

value: Patient Derived GSCs grown in a 3D bioprinted tetra-culture model


title: pA044: genomic DNA from normal colon mucosa

value: yes


title: T29

description:
S62
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

tag: population


title: C044: genomic DNA from normal colon mucosa

tag: clonic location

value: distal


title: Macrophage-THP1-3D-1

value: THP1-derived macrophage


title: pC044: genomic DNA from normal colon mucosa

tag: disease state


title: T284

description:
S58
ACGEJ123pairs_gene_expression_hg19.txt

value: Chinese


title: T282

description:
S57
ACGEJ123pairs_gene_expression_hg19.txt


title: A056: genomic DNA from normal colon mucosa

tag: age (years)


title: GSC-CW468-Tetraculture-1


title: GSC-CW468-Sphere-2

value: Patient Derived GSCs grown in traditional sphere cell culture


title: pC037: genomic DNA from normal colon mucosa

value: normal

tag: aspirin


title: T281

description:
S56
ACGEJ123pairs_gene_expression_hg19.txt


title: C037: genomic DNA from normal colon mucosa

value: nonuser

tag: bmi


title: GSC-CW468-Sphere-1

tag: batch


title: T280

description:
S55
ACGEJ123pairs_gene_expression_hg19.txt


title: pC018: genomic DNA from normal colon mucosa

value: high


title: A037: genomic DNA from normal colon mucosa

value: colon


title: pC135: genomic DNA from normal colon mucosa

value: female


title: T279

description:
S54
ACGEJ123pairs_gene_expression_hg19.txt


title: pA018: genomic DNA from normal colon mucosa

value: proximal


title: 11_C11_Mid-4

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

data_processing:
The reads were mapped on human genome hg38 using STAR (v2.5.2b; Dobin et al., 2013).
differential expression was analyzed using DESeq2 (v1.20.0; Love et al., 2014).
Genes represented by less than 3 reads per million were not considered further.
FDR is noted in the text.

growth_protocol: Cell were cultured in DMEM/F12 supplemented with 5%fetal bovine serum and penicillin-streptomycin at 37°C and 5% CO2

extract_protocol:
For RNA extraction, RNA easy mini Kit (Qiagen) were used according to the manufaturer recommandation.
library protocol ribodep stranded RNA

treatment_protocol: Cells were dissociated using Trypsin and resuspended in PBS with 1%BSA at a density of 1.107cells/ml. Mouse primary antibody mVSIG1 (R&D MAB4818) was added at 5µg/ml final concentration for 30’ at RT with agitation. After two washes with PBS cells were again resuspended at 1.107 cells/ml in PBS with 1% BSA. Cells were then incubated with secondary antibodies at 2µg/ml for 30’ with agitation. Two final PBS washes were performed and the cells FACS analyzed or sorted ( Beckman Coulter MoFlo Astrios).

value: CC14 Colon Cancer derived clone

tag: passage

tag: if antibody

value: mVSIG1 (R&D MAB4818)

tag: vsig expression

value: Middle


title: 12_C11_High-4

tag: cell type

value: High


title: T275

description:
S53
ACGEJ123pairs_gene_expression_hg19.txt


title: C018: genomic DNA from normal colon mucosa

value: no

value: longterm


title: A018: genomic DNA from normal colon mucosa


title: Macrophage-THP1-2D-2

tag: growth protocol

value: Macrophages derived from THP1 cells and grown in traditional cell culture


title: pA037: genomic DNA from normal colon mucosa

tag: tissue


title: T274

description:
S52
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue


title: A044: genomic DNA from normal colon mucosa

tag: time point

value: yes


title: pC010: genomic DNA from normal colon mucosa

tag: gender

value: distal


title: 10_C11_Low-4

value: Low


title: pA010: genomic DNA from normal colon mucosa

tag: polyp

value: normal


title: C010: genomic DNA from normal colon mucosa

value: nonuser


title: T272

description:
S51
ACGEJ123pairs_gene_expression_hg19.txt

tag: patient

value: Chinese


title: A010: genomic DNA from normal colon mucosa

value: colon


title: pC005: genomic DNA from normal colon mucosa

value: female


title: 8_C11_High-3


title: T271

description:
S50
ACGEJ123pairs_gene_expression_hg19.txt

tag: population


title: pA005: genomic DNA from normal colon mucosa

tag: clonic location

value: proximal


title: C005: genomic DNA from normal colon mucosa

tag: disease state


title: A005: genomic DNA from normal colon mucosa

tag: age (years)


title: 7_C11_Mid-3

value: CC14 Colon Cancer derived clone


title: T270

description:
S49
ACGEJ123pairs_gene_expression_hg19.txt


title: 6_C11_Low-3

value: mVSIG1 (R&D MAB4818)


title: TA180_18

city: Wuhan

first: Jing

last: Yang

address: No. 1, Gold industrial park, Zhengdian street, Jiangxia district

institute: Wuhan Institute of Biological Products Co., Ltd.

data_processing:
Illumina Casava1.7 software used for basecalling.
The clustering of the index-coded samples was performed on a cBotCluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform (Illumina NovaSeq 6000) and 125 bp/150 bp paired-end reads were generated.
Hisat2 v2.0.5 was used for building index of the GRCh38 (hg19) reference genome, as well as the alignment of paired-end clean reads to the reference genome.
The Conditional Quantile Normalization was applied to gene counts to adjust for GC content and gene length. Genes numbers mapped to each gene were counted by FeatureCounts v1.5.0-p3. Subsequent analyses were based on the normalized values.
Genome_build: GRCh38 (hg19)
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: Venous blood

extract_protocol:
Total RNA was extracted from whole blood samples using TRIzol (Bio Basic Inc.) according to the manufacturer’s instructions, and analyzed using RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) and Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
mRNA sequencing libraries were built using 3 µg RNA and NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations. Poly-T oligo-attached magnetic beads were employed to isolate poly-A RNA. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. After adenylation of 3’ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBotCluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

value: Female

tag: group

value: D180 _NMT65yrs


title: 9_C11_Neg-4

value: Negative


title: T267

description:
S47
ACGEJ123pairs_gene_expression_hg19.txt


title: 4_C11_High-2

value: High


title: 5_C11_Neg-3


title: TA180_26

value: D180 _MT65yrs

tag: bmi


title: TA180_28

value: Male


title: T265

description:
S46
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue


title: TA180_12


title: 2_C11_Low-2


title: TA180_11


title: C223: genomic DNA from normal colon mucosa

value: no

value: distal

tag: aspirin

value: longterm

value: high

tag: batch


title: 3_C11_Mid-2

tag: passage

tag: if antibody

value: Middle


title: 1_C11_Neg-2

tag: cell type

tag: vsig expression


title: input_MAC-T cells infected by inactivated E. coli_rep2

first: Changmin

last: Hu

state: Hubei

address: No.1 Shizishan Street

institute: Huazhong Agricultural University

data_processing:
Library strategy: meRIP-seq
quality controlled by Q30
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
clean reads of input libraries were aligned to reference genome (ARS-UCD1.2) by bowtie2 software
clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Genome_build: bosTau9
Supplementary_files_format_and_content: peak files

organism: Bos taurus

source_name: Bovine mammary epithelial cells (MAC-T cells)

growth_protocol: MAC-T cells were cultured in DME/F12 medium (Hyclone, Tauranga, New Zealand) supplemented with 10% fetal bovine serum (Gibco, New York, United States), and incubated at 37°C in a 5% CO2-humidified incubator. The cells were digested and passaged using 0.25% trypsin-0.02% EDTA.

extract_protocol:
Total RNA was extracted according to commercial reagent manufacturers' instructions (Invitrogen) and RNA isolation procedures.And m6A RNA immunoprecipitation was performed with m6A antibody (Millipore, ABE572) by following the manufacturers instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One replicate was inactived S. aureus/ E. coli treated for 24 hours.

tag: tissue

value: Bovine mammary epithelial

tag: cell line

value: MAC-T

tag: treatment

value: inactivated E. coli

tag: sample type

value: input


title: input_MAC-T cells infected by inactivated E. coli_rep3


title: T261

description:
S43
ACGEJ123pairs_gene_expression_hg19.txt

tag: patient

value: Chinese


title: T263

description:
S44
ACGEJ123pairs_gene_expression_hg19.txt

tag: population


title: T269

description:
S48
ACGEJ123pairs_gene_expression_hg19.txt


title: Exome sequencing C11 clone dirived from CC14

description: clone derived from CC14 culture with lower metastatic potential

data_processing:
Variants were called following GATK best practices v3.6
PCR duplicates were marked using Picard Tools v2.5.0 MarkDuplicates, and  Indel realignment done followed by Picard Tools FixMateInformation
Base quality scores were recalibrated using GATK BaseRecalibrator and BQSR. GATK haplotypecall was then used to produce genotype GVCFs for individual samples
Joint genotyping on gVCF files was done using GATK GenotypeGVCFs producing the variant VCF-file. The variants were then separated as SNPs and INDELs and GATK hard filters were applied with the parameters: --filterExpression "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 for SNPs and --filterExpression "QD < 2.0 || FS > 200.0 || ReadPosRankSum < -20.0" for INDELs
Genome_build: UCSC hg19
Supplementary_files_format_and_content: excel file containing variants

source_name: primary colon cancer cell

growth_protocol: All primary cells and derived clones were cultured in DMEM/F12, supplemented with 5% FBS and 1% penicillin-streptomycin.

extract_protocol:
DNA extraction was performed with DNeasy Blood & Tissue Kit (Qiagen Cat No.69504)
Agilent SureSelect Human All Exon V4

value: clone drived from primary culture CC14


title: TA180_14

tag: gender

value: Female

tag: time point


title: input_MAC-T cells infected by inactivated E. coli_rep1


title: T260

description:
S42
ACGEJ123pairs_gene_expression_hg19.txt


title: TA180_16

value: D180 _NMT65yrs


title: input_MAC-T cells infected by inactivated S. aureus_rep3

value: inactivated S. aureus


title: T26

description:
S41
ACGEJ123pairs_gene_expression_hg19.txt


title: TA180_29


title: Exome sequencing E3 clone derived from CC14

description: clone derived from CC14 culture with higher metastatic potential

value: clone derived from primary  culture CC14


title: TA180_07


title: input_MAC-T cells infected by inactivated S. aureus_rep2


title: TA180_25

value: Male

value: D180 _MT65yrs


title: T264

description:
S45
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue


title: Exome sequencing CC14 primary colon cancer cell line

description: primary colon cancer culture with medium metastatic potential

value: primary culture from Colon cancer patient


title: T258

description:
S40
ACGEJ123pairs_gene_expression_hg19.txt


title: input_MAC-T cells infected by inactivated S. aureus_rep1


title: TA180_15


title: P3E3M3C

description: condition 3= E3GFP facs sorted from coColture with C11 shVSIG3

data_processing:
The reads were mapped on human genome hg38 using STAR
Differential expression was analyzed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: excel file compiling the raw / normalized counts of each samples + DEG analysis values

source_name: clone FACS sorted for gfp previously cocoltured for 48h with different cells

extract_protocol:
RNA extraction was perfomed using Trizol following manufacturer’s instructions
ribosomal-RNA depleted libraries from 3 independent experiments were sequenced on the Illumina Hiseq 4000 platform as single-end 50bp reads.

tag: condition

value: E3GFP SORTED FROM  Cocolture WITH C11shVSIG1 WHITE


title: P3E3M3B

description: condition 3= E3GFP facs sorted from coColture with C11 shVSIG2


title: TA180_54

tag: group


title: TA180_04

tag: bmi


title: input_MAC-T cells_rep3

value: LB broth


title: P3E3M3A

description: condition 3= E3GFP facs sorted from coColture with C11 shVSIG1


title: input_MAC-T cells_rep2


title: T252

description:
S38
ACGEJ123pairs_gene_expression_hg19.txt


title: TA180_45


title: input_MAC-T cells_rep1


title: T250

description:
S37
ACGEJ123pairs_gene_expression_hg19.txt


title: P3E3M2C

description: condition 2= E3GFP facs sorted from coColture with C11 plko

value: E3GFP SORTED FROM Cocolture WITH C11 WHITE


title: TA28_54

value: D28 _NMT65yrs


title: T249

description:
S36
ACGEJ123pairs_gene_expression_hg19.txt


title: meRIP-seq_MAC-T cells infected by inactivated E. coli_rep3

value: Bovine mammary epithelial

value: MAC-T

value: meRIP-seq


title: P3E3M2B


title: T247

description:
S35
ACGEJ123pairs_gene_expression_hg19.txt

value: Chinese


title: TA28_53

value: D28 _MT65yrs


title: meRIP-seq_MAC-T cells infected by inactivated E. coli_rep2

value: inactivated E. coli


title: T256

description:
S39
ACGEJ123pairs_gene_expression_hg19.txt


title: meRIP-seq_MAC-T cells infected by inactivated E. coli_rep1


title: P3E3M1C

description: control of the experiment (E3GFP FACS sorted from coColture with E3 white cells).

value: E3GFP SORTED FROM Cocolture WITH E3 WHITE


title: T245

description:
S34
ACGEJ123pairs_gene_expression_hg19.txt


title: TA28_32

value: Female


title: TA180_53


title: TA28_45


title: T244

description:
S33
ACGEJ123pairs_gene_expression_hg19.txt


title: TA28_29


title: meRIP-seq_MAC-T cells infected by inactivated S. aureus_rep3

value: inactivated S. aureus


title: T24

description:
S32
ACGEJ123pairs_gene_expression_hg19.txt


title: meRIP-seq_MAC-T cells infected by inactivated S. aureus_rep2


title: P3E3M1A


title: meRIP-seq_MAC-T cells infected by inactivated S. aureus_rep1


title: pAk015: genomic DNA from normal colon mucosa

value: colon

value: female

tag: polyp

value: yes

tag: clonic location

value: proximal

tag: disease state

value: normal

tag: age (years)

tag: aspirin

value: longterm

value: high


title: meRIP-seq_MAC-T cells_rep3

value: LB broth


title: TA28_26


title: E3pTW_2

description: clone with high metastatic potential infected with Pween (control lentivirus)

data_processing:
The reads were mapped on human genome hg38 using STAR
Differential expression was analyzed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values(cpm = count per millions) for each Sample

source_name: primary colon cancer cell lentiviral infected

tag: cell type

value: clone derived from primary colon cancer cell culture

value: cells infected with lentivirus


title: TA28_25

value: Male


title: TA28_28

value: D28 _NMT65yrs


title: T212

description:
S30
ACGEJ123pairs_gene_expression_hg19.txt

tag: tissue

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

value: Chinese


title: P3E3M2A

value: E3GFP SORTED FROM Cocolture WITH C11 WHITE


title: P3E3M1B

value: E3GFP SORTED FROM Cocolture WITH E3 WHITE


title: E3pTW_1


title: meRIP-seq_MAC-T cells_rep2

value: Bovine mammary epithelial

tag: cell line

value: MAC-T

value: meRIP-seq


title: T167

description:
S28
ACGEJ123pairs_gene_expression_hg19.txt


title: TA28_18

value: Female


title: meRIP-seq_MAC-T cells_rep1

tag: treatment


title: T166

description:
S27
ACGEJ123pairs_gene_expression_hg19.txt


title: TA28_16


title: T18

description:
S29
ACGEJ123pairs_gene_expression_hg19.txt


title: E3VSIG1V2_3

description: clone with high metastatic potential lentiviral infected with VSIG1 cDNA


title: E3VSIG1V2_2


title: T236

description:
S31
ACGEJ123pairs_gene_expression_hg19.txt


title: T163

description:
S26
ACGEJ123pairs_gene_expression_hg19.txt


title: E3VSIG1V2_1


title: T162

description:
S25
ACGEJ123pairs_gene_expression_hg19.txt


title: TA28_14

value: D28 _MT65yrs


title: pA056: genomic DNA from normal colon mucosa

value: colon

value: female

value: no

value: proximal

value: normal

value: nonuser

tag: batch


title: T157

description:
S24
ACGEJ123pairs_gene_expression_hg19.txt

tag: patient


title: E3pTW_3

value: clone derived from primary colon cancer cell culture

value: cells infected with lentivirus


title: E3VSIG1V1_2


title: TA28_07

value: D28 _NMT65yrs


title: T156

description:
S23
ACGEJ123pairs_gene_expression_hg19.txt

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

tag: population

value: Chinese


title: T153

description:
S22
ACGEJ123pairs_gene_expression_hg19.txt


title: E3VSIG1V1_1


title: TA28_11

tag: gender

value: Male


title: T148

description:
S21
ACGEJ123pairs_gene_expression_hg19.txt


title: C11shVSIG95_2

description: clone with low metastatic potential knocked down for VSIG1 gene

data_processing:
The reads were mapped on human genome hg38 using STAR
Differential expression was analyzed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values(cpm = count per millions) for each Sample …

value: Patient-derived Colon cancer cells

tag: passage


title: Mouse Islet 17 [KH34229_gene-level]

data_processing: Raw probe cell intesity data was analyzed at both the gene- and exon-level using the Robust Multichip Analysis (RMA) algorithm within the Affymetrix Expression Console 1.3 software package. Data extracted and processed using Affymetrix Command Console version 3.2.4.1515W.

tag: age

value: 6 months

tag: Sex

value: male

tag: genotype

value: Gaz KO

tag: diet

value: High Fat

value: Pancreatic islets


title: T145

description:
S20
ACGEJ123pairs_gene_expression_hg19.txt

data_processing:
We used HISAT2 (v2.1.0) to align RNA sequence reads to the UCSC hg19 human genome and then used StringTie (v1.3.3b) to re-assemble transcriptome and quantify the expression level of each gene in each sample. The assembly process was guided by the reference annotations from GENCODE (v19). Gene expression levels were quantified by Transcript per Million (TPM).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ACGEJ123pairs_gene_expression_hg19.txt: Tab-delimited text file containing the expression abundance (TPM) of each gene in each sample.


title: C11shVSIG95_3


title: TA28_15

value: Female

tag: time point

tag: group

value: D28 _MT65yrs

tag: bmi


title: TA28_04


title: TA28_12


title: E3VSIG1V1_3


title: TA03_54

value: D3 _NMT65yrs


title: T142

description:
S19
ACGEJ123pairs_gene_expression_hg19.txt


title: Mouse Islet 18 [KH34230_gene-level]


title: C11shVSIG95_1


title: C11pLKO_3

description: clone with low metastastic potential infected with control lentivirus (PLKO)


title: TA03_45

value: D3 _MT65yrs


title: TA03_53


title: T141

description:
S18
ACGEJ123pairs_gene_expression_hg19.txt


title: C11pLKO_2


title: TA03_32


title: T140

description:
S17
ACGEJ123pairs_gene_expression_hg19.txt


title: C11pLKO_1


title: TA03_29


title: Mouse Islet 16 [WH33896_gene-level]

value: WT


title: F3Z_2

description: clone with low metastatic potential

value: clone derived from primary colon cancer cell culture


title: F3Z_3

description: clone with low metastatic potential


title: T133

description:
S15
ACGEJ123pairs_gene_expression_hg19.txt


title: TA03_26


title: F3Z_1

description: clone with low metastatic potential


title: TA03_25


title: T130

description:
S13
ACGEJ123pairs_gene_expression_hg19.txt


title: TA03_28


title: E6Z_3

description: clone with high metastatic potential


title: Mouse Islet 14 [WL32833_gene-level]

value: Control


title: Mouse Islet 15 [WL33212_gene-level]


title: E6Z_2

description: clone with high metastatic potential


title: T13

description:
S12
ACGEJ123pairs_gene_expression_hg19.txt


title: T131

description:
S14
ACGEJ123pairs_gene_expression_hg19.txt


title: Mouse Islet 13 [KL32832_gene-level]


title: Mouse Islet 12 [KL32825_gene-level]


title: Mouse Islet 11 [KH32612_gene-level]


title: Mouse Islet 10 [KH32609_gene-level]


title: Mouse Islet 7 [WH30718_gene-level]


title: Mouse Islet 6 [WL30656_gene-level]


title: TA03_15


title: Mouse Islet 9 [WH30720_gene-level]


title: E6Z_1

description: clone with high metastatic potential


title: Mouse Islet 8 [WH30719_gene-level]


title: B2Z_CTRL_3

description: clone with medium metastatic potential


title: T126

description:
S10
ACGEJ123pairs_gene_expression_hg19.txt


title: T125

description:
S9
ACGEJ123pairs_gene_expression_hg19.txt


title: TA03_14


title: Mouse Islet 3 [KL29172_gene-level]


title: Mouse Islet 2 [KL28846_gene-level]


title: B2Z_CTRL_2

description: clone with medium metastatic potential


title: Mouse Islet 1 [KL28845_gene-level]


title: TA03_18


title: TA03_16


title: T128

description:
S11
ACGEJ123pairs_gene_expression_hg19.txt


title: T115

description:
S8
ACGEJ123pairs_gene_expression_hg19.txt


title: Mouse Islet 5 [WL30651_gene-level]


title: TA03_12


title: TA03_11


title: T112

description:
S7
ACGEJ123pairs_gene_expression_hg19.txt


title: E3_3

description: clone with high meteastatic potential compared to the parental primary culture


title: Mouse Islet 4 [WL30650_gene-level]


title: T11

description:
S6
ACGEJ123pairs_gene_expression_hg19.txt


title: E3_2


title: TRAMP-C1 cells with HFD-gWAT [B4]

city: Ciudad Autónoma de Buenos Aires

first: Cintia

middle: Lorena

last: Massillo

state: Buenos Aires

address: Vuelta de Obligado 2490

country: Argentina

institute: Instituto de Biología y Medicina Experimental

description: co-culture medium between TRAMP-C1 cells with HFD-gWAT

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C

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

data_processing:
Data were processed using pd.mirna.4.0 and limma packages in R/Bioconductor environment. Background correction, normalization and gene level expreession were calcualted with RMA .
probe group file: Mm_miRNA-4_0-st-v1.txt
meta-probeset file: Mm_miRNA-4_0-st-v1.GRCm38.txt

source_name: TRAMP-C1 cells with HFD-gWAT

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

growth_protocol: TRAMP-C1 cells were co-cultured in 24-transwell plates with gWAT obtained from CD or HFD C57BL/6J mice

extract_protocol: RNA from co-culture medium was isolated with NucleoSpin® miRNA columns.

treatment_protocol: Culture medium from co-cultures was collected for RNA isolation followed by miRNA microarrays hybridization

tag: strain background

value: 4 weeks

value: TRAMP C1 cells

tag: co-cultured with

value: gWAT obtained from HFD C57BL/6J

value: wild-type


title: T108

description:
S5
ACGEJ123pairs_gene_expression_hg19.txt

tag: tissue

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

value: Chinese


title: TA03_04

value: Male


title: E3_1

tag: cell type

value: Patient-derived Colon cancer cells


title: T107

description:
S4
ACGEJ123pairs_gene_expression_hg19.txt


title: TA00_54

value: D0 _NMT65yrs


title: TA00_53

value: D0 _MT65yrs


title: 10x, abdomen, sample 4

city: Boston

first: Yifang

last: Liu

state: MA

address: 77 Avenue Louis Pasteur, NRB 336

institute: Harvard Medical School

description:
T1
processed data file: 2020-09-05_matrix_10x_3_4.csv.gz
processed data file: 2020-09-05_metadata_10x_3_4.csv.gz

data_processing:
We used cellranger count pipeline (version 3.1.0) to analyze the demultiplexed FASTQ data and generated the single cell count matrix, once for each sample. We aligned the reads to a custom “pre-mRNA” reference which was generated as described by 10X Genomics based on FlyBase R6.29.
We applied SoupX (version 0.3.1) (Young et al., 2020) to directly correct the count matrix from cellranger with fixed contamination value equals 0.45 for each sample.
We filtered the cells beyond UMI counts ± 2-fold SD of the average total sample counts (log10) after SoupX, which were regarded as doublets or dead cells in droplet.
The quality filtered datasets were combined into a single Seurat (version 3.1.2) object (Stuart et al., 2019) and integrated using Harmony (version 1.0) (Korsunsky et al., 2019) with default analysis workflow and parameters. FindClusters function in Seurat was applied to identify cell clusters with a resolution = 0.4
Genome_build: Drosophila, FlyBase release r6.29
Supplementary_files_format_and_content: 2020-09-05_matrix_10x_3_4.csv.gz: A gzipped CSV gene x cell matrix of UMI counts. 2020-09-05_metadata_10x_3_4.csv.gz: a gzipped CSV of cells x metadata . The metadata file includes the UMAP coordinates for each cell. UMAP (Uniform Manifold Approximation and Projection) is a dimension reduction technique.
Supplementary_files_format_and_content: 2020-09-05_supplementary_file_10x_3_4.xlsx: includes cell ID/barcode and associated GSM and raw file name.

organism: Drosophila melanogaster

source_name: abdomen

growth_protocol: Fly strains of the genotypes w1118; UAS-2xEGFP/+ ; PromE-GAl4, tub-Gal80ts/+ and w1118; UAS-Tsc1/2/+ ; PromE-GAl4, tub-Gal80ts/+ were routinely kept at 18 °C on standard lab food composed of 15g yeast, 8.6g soy flour, 63g corn flour, 5g agar, 5g malt, 74 ml corn syrup per liter. For temperature dependent induction of EGFP or Tsc1/2, flies were shifted to 29 °C for 4 days, prior to the isolation of nuclei.

extract_protocol:
40 adult male abdomens were quickly dissected in ice cold relaxing buffer (1xPBS, 10 mM EGTA and 10 mM MgCl2) by cutting off the last 2nd and abdominal segment with micro-scissors and hollowing out the abdomen by removing the intestines and male reproductive organs. The dissected tissue was then roughly chopped and transferred to a Dounce homogenizer. The relaxing buffer was replaced with 1.3 ml of nuclei lysis buffer from the Sigma NUC-201 Nuclei isolation kit. Single nuclei suspension from the homogenate was prepared according to the manufacturer’s instruction the in the NUC-201 kit. Briefly, a 1.5 M sucrose cushion was used for generating the gradient for density gradient centrifugation. Density gradient centrifugation was performed in 2 ml tubes using a SW55Ti rotor on a Beckman ultracentrifuge.
Libraries were generated according to 10X genomics v2 protocol.

tag: technology

value: 10x genomics

value: w1118; UAS-Tsc1, UAS-Tsc2/+ ; PromE-GAl4, tub-Gal80ts/+

value: Abdominal cuticle which consists of oenocytes, adipose tissue, and muscle

value: male

tag: developmental stage

value: adult


title: T106

description:
S3
ACGEJ123pairs_gene_expression_hg19.txt

tag: patient


title: C11_2

description: clone with low metastatic potential compared to the parental primary culture

value: clone derived from primary colon cancer cell culture


title: 10x, abdomen, sample 2

description:
G1
processed data file: 2020-09-02_matrix.csv.gz
processed data file: 2020-09-02_metadata.csv.gz

data_processing:
We used cellranger count pipeline (version 3.1.0) to analyze the demultiplexed FASTQ data and generated the single cell count matrix, once for each sample. We aligned the reads to a custom “pre-mRNA” reference which was generated as described by 10X Genomics based on FlyBase R6.29.
We applied SoupX (version 0.3.1) (Young et al., 2020) to directly correct the count matrix from cellranger with fixed contamination value equals 0.45 for each sample.
We filtered the cells beyond UMI counts ± 2-fold SD of the average total sample counts (log10) after SoupX, which were regarded as doublets or dead cells in droplet.
The quality filtered datasets were combined into a single Seurat (version 3.1.2) object (Stuart et al., 2019) and integrated using Harmony (version 1.0) (Korsunsky et al., 2019) with default analysis workflow and parameters. A resolution of 0.1 was chosen as clustering parameter.
Genome_build: Drosophila, FlyBase release r6.29
Supplementary_files_format_and_content: 2020-09-02_matrix.csv.gz: A gzipped CSV gene x cell matrix (13955 x 15280) of UMI counts. 2020-09-02_metadata.csv.gz: a gzipped CSV of cells x metadata (15280 x 4).  The metadata file includes the UMAP coordinates for each cell. UMAP (Uniform Manifold Approximation and Projection) is a dimension reduction technique.
Supplementary_files_format_and_content: 2020-09-04_supplementary_file.xlsx: includes cell ID/barcode and associated GSM and raw file name.

growth_protocol: Fly strains of the genotype w1118; UAS-2xEGFP/+ ; PromE-GAl4, tub-Gal80ts/+ were routinely kept at 18 °C on standard lab food composed of 15g yeast, 8.6g soy flour, 63g corn flour, 5g agar, 5g malt, 74 ml corn syrup per liter. For temperature dependent induction of EGFP, flies were shifted to 29 °C for 4 days, prior to the isolation of nuclei.


title: B2Z_CTRL_1

description: clone with medium metastatic potential


title: TA00_45

value: Female


title: T104

description:
S2
ACGEJ123pairs_gene_expression_hg19.txt

tag: population


title: 10x, abdomen, sample 1

description:
G0
processed data file: 2020-09-02_matrix.csv.gz
processed data file: 2020-09-02_metadata.csv.gz

value: w1118; UAS-2xEGFP/+ ; PromE-GAl4, tub-Gal80ts/+


title: T100

description:
S1
ACGEJ123pairs_gene_expression_hg19.txt


title: TA03_07

tag: gender

value: D3 _NMT65yrs


title: C11_1

tag: passage


title: 29ZB

description: clone with low migratory potential

data_processing:
The reads were mapped on human genome hg38 using STAR
Differential expression was analyzed using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: excel file compiling the normalized counts of each samples + DEG analysis values


title: 29ZC

description: clone with low migratory potential


title: TFAP2A_KD_AR_rep2_RNAseq

city: Shanghai

first: Le

middle: Le

last: Zhang

address: 241 Huaihai West Rd

department: Shanghai chest hospital

institute: Shanghai Jiaotong university

data_processing:
Raw sequencing reads were trimmed for adaptor sequences. For RNA-Seq, clipped reads were aligned to human genome (hg19)  using STAR. For ATAC-Seq, clipped reads were mapped to human genome (hg19) using Bowtie2 (v2.3.3.1) with the parameters: -t -q -N 1 -L 25 -X 2000 –no-mixed –nodiscordant.
MACS2 (v2.1.1.20160309) was used for peak-calling .
Reads of RNAseq were counted by featureCounts with paraments: -p -Q 10 -s 2.
BigWig files of ATAC-Seq was generated by deeptools (v3.3.0).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: lung

growth_protocol: All cells were cultured in RPMI 1640 medium supplemented with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin at 37°C incubator with 5% CO2.

extract_protocol:
RNA-Seq: Total RNA was extracted by trizol, following the standard protocol; ATAC-Seq: Chromatin accessible genomic DNA was got by using Tn5 transposase.
RNA-Seq: 1 ug of total RNA from each sample were used for RNA-seq library preparation according manufacturer's instructions of NEBNext Ultra Directional RNA Library Prep Kit (NEB). ATAC-seq: ATAC-seq library processing was performed following the Omni-ATAC protocol (M Ryan Corces et al. 2017), and Vazyme Tn5 transposase (TD501) was used for transposition.

tag: cell line

tag: cell state

value: TFAP2A knock down Anlotinib resistant


title: 10x, abdomen, sample 3

description:
T0
processed data file: 2020-09-05_matrix_10x_3_4.csv.gz
processed data file: 2020-09-05_metadata_10x_3_4.csv.gz

tag: genotype

tag: Sex


title: C11_3


title: TFAP2A_KD_AR_rep1_RNAseq


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M20_P1]

data_processing:
QC of raw sequencing reads and trimming were performed in Trim Galore! 0.4.5 (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), using a phred score cutoff of 20 and minimum sequence length of 20 after trimming.
A pseudo-hybrid (Mus domesticus X Mus spretus) genome using was generated based on the mouse genome (GRCm38.89) using  the genome preparation tool of the program SNPsplit (Brabraham Bioinformatics). All placenta samples were mapped to the pseudo-hybrid genome.
The RRBS reads were mapped to the converted pseudo-hybrid genome using the Bismark Bisulfite Aligner (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/bismark/).
We filtered the resulting alignment files using SAMtools 0.1.19 (Li et al. 2009), retaining only high quality (MAPQ score 40), uniquely mapped, paired reads for analysis.
We randomly downsampled all alignment files to the same number of reads (~10 million reads) using SAMtools 0.1.19 (Li et al. 2009).
To analyze allele specific methylation (ASM) in hybrids we split the hybrid alignment files with SNPsplit as described above for RNAseq alignments, but using the bisulfite option of the program.
CpG methylation information was extracted from the alignment files using the Bismark-methylation-extractor tool (Babraham Bioinformatics).
Differential methylation (DM) and ASM were analyzed in SeqMonk (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: All samples were mapped to the pseudo-hybrid genome (Mus domesticus X Mus spretus) based on the mouse genome (GRCm38.89)
Supplementary_files_format_and_content: tab-delimited supplementary text files include bismark methylation counts (e.g.: DOM_RRBS_M15_P1_meth.txt.gz) and differential methylation analysis (e.g.: DMR_DOMvsSPRET_female.txt) and allele specific methylation analysis outputs (e.g.: ASM_males) for each comparison

organism: Mus musculus domesticus x Mus spretus

extract_protocol:
Pregnant females (n=5/type of pregnancy) were euthanized by cervical dislocation between 10:00 and 11:00 AM on embryonic day 17-18 (e17.5) and the maternal brain was extracted. Embryos were separated from placentas and placentas were weighed, and the maternally-derived decidual layer was removed as previously described (Qu et al. 2014) and discarded.  Only fetally-derived placental tissue was used in this study. All tissues were transferred immediately to RNAlater (Thermo Fisher, USA), kept at 4°C overnight to allow RNAlater perfusion, and stored at -20°C until DNA and RNA extraction.
library preparation and sequencing were performed by the sequencing facility (NXT-Dx, Ghent, Belgium).
Sequencing was performed on the Illumina HiSeq 4000 platform, producing >13 million 50bp paired-end reads per sample.

tag: pregnancy type code

value: HYBRID

tag: placenta weight (g)

tag: embryo weight (g)

tag: placenta (percent embryo weight)

tag: embryo sex

value: m

tag: # males in litter

tag: # females in litter

tag: litter size

tag: proportion males in litter

value: placenta

tag: molecule subtype

value: bisulfite converted DNA


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M9_P1]

value: f

tag: tissue


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M9_P3]


title: TA00_32

tag: gender

tag: time point

tag: group

value: D0 _NMT65yrs

tag: bmi


title: 29ZA

description: clone with low migratory potential

tag: cell type

value: Patient-derived Colon cancer cells

tag: passage


title: AR_rep2_ATACseq

tag: cell line

tag: cell state

value: Anlotinib resistant


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M19_P2]

tag: pregnancy type code

tag: placenta weight (g)

tag: embryo weight (g)


title: 1ZC

description: clone with high migratory potential


title: 1ZB

description: clone with high migratory potential


title: TA00_29

value: Male


title: AR_rep1_ATACseq


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M19_P1]

tag: placenta (percent embryo weight)

tag: embryo sex

tag: # males in litter


title: WT_rep2_ATACseq

value: wild type


title: 1ZA

description: clone with high migratory potential


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M11_P2]

tag: # females in litter

tag: litter size

tag: proportion males in litter


title: TRAMP-C1 cells with HFD-gWAT [B3]

tag: strain background

tag: age

value: 4 weeks

tag: Sex

value: male

value: TRAMP C1 cells

tag: co-cultured with

value: gWAT obtained from HFD C57BL/6J

tag: genotype

value: wild-type


title: TRAMP-C1 cells with CD-gWAT [A1]

description: co-culture medium between TRAMP-C1 cells with CD-gWAT

source_name: TRAMP-C1 cells with CD-gWAT

tag: cell type

value: gWAT obtained from CD C57BL/6J


title: TRAMP-C1 cells with CD-gWAT [A2]


title: TA00_18

tag: gender

value: Female

tag: time point

tag: group

tag: bmi


title: TA00_26

value: D0 _MT65yrs


title: WT_rep1_ATACseq

tag: cell line

tag: cell state


title: TA00_15


title: TA00_16


title: TA00_25


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M11_P1]

tag: pregnancy type code

value: HYBRID

tag: placenta weight (g)

tag: embryo weight (g)

tag: placenta (percent embryo weight)

tag: embryo sex

tag: tissue

tag: molecule subtype


title: TA00_28


title: shYTHDF2-MeRIP-rep3

city: Hangzhou

first: Jiangfeng

last: Li

address: Qingchun Road 79

institute: First Affiliated Hospital, School of medicine, Zhejiang University

data_processing:
Basecall was performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
The IP and Input reads were aligned to genome reference sequences using HISAT2 software (v2.1.0)
Peaks were called with MeRIP-PF method, and statistically significant MeRIP enriched regions (peaks) were identified for each sample at a p value threshold of 0.05. The MeRIP enriched regions (peaks) were annotated by the overlapped gene using the newest UCSC RefSeq database.
Genome_build: hg19

source_name: prostate cancer cell line

extract_protocol:
The intact mRNA isolated from total RNA samples was chemically fragmented into 100-nucleotide-long fragments by incubation in fragmentation buffer, and then was enriched with m6A antibody
RNA-seq libraries of m6A antibody enriched mRNAs and input mRNAs were prepared using KAPA Stranded mRNA-seq Kit (Illumina) as the following steps: 1) first strand cDNA synthesis; 2) second strand cDNA synthesis; 3) A-tailing; 4) Adapter ligation; 5) PCR amplification; 6) Library purification. QC of the completed libraries was performed with Agilent 2100 Bioanalyzer.

value: prostate cancer cell line

tag: merip antibody

value: Anti-m6A (Abcam, ab208577)


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M10_P2]

value: f

tag: # males in litter

tag: # females in litter

tag: litter size

tag: proportion males in litter

value: placenta

value: bisulfite converted DNA


title: AR_rep2_RNAseq

value: Anlotinib resistant


title: shYTHDF2-MeRIP-rep2

tag: cell type


title: Mus domesticus X Mus spretus e17.5 placenta [HYBRID_M10_P1]

value: m


title: TA00_14

tag: gender

tag: time point

tag: group


title: WT_rep2_RNAseq

tag: cell line

tag: cell state

value: wild type


title: TA00_12

value: Male

tag: bmi


title: MsmegUvrD5minR2

city: Chapel Hill

first: Yanyan

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: replicate 2

data_processing:
adaptor trimming
filtering reads based on length
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: M. smegmatis wild type strain MC2155 (GCA_000015005.1 was downloaded from EnsemblBacteria)
Supplementary_files_format_and_content: bigwig

organism: Mycolicibacterium smegmatis

source_name: Mycolicibacterium smegmatis MC2 155

extract_protocol: We apply XR-seq in Mycolicibacterium smegmatis MC2 155, the cells were were grown with shaking at 37 °C in Luria Broth containing 0.5% (w/vol) Tween 80. Exponentially growing cells were transferred to R250 tissue culture dishes in volumes of 15 mL and were irradiated at an OD600 of ∼0.6 at room temperature with 100 J/m2. dishes were then incubated for 10 min at room temperature, and then cells were harvested, chilled, and maintained on ice. Excision products were then isolated using a modified Hirt procedure that employs shearing to assist cell lysis.  Cells were pelleted at 4 °C, resuspended in ice-cold TE [Tris (10 mM)-EDTA (1 mM) (pH 8.0)], transferred to ice cold Eppendorf tubes, and pelleted at 4 °C, and the supernatants were removed. Pellets were then resuspended with 360 μL of ice-cold TE. Then, 50 μL of room temperature 10% (wt/vol) SDS was added, and cells were lysed by passage through a 26G needle 40 times followed by incubation at room temperature for 20 min. A 120-μL volume of room temperature NaCl (5 M) was then added, tubes were gently mixed, and suspensions were incubated at 4 °C overnight. After centrifuging at high speed for 1 h in a microfuge at 4 °C, supernatants (about 480 μL each) were taken, and each was mixed with and incubated with 12 μL of RNaseA (R4642; Sigma) for 1 h at 37 °C, and then with 12 μL of proteinase K (P8107S; NEB) for 1.5 h at 60 °C. Samples were then extracted twice with phenol/chloroform/isoamyl alcohol and precipitated with ethanol. Samples were immunoprecipitated with an anti-CPD antibody and then ligated to adapters and processed for sequencing (XR-seq). XR-seq libraries were pooled and then sequenced on the HiSeq 2500Rapid Run platform at the UNC-Chapel Hill High-Throughput Sequencing Facility.

tag: strain

tag: treatment

value: UV

tag: genotype

value: uvrD-


title: TA00_11

value: D0 _NMT65yrs


title: MsmegWT5minR2

description: replicate 2


title: shYTHDF2-Input-rep2

value: none (input)


title: shYTHDF2-Input-rep3


title: Mus spretus e17.5 placenta [SPRET_M7_P1]

first: Polly

address: 3401 Watkins Drive

institute: University of California Riverside

organism: Mus spretus

source_name: Mus spretus e17.5 placenta

tag: pregnancy type code

value: SPRET

tag: placenta weight (g)

tag: embryo weight (g)

tag: placenta (percent embryo weight)

tag: embryo sex

tag: tissue


title: Mus spretus e17.5 placenta [SPRET_M6_P3]

tag: # males in litter

tag: # females in litter

tag: litter size

tag: proportion males in litter

tag: molecule subtype


title: TA00_07

tag: gender

value: Female

tag: time point

tag: group


title: Mus spretus e17.5 placenta [SPRET_M6_P2]


title: shYTHDF2-Input-rep1

tag: cell line

tag: cell type

tag: merip antibody


title: TA00_04

tag: bmi


title: shYTHDF2-MeRIP-rep1


title: Mus spretus e17.5 placenta [SPRET_M14_P4]

tag: pregnancy type code

tag: placenta weight (g)


title: GSC-CW468-TetracultureHIPSC-batch2-1

description: Bioprinting_RNAseq_Batch2_Processed_Data.xlsx

data_processing:
Paired-end FASTQ sequencing reads were trimmed using Trim Galore version 0.6.2 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using cutadapt version 2.3. Transcript quantification was performed using Salmon version 0.13.1 in the quasi-mapping mode from transcripts derived from human Gencode release 30 (GRCh38.12). Salmon “quant” files were converted using Tximport (https://bioconductor.org/packages/release/bioc/html/tximport.html) and differential expression analysis was performed using DESeq2 in the R programming language.
Genome_build: human Gencode release 30 (GRCh38.12).
Supplementary_files_format_and_content: Salmon Quant Text file, Excel File containing gene expression (Transcripts per Million) and differential expression analysis

value: Patient Derived Glioblastoma Stem Cell

tag: growth protocol

value: Patient Derived GSCs grown in a 3D bioprinted tetra-culture model containing human induced pluripotent stem cell derived macrophages

tag: batch


title: Mus spretus e17.5 placenta [SPRET_M14_P3]

tag: embryo weight (g)

tag: placenta (percent embryo weight)

tag: embryo sex

tag: tissue


title: shNC-MeRIP-rep2

value: prostate cancer cell line


title: GSC-CW468-TetracultureTHP1-batch2-2

value: Patient Derived GSCs grown in a 3D bioprinted tetra-culture model


title: Mus spretus e17.5 placenta [SPRET_M7_P3]

value: f

tag: # males in litter

tag: # females in litter

tag: litter size

tag: proportion males in litter


title: Mus spretus e17.5 placenta [SPRET_M13_P4]

value: placenta

tag: molecule subtype


title: GSC-CW468-TetracultureTHP1-batch2-1


title: Lit cells2

city: Seattle

first: Vivek

last: Srinivas

state: WA

address: 401 Terry Ave N

institute: ISB

description: Mycobacterium smegmatis (mc1522)

data_processing:
Base calls were performed with Illumina (online) base calling protocol
Reads (fastq files) were alligned to the transcript sequences of M. smegmatis (1522) and gene expression was obtained with Kallisto
Genome_build: NC_008596
Supplementary_files_format_and_content: Read counts

source_name: MSM-mEos2, Bone marrow derived macrophages

growth_protocol: MSM-mEos2 was grown in 7H9 media under optimal growth conditions.

extract_protocol:
Dim and lit cells (n= 300,000) were PerSorted into 1 mL TriZol having ~ 1000 bone marrow derived macrophage cells. RNA was extracted with phenol chloroform method described previously by Peterson et al., 2019. rRNA was depleted with Illumina rRNA depletion kit (20040526), and mycobacterium RNA was enriched with Path-seq methodology described previously in Peterson et al., 2019. A total of 100,240 probes were designed to cover M. smegmatis mc2155 (Agilent probe library ELID number S3206492). cDNA was made with   Invitrogen SuperScript II (18064022).
Library was constructed with Illumina Nextera XT DNA Library Preparation Kit (FC-131-1024) using their suggested protocol.

treatment_protocol: Dim and lit cells (n=300,000) were isolated with PerSort from Atc (500 ng/ml) treated cultures of MSM-mEos2

tag: strain

value: Lit cells (translationally active cells)

tag: treatment

value: PerSorted into TriZol having mouse bone marrow derived macrophage cells


title: Lit cells3

description: Mycobacterium smegmatis (mc1522)

tag: cell type


title: Dim cells4

description: Mycobacterium smegmatis (mc1522)

value: Dim cells (translationally dormant cells)


title: GSC-CW468-Triculture-batch2-2

value: Patient Derived GSCs grown in a 3D bioprinted tri-culture model


title: shNC-Input-rep3

tag: cell line

tag: merip antibody


title: shNC-MeRIP-rep1

value: Anti-m6A (Abcam, ab208577)


title: Dim cells3

description: Mycobacterium smegmatis (mc1522)


title: T138

first: Chen

address: 17 Panjiayuan Nanli, Chaoyang District

institute: Cancer Hospital, Chinese Academy of Medical Sciences

description:
S16
ACGEJ123pairs_gene_expression_hg19.txt

source_name: Tumor tissue sample

extract_protocol:
Total RNA were extracted from tissue samples using the AllPrep DNA/RNA Kit (Qiagen).
RNA degradation and contamination were monitored on 1% agarose gels. RNA concentration was measured by Qubit® RNA Assay Kit in Qubit® 2.0. RNA library preparation used NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina and 3 nanograms RNA per sample as the initial materials. Ribosomal RNA was removed using Epicentre Ribo-ZeroTM Gold Kits. Library fragments were purified using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China).

value: Adenocarcinoma at the gastroesophageal junction (ACGEJ) tumor tissue

tag: patient

tag: population

value: Chinese


title: shNC-Input-rep2


title: Mus spretus e17.5 placenta [SPRET_M13_P1]

city: Riverside

last: Campbell

tag: pregnancy type code

tag: placenta weight (g)

value: m

value: bisulfite converted DNA


title: Lit cells4

description: Mycobacterium smegmatis (mc1522)


title: GSC-CW468-Triculture-batch2-1

tag: growth protocol

tag: batch


title: Dim cells2

description: Mycobacterium smegmatis (mc1522)


title: shNC-MeRIP-rep3


title: Mus spretus e17.5 placenta [SPRET_M12_P2]

value: SPRET

tag: embryo weight (g)

tag: placenta (percent embryo weight)

tag: embryo sex

tag: tissue


title: shNC-Input-rep1

value: none (input)


title: GSC-CW468-Sphere-batch2-2

value: Patient Derived Glioblastoma Stem Cell

value: Patient Derived GSCs grown in traditional sphere cell culture


title: Mus spretus e17.5 placenta [SPRET_M12_P1]

tag: # males in litter

tag: # females in litter

tag: litter size

tag: proportion males in litter


title: Dim cells1

description: Mycobacterium smegmatis (mc1522)

tag: strain

tag: cell type

tag: treatment


title: ZM44 [sgTRAF2-4-RFP + DMSO]

status: Public on Nov 08 2020

first: Rajkumar

last: Balakrishnan

state: California

address: 10300 Campus Point Drive, Suite 100,

department: Informatics & Predictive Sciences

institute: Bristol Myers Squibb

data_processing:
Raw fastq files were merged so that each sample had one R1 and one R2 files. The quality of the fastq files was evaluated using FastqQC (v 0.11.5). The fastq files were tested using bbmap reformat (v.37.24) for compliance with the fastq format and to convert the quality encoding to q33. Illumina adapters were trimmed using cutadapt (v1.15) and used for Salmon and any other downstream process.    In all analyses the primary assembly of hg38 was used (ENCODE version) and the annotation from Gencode v24. Alignment was performed using a two pass mode with STAR (v2.5.2b) on the full genome and counts were obtained using the quantmode GeneCounts option, STAR was also used to trim the reads on the fly using the clip3pAdapterSequence option. Salmon (v 0.7) was used to obtain pseudoalignments on genes on the trimmed fastq files.
Supplementary_files_format_and_content: Salmon Raw Counts

source_name: B lymphocyte

growth_protocol: SU-DHL-4 was maintained in RPMI 1640 medium (RPMI; #11875085, Thermo Fisher) supplemented with 10% fetal bovine serum, 1X sodium pyruvate, 1X non-essential amino acids, 100 U/mL penicillin, and 100 µg/mL streptomycin. Cells were cultured at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Duplicates of about 1 million freshly frozen, pelleted cells for each condition were shipped to GENEWIZ (South Plainfield, NJ). The RNA extraction was performed using QIAGEN RNeasy Plus Mini Kit and the mRNA was enriched through poly-A+ mRNA.
The RNA extraction, library preparation, and mRNAseq were performed by GENEWIZ using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (#7765, New England Biolabs). ERCC RNA spike-in mix (#4456653, invitrogen) was spiked into each sample after RNA extraction and universal human reference RNA (#14919, Thermal fisher) was included for quality control purpose.

treatment_protocol: SU-DHL-4 cells were transduced with a lentiviral vector expressing a sgRNA targeting either CYLD (sgCYLD-2, sgCYLD-5), NFKBIA (sgNFKBIA-5, sgNFKBIA-8 ), TRAF3 (sgTRAF3-4, sgTRAF3-7) or TRAF2 (sgTRAF2-3, sgTRAF2-4) and then selected by puromycin (2µg/mL) for three days.  Cells were then spin down and resuspended with fresh medium and seeded in 6 well plates at one million cells per mL and treated with either DMSO or 10 µM CC-122 for 24 hours. Cells were washed once by ice cold PBS and then the cell pellets were snap frozen and kept at -80 °C. One cell pellet from each condition was subjected to western blot to check the CRISPR editing of target genes and Ikaros degradation.

tag: cell line


title: ZM41 [sgTRAF2-3-RFP + CC-122]


title: ZM43 [sgTRAF2-4-RFP + DMSO]


title: ZM53 [sgTRAF3-4-RFP + CC-122]


title: ZM42 [sgTRAF2-3-RFP + CC-122]


title: ZM38 [sgTRAF2-3-RFP + DMSO]


title: ZM47 [sgTRAF2-4-RFP + CC-122]


title: ZM49 [sgTRAF3-4-RFP + DMSO]


title: ZM55 [sgTRAF3-7-RFP + DMSO]


title: ZM48 [sgTRAF2-4-RFP + CC-122]


title: ZM54 [sgTRAF3-4-RFP + CC-122]


title: ZM60 [sgTRAF3-7-RFP + CC-122]


title: Lit cells1

description: Mycobacterium smegmatis (mc1522)


title: ZM59 [sgTRAF3-7-RFP + CC-122]


title: ZM31 [sgNFKBIA-8-RFP + DMSO]


title: ZM32 [sgNFKBIA-8-RFP + DMSO]


title: ZM35 [sgNFKBIA-8-RFP + CC-122]


title: ZM37 [sgTRAF2-3-RFP + DMSO]


title: ZM50 [sgTRAF3-4-RFP + DMSO]


title: ZM36 [sgNFKBIA-8-RFP + CC-122]


title: ZM30 [sgNFKBIA-5-RFP + CC-122]


title: ZM29 [sgNFKBIA-5-RFP + CC-122]


title: ZM26 [sgNFKBIA-5-RFP + DMSO]


title: ZM25 [sgNFKBIA-5-RFP + DMSO]


title: ZM20 [sgCYLD-5-RFP + DMSO]


title: ZM23 [sgCYLD-5-RFP + CC-122]


title: ZM19 [sgCYLD-5-RFP + DMSO]


title: ZM18 [sgCYLD-2-RFP + CC-122]


title: ZM56 [sgTRAF3-7-RFP + DMSO]


title: ZM17 [sgCYLD-2-RFP + CC-122]


title: ZM14 [sgCYLD-2-RFP + DMSO]


title: ZM13 [sgCYLD-2-RFP + DMSO]


title: circRNA of IgAN2

city: Changsha

first: Hong

state: Hunan

address: Renmin Road 139#

department: Nephrology

institute: The Second Xiangya Hospital, Central South University

description: re-analysis of GSE145652

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Hisat to map reads to the genome of species.
Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion. All samples were generated unique circular RNAs.
The differentially expressed circRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package–edgeR.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: PBMCs

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Agilent 2100 with RIN number >7.0.
Approximately 5 mg of total RNA was used to deplete ribosomal RNA according to the manuscript of the  Ribo-Zero™ rRNA Removal Kit  (Illumina, San Diego, USA). After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under high temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA,which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP.. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs,The ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed the paired-end sequencing on an Illumina Hiseq 4000 following the vendor's recommended protocol.

tag: condition

value: IgAN


title: circRNA of IgAN3

description: re-analysis of GSE145652


title: circRNA of IgAN1

description: re-analysis of GSE145652


title: circRNA of Control 3

description: re-analysis of GSE145652

value: Control


title: circRNA of Control 2

description: re-analysis of GSE145652


title: cpl2_rep1

city: shanghai

first: Yizhe

address: No.300 Fenglin Road

institute: Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences

description:
cpl2_1
12-day-old seedlings
mRNA
expression_value_FPKM.txt

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using TopHat software. The mapping criteria of bowtie was as follows: sequencing reads should be uniquely matched to the genome allowing up to 2 mismatches, without insertions or deletions. Then the region of gene were expanded following depths of sites and the operon was obtained. In addition, the whole genome was split into multiple 15kb windows that share 5kb. New transcribed regions were defined as more than 2 consecutive windows without overlapped region of gene, where at least 2 reads mapped per window in the same orientation.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) method. RSEM was used to quantify gene abundances. R statistical package software EdgeR was utilized for differential expression analysis. In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS 2.1.1
Genome_build: not provided
Supplementary_files_format_and_content: expression_value_FPKM.txt: Tab-delimited text file includes expression matrix.

organism: Arabidopsis thaliana

source_name: plant tissues

growth_protocol: All the plant seeds were sown and grown on 1/2 MS medium containing 1% sucrose. The seedlings were grown under a long- (16 h light/8 h dark) photoperiod at 23 °C.

extract_protocol:
Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen).
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 (2×150bp read length).

tag: ecotype/background

tag: genotype/variation

tag: age

value: 12 days

value: Seedling