title: mRNA WT primed + triggered rep 3

city: Philadelphia

first: Diep

middle: R

last: Ganguly

address: 433 S University Ave

department: Department of Biology

institute: University of Pennsylvania

data_processing:
Bisulfite-seq
Raw reads were quality controlled using FastQC (v0.11.2), Cutadapt (v1.9), Trim Galore! (v.0.3.7).
Single-end alignments of trimmed raw reads were aligned to the TAIR10 reference using Bismark (v0.14.5) and Bowtie2 (v2.2.9) with the flags -N 0 and -L 20.
Per cytosine methylation levels were calculated using Bismark methylation extractor with default settings. Bisulfite conversion efficiency was calculated as the proportion of methylated cytosines in the CHH context within the chloroplast genome, which itself should be fully unmethylated.
Weighted methylation levels were used to calculate the proportion of CG, CHG, and CHH at single cytosine resolution to account for sequencing depth.  This output was utilized in DMR identification using DSS.
mRNA-seq
Raw reads were diagnosed using FastQC (v0.11.2). Due to strong nucleotide sequence content bias Trim Galore! and Cutadapt were used to trim low-quality reads with PHRED score < 20 (-q 20) and to make a hard clip of 10 bp and 1 bp from the 5’ and 3’ ends, respectively.
Single-end alignments of trimmed raw reads were aligned to the TAIR10 reference genome using Subread (v1.6.2) with the flags -t 0 and -u to report uniquely mapping reads, prior to sorting, indexing and compressing using Samtools (v1.2).
Transcript quantification was performed at the gene-level with the Araport11 annotation using featureCounts (with flag -s 2 for reverse strand specificity). This output was utilized in differential gene expression testing with edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: .bed.gz: weighted methylation levels at single cytosines. Separate files have been produced for each sequence of DNA methylation: CG, CHG, and CHH; . counts: counts per gene-level feature across the Araport11 annotation for each sample.
Supplementary_files_format_and_content: bed: chromosome, start, end, proportion methylated, counts methylated, counts un-methylated, total counts

organism: Arabidopsis thaliana

source_name: 3 week old Col-0 leaf tissue

growth_protocol: Plants grown on soil, with approximately 3g/L osmocote fertilizer, under a 12-hour photoperiod of 100-150μ mol photons m-2 s -1, 20 (±0.5) °C, and 55 (±5) % RH.

extract_protocol:
Bisulfite-seq: Genomic DNA was extracted using the Qiagen DNeasy Plant Mini Kit (Limburg, Netherlands), as per the manufacturer’s instructions. 100-200 ng of fragmented (Covaris) and purified gDNA was bisulfite converted using the Zymo DNA-Gold bisulfite conversion kit (Zymo Research; CA, USA).
mRNA-seq: Total RNA was extracted using TRIzol reagent.
Whole genome bisulfite sequencing libraries were constructing using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences; MI, USA) as per the manufacturer’s instructions.
PolyA-enriched RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit (Illumina, CA, USA) using 1.3 μg input of extracted total RNA. The following modifications to the manufacturer’s instructions were made: reagent volumes were adjusted for 1/3 reactions; and Invitrogen SuperScript III Reverse Transcriptase (Invitrogen, Life Technologies Australia Pty Ltd) was used for first strand synthesis with adjusted reaction temperature of 50 °C.

treatment_protocol: For excess-light treatments, exposure to approximately 10X growth irradiance (1000 μ mol photons m-2 s-1) was applied using a mixture of 250W metal halide lamps (Venture Lighting, MH 250W/U) and high pressure sodium lamps (Phillips, SON-T 250W E E40 SL/12) providing a source of ‘warm’ light (similar to sunlight). This was applied for one hour repeated thrice daily at 9:30 am, 1:30pm, and 5:30 pm.

value: true leaves 4 - 9

tag: ecotype


title: mRNA WT primed + triggered rep 2

status: Public on Nov 27 2018

type: SRA

state: PA

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: tissue


title: mRNA WT primed + triggered rep 1


title: UC female36

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: NIDDK_ID: 8680

data_processing:
Reads were quantified by kalliso using Gencode v25 as the reference genome with transcripts per million as the output.
We included 14085 protein-coding mRNA genes with TPM >1 in 20% of the samples.

molecule: total RNA

organism: Homo sapiens

source_name: Rectal mucosal biopsy from UC Female age 16 at diagnosis

extract_protocol:
RNA was isolated using the Qiagen AllPrep RNA/DAN Mini Kit.  We employed polyA-RNA selection.
TrueSeq RNAsample prep, with paired-end 75bp reads on the Illumina HiSeq2500.

treatment_protocol: Rectal mucosal biopsies were obtained during diagnostic colonoscopies.

value: Rectal mucosal biopsy

tag: diagnosis

value: Ulcerative Colitis

tag: Sex

value: Female

tag: age at diagnosis

tag: pucai

tag: total mayo score

tag: eosinophil grade ≥ 32

value: Y

tag: week 4 remission

value: Yes

tag: histology severity score

tag: initial treatment

value: CS-Oral

tag: baseline calprotectin

tag: week 4 calprotectin


title: mRNA WT naïve + triggered rep 3


title: mRNA WT primed rep 3


title: mRNA WT primed rep 1


title: UC female35

description: NIDDK_ID: 1087

source_name: Rectal mucosal biopsy from UC Female age 12 at diagnosis

value: No


title: mRNA WT naïve + triggered rep 2


title: UC female33

description: NIDDK_ID: 9191

value: unknown


title: mRNA WT naïve + triggered rep 1


title: UC female31

description: NIDDK_ID: 10473

source_name: Rectal mucosal biopsy from UC Female age 13 at diagnosis

value: CS-IV


title: UC female32

description: NIDDK_ID: 14748

source_name: Rectal mucosal biopsy from UC Female age 6 at diagnosis


title: UC female37

description: NIDDK_ID: 7939

source_name: Rectal mucosal biopsy from UC Female age 15 at diagnosis


title: mRNA WT naive rep 3


title: mRNA WT naive rep 1


title: mRNA WT naive rep 2


title: UC female30

description: NIDDK_ID: 4892

source_name: Rectal mucosal biopsy from UC Female age 10 at diagnosis


title: UC female29

description: NIDDK_ID: 8244


title: MethylC WT rep 3

description: bisulfite treated genomic DNA

library_source: genomic

molecule: genomic DNA


title: MethylC strs2 rep 1

description: bisulfite treated genomic DNA


title: MethylC WT rep 2

description: bisulfite treated genomic DNA


title: UC female28

description: NIDDK_ID: 14195

value: N


title: MethylC WT rep 1

description: bisulfite treated genomic DNA


title: HTR_lncRNA overexpression_rep3

city: Nanjing

first: Zhenyao

last: Huang

address: Dongshan

country: China

institute: Nanjing Medical University

description:
HTR-10/SVneo cells transfected with overexpressed lncRNA
Slc-4

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  whole genome using tophat with default parameters
Reads Per Kilo bases per Million reads(RPKM) were calculated using a protocol from Wagner GP et al., Theory Biosci. 2012 Dec;131(4):281-5.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Human trophoblastic cells

extract_protocol:
RNA was extracted by RNeasy Kits (Qiagen, Hilden, NRW, Germany) and treated with DNase I (Thermo Fisher Scientific, Wilmington, DE, USA) according to standard protocols. RNA-sequencing was done in Ribo (Ribo, Guangzhou, China). Briefly, intact RNA was fragmented, end repaired, adapter ligation and PCR amplified following illumina protocol. Libraries were sequencing by illumins Hiseq 3000. polyA tail-grabbed mRNA was used to construct a library and sequence, and then to detect the differential expression or structural variation of all genes and transcripts containing polyA structure.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: HTR-8/SVneo cells

tag: treatment


title: mRNA WT primed rep 2


title: WT 2

city: St. Louis

first: John

middle: R.

last: Edwards

state: MO

address: 660 S. Euclid Ave, Campus Box 8220

department: Center for Pharmacogenomics

institute: Washington University School of Medicine

data_processing:
ERRBS data were filtered for sequence adapters, limited to the first 29 bp of the read, and mapped to the zebrafish genome (danRer7) using BSmap (v 2.90).
Genome_build: danRer7
Supplementary_files_format_and_content: Processed data files are the output files from the methratio.py script in bsmap. Output format: tab delimited txt file with the following columns:      1) chromorome      2) coordinate (1-based)      3) strand      4) sequence context (CG|CHG|CHH)      5) methylation ratio, calculated as #C_counts / #eff_CT_counts      6) number of effective total C+T counts on this locus (#eff_CT_counts)               CT_SNP="no action", #eff_CT_counts = #CT_counts              CT_SNP="correct", #eff_CT_counts = #CT_counts * (#rev_G_counts / #rev_GA_counts)      7) number of total C counts on this locus (#C_counts)      8) number of total C+T counts on this locuso (#CT_counts)      9) number of total G counts on this locus of reverse strand (#rev_G_counts)      10) number of total G+A counts on this locus of reverse strand (#rev_GA_counts)      11) lower bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.      12) upper bound of 95% confidence interval of methylation ratio, calculated by Wilson score interval for binomial proportion.

organism: Danio rerio

source_name: Fin

extract_protocol:
50 ng of high quality genomic DNA was prepared from fin tissue from adult zebrafish at 25 wpf.
ERRBS was performed as in Garrett-Bakelman, F.E.,  et al. (2015) J Vis Exp, e52246 using MspI for digestion.

tag: development stage

value: Adult (25 wpf)

tag: genotype/variation

value: WT


title: WT 1


title: WT 3


title: HTR_lncRNA overexpression_rep2

description:
HTR-9/SVneo cells transfected with overexpressed lncRNA
Slc-3


title: UC female34

description: NIDDK_ID: 1115

source_name: Rectal mucosal biopsy from UC Female age 8 at diagnosis


title: UC female26

description: NIDDK_ID: 7272


title: HTR_lncRNA overexpression_rep1

description:
HTR-8/SVneo cells transfected with overexpressed lncRNA
Slc-2


title: UC female27

description: NIDDK_ID: 2970


title: UC female25

description: NIDDK_ID: 9872


title: zbtb24 mutant 3

value: zbtb24 mutant


title: zbtb24 mutant 2


title: HTR_control_rep3

description:
HTR-8/SVneo cells transfected with unloaded plasmid
Control-4

value: cells transfected with unloaded plasmid


title: UC female24

description: NIDDK_ID: 1456

source_name: Rectal mucosal biopsy from UC Female age 7 at diagnosis


title: MethylC strs2 rep 2

description: bisulfite treated genomic DNA

tag: ecotype


title: UC female23

description: NIDDK_ID: 1450

tag: tissue


title: HTR_control_rep1

description:
HTR-8/SVneo cells transfected with unloaded plasmid
Control-2


title: HTR_control_rep2

description:
HTR-8/SVneo cells transfected with unloaded plasmid
Control-3


title: zbtb24 mutant 1


title: UC female22

description: NIDDK_ID: 1178

tag: diagnosis


title: HH28_DHL_WT_input

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: chick HH28 WT distal hindlimb input

data_processing:
Demultiplexed ChIP-seq reads were mapped onto the galGal5 or mm10 using Bowtie (Version 0.12.7) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al. 2014), and PCR duplicates were removed from mapped reads using samtools (Version 0.1.18) (Li et al., 2009)
By using bamCompare (Version 2.5.0), The ChIP data from H3K27ac, H3K27me3 and H3K4me1 and the input data were normalized and compared to compute the log2 of the number of reads ratio.
The CTCF ChIP data was normalized to obtain 1x depth of coverage by using bamCoverage (Version 2.5.0) (Ramirez et al. 2014, 2016). Peaks of CTCF were called by using MACS2 (Version 2.1.0.20151222) with q-value (0.01) and used for the CTCF motif orientation analysis as previously described (Rodríguez-Carballo et al. 2017)
All analysis was done with our Galaxy server (the Bioteam Appliance Galaxy Edition, https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: bedgraph of log2 of the normalized number of reads ratio histone marks ChIP versus Input; bedgraph of the normalized 1x depth of CTCF coverage; bed of CTCF narrow peaks with q-value=0.01

organism: Gallus gallus

source_name: Hindlimb

extract_protocol:
Chromatin immunoprecipitated experiment was performed as previously described (Beccari et al. 2016). Micro-dissected limb tissues from mouse and chick embryos were cross-linked with 1% formaldehyde/PBS for 15 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with anti-H3K27ac (ab4729, Abcam), anti-H3K27me3 (07-449, Merck Millipore), anti-H3K4me1 (ab8895, Abcam) and anti-CTCF (61311, Active Motif), respectively.
Libraries were prepared with at least 5 ng of purified DNA following Illumina TruSeq ChIP library preparation guide. Sequencing was performed with 100-bp single-end.

tag: breed

value: White Leghorn

tag: age

tag: tissues

value: Distal hindlimb

tag: genotype

value: wild type

tag: antibody


title: UC female21

description: NIDDK_ID: 14523

source_name: Rectal mucosal biopsy from UC Female age 17 at diagnosis

value: Rectal mucosal biopsy

value: Ulcerative Colitis

tag: Sex

tag: age at diagnosis

tag: pucai

tag: total mayo score

tag: eosinophil grade ≥ 32

tag: week 4 remission


title: HH28_DHL_WT_H3K27ac

description: chick HH28 WT distal hindlimb H3K27ac


title: UC female20

description: NIDDK_ID: 10750

source_name: Rectal mucosal biopsy from UC Female age 9 at diagnosis

value: Female

tag: initial treatment

tag: baseline calprotectin

tag: week 4 calprotectin


title: HH28_PHL_WT_H3K27me3

description: chick HH28 WT proximal hindlimb H3K27me3

value: Proximal hindlimb


title: UC female19

description: NIDDK_ID: 3044

value: Y

tag: histology severity score


title: HH28_PHL_WT_input

description: chick HH28 WT proximal hindlimb input


title: HH28_PHL_WT_H3K27ac

description: chick HH28 WT proximal hindlimb H3K27ac


title: UC female16

description: NIDDK_ID: 6659

tag: tissue

value: Yes


title: UC female17

description: NIDDK_ID: 3989

tag: diagnosis

value: No

value: unknown


title: HH28_DFL_WT_H3K27me3

description: chick HH28 WT distal forelimb H3K27me3

source_name: Forelimb

tag: breed

value: Distal forelimb


title: HH28_DFL_WT_input

description: chick HH28 WT distal forelimb input

tag: age


title: UC female18

description: NIDDK_ID: 1545

value: CS-IV


title: HH28_PFL_WT_H3K27me3

description: chick HH28 WT proximal forelimb H3K27me3

tag: tissues

value: Proximal forelimb


title: UC female13

description: NIDDK_ID: 4522

value: CS-Oral


title: UC female14

description: NIDDK_ID: 10705

value: N


title: ifih1WT_z24WT_3

data_processing:
Raw RNA-seq FASTQ reads were trimmed for adapters and preprocessed to remove low-quality reads using Trimmomatic v0.33 (arguments: LEADING:3 TRAILING:3 MINLEN:36) (Bolger et al., 2014) prior to mapping to the Danio rerio GRCz10 reference genome assembly. Reads were mapped using TopHat v2.1.1 (Kim et al., 2013) supplied with a reference General Features File (GFF) to the Danio rerioGRCz10 reference genome assembly, and with the following arguments: -i 10 -I 5000 --library-type fr-firststrand. Gene expression was estimated using Cuffquant (a tool from Cufflinks v2.2.1), with following arguments --library-type fr-firststrand.  Expression level were normalized in FPKM units by Cuffnorm (a tool from Cufflinks v2.2.1), with following arguments --library-type fr-firststrand.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited normalized RNA-seq FPKM for each sample.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) and precipitated with isopropanol.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 2500 High Output in a 50bp/50bp paired end run, using the TruSeq SBS v4 Kit (Illumina).

tag: development stage

value: Larvae

tag: genotype/variation

value: ifih1 WT

tag: tag

value: zbtb24 WT


title: HH28_DHL_WT_H3K27me3

description: chick HH28 WT distal hindlimb H3K27me3

value: White Leghorn

value: Distal hindlimb

tag: genotype

value: wild type

tag: antibody


title: UC female12

description: NIDDK_ID: 6424

value: Rectal mucosal biopsy

value: Ulcerative Colitis

tag: Sex

value: Female

tag: age at diagnosis

tag: pucai

tag: total mayo score


title: UC female11

description: NIDDK_ID: 8273

tag: eosinophil grade ≥ 32

tag: week 4 remission

value: Yes

tag: initial treatment

tag: baseline calprotectin


title: UC female10

description: NIDDK_ID: 41

tag: tissue

tag: diagnosis

value: Y

value: No

tag: histology severity score

tag: week 4 calprotectin


title: ifih1WT_z24WT_1

tag: development stage


title: HH28_PFL_WT_input

description: chick HH28 WT proximal forelimb input

tag: breed

tag: age

tag: tissues


title: ifih1WT_z24Mu_3

tag: genotype/variation

tag: tag

value: zbtb24 Mutant


title: ifih1WT_z24Mu_2


title: HH19_FL_WT_input

description: chick HH19 WT whole forelimb bud input

value: Whole forelimb bud

tag: genotype

tag: antibody


title: HH19_FL_WT_H3K27ac

description: chick HH19 WT whole forelimb bud H3K27ac


title: UC female9

description: NIDDK_ID: 13450

source_name: Rectal mucosal biopsy from UC Female age 11 at diagnosis

tag: Sex

tag: age at diagnosis

tag: pucai

tag: total mayo score


title: ifih1WT_z24Mu_1


title: UC female15

description: NIDDK_ID: 7694

tag: eosinophil grade ≥ 32

tag: week 4 remission

tag: initial treatment

value: CS-IV

tag: baseline calprotectin


title: HH30_DHL_WT_Hoxd13vp

description: chick HH30 WT distal hindlimb Hoxd13 viewpoint

data_processing:
Library strategy: 4C-Seq
De-multiplexing, mapping and 4C analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to either the mm10 or galGal5 chicken genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters “--end-to-end --sensitive -k 20”. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads.
Fragments scores are normalized to the mean score of fragments falling into a region defined as the bait coordinated either ± 1Mb or ± 2Mb and the data was smoothed by using a running mean with window size of 11 fragments. During the procedure, information of excluded fragments at specific regions from the analysis were described in Supplemental Table 3 in Yakushiji-Kaminatsui et al. (2018).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: Smoothed/normalized data (bedgraph)

extract_protocol:
The dissected limb bud tissues were dissociated with collagenase (Sigma Aldrich) and filtered through cell strainer to obtain single cells. Cells were fixed with 2% formaldehyde for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of samples were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. All primer and barcode information are described in Supplemental Table 3 in Yakushiji-Kaminatsui et al. (2018).


title: UC female7

description: NIDDK_ID: 5175

source_name: Rectal mucosal biopsy from UC Female age 14 at diagnosis

tag: tissue

tag: diagnosis

tag: histology severity score

value: unknown

tag: week 4 calprotectin


title: UC female8

description: NIDDK_ID: 10897

value: CS-Oral


title: ifih1Mu_z24WT_2

tag: development stage

value: Larvae

value: ifih1 Mutant


title: ifih1Mu_z24WT_3

tag: genotype/variation

value: zbtb24 WT


title: ifih1WT_z24WT_2

value: ifih1 WT

tag: tag


title: UC female6

description: NIDDK_ID: 458

value: N


title: HH30_PHL_WT_Hoxd13vp

description: chick HH30 WT proximal hindlimb Hoxd13 viewpoint

tag: breed

value: White Leghorn

tag: age

tag: tissues

value: Proximal hindlimb

tag: genotype

value: wild type


title: ifih1Mu_z24WT_1


title: HH30_DFL_WT_Hoxd13vp

description: chick HH30 WT distal forelimb Hoxd13 viewpoint

value: Distal forelimb


title: HH30_PFL_WT_Hoxd13vp

description: chick HH30 WT proximal forelimb Hoxd13 viewpoint

value: Proximal forelimb


title: UC female3

description: NIDDK_ID: 5087

value: Rectal mucosal biopsy

value: Ulcerative Colitis

tag: Sex

value: Female

tag: age at diagnosis

tag: pucai

value: Y

value: Yes


title: ifih1Mu_z24Mu_3

value: zbtb24 mutant


title: MethylC strs2 rep 3

description: bisulfite treated genomic DNA

source_name: 3 week old Col-0 leaf tissue

value: true leaves 4 - 9

tag: ecotype


title: ifih1Mu_z24Mu_2

value: Larvae


title: ifih1Mu_z24Mu_1

value: ifih1 Mutant


title: HH30_DHL_WT_Hoxd12vp

description: chick HH30 WT distal hindlimb Hoxd12 viewpoint

value: Distal hindlimb


title: UC female2

description: NIDDK_ID: 9658

tag: total mayo score

tag: eosinophil grade ≥ 32

tag: week 4 remission

tag: initial treatment

value: CS-Oral


title: HH30_DFL_WT_Hoxd12vp

description: chick HH30 WT distal forelimb Hoxd12 viewpoint


title: Mut3

data_processing:
Reads were mapped to the Zebrafish genome (danRer7) using the rnaStar aligner v2.5.0a. We used the 2 pass mapping method outlined in Engström et.al (Nat. Meth. 2013). The first mapping pass used a list of known annotated junctions from Ensemble. Novel junctions found in the first pass were then added to the known junctions and a second mapping pass was done (on the second pass the RemoveNoncanoncial flag was used). Expression counts were computed from the mapped reads using HTSeq v0.5.3 and Ensemble D.rerio v79 gene annotations. Normalization and differential expression was performed using DESeq.
Genome_build: danRer7
Supplementary_files_format_and_content: Tab-delimited normalized RNA-seq counts per million for each sample.

value: Mutant


title: HH30_PHL_WT_Hoxd12vp

description: chick HH30 WT proximal hindlimb Hoxd12 viewpoint

value: White Leghorn


title: UC female1

description: NIDDK_ID: 11983

tag: tissue

tag: diagnosis

value: No

tag: histology severity score

tag: baseline calprotectin


title: Controls male9

description: NIDDK_ID: Control20

source_name: Rectal mucosal biopsy from Ctl Male age 12 at diagnosis

value: Control

value: Male

tag: week 4 calprotectin


title: Mut2

tag: development stage

tag: genotype/variation


title: HH30_PFL_WT_Hoxd12vp

description: chick HH30 WT proximal forelimb Hoxd12 viewpoint

tag: breed

tag: age

tag: tissues

value: Proximal forelimb

value: wild type


title: UC female5

description: NIDDK_ID: 3800

value: Rectal mucosal biopsy

value: Ulcerative Colitis

tag: Sex

tag: age at diagnosis


title: WT2A

value: WT


title: HH30_DHL_WT_Hoxd10-11vp

description: chick HH30 WT distal hindlimb Hoxd10-11 viewpoint

tag: genotype


title: UC female4

description: NIDDK_ID: 5170

value: Female

tag: pucai

tag: total mayo score

value: Y


title: WT1A


title: Controls male7

description: NIDDK_ID: Control18

source_name: Rectal mucosal biopsy from Ctl Male age 16 at diagnosis

tag: eosinophil grade ≥ 32

tag: week 4 remission


title: Controls male6

description: NIDDK_ID: Control17

tag: tissue

tag: initial treatment


title: HH30_DFL_WT_Hoxd10-11vp

description: chick HH30 WT distal forelimb Hoxd10-11 viewpoint

value: Distal forelimb


title: Controls male5

description: NIDDK_ID: Control16

source_name: Rectal mucosal biopsy from Ctl Male age 17 at diagnosis

tag: diagnosis

tag: histology severity score


title: HH30_PHL_WT_Hoxd10-11vp

description: chick HH30 WT proximal hindlimb Hoxd10-11 viewpoint

value: Proximal hindlimb


title: Controls male4

description: NIDDK_ID: Control15

source_name: Rectal mucosal biopsy from Ctl Male age 14 at diagnosis

tag: baseline calprotectin

tag: week 4 calprotectin


title: HH30_PFL_WT_Hoxd10-11vp

description: chick HH30 WT proximal forelimb Hoxd10-11 viewpoint


title: Embryo-3

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description: allSamples_genes.read_group_tracking:Emb_2

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
bowtie2 v2.2 was used to subtract reads mapping to canine rRNA genes and other small noncoding, non-polyA+ RNAs such as microRNAs, snoRNAs, snRNAs, etc (default mapping params, --un-gz to write non-rRNA reads to a new fastq file).
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map non-rRNA reads to the canine CanFam3 reference genome+transcriptome (Ensembl).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts based on the canine CanFam3 transcriptome (Ensembl).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the canine CanFam3 transcriptome (Ensembl).
Genome_build: CanFam3
Supplementary_files_format_and_content: Tab delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The 'gene_exp.diff' files contain average FPKM values for sample groups (per condition) as well as results for statistical testing for differential expression. The 'genes.read_group_tracking' files contain raw mapped read counts and FPKM values for individual samples.

organism: Canis lupus familiaris

source_name: embryonic hip

growth_protocol: primary canine hip tissue, different ages and disease states at collection

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of a second ethanol wash of the RNA pellet to remove residual salt.
Ribosomal RNA was subtracted from 1.5-2.5ug total RNA with the Ribozero Gold HMR kit (Illumina). Diretional RNA-seq libraries were prepared from 100 ng rRNA-subtracted RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: embryonic hip

tag: sample group

value: embryo

tag: dog id


title: Embryo-1

description: allSamples_genes.read_group_tracking:Emb_0

tag: age


title: Embryo-2

description: allSamples_genes.read_group_tracking:Emb_1


title: Young-Ligament-4

description: allSamples_genes.read_group_tracking:Lig_13

source_name: teres ligament

value: teres ligament

value: young


title: HH30_DHL2_WT_RNA-seq

description:
chick HH30 WT distal hindlimb (metatarsals) RNA-seq
HH30DHL_coverage_unique_norm_fwd.bedgraph, HH30DHL_coverage_unique_norm_rev.bedgraph

data_processing:
Demultiplexed RNA-seq reads were mapped onto mm10 genome or galGal5, respectively. Regarding chick distal hindlimb at HH30, the two fastq files derived from phalanges and metatarsals were concatenated and used for analysis.
The RNA-seq data were aligned against respective genomes using Tophat2 (Version 2.0.9)(Kim et al. 2013) and the unique mapped reads were extracted. The number of uniquely mapped reads was calculated using FLAGSTAT (Samtools, Version 0.1.18) (Li et al. 2009) and this value was used for the subsequent normalization of each coverage data to be the million reads number.
All analysis was done by our Galaxy server (the Bioteam Appliance Galaxy Edition; https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: bedgraph of the forward or reverse strand unique read coverage, divided by the number of millions of mapped reads in each sample.

extract_protocol:
Micro-dissected limb tissues either from mouse or chick were used for RNA extraction by using the RNeasy Micro Kit (QIAGEN) according to manufacturer instruction.
A total of 100 ng of pure total RNA was amplified following standard Illumina procedure for polyA-selected RNA. Libraries were prepared with the Illumina TruSeq Stranded mRNA protocol and sequenced on either Illumina HiSeq 2500 or NextSeq 500.

tag: breed

value: White Leghorn

tag: tissues

value: Distal hindlimb (metatarsals)


title: Controls male2

description: NIDDK_ID: Control13

source_name: Rectal mucosal biopsy from Ctl Male age 11 at diagnosis

value: Control

tag: Sex

tag: age at diagnosis


title: Controls male3

description: NIDDK_ID: Control14

value: Male

tag: pucai


title: Controls male8

description: NIDDK_ID: Control19

source_name: Rectal mucosal biopsy from Ctl Male age 9 at diagnosis

tag: total mayo score


title: Mut1

source_name: Fin

tag: development stage

value: Larvae

tag: genotype/variation

value: Mutant


title: HH30_PHL_WT_RNA-seq

description: chick HH30 WT proximal hindlimb RNA-seq

tag: genotype

value: wild type


title: Controls male1

description: NIDDK_ID: Control12

tag: tissue

value: Rectal mucosal biopsy

tag: eosinophil grade ≥ 32

tag: week 4 remission

tag: initial treatment


title: Control female11

description: NIDDK_ID: Control11

source_name: Rectal mucosal biopsy from Ctl Female age 17 at diagnosis

tag: diagnosis

tag: histology severity score

tag: baseline calprotectin

tag: week 4 calprotectin


title: HH30_DFL_WT_RNA-seq

description: chick HH30 WT distal forelimb RNA-seq

tag: breed

tag: age


title: Young-Ligament-2

description: allSamples_genes.read_group_tracking:Lig_9

tag: sample group

tag: dog id


title: HH30_PFL_WT_RNA-seq

description: chick HH30 WT proximal forelimb RNA-seq

tag: tissues

value: Proximal forelimb


title: Young-Ligament-1

description: allSamples_genes.read_group_tracking:Lig_7


title: Ctrl-Ligament-3

description:
allSamples_genes.read_group_tracking:Lig_8
Ligament_genes.read_group_tracking:Ctl_2
Ligament_gene_exp.diff:Ctl_2

value: control

value: adult


title: HH20_HL_WT_CTCF

description:
chick HH20 WT whole hindlimb bud CTCF
HH20HL_CTCF_narrowPeaks.bed

source_name: Hindlimb

value: Whole hindlimb bud

tag: antibody


title: Control female9

description: NIDDK_ID: Control9

source_name: Rectal mucosal biopsy from Ctl Female age 9 at diagnosis

tag: Sex

value: Female

tag: age at diagnosis

tag: pucai

tag: total mayo score


title: HH20_HL_WT_H3K27me3

description: chick HH20 WT whole hindlimb bud H3K27me3

tag: genotype


title: Control female7

description: NIDDK_ID: Control7

source_name: Rectal mucosal biopsy from Ctl Female age 14 at diagnosis

tag: tissue

tag: eosinophil grade ≥ 32

tag: week 4 remission


title: Control female8

description: NIDDK_ID: Control8

source_name: Rectal mucosal biopsy from Ctl Female age 16 at diagnosis

tag: diagnosis

tag: histology severity score

tag: initial treatment


title: Ctrl-Ligament-1

description:
allSamples_genes.read_group_tracking:Lig_5
Ligament_genes.read_group_tracking:Ctl_0
Ligament_gene_exp.diff:Ctl_0

value: Sandy


title: HH20_HL_WT_input2_for_H3K27

description: chick HH20 WT whole hindlimb bud input2 for H3K27

tag: breed


title: Control female6

description: NIDDK_ID: Control6

tag: baseline calprotectin

tag: week 4 calprotectin


title: Ctrl-Ligament-2

description:
allSamples_genes.read_group_tracking:Lig_6
Ligament_genes.read_group_tracking:Ctl_1
Ligament_gene_exp.diff:Ctl_1

tag: sample group

tag: age

tag: dog id

value: Georgia


title: HH30_DHL1_WT_RNA-seq

description:
chick HH30 WT distal hindlimb (phalanges) RNA-seq
HH30DHL_coverage_unique_norm_fwd.bedgraph, HH30DHL_coverage_unique_norm_rev.bedgraph

tag: tissues

value: Distal hindlimb (phalanges)


title: Aff-Ligament-6

description:
allSamples_genes.read_group_tracking:Lig_2
Ligament_genes.read_group_tracking:Aff_5
Ligament_gene_exp.diff:Aff_5

value: teres ligament

value: affected


title: HH20_HL_WT_H3K27ac

description: chick HH20 WT whole hindlimb bud H3K27ac

value: White Leghorn

tag: antibody


title: Control female5

description: NIDDK_ID: Control5

value: Control

tag: Sex

tag: age at diagnosis

tag: pucai


title: Control female4

description: NIDDK_ID: Control4

source_name: Rectal mucosal biopsy from Ctl Female age 8 at diagnosis

tag: tissue

tag: total mayo score


title: Young-Ligament-3

description: allSamples_genes.read_group_tracking:Lig_12

value: young


title: HH20_FL_WT_H3K27me3

description: chick HH20 WT whole forelimb bud H3K27me3

source_name: Forelimb

value: Whole forelimb bud

tag: genotype


title: Control female10

description: NIDDK_ID: Control10

tag: diagnosis

tag: eosinophil grade ≥ 32

tag: week 4 remission


title: Control female2

description: NIDDK_ID: Control2

source_name: Rectal mucosal biopsy from Ctl Female age 11 at diagnosis

tag: histology severity score

tag: initial treatment


title: HH20_FL_WT_H3K27ac

description: chick HH20 WT whole forelimb bud H3K27ac

tag: breed


title: HH20_FL_WT_input_for_H3K27

description: chick HH20 WT whole forelimb bud input


title: Control female3

description: NIDDK_ID: Control3

tag: baseline calprotectin

tag: week 4 calprotectin


title: Control female1

description: NIDDK_ID: Control1


title: Aff-Ligament-3

description:
allSamples_genes.read_group_tracking:Lig_10
Ligament_genes.read_group_tracking:Aff_2
Ligament_gene_exp.diff:Aff_2

tag: sample group

tag: age

tag: dog id


title: Aff-Ligament-4

description:
allSamples_genes.read_group_tracking:Lig_11
Ligament_genes.read_group_tracking:Aff_3
Ligament_gene_exp.diff:Aff_3


title: Aff-Ligament-2

description:
allSamples_genes.read_group_tracking:Lig_3
Ligament_genes.read_group_tracking:Aff_1
Ligament_gene_exp.diff:Aff_1


title: Aff-Ligament-1

description:
allSamples_genes.read_group_tracking:Lig_0
Ligament_genes.read_group_tracking:Aff_0
Ligament_gene_exp.diff:Aff_0


title: Young-Capsule-6

description: allSamples_genes.read_group_tracking:Cap_14

source_name: hip joint capsule

value: hip joint capsule


title: Aff-Ligament-7

description:
allSamples_genes.read_group_tracking:Lig_4
Ligament_genes.read_group_tracking:Aff_6
Ligament_gene_exp.diff:Aff_6


title: HH20_HL_WT_input1_for_H3K27

description: chick HH20 WT whole hindlimb bud input1 for H3K27

tag: tissues

value: wild type

tag: antibody


title: HH20_FL_WT_CTCF

description:
chick HH20 WT whole forelimb bud CTCF
HH20FL_CTCF_narrowPeaks.bed


title: Young-Capsule-5

description: allSamples_genes.read_group_tracking:Cap_13


title: roX1roX2 replicate 2

city: Umeå

first: Jan

last: Larsson

address: University Hospital, byggnader 6 K och 6 L

department: Department of Molecular biology

country: Sweden

institute: Umeå university

data_processing:
Clustering was done by ‘cBot’ and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2x126 setup using ‘HiSeq SBS Kit v4’ chemistry. The Bcl to FastQ conversion was performed using bcl2fastq-1.8.4 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+. Raw sequencing data was demultiplexed and converted to FastQ.
Reads were mapped to Drosophila melanogaster genome version 6.09 using STAR v2.5.1b with default settings
Read counts were obtained with HTseq version 0.6.1 using htseq count with default settings
Differential expression was calculated using the DESeq2 software package. Genes with less than 20 reads as a sum of all samples were excluded from the analysis. Out of the 1000 most variable genes, the ones with an adjusted p-value for differential expression between WT and each of the three roX mutants above 0.01 were also excluded from this analysis
Genome_build: Dmel 6.09
Supplementary_files_format_and_content: Excel files with 1) counts and 2) differential expression between WT and mutants with gene annotation.

organism: Drosophila melanogaster

source_name: roX1roX2, first instar larvae

growth_protocol: Flies were cultivated at 25˚C in vials containing potato mash-yeast-agar.

extract_protocol:
Total RNA was extracted with 1 mL of Tri Reagent (Ambion) per sample.
Libraries were prepared with a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.

value: whole larvae

tag: developmental stage

value: first instar larvae

tag: strain


title: Young-Capsule-4

description: allSamples_genes.read_group_tracking:Cap_12

tag: tissue


title: roX2 replicate 4

source_name: roX2, first instar larvae

tag: genotype


title: Aff-Ligament-5

description:
allSamples_genes.read_group_tracking:Lig_1
Ligament_genes.read_group_tracking:Aff_4
Ligament_gene_exp.diff:Aff_4


title: roX1roX2 replicate 3


title: Young-Capsule-3

description: allSamples_genes.read_group_tracking:Cap_11


title: roX1roX2 replicate 4


title: Young-Capsule-2

description: allSamples_genes.read_group_tracking:Cap_8


title: roX2 replicate 3


title: roX1 replicate 4

source_name: roX1, first instar larvae


title: roX2 replicate 2


title: Ctrl-Capsule-5

description:
allSamples_genes.read_group_tracking:Cap_9
Capsule_genes.read_group_tracking:Ctl_4
Capsule_gene_exp.diff:Ctl_4

value: control


title: roX1 replicate 3


title: whole fly female -HIgh_elevation_24C-3

type: RNA

city: Hilo

first: M. Renee

last: Bellinger

state: Hawaii

address: 200 W. Kawili St.

department: Biology

institute: University of Hawaii

hyb_protocol: low-input quickAmp Labeling kit

scan_protocol: Agilent scanner G2565CA

data_processing: intensities of the adhered dye recorded using Feature extraction software (Aligent Technologies, Santa Clara, CA) ; prepared using GeneSpring  software

organism: Drosophila sproati

label_protocol: Cyanine-3 CTP

growth_protocol: two populations founded from high and low elevation areas were raised for five generations at 18C

extract_protocol: whole RNA

treatment_protocol: The 6th generation populations were held at 18C for one week, then split into two groups, one kept at 18C and one exposed to 24C for one week. Gene expression was measured during week 4 of maturation after a one-week rest period.

value: whole fly

tag: gender

value: female

value: four weeks

value: reproductively mature

tag: treatment

value: elevated temperature (24C)

tag: source population

value: high elevation


title: whole fly female -HIgh_elevation_18C-5


title: whole fly female -HIgh_elevation_24C-1


title: roX1 replicate 2


title: Ctrl-Capsule-4

description:
allSamples_genes.read_group_tracking:Cap_7
Capsule_genes.read_group_tracking:Ctl_3
Capsule_gene_exp.diff:Ctl_3

value: adult


title: whole fly female -HIgh_elevation_24C-2


title: whole fly female -HIgh_elevation_18C-6


title: whole fly female -HIgh_elevation_18C-2


title: roX1 replicate 1


title: whole fly female -HIgh_elevation_18C-3


title: Ctrl-Capsule-3

description:
allSamples_genes.read_group_tracking:Cap_5
Capsule_genes.read_group_tracking:Ctl_2
Capsule_gene_exp.diff:Ctl_2

value: Sandy


title: whole fly female -HIgh_elevation_18C-4


title: wt replicate 4

source_name: wt, first instar larvae

value: wt


title: Ctrl-Capsule-1

description:
allSamples_genes.read_group_tracking:Cap_2
Capsule_genes.read_group_tracking:Ctl_0
Capsule_gene_exp.diff:Ctl_0


title: Ctrl-Capsule-2

description:
allSamples_genes.read_group_tracking:Cap_3
Capsule_genes.read_group_tracking:Ctl_1
Capsule_gene_exp.diff:Ctl_1


title: wt replicate 3


title: Aff-Capsule-4

description:
allSamples_genes.read_group_tracking:Cap_4
Capsule_genes.read_group_tracking:Aff_3
Capsule_gene_exp.diff:Aff_3

value: affected


title: Young-Capsule-1

description: allSamples_genes.read_group_tracking:Cap_6

value: young


title: Aff-Capsule-2

description:
allSamples_genes.read_group_tracking:Cap_0
Capsule_genes.read_group_tracking:Aff_1
Capsule_gene_exp.diff:Aff_1


title: whole fly female -Low_elevation_24C-4

value: low elevation


title: whole fly female -Low_elevation_24C-2


title: whole fly female -Low_elevation_24C-3


title: whole fly female -HIgh_elevation_18C-1


title: whole fly female -Low_elevation_18C-5

value: control (18C)


title: HH20_HL_WT_RNA-seq

description: chick HH20 WT whole hindlimb RNA-seq

value: White Leghorn

value: Whole hindlimb bud

value: wild type


title: whole fly female -Low_elevation_24C-1


title: whole fly female -Low_elevation_18C-6


title: HH20_FL_WT_RNA-seq

description: chick HH20 WT whole forelimb RNA-seq

value: Whole forelimb bud


title: whole fly female -Low_elevation_24C-5

value: whole fly


title: dek-B

city: Taian

first: Ru Chang

last: Ren

address: Daizong

department: College of Life Sciences

institute: Shandong Agricultural University

data_processing:
We use internal software to filter reads, fllowed as:  1) Remove reads with adaptors;  2) Remove reads in which unknown bases(N) are more than 5%;  3) Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 20% in a read).
We use HISAT to perfrom genome mapping,HISAT:  version: v0.1.6-beta
we use GATK to call SNP and INDEL for each sample
we mapped clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

extract_protocol:
Total RNAs were extracted from the endosperm of WT and mutant at 10 DAP used CTAB-based method
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: mutant

tag: time point

value: 10 days after pollination

value: endosperm


title: wt replicate 1

value: whole larvae

value: first instar larvae


title: dek-A


title: whole fly female -Low_elevation_18C-2

value: female

value: four weeks

value: reproductively mature


title: whole fly female -Low_elevation_18C-3


title: Aff-Capsule-1

description:
allSamples_genes.read_group_tracking:Cap_10
Capsule_genes.read_group_tracking:Aff_0
Capsule_gene_exp.diff:Aff_0

value: hip joint capsule

value: affected

value: adult


title: whole fly female -Low_elevation_18C-4

value: control (18C)

value: low elevation


title: WT-B


title: Aff-Capsule-3

description:
allSamples_genes.read_group_tracking:Cap_1
Capsule_genes.read_group_tracking:Aff_2
Capsule_gene_exp.diff:Aff_2


title: WT-A


title: GRA15

city: BEIJING

first: Peiyan

last: Wang

state: 北京

address: NO.38 ROAD XUEYUAN, DISTRICT HAIDIAN, BEIJING, CHINA, 北京市海淀区学院路38号北京大学医学部

institute: Peking University

data_processing:
RNA sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB), and sequenced on an Illumina Novaseq platform.
Illumina Casava 1.8 software used for basecalling and raw reads were gained.
After eliminating low-quality reads and reads with adaptors, clean reads were mapped to mouse genome reference sequence (GRCm38/mm10 Ensembl release 81) using HISAT2.
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include ensemble gene ID and RPKM values for each Sample

organism: Mus musculus

source_name: Bone marrow

growth_protocol: Immortalized bone marrow derived macrophages were cultured in DMEM containing 10% FBS, 1% glutamine, 1% streptomycin-penicillin on 10 cm dish for further experiments.

extract_protocol:
Supernatant was removed and cells were covered with 350ul Buffer RLT at the end of treatment. Total RNA was extracted following the strandard protocol of RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected by lenti-virus containing GRA15II gene and selected by applying puromycin in culture medium

tag: transfection

tag: cell type


title: F14039 Infected3

city: Berlin

last: zur Brügge

address: Oertzenweg 19b

department: Veterinary Medicine

country: Germany

institute: Freie Universität Berlin

description:
RawCounts_ALLSAMPLE.xlsx
NormalizedCountsDeq2_ALLSAMPLE.xlsx

data_processing:
Alignment of fastq files using spliced-read aligner Tophat2 (Galaxy version 2.1.0)
Ab initio transcriptome assembly with Cufflinks (Galaxy version 2.2.1) using uniquely mapped and properly paired reads to identify annotated and novel transcripts
Generated single assembly GTF file from the individual Cufflinks assemblies with Cuffmerge (Galaxy version 2.2.1.0).
Estimation of number of fragments in all paired-end libraries using featureCounts (version 1.5.2)
Estimation of normalized count using DESeq (version 1.16.1)
Genome_build: bosTau8 June 2014
Supplementary_files_format_and_content: raw count generated using featureCounts; normalized count data generated using DESeq2

organism: Bos taurus

source_name: bovine macrophages

growth_protocol: Blood mononuclear cells were isolated by Ficoll-Paque Plus , centrifugation, three washing steps with PBS and subsequent attachment to cell-culture plate surface. Cells were cultivated at 37°C and 5% CO2 for 6 days in six well plates in 1.5 ml IMDM medium containing 10% FCS, 10 μg/ml gentamycin, 30 ng/ml M-CSF  and 1 x Penicillin-Streptomycin-Amphotericin B. The media was changed one to two times during cultivation.

extract_protocol:
For RNA extraction, cells were washed three times with PBS, lysed with RNA lysis buffer (mirVANA) and total RNA was isolated according to the manufacturer’s instruction.
Sequencing libraries were constructed using the Illumina TruSeq stranded total RNA kit according to manufacturer’s instructions with an input of 500 ng total RNA  per sample. This kit includes ribosomal RNA removal by Ribozero treatment. The quality of final libraries was checked on a TapeStation2200 using the D1000 Screen Tape.
Libraries were sequenced on an Illumina HiSeq4000 (Illumina) with 2 x 75 bp paired end reads and six samples per lane.

treatment_protocol: Approximately 2 × 107 bacterial cells were inoculated on 2 × 105 primary bovine macrophages (multiplicity of infection [MOI] = 100) and incubated at 37 °C and 5% CO2. Non-infected cells served as a negative control. After 2 h of infection, cells were washed three times with PBS and incubated in fresh media containing 10% FCS for another 4 h to remove remaining extracellular bacteria. Samples were taken 6 h after infection.

value: Monocyte derived macrophages

value: primary cells

tag: source

value: whole blood

tag: infected

value: Mycobacterium avium subspecies paratuberculosis


title: vector

value: vector

value: Immortalized bone marrow derived macrophages

value: wild type


title: F14040 Neg Control3


title: F14038 Neg Control2


title: whole fly female -Low_elevation_18C-1

value: whole fly

tag: age


title: whole fly male -High_elevation_24C-3

value: male

value: high elevation


title: whole fly male -High_elevation_24C-5

value: four weeks


title: whole fly male -High_elevation_18C-7

value: reproductively mature


title: whole fly male -High_elevation_24C-2


title: F14037 Infected2


title: whole fly male -High_elevation_24C-8


title: whole fly male -High_elevation_18C-6


title: F14035 Infected1


title: ncapg2_gRNA3_Cas9_rep5

city: Chicago

first: Erica

last: Davis

state: IL

address: 225 E Chicago Avenue

department: Advanced Center for Translational and Genetic Medicine (ACT-GeM)

institute: Ann & Robert H Lurie Children's Hospital of Chicago

description: DifferentialExpression.xls

data_processing:
Data were demultiplexed and Fastq files generated using Bcl2Fastq (Illumina).
RNAseq data were processed with the TrimGalore toolkit which employs Cutadapt to trim low quality bases and sequencing adapters from 3’ ends of the reads. Only reads > 20nt after trimming were kept.
Reads were mapped to the Zv10r87 version of the zebrafish genome and transcriptome using the STAR RNA-seq alignment tool.
Gene counts were compiled using the HTSeq tool. Only genes that had >10 reads were used in subsequent analysis.
Normalization and differential expression were carried out with the DESeq2 Bioconductor38 package with the R statistical programming environment.
Genome_build: Zv10r87
Supplementary_files_format_and_content: Excel file include RPKM values for each Sample

growth_protocol: Embryos were obtained from natural matings of adult wild-type zebrafish that were maintained on a 14h/10h light/dark cycle. Embryos were reared in embryo media (0.3 g/L NaCl, 75 mg/L CaSO4, 37.5 mg/L NaHC03, 0.003% methylene blue) at 28°C until 2 dpf.

extract_protocol:
We extracted total RNA from embryo heads with Trizol (ThermoFisher), according to manufacturer's instructions. N=20 embryos/pool
RNAseq libraries were prepared using the Stranded mRNA-Seq Kit (KAPA) following the manufacturer’s protocol. In brief, mRNA transcripts were captured using magnetic oligo-dT beads, fragmented with heat and magnesium, and reverse transcribed with random primers. Illumina sequencing adapters were ligated to dscDNA fragments and amplified to produce RNA-seq libraries. Libraries were dual indexed; fragment length distribution and QC was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies). All libraries were pooled in equimolar ratio (5 libraries/lane) and sequenced on an Illumina HiSeq 4000 flow cell to yield ~66 million 50 bp single-end sequences per sample.

value: embryo head

value: 2 day post-fertilization


title: ncapg2_gRNA3_Cas9_rep2

description: DifferentialExpression.xls


title: ncapg2_gRNA3_Cas9_rep4

description: DifferentialExpression.xls


title: ncapg2_gRNA3_Cas9_rep3

description: DifferentialExpression.xls


title: E12_PHL_HoxDdel(8-13);HoxDdel(attp-SB3)_H3K4me1

description: mouse E12.5 del(8-13);del(attp-SB3) proximal hindlimb H3K4me1

value: Proximal hindlimb


title: whole fly male -High_elevation_18C-2

value: control (18C)


title: whole fly male -High_elevation_24C-7


title: whole fly male -High_elevation_18C-1


title: E12_PHL_HoxDdel(8-13);HoxDdel(attp-SB3)_input

description: mouse E12.5 del(8-13);del(attp-SB3) proximal hindlimb input


title: ncapg2_gRNA3_Cas9_rep1

description: DifferentialExpression.xls


title: F14036 Neg Control1


title: whole fly male -High_elevation_18C-4


title: whole fly male -Low_elevation_24C-7

value: elevated temperature (24C)

value: low elevation


title: E12_PFL_HoxDdel(8-13);HoxDdel(attp-SB3)_H3K4me1

description: mouse E12.5 del(8-13);del(attp-SB3) proximal forelimb H3K4me1

value: Proximal forelimb


title: whole fly male -Low_elevation_24C-3


title: whole fly male -Low_elevation_24C-8


title: E12_PFL_HoxDdel(8-13);HoxDdel(attp-SB3)_input

description: mouse E12.5 del(8-13);del(attp-SB3) proximal forelimb input


title: whole fly male -Low_elevation_24C-1


title: ncapg2_gRNA3_rep5

description: DifferentialExpression.xls


title: whole fly male -Low_elevation_24C-6


title: whole fly male -Low_elevation_24C-2


title: E12_PHL_HoxDdel(8-13)_H3K4me1

description: mouse E12.5 del(8-13) proximal hindlimb H3K4me1


title: whole fly male -Low_elevation_18C-8


title: ncapg2_gRNA3_rep3

description: DifferentialExpression.xls


title: whole fly male -Low_elevation_24C-5


title: E12_PHL_HoxDdel(8-13)_input

description: mouse E12.5 del(8-13) proximal hindlimb input


title: whole fly male -Low_elevation_18C-4


title: ncapg2_gRNA3_rep2

description: DifferentialExpression.xls


title: E12_PFL_HoxDdel(8-13)_H3K4me1

description: mouse E12.5 del(8-13) proximal forelimb H3K4me1


title: ncapg2_gRNA3_rep1

description: DifferentialExpression.xls


title: E12_PFL_HoxDdel(8-13)_input

description: mouse E12.5 del(8-13) proximal forelimb input


title: phenol_red_rep5

description: DifferentialExpression.xls

value: phenol red


title: ncapg2_gRNA3_rep4

description: DifferentialExpression.xls


title: ΔrrnI - ribosome profiling data rep2

city: Seoul

first: Seong-il

last: Eyun

address: 84 Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

description:
ribosome protected mRNA
rrnI-deleted strain
ΔrrnI - RP#2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to vibrio vulnificus CMCP6 whole genome (NCBI Reference Sequence: NC_004459.3, NC_004460.2) using  Bowtie2 or BWA.
Coordinates of mapped reads were obtained by processing BAM formatted files using BEDOPS tools and were stored in BED formatted files. Coordinates of genome features such as protein coding genes were extracted from the genome annotation data.
Boundaries of features such as transcription start sites and gene segments were prepared: a transcription start site was defined as positions from -60 to +60 (the first nucleotide of a start codon was numbered as +1) and a gene segment as positions from -60 to the end of the stop codon. Overlapping genome-mapped RNA-seq reads were assigned to these features.
The normalized abundance of reads was measured as number of reads per million mapped reads (RPM).
Genome_build: vibrio vulnificus CMCP6 (NCBI Reference Sequence: NC_004459.3, NC_004460.2)
Supplementary_files_format_and_content: exell file include Fold Change values(ΔrrnIcomp strain versus ΔrrnI strain)

organism: Vibrio vulnificus CMCP6

source_name: ΔrrnI - ribosome profiling data rep2

growth_protocol: Cells were grown at 30 °C in LBS media containing 0.2 μg/ml tetracycline (Tc) to an OD600 of 0.7. After treatment with 100 µg/ml chloramphenicol to stop translation, the cells were incubated at 30 °C for 5 min.

extract_protocol:
ribosome profiling: The culture was cooled on ice and harvested by centrifugation. The pellet was washed with pre-chilled buffer A (50 mM Tris-HCl, pH 7.6, 10 mM MgCl2, 100 mM NH4Cl, 6 mM 2-mercaptoethanol, 0.5 mM EDTA) containing 1 mM of chloramphenicol and was lysed using a French press. Cellular debris was removed by centrifuging for 30 min at 30,000 × g. The clarified lysate (supplemented with 5 mM CaCl2) was digested with micrococcal nuclease for 1 h at 25 °C and quenched with EGTA to a final concentration of 6 mM. The resulting lysate was loaded onto a 30% sucrose cushion. Crude ribosomes were pelleted by centrifugation at 100,000 × g for 16 h at 4 °C. The pellets were resuspended and loaded onto a 15–40% sucrose gradient and centrifuged at 79,500 × g for 13.5 h at 4 °C. After centrifugation, monosomes were obtained by fractionation and measurement of optical density at 260 nm. Monosomal RNA was obtained by phenol extraction and ethanol precipitation and was resuspended in RNase-free water. To obtain ribosome-protected mRNAs, extracted monosomal RNA was resolved on a 15% polyacrylamide-8 M urea-TBE gel. A band between 28 and 42 bp was excised, gel puriﬁed, precipitated, and resuspended in RNase-free water.
transcriptome: Total cellular RNA was extracted from cells using TRIzol according to the manufacturer’s instructions.
ribosome profiling: Isolated RNAs were used to construct a cDNA library for Illumina sequencing using the TruSeq Small RNA Sample Prep Kit according to the manufacturer’s instructions.
transcriptome: The mRNA in total RNA was converted into a library of template molecules suitable for subsequent cluster generation using the reagents provided in the TruSeq RNA Sample Preparation Kit  according to the manufacturer’s instructions.

value: rrnI::KmR, contain pRK415


title: phenol_red_rep4

description: DifferentialExpression.xls


title: ΔrrnI - transcriptome data rep2

description:
total RNA
rrnI-deleted strain
I-2-Total.fastq.gz
ΔrrnI - Tc#2

source_name: ΔrrnI - transcriptome data rep2


title: ΔrrnIcomp - ribosome profiling data rep2

description:
ribosome protected mRNA
rrnI-complemented strain
ΔrrnIcomp - RP#2

value: rrnI::KmR, contain pRK415-rrnI


title: phenol_red_rep3

description: DifferentialExpression.xls


title: whole fly male -Low_elevation_18C-3


title: phenol_red_rep2

description: DifferentialExpression.xls


title: ΔrrnIcomp - transcriptome data rep2

description:
total RNA
rrnI-complemented strain
Com-2-Total.fastq.gz
ΔrrnIcomp - Tc#2

source_name: ΔrrnIcomp - transcriptome data rep2


title: ΔrrnI - ribosome profiling data rep1

description:
ribosome protected mRNA
rrnI deleted strain
ΔrrnI - RP#1

source_name: ΔrrnI - ribosome profiling data rep1


title: whole fly male -Low_elevation_18C-2


title: ΔrrnIcomp - ribosome profiling data rep1

description:
ribosome protected mRNA
rrnI-complemented strain
ΔrrnIcomp - RP#1


title: ΔrrnI - transcriptome data rep1

description:
total RNA
rrnI deleted strain
ΔrrnI - Tc#1

source_name: ΔrrnI - transcriptome data rep1


title: phenol_red_rep1

description: DifferentialExpression.xls


title: ΔrrnIcomp - transcriptome data rep1

description:
total RNA
rrnI-complemented strain
ΔrrnIcomp - Tc#1

source_name: ΔrrnIcomp - transcriptome data rep1


title: whole fly male -Low_elevation_18C-7


title: whole fly male -Low_elevation_18C-6


title: whole fly male -Low_elevation_18C-1


title: Mouse_3_DNMT3A_WT (RRBS)

status: Public on Nov 26 2018

city: Edinburgh

first: Duncan

last: Sproul

state: Mid Lothian

address: Crewe Road South

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw Illumina sequencing output from the NextSeq were converted to paired FASTQ files without demultiplexing using ‘bcl2fastq’ and default settings (v2.17.1.14). These FASTQ files were then demultiplexed using custom python scripts considering indexes with perfect matches to the sample indexes. The different lanes for each sample were then combined.
Sequencing quality was assessed with FASTQC (v0.11.4). Low quality reads and remaining adaptors were removed using TrimGalore (v0.4.1, Settings: --adapter AGATCGGAAGAGC --adapter2 AAATCAAAAAAAC). NuGen adaptors contain extra diversity bases to facilitate sequencing. These were removed using the ‘trimRRBSdiversityAdaptCustomers.py’ Python script provided by NuGen (v1.11). The paired end reads were then aligned to the mm10 genome using Bismark (v 0.16.3 with Bowtie2 v2.2.6 with settings: -N 0 -L 20) before PCR duplicates were identified and removed using the 6bp UMIs present in the index reads and the ‘nudup.py’ Python script supplied by NuGen (v2.3). Aligned BAM files were processed to report coverage and number of methylated reads for each CpG observed. Forward and reverse strands were combined using Bismark’s methylation extractor and bismark2bedgraph modules with custom Python and AWK scripts.
Processed RRBS files were assessed for conversion efficiency based on the proportion of methylated reads mapping to the λ genome spike-in (>99.5% in all cases).
BigWigs were generated from RRBS data using CpGs with coverage ≥5
Genome_build: mm10
Supplementary_files_format_and_content: Processed coverage values for each CpG observed in sample. CpG position and total coverage (T) and methylated coverage (M) combining both strands. Columns = chr, start, end, T, M. Positions are 0-based, ie BED format.
Supplementary_files_format_and_content: bigWig files for each sample also supplied. Only contain CpGs with coverage >= 5 in that sample.

source_name: Mouse cortex

growth_protocol: For neural differentiation mES cells were differentiated as described previously (Plloard et al, PMID: 17141035). Briefly, cells were plated in 0.1% gelatine coated dishes in Neurobasal/DMEM/F12 (Life Technologies) supplemented with 1x B27 (Life Technologies), 1 x N2 (Life Technologies) and penicillin-streptomycin antibiotics. Cells were fed daily and harvested after 9 days of differentiation.

extract_protocol:
Genomic DNA isolated with DNeasy Blood & Tissue Kit (QIAGEN) or Nucleon BACC2 Genomic DNA Extraction Kit (illustra) and quantified by Qubit (Invitrogen). DNA from mouse cortex samples were concentrated using Agencourt AMPure XP technology.
200ng of purified DNA samples were processed using the Ovation RRBS Methyl-Seq system kit according to instructions with the following modifications (NuGen Technologies). Briefly, unmethylated phage λ DNA 0.5ng (NEB) was spiked into each sample to allow assessment of bisulfite conversion efficiency. The methylation-insensitive restriction enzyme MspI was then used to digest the gDNA, and digested fragments were ligated to adapters. Adapter ligated fragments were then repaired before bisulfite conversion with the Qiagen Epitect fast bisulfite conversion kit. Bisulfite-treated adapter-ligated fragments were amplified by 9 cycles of PCR and purified using Agencourt RNAClean XP beads. Libraries were quantified using the Qubit dsDNA HS assay and assessed for size and quality using the Agilent Bioanalyzer DNA HS kit. Sequencing was performed using the NextSeq 500/550 high-output version 2 kit (75bp paired end reads) on the Illumina NextSeq 550 platform. As instructed for the NuGen RRBS kit, 12bp index reads were generated to sequence the Unique Molecular Identifiers (UMI) in addition to the index present in the adaptors. Libraries were combined into equimolar pools and run on a single flow cell. 10% PhiX control library was spiked in to facilitate sequencing by generating additional sequence diversity. Library preparation and sequencing performed by WTCRF, Edinburgh.

value: cortex


title: Mouse_2_DNMT3A_WT (RRBS)


title: Mouse_1_DNMT3A_WT (RRBS)


title: Mouse_5_DNMT3A_heterozygous_mutant (RRBS)


title: WT_clone_3_NPC (RRBS)

source_name: ES cells differentiated to neurons

value: NPC cells

value: WT


title: Mouse_4_DNMT3A_heterozygous_mutant (RRBS)


title: WT_clone_2_NPC (RRBS)


title: DNMT3A_heterozygous_mutant_clone_1_NPC (RRBS)


title: DNMT3A_homozygous_mutant_clone_1_NPC (RRBS)


title: DNMT3A_homozygous_mutant_clone_2_NPC (RRBS)


title: WT_clone_1_NPC (RRBS)


title: DNMT3A_homozygous_mutant_clone_3_NPC (RRBS)


title: Mouse_6_DNMT3A_heterozygous_mutant (RRBS)


title: WT_clone_2_NPC

data_processing:
RNA-seq read quality was analysed using FASTQC (v0.11.4), with low quality reads and adaptors removed using trim-galore with default settings (v0.4.1). Reads were aligned to the mm10 genome using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 -- no-unal). Multi-mapping reads excluded using SAMtools (v1.6, with settings: -bq 10) respectively.
The number of reads mapping to each ENSEMBL annotated gene (Release 91/mm10) was calculated using the featureCounts module of the subread aligner (v1.5.2). Only reads mapping to exons were considered. Gene read counts were then analysed using EdgeR (v3.18.1) with Trimmed Mean of M-values (TMM) normalization. The log2 normalized counts per million (CPM) and log2 ratios calculated by EdgeR were then subject to further analysis. Only genes where CPM was >1 in ≥2 samples and that are annotated as protein coding in ENSEMBL were considered for analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TMM normalized RPKM values for protein coding genes following exclusion as described above.
Supplementary_files_format_and_content: Raw counts derived from featureCounts also supplied for all ENSEMBL genes.

extract_protocol:
RNA was extracted using the RNeasy kit (QIAGEN) according to manufacturer instructions with DNAseI (QIAGEN) treatment.
Random primed cDNA from poly-A selected RNA was converted into an Illumina sequencing library and single-end 50bp reads generated on an Illumina HiSeq machine (GATC Biotech Konstanz, Germany).


title: DNMT3A_homozygous_mutant_clone_2_NPC


title: OT-I cells: control_input

city: Stanford

first: Mark

state: CA

address: Stanford University

institute: Institute for Immunity, Transplantation and Infection

data_processing:
Map the sequencing reads to the Mus musculus genome (version mm10) using Bowtie2 with no more than two mismatches.
Remove PCR duplicates by samtools
Use MACS2 for peak calling, compare with each input control with FDR less than 0.001.
Genome_build: mm10
Supplementary_files_format_and_content: peak files with quantitative data for each sample

source_name: CD8+ T cells

growth_protocol: CD8+ T cells were isolated from spleen and lymph nodes of OT-I mice using Dynabeads Flowcomp mouse CD8 kit (Invitrogen). Then the cells were stimulated with SIINFEKL peptide (OVA257-264) at 2.5 ng/mL in the presence of 10U/mL IL-2 for 24 hr. Retroviral supernatants were harvested, filtered, and supplemented with 6μg/mL polybrene. OT-I T cell cultures were spinduced with the retroviral supernatant for 90 min at 1800 rpm, 32ºC. 48 hr later, hCD2+ cells were sorted prior to re-stimulation.

extract_protocol:
Re-stimulated control or Eomes-overexpressing OT-I cells were harvested, fixed with 1% formaldehyde for 10min at room temperature and stopped by adding glycine to 125mM. ChIP experiment was done following instructions of Active Motif’s ChIP assay kit (53035) with slight modifications, in which 10 cycles of sonication (Bioruptor) were added after enzyme digestion, and dynabeads protein G (Life Technologies) were used for immunoprecipitations. 5μg anti-TBR2/Eomes antibodies (ab23345, abcam) were used for each reaction.
The precipitated DNA was sent to BGI genomics for library construction.

treatment_protocol: hCD2+ OT-I cells were plated at 40,000 cells/well in 96-well plates and re-stimulated with 2.5ng/mL OVA with 10U/mL IL-2 for 3 days before harvested for RNAseq analysis.

value: spleen and lymph nodes

value: OT-I transgenic

value: none (input)


title: OT-I cells: eomes

value: anti-TBR2/Eomes antibodies (ab23345, abcam)


title: OT-I cells: control


title: OT-I cells: eomes_input


title: OT-I cells: Eomes_1

data_processing:
Use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution
Use internal software SOAPnuke to filter reads
Use hisat2 to map to mm10 genome
Map clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM
Detect DEGs with PossionDis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

extract_protocol:
Total RNA was extracted by TRIZOL.
cDNA was made and library was constructed by BGI Genomics.


title: OT-I cells: Ctrl_1


title: WT_clone_3_NPC


title: WT_clone_1_NPC


title: DNMT3A_homozygous_mutant_clone_1_NPC


title: DNMT3A_homozygous_mutant_clone_3_NPC


title: LG-8_160816_L004

city: Medford

first: Eric

last: Reed

state: MA

address: 419 Boston Ave.

department: Data Intensive Studies Center

institute: Tufts University

data_processing:
FASTQ files were quality checked via FASTQC and possessed Phred quality scores > 30 (i.e. less than 0.1% sequencing error).
Raw Fastq files were aligned using TopHat v2.1.1.
Reads were counted using FeatureCountes v1.5.0.
Genome_build: mm38
Supplementary_files_format_and_content: counts

source_name: striatum

growth_protocol: C57BL/6J (B6J) and C57BL/NJ (B6NJ) mice were purchased from JAX at 7 weeks of age and were habituated in the vivarium one week prior to experimental testing that occurred next door. All behavioral testing was performed during the light phase of the 12 h light/dark cycle (0800 h to 1300 h). For QTL mapping, B6J females were crossed to B6NJ males to generate B6J x B6NJ-F1 mice and B6J x B6NJ F1 offspring were intercrossed to generate B6J x B6NJ F2 mice. Mice were 50-100 days old at the time of testing. All experiments were performed during the light cycle, and the study was approved by the Institutional Animal Care and Use Committee of Boston University School of Medicine. All studies were carried out in accordance with the National Institutes of Health’s Guide for the Care and Use of Laboratory Animals.

extract_protocol:
Brains were rapidly removed, sectioned with a brain matrix to obtain a 3 mm thick section, and a 2 mm diameter punch of the striatum was collected. Harvested left and right striatum punches were pooled and immediately placed in RNAlater (Life Technologies, Grand Island, NY, USA) for 48 h prior to storage in a -80°C freezer. Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA, USA) as described57.
RNA was shipped to the University of Chicago Genomics Core Facility for cDNA library preparation using the Illumina TruSeq (oligo-dT; 100 bp paired-end reads).

treatment_protocol: During the four days prior to baseline hot plate assessment, F2 mice recieved four daily OXY injections (20 mg/kg, i.p.).

tag: strain background

value: C57BL/6J (B6J) X C57BL/NJ (B6NJ)

tag: sample id

tag: run

tag: lane

tag: cage _id

tag: Sex

value: M


title: LG-9_160823_L007

value: F


title: LG-8_160830_L007


title: LG-8_160823_L008


title: LG-9_160830_L008


title: LG-9_160830_L007


title: LG-8_160830_L008


title: LG-8_160823_L007


title: LG-9_160823_L008


title: LG-9_160816_L004


title: LG-7_160823_L008


title: LG-7_160823_L007


title: LG-7_160816_L004


title: LG-7_160830_L007


title: LG-7_160830_L008


title: LG-6_160830_L007


title: LG-6_160830_L008


title: LG-6_160823_L007


title: LG-5_160816_L004


title: LG-4_160823_L008


title: LG-6_160823_L008


title: LG-4_160823_L007


title: LG-6_160816_L004


title: LG-5_160830_L007


title: LG-5_160823_L008


title: LG-5_160823_L007


title: LG-5_160830_L008


title: LG-4_160830_L007


title: LG-4_160816_L004


title: LG-4_160830_L008


title: LG-3_160830_L007


title: LG-23_160816_L004


title: LG-23_160823_L008


title: LG-3_160830_L008


title: LG-3_160823_L008


title: LG-22_160830_L007


title: LG-3_160823_L007


title: LG-23_160830_L007


title: LG-23_160830_L008


title: LG-3_160816_L004


title: LG-23_160823_L007


title: LG-22_160816_L004


title: LG-22_160823_L008


title: LG-22_160830_L008


title: LG-22_160823_L007


title: LG-21_160816_L004


title: LG-2_160830_L007


title: LG-20_160830_L007


title: LG-20_160823_L008


title: LG-21_160823_L007


title: LG-21_160823_L008


title: LG-20_160823_L007


title: LG-20_160816_L004


title: LG-2_160823_L007


title: LG-21_160830_L008


title: LG-2_160830_L008


title: LG-21_160830_L007


title: LG-19_160830_L008


title: LG-2_160823_L008


title: LG-19_160823_L007


title: LG-19_160816_L004


title: LG-18_160823_L007


title: LG-18_160830_L007


title: LG-17_160816_L004


title: LG-18_160823_L008


title: LG-17_160830_L007


title: LG-17_160823_L007


title: LG-19_160830_L007


title: LG-19_160823_L008


title: LG-18_160816_L004


title: LG-18_160830_L008


title: LG-17_160823_L008


title: LG-17_160830_L008


title: LG-20_160830_L008


title: LG-16_160830_L007


title: LG-2_160816_L004


title: LG-16_160816_L004


title: LG-16_160823_L008


title: LG-16_160830_L008


title: LG-16_160823_L007


title: LG-15_160816_L004


title: LG-14_160823_L007


title: LG-15_160823_L007


title: LG-15_160823_L008


title: LG-15_160830_L008


title: LG-15_160830_L007


title: LG-14_160823_L008


title: LG-14_160816_L004


title: LG-14_160830_L007


title: LG-13_160830_L007


title: LG-14_160830_L008


title: LG-13_160830_L008


title: LG-13_160823_L008


title: LG-13_160823_L007


title: LG-11_160816_L004


title: LG-12_160830_L008


title: LG-12_160823_L007


title: LG-12_160830_L007


title: LG-11_160823_L008


title: LG-11_160823_L007


title: LG-12_160816_L004


title: LG-11_160830_L008


title: LG-10_160830_L007


title: LG-10_160823_L008


title: LG-10_160823_L007


title: LG-11_160830_L007


title: LG-10_160830_L008


title: LG-10_160816_L004


title: LG-1_160823_L008


title: LG-1_160816_L004


title: LG-1_160830_L008


title: LG-1_160830_L007


title: LG-1_160823_L007


title: LG-13_160816_L004


title: LG-12_160823_L008


title: IA42

city: Utrecht

first: Ynte

last: Ruigrok

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

data_processing:
Mapping with STAR 2.3.1, allowing for two mismatches.
SAMtools 0.1.185 was used to sort the aligned reads.
Gene level quantification was performed with HTSeq-0.5.4 using -- mode=union -- stranded=no, using Ensembl version 71 as gene annotation database
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: raw counts txt files containing readcounts were generated using HTSeq-0.5.4 and Ensembl version 71 on RNA-seq data

source_name: Unruptured intracranial aneurysm

extract_protocol:
Frozen in liquid nitrogen, RNA extraction.
Illumina TruSeq DNA library protocol.

value: Female

tag: aneurysm location

value: ACM (M2 or more distal)

tag: tissue/status

value: Unruptured intracranial aneurysm


title: IA41

value: Male


title: IA40

source_name: Unknown rupture status

value: ACOM

value: Unknown rupture status


title: IA44

value: ACM (M1)


title: IA43

source_name: Ruptured intracranial aneurysm

value: Ruptured intracranial aneurysm


title: IA38


title: IA36


title: IA35


title: IA30


title: IA29


title: IA27


title: IA26


title: IA28


title: IA21


title: IA23


title: IA33

value: PCOM


title: IA24


title: IA25


title: IA22


title: IA20


title: IA17


title: IA19


title: IA18

value: ACA (A2 or more distal)


title: IA16


title: IA39


title: IA15


title: IA14


title: IA12


title: IA32


title: IA8


title: IA37


title: IA7


title: IA9


title: IA11


title: IA31


title: IA5


title: IA3


title: IA6

source_name: Unknown intracranial aneurysm

value: Unknown intracranial aneurysm


title: IA2


title: IA4


title: CO16

source_name: Intracranial cortical artery

value: Intracranial cortical artery


title: CO15


title: IA1


title: CO13


title: CO14


title: CO12


title: CO10


title: CO8


title: CO7


title: CO9


title: CO6


title: IA13


title: IA10


title: CO5


title: CO4


title: CO3


title: CO2


title: CO1


title: Non-db-derived-neutrophil_Pool8

city: Kitakyushu

first: Takahiro

last: Umehara

address: 1-1 Iseigaoka Yahatanishiku

institute: University of Occupational and Environmental Health

description:
TU0106_08
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/+)
The expression of miRNA in non-db-derived neutrophils.
microRNA
Replicate 1

hyb_protocol: The dried Cy3-labelled miRNA was resuspended in 18 μL of nuclease-free water, 4.5 μL of the 10X GE Blocking Agent and 22.5 μL of 2x Hi-RPM Hybridization Buffer was added following the manufacturer’s instructions. After the sample was incubated at 100°C for 5 minutes, it was immediately transferred to an ice water bath for 5 minutes, and hybridized to Mouse miRNA Microarray 8x60K rel.21.0 (Agilent Technologies) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 5 minute with 37°C GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The GeneView files were generated using Agilent's Feature Extraction software version 11.5.1.1.

source_name: Neutrophils from bone marrow, non-diabetic

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng total RNA using the miRNA Complete Labeling and hyb kit (Agilent Technologies) according to the manufacturer's instructions.

extract_protocol: miRNA was purified from neutrophils using a microRNA isolation kit, Mouse Ago2 (Wako, Osaka, Japan). Microarray analysis was performed on a total of eight pools (four pools of three db BM samples and four pools of three non-db BM samples) using SurePrint G3 Mouse miRNA microarray, in accordance with the manufacturer’s instructions (Agilent Technologies, Tokyo, Japan).

treatment_protocol: Bone marrow (BM) was flushed from femurs and tibiae. Neutrophils from the pooled BM of three db or three non-db mice were isolated using a neutrophil isolation kit (Miltenyi Biotec GmbH, Germany).

tag: strain/background

value: BKS.Cg-Dock7(m) +/+ Lepr(db)/J

value: Lepr (db/+)

value: neutrophils from bone marrow

tag: gender

value: male

value: 8 weeks


title: Non-db-derived-neutrophil_Pool7

description:
TU0106_07
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/+)
The expression of miRNA in non-db-derived neutrophils.
microRNA
Replicate 1

tag: genotype/variation


title: control_2_fibroblast

data_processing:
RNA-seq read quality was analyzed using FASTQC (v0.11.4), with low quality reads and adaptors removed using trim-galore with default settings (v0.4.1). Reads were aligned to the hg19 genome using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 -- no-unal). Multi-mapping reads excluded using SAMtools (v1.6, with settings: -bq 10) respectively.
The number of reads mapping to each ENSEMBL annotated gene (Release 75/hg19) was calculated using the featureCounts module of the subread aligner (v1.5.2). Only reads mapping to exons were considered. Gene read counts were then analyzed using EdgeR (v3.18.1) with Trimmed Mean of M-values (TMM) normalization. The log2 normalized counts per million (CPM) and log2 ratios calculated by EdgeR were then subject to further analysis. Only genes where CPM was >1 in ≥2 samples and that are annotated as protein coding in ENSEMBL were considered for analysis.
Genome_build: hg19
Supplementary_files_format_and_content: TMM normalized RPKM values for protein coding genes following exclusion as described above.
Supplementary_files_format_and_content: Raw counts derived from featureCounts also supplied for all ENSEMBL genes.
Raw sequencing reads are available through EGA (protected patient data): EGAS00001003232

source_name: primary fibroblast cell line

growth_protocol: Fibroblast cell lines were maintained at 3% O2 in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) supplemented with 10% FBS and 5% penicillin-streptomycin antibiotics or in AmnioMAX-C100 (Life Technologies).

tag: disease state

value: healthy control

tag: cell line

value: primary fibroblast cell line

tag: genotype

value: control


title: Non-db-derived-neutrophil_Pool6

description:
TU0106_06
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/+)
The expression of miRNA in non-db-derived neutrophils.
microRNA
Replicate 1

tag: cell type


title: patient_1_fibroblast

value: microcephalic dwarfism

value: DNMT3A W330R heterozygous


title: control_1_fibroblast


title: Non-db-derived-neutrophil_Pool5

description:
TU0106_05
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/+)
The expression of miRNA in non-db-derived neutrophils.
microRNA
Replicate 1


title: CO11

value: Female


title: BS4

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

description:
asf1 replicate 2
NG-16175_asf1_lib259174_5955_4

data_processing:
Reads were trimmed for low quality bases and adapter removal with Trimmomatic (Bioinformatics 2014, 30:2114–2120; parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40).
Reads were mapped to the Sordaria macrospora genome and methylated cytosines identified using Bismarck (Bioinformatics 2011, 27:1571-2).
After mapping, reads were deduplicated, and methylated cytosines identified with the Bismarck methylation extractor (parameters --ignore_r2 2 --no_overlap).
Downstream analyses were performed with custom-written Perl scripts.
Genome_build: Sordaria macrospora genome version 02, accession numbers CABT02000001-CABT02001583
Supplementary_files_format_and_content: tab delimited text file containing methylation information for each analyzed cytosine with a minimum coverage of 10

organism: Sordaria macrospora

source_name: asf1 mutant_total sexual mycelium

growth_protocol: Samples were inoculated into liquid SWG medium from petri dishes grown for 2d on solid BMM medium at 25 °C.  Samples in SWG medium were grown for 4d at 25 °C in surface cultures to induce sexual development, and then harvested for DNA preparation

extract_protocol:
Mycelia were ground in liquid nitrogen, and DNA was purified by phenol/chloroform extraction and RNase-treated. DNA was purified using Amicon Ultra 30k columns with buffer 10 mM Tris-HCl pH 8.0.
DNA libraries of bisulfite treated DNA samples were used for library construction for sequencing in an Illumina HiSeq. Bisulfite treatment, library preparation and sequencing were performed at GATC Biotech AG (Konstanz, Germany).
Directional genomic libraries

treatment_protocol: Mycelia were harvested and frozen in liquid nitrogen for DNA extraction.

tag: tissue

value: total sexual mycelium


title: BS3

description:
wild type replicate 2
NG-16175_wt_lib259173_5956_6

source_name: WT_total sexual mycelium

value: wild type


title: BS2

description:
asf1 replicate 1
NG-15156_asf1_lib244005_5842_8


title: P10-EGFP-plus-Lam-mius-1

city: Kurume

first: Yuichi

last: Shima

state: Fukuoka

address: Asahimachi 67

department: Department of Anatomy

institute: Kurume University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and  mapped to mm 10 whole genome using Tophat v2.1.1. with the option -library-type fr-secondstrand.
Fragments Per Kilobase of exon per Million reads mapped (FPKM) were calculated using Cufflinks v2.2.1 with the option -u -library-type fr-secondstrand.
Genome_build: mm 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: EGFP-positive and Laminin-negative cells sorted from mFLE-Cre;CAG-CAT-EGFP mice at postnatal day 10.

extract_protocol:
Testicular interstitial cells were sorted from mFLE-Cre;CAG-CAT-EGFP mouse testes at postnatal day 10. Total RNA was extracted from the sorted cells by using RNeasy micro kit (Qiagen).
Libraries were constructed by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

tag: strain

value: testis

tag: age

value: postnatal day 10

tag: cell population


title: P10-EGFP-plus-Lam-mius-2

value: EGFP-positive and Laminin-negative cells sorted from mFLE-Cre;CAG-CAT-EGFP mice at postnatal day 10.


title: Db-derived-neutrophil_Pool1

description:
TU0106_01
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/db)
The expression of miRNA in db-derived neutrophils.
microRNA
Replicate 1

source_name: Neutrophils from bone marrow, diabetic

value: Lepr (db/db)


title: Db-derived-neutrophil_Pool2

description:
TU0106_02
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/db)
The expression of miRNA in db-derived neutrophils.
microRNA
Replicate 1

value: BKS.Cg-Dock7(m) +/+ Lepr(db)/J


title: Control 1 ChIPseq K27me3Rx Input

data_processing:
ChIP-seq read quality was analyzed using FASTQC (v0.11.4), with low quality reads and adaptors removed using trim-galore with default settings (v0.4.1). Reads were aligned to the hg19 genome using bowtie 2 (v2.3.1, with settings: -N 1 -L 20 -- no-unal). Multi-mapping reads excluded using SAMtools (v1.6, with settings: -bq 10). PCR duplicates excluded using SAMBAMBA (v0.5.9). For ChIP Rx-seq, reads were aligned to combined hg19 and dm6 genomes using the same settings.
Tracks for data visualization generated using Homer (v4.8)73. Aligned BAMs were converted to tag directories setting the fragment length to 180bp and converted to bigWig files using Homer’s makeUCSCfile function after filtering with the removeOutOfBounds.pl function.
ChIP-seq peaks were called from tag directories using Homer’s findPeaks function (settings: -style histone) and the corresponding input chromatin control sample.
Genome_build: hg19, dm6
Supplementary_files_format_and_content: bigWig files derived as described above.
Supplementary_files_format_and_content: BED file of Homer peaks for ChIP samples.
Raw sequencing reads are available through EGA (protected patient data): EGAS00001003232

extract_protocol:
Cross-linked chromatin immunoprecipitation was adapted from a previous publication (Illingworth et al, PMID: 27723457) with the following modifications. 2x106 cells were harvested, washed and crosslinked with 1% methanol-free formaldehyde in PBS. Crosslinked cells were lysed directly for 15 min on ice in cold lysis buffer (10 mM EDTA, 50 mM Tris-HCl (pH8), 1% SDS). All buffers used during chromatin capture were freshly supplemented with protease inhibitors (Roche) and 1 mM DTT. For ChIP-Rx crosslinked Drosophila chromatin (S2 cells) was spiked into samples before sonication (ratio of 20:1 human to Drosophila cells). Lysates were sonicated with two 30 sec pulses using a soniprep 150 plus (MSE) followed by 10 cycles (30 s on / 30 s off on ‘high’ setting at 4°C) on a Bioruptor Plus (Diagenode). Following centrifugation for 10 min at 20,000xg, 4°C, supernatant was supplemented with Triton X-100 (final concentration 1%) and 50 μg/ml BSA and then added to Protein A dynabeads (Invitrogen) pre-coupled with the respective antibody (H3K27me3 antibody (Cell Signaling; C36B11; Cat.no. 9733S); H3K4me3 (Millipore; 07-473); H3K36me3 (Active Motif; #61101)). 10% of input material was retained for use as a reference. The bead-chromatin mixture was incubated under rotation at 4°C overnight. Beads were then washed twice for 10 min at 4°C with each of the following buffers: IP dilution buffer (2 mM EDTA, 150 mM NaCl, 20 mM Tris HCl pH8, 1% Triton X-100), buffer A’ (20 mM Tris pH8, 500 mM NaCl, 1 mM EDTA pH8, 1% TritonX-100, 0.1% Na-deoxycholate, 0.1% SDS), buffer B’ (20 mM Tris pH8, 1 mM EDTA pH8, 250 mM LiCl, 1% NP-40, 0.1% Na-deoxycholate). Finally, beads were washed three times with 1xTE buffer (1 mM EDTA pH8, 10 mM Tris pH8). Captured chromatin was eluted, followed by reverse crosslinking through addition of Tris HCl pH6.8 (100 mM), NaCl (300 mM) and 20 μg RNAse A at 65°C overnight. Input material was similarly de-crosslinked. Degradation of proteins with 20 μg Proteinase K and incubation at 37°C for 2 hrs. Samples purified with the MinElute PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645) according to the manufacturer instructions using barcoded adapters (NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1 or 2), E7335; E7500S). For input reference libraries 50 ng material were used. Adapter197 ligated DNA was size selected for an insert size of 150 or 200 bp using AMPure XP beads. Libraries were amplified for 7 cycles in the final PCR amplification step. Amplified libraries were purified using AMPure XP beads and eluted in EB. Libraries were pooled in an equimolar ratios. For H3K27me3 single-end 50bp reads were generated on an Illumina HiSeq machine (GATC Biotech Konstanz, Germany). For H3K4me3, H3K36me3 ChIP-Rx and H3K27me3 ChIP-Rx single-end 75bp reads were generated on an Illumina NextSeq 550 machine.

tag: chip antibody


title: Patient 1 ChIPseq K27me3Rx ChIP

tag: spike-in

value: crosslinked Drosophila chromatin (S2 cells)

value: H3K27me3 (Cell Signaling; C36B11; Cat.no. 9733S)


title: Db-derived-neutrophil_Pool4

description:
TU0106_04
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/db)
The expression of miRNA in db-derived neutrophils.
microRNA
Replicate 1

value: neutrophils from bone marrow

value: male


title: Control 1 ChIPseq K27me3Rx ChIP

value: healthy control


title: Db-derived-neutrophil_Pool3

description:
TU0106_03
BKS.Cg-Dock7m +/+ Leprdb/J (Leprdb/db)
The expression of miRNA in db-derived neutrophils.
microRNA
Replicate 1

value: 8 weeks


title: patient_2_fibroblast

value: primary fibroblast cell line


title: Patient 1 ChIPseq K27me3Rx Input

value: microcephalic dwarfism


title: Control 2 ChIPseq K27me3 ChIP

value: control


title: Control 2 ChIPseq K27me3 Input


title: Low-fat-female [TW892_pool8-LF_MeDIP]

city: Aurora

first: Madeline

last: Keleher

state: CO

department: Pediatrics

institute: University of Colorado Anschutz

data_processing:
Raw reads were aligned to the mm9 genome
methylQA was used to process the BAM file and generate BED files
Genome_build: mm9
Supplementary_files_format_and_content: Bed files include reads for each sample

source_name: Liver

growth_protocol: Liver tissue was isolated from SM/J mice

extract_protocol:
Phenol chloroform was used to extract DNA
DNA libraries were prepared as described by: Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015;72:29-40.

value: hepatic

value: SM/J

tag: diet

value: Low-fat

value: female

value: adult


title: High-fat-female [TW890_pool6-HF_MeDIP]

value: High-fat

tag: Sex


title: Low-fat-female [TW891_pool7-LF_MeDIP]


title: P10-EGFP-plus-Lam-plus-1

source_name: EGFP-positive and Laminin-positive cells sorted from mFLE-Cre;CAG-CAT-EGFP mice at postnatal day 10.

value: testis

value: postnatal day 10


title: High-fat-female [TW887_pool5-HF_MeDIP]


title: Control 1 ChIPseq K27me3 ChIP


title: Low-fat-male [TW885_pool3-LM_MeDIP]


title: P10-EGFP-plus-Lam-plus-2

value: EGFP-positive and Laminin-positive cells sorted from mFLE-Cre;CAG-CAT-EGFP mice at postnatal day 10.


title: Patient 1 ChIPseq K27me3 ChIP

value: DNMT3A W330R heterozygous

value: H3K27me3 (Cell Signaling; C36B11; Cat.no. 9733S)


title: Control 1 ChIPseq K27me3 Input


title: High-fat-male [TW868_pool2-HM_MeDIP]

value: male


title: BS1

description:
wild type replicate 1
NG-15156_wt_lib241439_5842_8

value: wild type

value: total sexual mycelium


title: Patient 1 ChIPseq K27me3 Input

value: primary fibroblast cell line


title: Patient 2 ChIPseq K27me3ChIP

value: microcephalic dwarfism


title: Low-fat-female [TW875_pool7-LF_MRE]


title: High-fat-female [TW844_pool5-HF_MRE]


title: High-fat-female [TW874_pool6-HF_MRE]


title: Low-fat-male [TW843_pool4-LM_MRE]


title: Low-fat-male [TW842_pool3-LM_MRE]


title: RBPs footprints in H2B-APEX2 cells

city: Tel Aviv

first: Daniel

last: Benhalevy

address: Tel Aviv University, Green Bldg. Room 205

department: Shmunis School of Biomedicine and Cancer Research

country: Israel

institute: Tel-Aviv University

description: Pooled_LongAndShortFootprintsAnalysis.xlsx

data_processing:
Illumina HiSeq 3000 platform was used for sequencing
Basecalling was done using bcl2fastq V2.17.1
The reads were aligned to the hg19 genome using TopHat (for RNA seq) or PARalyzer (for RBP footprints)
RNAseq reads and RPKM values per gene were generated by RNAcounter
Genome_build: hg19
Supplementary_files_format_and_content: RNAcounter / PARalyzer output files

growth_protocol: Cells were grown and routinely passaged in DMEM supplemented with 10% FCS and 1% pen/strip, and selective agent as required.

extract_protocol:
Preadenylated, barcoded 3´adapter oligonucleotide was ligated followed by ligation of a 5´adapter. Ligation products were reverse transcribed and amplified by PCR.
Cells were extracted in RIPA buffer, RNA was isolated by Phenol-Chloroform extraction

treatment_protocol: 16 hours of 4SU labeling and Dox induction, BP addition for 30 min followed by Proximity biotinylation

value: T-Rex stable line inducibly expressing V5-H2B-APEX2


title: High-fat-male [TW841_pool2-HM_MRE]

value: hepatic


title: High-fat-male [TW840_pool1-HM_MRE]

value: SM/J


title: RBPs footprints in Connexin43-APEX2 cells

value: T-Rex stable line inducibly expressing Connexin43-EGFP-APEX2


title: RBPs footprints in APEX2-NES cells

value: T-Rex stable line inducibly expressing V5-APEX2-NES


title: RBPs footprints in negative control cells

value: T-Rex


title: Bound RNA in Connexin43-APEX2 cells

description:
2016_RNAseqTotalAndBound.xlsx
2017_RNAseq_TotalAndBound.xlsx

extract_protocol:
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina without rRNA depletion
Cells were extracted in RIPA buffer, RNA was isolated by Phenol-Chloroform extraction


title: Bound RNA in H2B-APEX2 cells


title: an010_WT

first: Nikolaus

last: Rajewsky

address: Robert-Rössle-Str. 10

department: BIMSB

institute: MDC Berlin

description: Drop-seq library

data_processing:
basecalling using bcl2fastq v2.18.0.12 with parameters --no-lane-splitting --fastq-compression-level=9 --mask-short-adapter-reads 15
FastqToSam, from package Picard-tools v.2.9.0, with default parameters
Cell barcode to tag in 2nd read. TagBamWithReadSequenceExtended, from package Drop-seq_tools v1.12 with parameters BASE_RANGE=1-12 DISCARD_READ=false TAG_NAMES=XC COMPRESSION_LEVEL=0
UMI to tag in 2nd read and removal of first read. TagBamWithReadSequenceExtended, from package Drop-seq_tools v1.12 with parameters BASE_RANGE=13-20 DISCARD_READ=true TAG_NAMES=XM COMPRESSION_LEVEL=0
Filter sequences with low quality barcodes. FilterBAM, from package Drop-seq_tools v1.12 with parameters TAG_REJECT=XQ
Trimming SMART adapter. TrimStartingSequence, from package Drop-seq_tools v1.12, with parameters SEQUENCE=AAGCAGTGGTATCAACGCAGAGTGAATGGG MISMATCHES=0 NUM_BASES=5
Trimming polyA. PolyATrimmer, from package Drop-seq_tools v1.12 with parameters MISMATCHES=0 NUM_BASES=6
SamToFastq, from package Picard-tools v.2.9.0 with default parameters
Alignment using STAR v2.5.3a with default parameters
SortSam, from package Picard-tools v.2.9.0 with default parameters
Merge barcode tags with mapped output. MergeBamAlignment, from package Picard-tools v.2.9.0 with parameters INCLUDE_SECONDARY_ALIGNMENTS=false PAIRED_RUN=false
TagReadWithGeneExon, from package Drop-seq_tools v1.12, with annotation Mus_musculus GRCm38.p4.gtf TAG=GE CREATE_INDEX=true
DetectBeadSynthesisErrors, from package Drop-seq_tools v1.12 with parameters NUM_BARCODES=12000, PRIMER_SEQUENCE=AAGCAGTGGTATCAACGCAGAGTAC
Custom R script that calculates the inflection point of the cumulative sum of reads and returns the number of barcodes until that point. Those barcodes and include in downstream steps
DigitalExpression, from package Drop-seq_tools v1.12, This step creates the dge.txt.gz which is provided as processed data files. Parameters the output of the previous step, custom R script
Genome_build: mm10
Supplementary_files_format_and_content: All dge.txt.gz files are digital gene expression matrices. These are matrices of raw counts (rows are genes, columns are cells). Values are separated by tab.

source_name: adult subventricular zone

extract_protocol:
SVZs were microdissected, dissociated to single cells, debris and dead cells removed. The single-cell suspension was subjected to Drop-seq.
Drop-seq and single-cell library generation was performed as described in Alles et al., 2017, BMC Biol 15:44 (based on Macosko et al., 2015, Cell 161, 1202–1214). Drop-seq libraries were sequenced in paired-end mode on Illumina Nextseq 500  sequencers with 1% PhiX spike-in for run quality control. We used Illumina Nextseq500/550 High  Output v2 kits (75 cycles). We sequenced in paired-end mode: Read 1: 20 bp (bases 1-12 cell barcode, bases 13-20 UMI); Read 2: 64 bp; Index read: 8 bp.

value: brain

tag: brain region

value: subventricular zone, SVZ

tag: fixation

tag: number of animals

tag: age (weeks)

tag: mouse strain

value: TCF/Lef_LacZ x Lrp2 <267> x FVBN

value: 2 wildtype and 2 heterozygous littermate controls


title: High-fat-male [TW884_pool1-HM_MeDIP]

value: High-fat

value: adult


title: an007_WT

description: Drop-seq library

value: male

value: 1 wildtype and 3 heterozygous littermate controls


title: Bound RNA in APEX2-NES cells

tag: genotype/variation


title: an007_KO

description: Drop-seq library

value: LRP2 knockout


title: Bound RNA in negative control cells

tag: cell line


title: an008

description: Drop-seq library

tag: genotype

value: wildtype


title: Patient 2 ChIPseq K27me3Input

tag: disease state

value: microcephalic dwarfism

value: primary fibroblast cell line

value: DNMT3A W330R heterozygous


title: an009

description: Drop-seq library

tag: tissue

value: mixed

value: 2 female, 2 male


title: Total RNA in Connexin43-APEX2 cells

extract_protocol:
Library was constructed using the NEBnext Ultra Directionsal RNA Library Prep Kit for Illumina with rRNA depletion
Cells were extracted in RIPA buffer, RNA was isolated by Phenol-Chloroform extraction

value: T-Rex stable line inducibly expressing Connexin43-EGFP-APEX2


title: daf-16;fer-15 Day7 rep3

city: Beijing

first: Wenhui

last: Li

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences

data_processing:
RNA-seq reads were aligned to the C. elegans reference genome (ws235) using HISAT2 (v2.0.4) with default parameters.
Gene-level read counts were calculated using HTSeq (v0.6.1p1) based on the Ensembl gene annotation v85.
Genome_build: ws235
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown on High Growth (HG) plates supplemented with OP50 bacteria at 25 °C and harvested on adult day 1 through day 7.

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

tag: strain/genotype

tag: developmental stage

value: Adult day 7


title: Low-fat-female [TW876_pool8-LF_MRE]

value: hepatic

tag: strain

value: SM/J

value: Low-fat

value: female

tag: age


title: daf-16;fer-15 Day7 rep2


title: daf-16;fer-15 Day7 rep1


title: an003_L

description: Drop-seq library

value: brain

value: subventricular zone, SVZ


title: an003_F

description: Drop-seq library

value: 80% Methanol/PBS


title: daf-16;fer-15 Day6 rep3

value: Adult day 6


title: an010_KO

description: Drop-seq library

value: male

value: TCF/Lef_LacZ x Lrp2 <267> x FVBN

value: LRP2 knockout


title: an002

description: Drop-seq library

value: wildtype


title: daf-16;fer-15 Day6 rep2


title: Total RNA in negative control cells

value: T-Rex


title: daf-16;fer-15 Day6 rep1