title: PBMC_E_m_53

tag: sequencingid

tag: studysubjectid

value: Etanercept

value: stopped

tag: rf

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD006_indexed

status: Public on Aug 24 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: MOs

tag: Sex

value: male

tag: age

tag: strain


title: AB17GFP_Brg1

city: Shanghai

first: Ze-Guang

last: Han

address: 800 Dongchuan Road

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
Reads were aligned to the mm10 reference genome using bowtie2;
Low-quality reads were removed by SAMtools;
PCR duplicates were removed using Picard tool (http://broadinstitute.github.io/picard)
The MACS2 with default parameters was deployed for peak calling, with corresponding inputs as background separately.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files

source_name: AB17: immortalized primary hepatocytes with Arid1afl/fl genotype.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone/TF-DNA complexes were isolated with antibody.
The ChIP libraries for Illumina sequencing were constructed using NEBNext® ChIP-Seq Library Prep Master Mix and sequenced on Illumina HiSeq-2500 instrument.

tag: treatment

value: AB17GFP cells infected by the adenoviral empty vector Ad-GFP as control.

tag: genotype

value: Arid1afl/fl, WT

tag: chip antibody

value: Brg1 (Santa Cruz Biotechnology, sc-17796)


title: AB17GFP_Arid1a

value: Arid1a (Cell Signaling Technology, 12354S)


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD004_indexed


title: DNA methylation_Adalimumab_noResponse_22

type: genomic

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

hyb_protocol: Genome-wide DNA methylation profiling was performed at the GenomeScan B.V (Leiden, Netherlands). DNA was subjected to quality control analysis using a PicoGreen assay (ThermoFisher) and bisulfite treated with an EZ DNA Methylation Kit (Zymo Research) before being subjected to whole genome amplification and subsequently hybridized to the Infinium MethylationEPIC BeadChip array (Illumina).

scan_protocol: Beadchip images were scanned on the iScan system

data_processing:
Infinium MethylationEPIC BeadChip images were scanned on the iScan system and the data quality was checked using minfi (version 1.30.0) R package35 with default settings, which shows every sample has a high quality of data. Raw data were read by ChAMP package (version 2.14.0) from IDAT files and converted to beta values, which is the ratio of methylated (M) intensity to the sum of methylated and unmethylated (U) intensity, i.e. β= M/(M+U +100). Probes that meet any one of the following criteria were excluded for further analyses: (1) probes with detection p-value (detPcut) > 0.01; (2) probes with bead count < 3 in at least 5% of samples; (3) probes targeting non-CpG positions; (4) probes targeting SNP sites; and (5) probes that aligned to multiple locations as described [36]. Finally, 735,297 probes were retained. Beta-mixture quantile normalization (BMIQ) was then applied to beta values to reduce the bias between Type I and Type II probes, followed by identification of differential methylation positions (DMPs) between responders and non-responders to either ADA or ETN, using the same ChAMP package.
MatrixSignal.csv:  Unmethylated and methylated signal intensities
MatrixProcessed_Raw.csv:  Average Beta.
The filtered and normalized (Beta-mixture quantile normalization) average Betas are represented in the Sample Data table.

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated from frozen PBMCs using a Qiacube (Qiagen) and AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer’s protocols.

tag: disease state

value: rheumatoid arthritis (RA)

tag: cell type

value: PBMC

value: f

tag: drug

value: Ada

tag: response

value: no

tag: height

tag: smokingstatus

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg

value: y

tag: anticcpposneg

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: AB17CRE_H3K27me3

tag: strain

value: AB17CRE cells infected by the adenoviral vector expressing Cre recombinase (Ad-Cre) to knock out Arid1a.

value: Arid1a-/-, KO


title: PBMC_E_n_52

description:
rawReadsData.csv
Counts_Normalization_PBMC.csv

library_source: transcriptomic

data_processing:
Reads were mapped, using STAR software (version 2.6.0a), to human reference genome GrCh38 (v83), obtaining 60,675 annotated genes.
The number of reads (counts) for each gene was determined using HTSeq python package (version 0.9.0)
Between-lane normalization from EDASeq R package (version 2.18.0) was performed to force the upper quartile of reads in each lane to be the same.
Normalized data not available for five samples that did not not pass QC (PBMC_A_g_09, CD14_E_g_32, CD14_E_g_39, CD4_A_m_63, CD4_E_g_32).
Genome_build: GrCh38 (v83)
Supplementary_files_format_and_content: Raw read counts; normalized counts

molecule: total RNA

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll-Paque™ (GE healthcare life Sciences, Little Chalfont, United Kingdom). The PBMCs were subsequently sorted using Magnetic Cell Isolation and Cell Separation (AutoMACS Pro 360; Miltenyi Biotec, Bergisch Gladbach, Germany), positively selected for monocytes using CD14 MicroBeads, human, and negatively selected for CD4+ T cells using the CD4+ T Cell Isolation Kit, human (both from Miltenyi Biotec), according to the manufacturer’s protocol. RNA was extracted using the RNeasy Mini Kit (Qiagen) and tested for quantity and purity by Nanodrop (Thermo Scientific) and quality by RIN-value with Agilent 2100 Bioanalyzer (Agilent technologies, Inc., Santa Clara, Ca, USA). All Samples were aliquoted and stored per 1.5-2.0 µg at -80°C until use.
Total RNA was sent to GenomeScan B.V. (Leiden, Netherlands) for library preparation and sequencing. Before sequencing, the RNA sample preparation was performed using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to manufacturer’s protocol. Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed.

tag: sequencingid

tag: Sex

value: m

tag: age

tag: studysubjectid

value: yes

tag: rf

value: Positive

tag: anti-ccp


title: DNA methylation_Adalimumab_moderateResponse_16

tag: disease state

tag: cell type

tag: drug

tag: response

value: moderate


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD007_indexed

tag: brain region

value: MOs

value: male


title: DNA methylation_Adalimumab_noResponse_15

tag: height

tag: smokingstatus

value: never

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg


title: DNA methylation_Etanercept_noResponse_18

value: Etn

value: n

tag: anticcpposneg

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Adalimumab_noResponse_14

value: rheumatoid arthritis (RA)

tag: Sex

tag: age

value: stopped


title: Wi38_40_2_HiC

city: Basel

first: Alejandro

last: Reyes

address: Fabrikstrasse 22

department: Data Sciences

country: Switzerland

institute: Novartis Institutes For BioMedical Research

data_processing:
Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
Methylation data processing. BSMAP version 2.74 (Xi et al., 2009) was used both to map the sequenced reads to the reference genome (hg19) and to calculate the fraction of methylated CpGs for each CpG across the genome. Data was further analyzed within the framework of the bsseq Bioconductor package (Hansen et al, 2012).
HiC Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using HiC-Pro (Servant et al., 2015). Within sample normalization was performed using the Iterative Correction and Eigenvector decomposition (ICE) method (Imakaev et al., 2012).
HiChip Data processing. Data were controlled for quality, mapped to the reference genome (hg19) and converted into interaction matrices using the HiC-Pro pipeline (Servant et al., 2015). Chromatin loops were called using the hichipper pipeline (Lareau et al. 2018) and diffloop (Lareau et al. 2017) was used for quality control, statistical inference of between-group differences and annotation of chromatin loops.
Reads were mapped to the reference genome (hg19) using bwa version 0.7.12 (Li et al., 2009). CTCF peaks were called using GCAPC with default parameters (Teng et al., 2015) and H3K27Ac peaks were called using MACS (Zhang et al., 2008).
Genome_build: hg19
Supplementary_files_format_and_content: Methylation data format (.cpg). As described by the bsmap manual. Output format: tab delimited txt file with the following columns: (1) chromorome, (2) coordinate (1-based), (3) strand, (4) sequence context (2nt upstream to 2nt downstream in Watson strand direction), (5) methylation ratio, (6) number of converted and unconverted Cs covering this locus (7) number of unconverted Cs covering this locus, (8) lower bound of 95% confidence interval of methylation ratio (9) upper bound of 95% confidence interval of methylation ratio.
Supplementary_files_format_and_content: HiC Interaction matrix files (.matrix). As provided by the HiCPro pipeline. A matrix, stored as standard triplet sparse format (i.e. list format). Based on the observation that a contact map is symmetric and usually sparse, only non-zero values are stored for half of the matrix.
Supplementary_files_format_and_content: HiChIP loop contacts (.bedpe). As provided by hichipper. Intrachromosomal looping between anchor loci where loops meet min/max distance requirements.
Supplementary_files_format_and_content: HiC all valid interaction read pairs (allValidPairs). As provided by the HiCPro pipeline. Columns are: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size.
Supplementary_files_format_and_content: ChIP-seq coverage tracks (.bw). Bigwig files, as specified by the UCSC genomic formats.

source_name: Cell line

extract_protocol: In situ HiC was performed as described previously (Rao et al., 2014).  In brief, crosslinked cells or tumor were thawed on ice in HiC lysis buffer. Tissue samples were mechanically disrupted with the Biomasher tissue grinder (Kimble Chase).  Tissue and cell line samples were permeabilized in 0.5% SDS at 37 degrees, quenched with Triton X100 and chromatin was digested with 100-200U MboI at 37 degrees overnight.  Nuclei were then pelleted, ends were marked with biotin-14-dATP (ThermoFisher 19524016) and chromatin was ligated for 5 hours by T4 DNA ligase (M0202).  Samples were treated with proteinase K at 55 degrees for 30 minutes and cross-links were reversed at 68 degrees overnight.  DNA was ethanol precipitated and sheared on a Covaris LE220 as per Rao et al., 2014.  DNA was cleaned up via AMPure XP beads (Beckman Coulter, A63881) and quantified by Qubit dsDNA High Sensitivity Assay (Life Technologies, Q32854).  Samples were bound to Dynabeads MyOne Streptavidin T1 beads (Life technologies, 65602) and washed.  End repair, dATP attachment and adapter ligation was performed.  Final PCR amplification was performed using barcoded sequencing primers and PCR.  Libraries were purified using AMPure XP beads and sequenced on either a NextSeq500 (150 cycle kit) or the HiSeq2500 (high output; 200 cycle kit).

tag: sample type

value: Cell line

tag: biological sample

tag: treatment

value: The primary fibroblast line WI38 was obtained from Coriell (AG06814-N) and was cultivated in EMEM with 15% FBS. Cells were passage serially (approximately twice weekly) for 14 weeks.


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD002_indexed

tag: strain


title: Wi38_40_1_HiC


title: PBMC_E_g_50

tag: sequencingid

tag: cell type

value: PBMC

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: good

tag: rf

tag: anti-ccp


title: PBMC_E_g_51

tag: height

tag: alcoholuseunitsweek

tag: weight

value: Negative

tag: hemoglobinecount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A1_AD001_indexed

tag: brain region

tag: Sex

tag: age


title: Wi38_30_2_HiC

tag: sample type

tag: biological sample

tag: treatment


title: PBMC_A_m_49

tag: sequencingid

tag: cell type

value: Adalimumab

tag: leucocytencount

tag: trombocytencount


title: AB17GFP_H3K27me3

tag: strain

value: AB17GFP cells infected by the adenoviral empty vector Ad-GFP as control.

tag: genotype

value: Arid1afl/fl, WT

tag: chip antibody


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A12_AD012_indexed

value: MOs


title: AB17GFP_H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: PBMC_E_g_48

value: m

tag: disease state

tag: studysubjectid

tag: drug

tag: response

tag: height

tag: rf

value: Positive

tag: anti-ccp


title: AB17GFP_Ctcf

value: Ctcf (Cell Signaling Technology, 3418S)


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A12_AD010_indexed

tag: brain region

tag: Sex

value: male

tag: age


title: AB17CRE_H3K27ac

tag: treatment

value: AB17CRE cells infected by the adenoviral vector expressing Cre recombinase (Ad-Cre) to knock out Arid1a.

value: Arid1a-/-, KO

value: H3K27ac (Abcam, ab4729)


title: PBMC_E_g_47

tag: sequencingid

tag: cell type

value: PBMC

value: rheumatoid arthritis (RA)

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: hemoglobinecount


title: DNA methylation_Adalimumab_goodResponse_09

value: Ada

value: good

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Etanercept_noResponse_11

tag: disease state

value: f

tag: drug

value: Etn

tag: response

value: no

tag: height

value: never


title: DNA methylation_Adalimumab_goodResponse_10

tag: Sex

value: m

value: yes


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A12_AD008_indexed

tag: brain region

value: MOs

tag: age

tag: strain


title: AB17CRE_H3K9me3

tag: treatment

tag: genotype

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: AB17GFP_H3K27ac

value: AB17GFP cells infected by the adenoviral empty vector Ad-GFP as control.

value: Arid1afl/fl, WT


title: Wi38_16_1_HiC

tag: sample type

value: Cell line

tag: biological sample

value: The primary fibroblast line WI38 was obtained from Coriell (AG06814-N) and was cultivated in EMEM with 15% FBS. Cells were passage serially (approximately twice weekly) for 14 weeks.


title: AB17CRE_H3K4me1

value: AB17CRE cells infected by the adenoviral vector expressing Cre recombinase (Ad-Cre) to knock out Arid1a.

value: Arid1a-/-, KO

value: H3K4me1 (Abcam, ab8895)


title: MGH3535_HiC

source_name: Colon tumor

value: Colon tumor


title: PBMC_A_n_45

tag: sequencingid

tag: cell type

value: PBMC

value: rheumatoid arthritis (RA)

tag: studysubjectid

value: Adalimumab

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf

value: Negative

tag: anti-ccp

tag: hemoglobinecount


title: Wi38_16_2_HiC


title: DNA methylation_Adalimumab_noResponse_12

tag: disease state

tag: Sex

value: m

tag: drug

value: Ada

tag: response

value: no

tag: height

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD001_indexed

tag: brain region

value: MOs

value: male

tag: age

tag: strain


title: PBMC_E_g_44

tag: sequencingid

tag: cell type

value: f

tag: studysubjectid

value: Etanercept

value: good

tag: alcoholuseunitsweek

tag: weight

value: Positive


title: AB17CRE_Input

tag: treatment

value: AB17CRE cells infected by the adenoviral vector expressing Cre recombinase (Ad-Cre) to knock out Arid1a.

tag: genotype

value: Arid1a-/-, KO

tag: chip antibody


title: AB17GFP_H3K4me1

value: AB17GFP cells infected by the adenoviral empty vector Ad-GFP as control.

value: Arid1afl/fl, WT

value: H3K4me1 (Abcam, ab8895)


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A12_AD002_indexed

tag: Sex


title: PBMC_E_n_43

value: PBMC

tag: disease state

value: rheumatoid arthritis (RA)

tag: drug

tag: response

tag: height

value: never

tag: rf

tag: anti-ccp

tag: hemoglobinecount


title: BRD3412_HiC

tag: sample type

value: Colon tumor

tag: biological sample


title: BRD3409N_HiC

source_name: Normal colon

value: Normal colon


title: BRD3462_HiC


title: PBMC_A_n_42

tag: sequencingid

tag: cell type

tag: age

value: Adalimumab

value: no

value: Negative

tag: leucocytencount

tag: trombocytencount


title: DNA methylation_Etanercept_moderateResponse_13

value: f

value: Etn

value: moderate

tag: smokingstatus

value: stopped

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg

value: n

tag: anticcpposneg


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A10_AD010_indexed

tag: brain region

value: MOs

tag: Sex

value: male

tag: strain


title: DNA methylation_Etanercept_noResponse_03

tag: disease state

value: m

tag: drug

tag: response

tag: height

value: y


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A12_AD007_indexed


title: AB17GFP_Input

tag: treatment

value: AB17GFP cells infected by the adenoviral empty vector Ad-GFP as control.

tag: genotype

value: Arid1afl/fl, WT

tag: chip antibody


title: BRD3378_HiC

tag: sample type

tag: biological sample


title: 14d-L-C_miRNA

city: Weifang

first: Guohui

last: wang

address: baotong west street 7166

institute: department of cell biology，Weifang Medical University

description: processed data file: Known_miRNA_Expression_Summary.txt

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water.

extract_protocol:
Total RNA was extracted from each tissue sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: The control group was exposed to natural light, while the experimental group was exposed to blue light (18 watt, PL-L, Philips) and surrounded by a dark container

tag: strain/model

value: Kunming (KM)

value: female

tag: age

value: 4 weeks old

value: experimental case; exposed to blue light

tag: tissue

value: eyeball


title: DNA methylation_Adalimumab_noResponse_08

value: rheumatoid arthritis (RA)

tag: cell type

value: PBMC

value: Ada

value: no

tag: smokingstatus

value: never

tag: alcoholuseunitsweek

tag: weight

tag: rfposneg

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: PBMC_A_n_41

tag: sequencingid

tag: Sex

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

tag: height

value: stopped

tag: rf

value: Positive

tag: anti-ccp


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD007_indexed

tag: brain region

value: MOs

value: male

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A10_AD008_indexed


title: HEK_3_rep3 [p3138_o6813/11]

city: Zurich

first: Weihong

last: Qi

address: Winterthurerstr. 190

department: FGCZ

institute: ETHZ

data_processing:
Raw reads were trimmed and filtered using fastp version version 0.20.0
Preprocessed reads were aligned to reference genomes using STAR version 2.7.3
Trancript level normalized counts were generated using kllisto version 0.44.0
Genome_build: Mus musculus Ensembl GRCm38.p5; Homo_sapiens Ensembl GRCh38.p10
Supplementary_files_format_and_content: Tab delimited text file containing transcript level normalized counts (TPM)

source_name: HEK293T_saKKH-CBE3 + RFP_48h

extract_protocol: TruSeq RNA stranded

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: mRNA transfection

tag: genotype/variation

value: saKKH-CBE3 + RFP


title: PBMC_E_n_40

tag: sequencingid

tag: cell type

value: Etanercept

tag: alcoholuseunitsweek

tag: weight

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 14d-L-B_miRNA

tag: strain/model

value: Kunming (KM)

tag: Sex

value: female

value: 4 weeks old

tag: treatment

value: experimental case; exposed to blue light

tag: tissue


title: HEK_2_rep3 [p3138_o6813/10]


title: 14d-B-B_miRNA

tag: age

value: control; exposed to natural light

value: eyeball


title: HEK_1high_rep3 [p3138_o6813/9]

tag: cell line/strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD008_indexed

tag: brain region

tag: strain


title: PBMC_E_g_39

value: PBMC

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

tag: response

value: good

tag: height

tag: rf

tag: anti-ccp


title: PBMC_E_n_38

tag: sequencingid

tag: cell type

value: m

value: no

tag: alcoholuseunitsweek

value: never

tag: weight

tag: hemoglobinecount

tag: leucocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A12_AD001_indexed

value: MOs

tag: Sex

value: male

tag: age


title: HEK_4_rep2 [p3138_o6813/8]

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: mRNA transfection

tag: genotype/variation


title: DNA methylation_Adalimumab_moderateResponse_02

tag: disease state

value: f

tag: drug

value: Ada

tag: response

value: moderate

tag: smokingstatus

tag: rfposneg

value: n

tag: anticcpposneg

value: y

tag: trombocytencount


title: DNA methylation_Adalimumab_noResponse_06

tag: cell type

tag: height

value: yes

tag: alcoholuseunitsweek

tag: weight


title: 14d-L-A_miRNA

tag: strain/model

value: Kunming (KM)

tag: Sex

value: female

tag: age

value: 4 weeks old

tag: treatment

value: experimental case; exposed to blue light

tag: tissue

value: eyeball


title: 14d-B-A_miRNA

value: control; exposed to natural light


title: DNA methylation_Etanercept_goodResponse_05

value: rheumatoid arthritis (RA)

value: PBMC

value: Etn

value: good

value: never

tag: hemoglobinecount

tag: leucocytencount


title: DNA methylation_Etanercept_noResponse_01

tag: disease state

value: f

tag: drug

value: no

value: stopped


title: 14d-L-C_RNA

description: processed data file: mRNA_Expression_Summary.txt


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A10_AD007_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD002_indexed


title: PBMC_A_g_46

tag: sequencingid

value: m

tag: studysubjectid

value: Adalimumab

tag: response

tag: rf

value: Negative

tag: anti-ccp


title: PBMC_A_g_36

tag: cell type

tag: height

tag: alcoholuseunitsweek

tag: weight

value: Positive

tag: trombocytencount


title: DNA methylation_Adalimumab_noResponse_04

tag: Sex

tag: age

value: Ada

tag: smokingstatus

tag: rfposneg

value: y

tag: anticcpposneg


title: HEK_3_rep2 [p3138_o6813/7]

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: mRNA transfection

tag: genotype/variation

value: saKKH-CBE3 + RFP


title: Wi38_30_1_HiC

tag: sample type

value: Cell line

tag: biological sample

tag: treatment

value: The primary fibroblast line WI38 was obtained from Coriell (AG06814-N) and was cultivated in EMEM with 15% FBS. Cells were passage serially (approximately twice weekly) for 14 weeks.


title: 14d-L-B_RNA

tag: strain/model

value: Kunming (KM)

value: female

value: 4 weeks old

value: experimental case; exposed to blue light

tag: tissue

value: eyeball


title: 14d-L-A_RNA


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A10_AD006_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: PBMC_E_g_35

tag: sequencingid

tag: cell type

value: PBMC

tag: Sex

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: Etanercept

tag: response

value: good

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: HEK_2_rep2 [p3138_o6813/6]

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: mRNA transfection

tag: genotype/variation


title: DNA methylation_Etanercept_moderateResponse_07

tag: disease state

tag: cell type

tag: Sex

tag: age

value: Etn

value: moderate

tag: smokingstatus

value: never

tag: rfposneg

value: y

tag: anticcpposneg


title: PBMC_A_n_37

tag: sequencingid

value: m

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Positive


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD006_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: 14d-B-B_RNA

tag: strain/model

value: Kunming (KM)

value: female

value: 4 weeks old

tag: treatment

value: control; exposed to natural light

tag: tissue

value: eyeball


title: PBMC_E_m_33

tag: cell type

value: PBMC

tag: Sex

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

value: Etanercept

value: stopped

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: HEK_4_rep1 [p3138_o6813/4]

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: mRNA transfection

tag: genotype/variation

value: saKKH-CBE3 + RFP


title: PBMC_A_m_34

tag: sequencingid

value: m

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

value: Negative


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A10_AD004_indexed

tag: brain region

value: MOs

tag: Sex

value: male

tag: age

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD012_indexed


title: 14d-B-A_RNA

tag: strain/model

value: Kunming (KM)

value: female

value: 4 weeks old

tag: treatment

tag: tissue


title: HEK_3_rep1 [p3138_o6813/3]

tag: cell line/strain

tag: cell/sample type

tag: time point

tag: treatment/method


title: PBMC_E_g_32

tag: sequencingid

tag: cell type

value: PBMC

tag: disease state

tag: studysubjectid

tag: drug

value: good

value: Positive

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A10_AD002_indexed

tag: brain region

tag: Sex

tag: age

tag: strain


title: HEK_2_rep1 [p3138_o6813/2]

tag: cell line/strain

tag: genotype/variation


title: PBMC_E_n_31

value: rheumatoid arthritis (RA)

value: Etanercept

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf


title: HEK_1high_rep2 [p3138_o6813/5]

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: mRNA transfection

value: saKKH-CBE3 + RFP


title: HEK_1high_rep1 [p3138_o6813/1]


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD010_indexed


title: s23

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Illumina CASAVA-1.8.2 used for basecalling
Reads were trimmed using trim_galore using standard parameters
Reads were aligned to the Mus musculus genome assembly mm10 using the bowtie2 aligner with standard parameters
Reads mapping to the genome were counted using featureCounts and the miRNA features in mirBase v. 21
Genome_build: mm10
Supplementary_files_format_and_content: Comma seperated value (csv) file with accession id, location and read counts of miRNAs in mirBase v. 21

source_name: subcutaneous adipose tissue

growth_protocol: Mice were house on 12-12 light-dark cycle at 22C and fed chow diet.

extract_protocol:
RNA was extracted with trizol accordingly to manufacturers instructions.
NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB7300) were used for library prep according to their protocol

treatment_protocol: Female mice were excised 1 hour  5 days pr. week on a treadmill for 6.5 weeks (16 m/min) on a moterised treadmill. In addition they had free access to running wheel during the whole experiment

tag: tissue

value: subcutaneous adipose

tag: genotype

value: WildType

tag: training status

value: Trained


title: PBMC_A_n_30

tag: sequencingid

tag: cell type

value: m

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

value: Negative

tag: anti-ccp

tag: hemoglobinecount

tag: leucocytencount

tag: trombocytencount


title: GFP control [p3138_6230/15]

source_name: HEK293T_GFP control

tag: cell line/strain

value: Plasmid transfection

tag: genotype/variation

value: GFP


title: PBMC_A_m_29

value: PBMC

tag: Sex

value: f

tag: age

tag: response

value: moderate

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A10_AD001_indexed

tag: brain region

value: MOs

value: male

tag: strain


title: 180426_CEMBA_mm_P56_P63_2B_CEMBA180305_2B_1_CEMBA180305_2B_2_A11_AD004_indexed


title: GFP control [p3138_6230/14]

tag: cell/sample type

tag: time point

tag: treatment/method


title: PBMC_A_g_28

tag: sequencingid

tag: cell type

tag: disease state

value: rheumatoid arthritis (RA)

tag: studysubjectid

tag: drug

value: good

value: stopped

value: Positive

tag: anti-ccp

tag: hemoglobinecount


title: s22

tag: tissue

value: subcutaneous adipose

tag: genotype

tag: training status

value: Sedentary

tag: Sex

value: female


title: GFP control [p3138_6230/13]

tag: cell line/strain

value: cell lysate

tag: genotype/variation


title: BE3-saCas, top 5% GFP [p3138_6230/12]

source_name: HEK293T_BE3-saCas, top 5% GFP

value: saKKH-CBE3 + GFP


title: PBMC_E_n_27

tag: age

value: Etanercept

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

value: never

tag: weight

tag: rf

tag: leucocytencount

tag: trombocytencount


title: s19

value: KinaseDead

value: Trained


title: s24

value: WildType


title: BE3-saCas, top 5% GFP [p3138_6230/11]

tag: cell/sample type

tag: time point

tag: treatment/method

value: Plasmid transfection


title: s18

tag: tissue


title: PBMC_A_n_25

tag: sequencingid

tag: cell type

value: PBMC

value: f

tag: disease state

tag: studysubjectid

tag: drug

value: Adalimumab

value: Negative

tag: anti-ccp

tag: hemoglobinecount


title: s17

tag: genotype

tag: training status

tag: Sex


title: BE3-saCas, top 5% GFP [p3138_6230/10]

tag: cell line/strain

tag: genotype/variation


title: PBMC_E_n_26

value: rheumatoid arthritis (RA)

tag: age

tag: response

tag: height

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: leucocytencount

tag: trombocytencount


title: PBMC_A_g_24

tag: sequencingid

tag: cell type

tag: disease state

tag: studysubjectid

value: good

value: stopped

value: Positive


title: s16

tag: tissue

value: subcutaneous adipose

tag: genotype

value: female


title: PBMC_E_n_23

tag: Sex

tag: drug

value: Etanercept

value: yes

tag: anti-ccp

tag: hemoglobinecount


title: BE3-spCas, top 5% GFP [p3138_6230/9]

source_name: HEK293T_BE3-spCas, top 5% GFP

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

tag: genotype/variation

value: saKKH-CBE3 + GFP


title: s21

value: KinaseDead

tag: training status

value: Sedentary


title: BE3-spCas, top 5% GFP [p3138_6230/8]

value: Plasmid transfection


title: smart_seq2_single_oocyteD4_4

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

description: applying single cell method to oocyte

data_processing:
Illumina Casava1.7 software used for basecalling.
5' and 3' sequences were extracted from paired-end sequences using Perl, Python and shell script
5' and 3' sequences were aligned  to mm10, using STAR (2.6.1a), with with parameters (--outFilterMultimapNmax 1 --outFilterScoreMinOverLread 0.6 --outFilterMatchNminOverLread 0.6).
Peaks were called with CAGEr (v 1.24.0) .
For smart-seq2 data, sequenced reads were trimmed for adaptor sequence using cutapapt (v 1.18) and aligned to mm10 using STAR  with with parameters as described above.
For Iso-seq data, sequence data were processed using the SMRTlink5.0 software. Circular consensus sequence (CCS) was generated from subread BAM files, parameters: min_length 200, max_drop_fraction 0.8, no_polish TRUE, min_zscore -9999, min_passes 1, min_predicted_accuracy 0.8, max_length 18000. CCS.BAM files were  classified into full length and non-full length reads using pbclassify.py script, ignore polyA false, minSeq Length 200. Non-full length and full-length fasta files produced were then fed into the cluster step, which does isoform-level clustering(ICE), followed by final Arrow polishing, hq_quiver_min_accuracy 0.99, bin_by_primer false, bin_size_kb 1, qv_trim_5p 100, qv_trim_3p 30.
Additional nucleotide errors in consensus reads were corrected using the Illumina RNA seq data with the software LoRDEC.
consensus reads were aligned to reference Genome using GMAP with parameters --no-chimeras --cross-species --expand-offsets 1 –B 5 –K 50000 –f samse –n 1 against reference genome.
Gene structure analysis was performed using TAPIS pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: [scRCAT-seq] tc*.txt reports the region and the normalized RPM values of each peak.
Supplementary_files_format_and_content: [Iso-seq] *gtf reports the isoform information which were detected by Iso-seq.

molecule: polyA RNA

source_name: oocyte

extract_protocol:
DRG, oocytes, hESC, HEK293T, ARPE, mESC, hESC_drived_organoid were dissected and dissociated into single cells. hESC, HEK293T, ARPE, mESC, hESC_drived_organoid were dissected respectively and mixed together.
The scRCAT-seq library was prepared according to the scRCAT-seq protocol.
The smart-seq2 library was prepared according to the smart-seq2 protocol.
The Iso-Seq library was prepared according to the Isoform Sequencing protocol.

tag: strain

value: oocyte


title: M6529

type: RNA

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

description:
M6529
F_3

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2500ng of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: mesenchymal stromal cells from bone marrow

label_protocol: 100ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations.

growth_protocol: The MSC expansion medium was Dulbecco´s Modified Eagle´s Medium (DMEM) Low Glucose (1 g/l glucose, Biochrom, FG0415) supplemented with 10 % (v/v) fetal bovine serum (not heat-inactivated, Thermo Fisher Scientific, Schwerte, Germany, HyClone, SV30160.03), 25 mM (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) (HEPES, Biochrom), 1 % (100 U/mL / 100 µg/mL) penicillin/streptomycin (Biochrom) and 2 ng/mL human recombinant fibroblast growth factor‑2 (from E. coli, PeproTech, Hamburg, Germany). The cells were cultured at 37 °C with 5 % CO2 at 85 % humidity. Media changes were performed every 3 - 4 days. The cells were passaged at a confluence of around 70 % by the use of 0.05 %/ 0.02 % (w/v) trypsin-ethylenediamine tetraacetic acid solution (Trypsin/EDTA; Biochrom L2153) and passaged with 2,000 cells per cm² for a maximum of five passages. Morphology was documented by phase contrast microscopy. Proliferation was documented by manual cell-counting with a Fuchs-Rosenthal chamber. Cells from three different donors (C, D and F) were randomly chosen. The conditions no heparin: 1 and high heparin: 3 (called cell pairs in the manuscript) were used and RNA obtained at day 0 before induction of osteogenic differentiation was subjected to the analyses.

extract_protocol: Duplicate samples from differentiated cells (osteogeneic and adipogenic induction) were lysed in 350 µl buffer RLT (Qiagen), lysates were stored at ‑ 80 °C. RNA was subsequently isolated with the RNeasy kit (Qiagen #74106) according to the instructions of the manufacturer including on-column-digestion with DNase I. Synthesis of cDNA was performed from 1 µg of RNA with oligo-dT18-primers according to the manufacturer´s suggestions (Fermentas). Total RNA from chondrogenic pellets was isolated with a homogenizer from Bertin technologies (PreCellys 24 lysis and homogenization; 2x 30 seconds, 6000 rpm with 40 seconds pause) and a Precellys® RNA Kit (732-3122, VWR). The isolation was carried out according to the manufacturer’s manual. RNA concentration was calculated by Nanodrop absorption measurement at 260/280 nm. Synthesis of cDNA was performed with 200 ng of RNA including treatment with DNase I and oligo-dT18-primers according to the manufacturer´s suggestions (Fermentas).

tag: gender

tag: treatment

value: bone marrow treated with 3.5 ml heparin

value: bone marrow

value: mesenchymal stromal cells


title: s14


title: PBMC_A_g_21

tag: sequencingid

tag: cell type

value: PBMC

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

value: Adalimumab

tag: response

tag: height

tag: alcoholuseunitsweek

value: never

tag: weight

tag: rf

tag: leucocytencount

tag: trombocytencount


title: s20

tag: tissue

value: subcutaneous adipose

tag: genotype

value: Trained

tag: Sex

value: female


title: smart_seq2_single_oocyteD4_3

description: applying single cell method to oocyte

tag: strain


title: M6526

description:
M6526
D_1

tag: gender

value: bone marrow treated without heparin


title: s13

value: WildType

tag: training status


title: M6525

description:
M6525
C_3

tag: treatment


title: M6527

description:
M6527
D_3

tag: cell type


title: RFP control [p3138_6230/6]

description: 20191029.A-c-intein_RFP_control_uppest5_RFP_3

source_name: HEK293T_RFP control

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

tag: genotype/variation

value: RFP


title: BE3-spCas, top 5% GFP [p3138_6230/7]

value: Plasmid transfection

value: saKKH-CBE3 + GFP


title: M6524

description:
M6524
C_1


title: PBMC_A_n_20

tag: sequencingid

tag: disease state

tag: age

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

tag: alcoholuseunitsweek

value: yes

tag: weight

value: Positive

tag: anti-ccp

tag: hemoglobinecount


title: smart_seq2_single_oocyteD4_2

description: applying single cell method to oocyte

tag: strain

tag: tissue

value: oocyte


title: s15

tag: genotype

value: KinaseDead

tag: training status

tag: Sex


title: M6528

description:
M6528
F_1

tag: gender

tag: treatment

value: bone marrow

tag: cell type

value: mesenchymal stromal cells


title: s11

value: Sedentary


title: RFP control [p3138_6230/4]

description: 20191029.A-c-intein_RFP_control_uppest5_RFP_1

tag: cell line/strain

tag: cell/sample type

tag: time point

tag: treatment/method

tag: genotype/variation


title: smart_seq2_single_oocyteD4_1

description: applying single cell method to oocyte


title: RFP control [p3138_6230/5]

description: 20191029.A-c-intein_RFP_control_uppest5_RFP_2


title: s10

value: subcutaneous adipose


title: PBMC_A_n_22

tag: sequencingid

value: PBMC

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: rf

tag: leucocytencount

tag: trombocytencount


title: PBMC_A_g_17

tag: cell type

tag: Sex

value: good

value: never

tag: weight

value: Negative

tag: anti-ccp

tag: hemoglobinecount


title: PBMC_E_n_18

value: Etanercept

value: no


title: Full intein, top 5% RFP [p3138_6230/3]

source_name: HEK293T_Full intein, top 5% RFP

tag: cell line/strain

tag: cell/sample type

value: cell lysate

tag: time point

tag: treatment/method

value: Plasmid transfection

tag: genotype/variation

value: saKKH-CBE3 + RFP


title: smart_seq2_single_DRG_19

description: applying single cell method to DRG neuron

source_name: Dorsal root ganglion neuron

tag: strain

tag: tissue

value: Dorsal root ganglion neuron


title: smart_seq2_single_DRG_18


title: PBMC_A_m_16

tag: sequencingid

tag: disease state

tag: age

tag: studysubjectid

tag: drug

tag: response

value: moderate

tag: height

value: yes

value: Positive


title: smart_seq2_single_DRG_17


title: Full intein, top 5% RFP [p3138_6230/2]


title: PBMC_A_n_15

tag: cell type

value: PBMC

tag: Sex

tag: alcoholuseunitsweek

tag: weight

tag: rf

tag: leucocytencount

tag: trombocytencount


title: s8

value: subcutaneous adipose

tag: genotype

value: WildType

tag: training status

value: Sedentary

value: female


title: s9

tag: tissue

value: KinaseDead


title: smart_seq2_single_DRG_16

tag: strain


title: s12


title: s7


title: smart_seq2_single_DRG_15


title: Full intein, top 5% RFP [p3138_6230/1]

tag: cell line/strain

tag: cell/sample type

tag: time point

tag: treatment/method

tag: genotype/variation


title: PBMC_A_n_14

tag: sequencingid

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

tag: height

value: stopped

tag: anti-ccp

tag: hemoglobinecount


title: PBMC_E_m_13

tag: cell type

tag: Sex

value: Etanercept

tag: alcoholuseunitsweek

tag: weight

tag: rf

value: Negative

tag: leucocytencount

tag: trombocytencount


title: s6

tag: tissue

tag: genotype

tag: training status

value: Trained


title: 81.2

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20 –trim-n
Trimmed reads were mapped against the human genome (hg38 UCSC) using HISAT2 (v 2.1.0) with parameters  -p 6 –rna-strandness RF --dta -k 5
Only primary alignments were reported, files were sorted and indexed with samtools (v 1.9)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -T 6 -M -t exon -g gene_id and Ensembl gene annotations (GRCh38.89)
Data normalization was assessed using R/edgeR (v 3.23.8) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated text file including TMM normalized FPKM values for each sample

source_name: primary ovarian tumor

extract_protocol:
RNA extraction was performed using TRIZOL, according to the manufacturer's instructions.
Poly-A RNA was enriched using oligo(dT) beads. RNAs are fragmented randomly by adding fragmentation buffer. cDNA is synthesized by using random hexamers primer followed by second strand synthesis. Strand-specific double-stranded cDNA libraries are completed by size selection (250-300bp) and PCR enrichment. Completed libraries are sequenced on an Illumina HiSeq platform.

tag: tumor subtype

value: serous ovarian carcinoma

value: ovary

tag: histology

value: serous-papillary

tag: primary or metastasis

value: primary

tag: figo stage

tag: grade


title: onk 83.1


title: s5


title: smart_seq2_single_DRG_14

tag: strain

value: Dorsal root ganglion neuron


title: PBMC_A_n_12

tag: sequencingid

value: PBMC

value: m

tag: disease state

tag: age

tag: studysubjectid

tag: drug

tag: response

value: no

tag: height

value: yes

value: Positive

tag: anti-ccp

tag: hemoglobinecount


title: smart_seq2_single_DRG_13

tag: tissue


title: onk 79.2


title: s4

value: subcutaneous adipose

tag: genotype

value: KinaseDead

tag: training status

tag: Sex

value: female


title: PBMC_E_n_11

tag: cell type

value: f

value: rheumatoid arthritis (RA)

tag: alcoholuseunitsweek

value: never

tag: weight

tag: rf

tag: leucocytencount

tag: trombocytencount


title: onk 74.2

tag: tumor subtype

tag: histology

tag: primary or metastasis

tag: figo stage

tag: grade


title: s3

value: Sedentary


title: onk 73.2

value: serous ovarian carcinoma


title: smart_seq2_single_DRG_12

tag: strain


title: PBMC_A_m_19

tag: sequencingid

tag: disease state

tag: age

tag: studysubjectid

tag: drug

value: Adalimumab

tag: response

value: moderate

tag: height

value: Negative

tag: anti-ccp

tag: hemoglobinecount


title: smart_seq2_single_DRG_11

tag: tissue

value: Dorsal root ganglion neuron


title: s2

tag: genotype

value: WildType

tag: training status

value: Trained

tag: Sex


title: Xrcc4-/- p53-/- Released rep6

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

country: France

institute: Institut Pasteur

data_processing:
library strategy: linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS)
Sequencing reads in FASTQ files were decoded and adaptor sequence trimmed using by ea-utils tool. Paired-end reads with less than 20 nucleotides bait sequence in the 5’ end of read1 were filtered out. Paired-end reads were mapped to the mouse mm9 reference genome using BWA mem with default settings.
Paired-end reads with a mapping quality less than 10 and multiple mapped reads were filtered out. Mapped reads were then further analyzed using read2.
Among non-split mapped, those with more than three quarters length of mapped sequence were defined as mapped with >=75% sequence reads. Among them, those that were not split mapped and mapped within the IgkJ4 bait to IgkJ2 regions were defined as germline.
The rest of non-germline sequence and read2 split mapped with breakpoint sequence with were further classified according to prey genomic location: trans-joins with antigen receptor (AgR) genes (Igh, Igl, Tcra, Tcrd, Tcrg, Tcrb), cis-joins with Igk V region and trans-joins with non AgR loci (else).
Genome_build: mm9
Supplementary_files_format_and_content: WIG files contain all captured prey sequence with both cis-rearrangement and trans-rearrangement

source_name: Xrcc4-/- p53-/- Released

extract_protocol:
Genomic DNA was extracted with proteinase K digestion overnight and phenol/chloroforme extraction.
Briefly, DNA was purified and sonicated (Bioruptor, Diagenode) into 500–1,000 bp fragments. LAM-PCR was performed using bait primer coupled with biotin, 1U Phusion polymerase (Thermo Scientific) and the following cycles: 1x (98 °C for 120 s); 80x (95 °C for 30 s; 58 °C for 30 s; 72 °C for 90 s); and 1x (72 °C for 360 s). Biotinylated PCR fragments were incubated with MyOne streptavidin C1 beads (Invitrogen) and rotated for 4 h in 1 M NaCl and 5 mM EDTA buffer at room temperature. After washes with B&W buffer (1 M NaCl; 5 mM Tris-HCl, 0.5 mM EDTA), on-bead ligation was performed using 2.5 mM bridge adaptor, 1 mM hexamine cobalt chloride (Sigma), 15 U T4 DNA ligase (Promega), 15% PEG-8000 (Sigma) and the following cycles: 25 °C for 1 h; 22°C for 2 h; and 16°C O/N. After washing three times with B&W buffer (1 M NaCl, 5 mM Tris-HCl (pH 7.4) and 0.5 mM EDTA (pH 8.0)), the on-bead ligated products were subjected to nested PCR using Phusion polymerase, locus-specific and adaptor primers and the following cycles: 1x (95 °C for 300 s); 15x (95 °C for 60 s; 72 °C 60 s); and 1x (72 °C 600 s). Blocking digestion was then performed with I-SceI for 1 h to remove uncut germline DNA. After purification using a Qiagen column, recovered DNA was PCR-amplified using Illumina primers, Phusion polymerase and the following cycles: 1x (95°C for 180 s); 10x (95°C for 30 s; 60°C for 30 s; 72°C for 60 s); and 1x (72°C for 360 s). The tagged PCR products were size-selected for DNA fragments between 500–1000 bp on a 1% agarose gel and purified using a Qiagen column before loading onto an Illumina Miseq machine for paired-end 2X250 bp sequencing.

treatment_protocol: 1 million/ml v-abl pro-B cells were treated with 3uM v-abl kinase inhibitor (STI571) for 3 days. After washing off inhibitor, cells were released into fresh medium.

tag: genotype/cell type

value: Xrcc4-/- p53-/- v-abl/Bcl2 transformed mouse pro-B cells

tag: treatment

value: Released cells from 3 days v-abl kinease inhibitor treatment


title: smart_seq2_single_DRG_10


title: s1


title: PBMC_A_g_09

tag: cell type

value: PBMC

value: m

value: good

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf

value: Positive

tag: leucocytencount

tag: trombocytencount


title: PBMC_A_n_08

tag: sequencingid

value: f

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

tag: studysubjectid

tag: drug

value: no


title: 70.7

tag: tumor subtype

value: serous ovarian carcinoma

tag: tissue

value: ovary

tag: histology

value: serous-papillary

tag: primary or metastasis

value: primary

tag: figo stage

tag: grade


title: smart_seq2_single_DRG_9

tag: strain

value: Dorsal root ganglion neuron


title: 63.5


title: 72.3


title: Xrcc4-/- p53-/- Released rep5

description: linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS)

tag: genotype/cell type

tag: treatment


title: Xrcc4-/- p53-/- Released rep4


title: smart_seq2_single_DRG_8


title: PBMC_A_n_06

tag: cell type

tag: Sex

value: Adalimumab

tag: response

tag: height

tag: alcoholuseunitsweek

value: yes

tag: weight

tag: rf

value: Negative

tag: anti-ccp

tag: hemoglobinecount


title: 61.1.2

tag: tumor subtype

tag: tissue


title: Xrcc4-/- p53-/- Released rep3

value: Xrcc4-/- p53-/- v-abl/Bcl2 transformed mouse pro-B cells

value: Released cells from 3 days v-abl kinease inhibitor treatment


title: PBMC_E_g_05

tag: sequencingid

value: PBMC

tag: disease state

tag: age

tag: studysubjectid

tag: drug

value: Etanercept

value: never

tag: leucocytencount

tag: trombocytencount


title: smart_seq2_single_DRG_6

tag: strain


title: PBMC_A_g_10

tag: cell type

tag: Sex

value: m

tag: response

value: good

value: Positive


title: onk 56.1.2

tag: histology

tag: primary or metastasis

tag: figo stage

tag: grade


title: Xrcc4-/- p53-/- Released rep2

tag: genotype/cell type

tag: treatment


title: onk 57.1.2

tag: tumor subtype

tag: tissue


title: PBMC_A_n_04

tag: sequencingid

tag: disease state

value: rheumatoid arthritis (RA)

tag: age

value: no

tag: height

tag: alcoholuseunitsweek

value: stopped

tag: weight

tag: rf

tag: anti-ccp

tag: hemoglobinecount


title: onk 55.1.3

value: serous ovarian carcinoma

value: ovary

tag: histology

value: serous-papillary


title: smart_seq2_single_DRG_5

tag: strain

value: Dorsal root ganglion neuron


title: Xrcc4-/- p53-/- Released rep1


title: PBMC_E_n_03

tag: cell type

tag: Sex

tag: studysubjectid

tag: drug

tag: response

tag: leucocytencount

tag: trombocytencount


title: smart_seq2_single_DRG_4

tag: tissue


title: Xrcc4-/- p53-/- ABLKi rep3

source_name: Xrcc4-/- p53-/- ABLKi

tag: genotype/cell type

tag: treatment

value: v-abl kinease inhibitor STI571(ABLKi) for 3 days


title: PBMC_E_m_07

tag: sequencingid

value: f

tag: disease state

tag: age

value: moderate

tag: height

tag: alcoholuseunitsweek


title: onk 52.2.1

tag: tumor subtype

tag: histology

tag: primary or metastasis

value: primary

tag: figo stage

tag: grade


title: PBMC_A_m_02

tag: cell type

value: PBMC

tag: Sex

tag: studysubjectid

tag: drug

value: Adalimumab

tag: weight

tag: rf

value: Negative

tag: anti-ccp

tag: hemoglobinecount


title: 51 OVAR 2.2

tag: tissue


title: smart_seq2_single_DRG_3

tag: strain


title: PBMC_E_n_01

tag: sequencingid

tag: disease state

tag: age

value: Etanercept

tag: response

tag: height

tag: leucocytencount

tag: trombocytencount


title: smart_seq2_single_DRG_2


title: combined input 2

city: San Francisco

first: Bassem

last: Al-Sady

address: 513 Parnassus Ave HSW1501

institute: UC San Francisco

data_processing:
ChIP-Seq reads were mapped to the S. pombe genome with with Bowtie2 version 2.3.4.2
Merge input files and wild-type H3K9me2 files were generated with samtools "merge" for normalization
Input or WT normalized signal tracks were generated using the MACS2 version 2.1.1.20160309 functions "callpeak" and "bdgcmp"
Genome_build: pombase.org September 2018 release
Supplementary_files_format_and_content: bigWig files for input and WT normalized ChIP-Seq data

organism: Schizosaccharomyces pombe

source_name: log phase fission yeast culture

growth_protocol: 50mL of cells were grown to OD=0.6-0.8 overnight from OD=0.025 in rich media (YES). Base on OD measurements, 300x10^6 cells per sample were fixed in 1% formaldehyde and flash frozen

extract_protocol:
ChIP DNA was extracted using a bead beater and 0.5mm zirconia beads. Lysates were clarfied following shearing by sonication and then DNA/histone complexes were immunoprecipitated with antibody.
Libraries were constructed first with end repair via the Fast End Repair Kit (Thermo) then A-tailed using Klenow fragment (NEB). Illumina adaptors were ligated using Rapid T4 DNA Ligase (Enzymatics), followed by PCR amplification for 15 cycles, and size selection between 200-500bp by bead purification and gel extraction.

value: PAS99, PAS525, PAS528 mixture

tag: genotype

value: mixture

tag: chip antibody


title: smart_seq2_single_DRG_1


title: smart_seq2_single_DRG_7


title: combined input 1


title: Xrcc4-/- p53-/- ABLKi rep1

tag: genotype/cell type

value: Xrcc4-/- p53-/- v-abl/Bcl2 transformed mouse pro-B cells

tag: treatment


title: wild type isolate D H3K9me2

value: wild type


title: scRCAT-seq_single_oocyteD4_8

description: applying single cell method to oocyte

value: oocyte


title: p53-/- Released rep3

source_name: p53-/- Released

value: p53-/- v-abl/Bcl2 transformed mouse pro-B cells

value: Released cells from 3 days v-abl kinease inhibitor treatment


title: ovar 43.1.1

tag: tumor subtype

value: serous ovarian carcinoma

value: ovary

tag: histology

value: serous-papillary

tag: primary or metastasis

tag: figo stage

tag: grade


title: scRCAT-seq_single_oocyteD4_7

description: applying single cell method to oocyte

tag: strain

tag: tissue


title: 44.9.2


title: Xrcc4-/- p53-/- ABLKi rep2

value: v-abl kinease inhibitor STI571(ABLKi) for 3 days


title: p53-/- Released rep2


title: p53-/- Released rep1


title: scRCAT-seq_single_oocyteD4_5

description: applying single cell method to oocyte


title: scRCAT-seq_single_oocyteD4_6

description: applying single cell method to oocyte


title: p53-/- ABLKi rep3

source_name: p53-/- ABLKi


title: ovar 42.2.1


title: 41 OVAR 1.2


title: ovar 50.2.1


title: p53-/- ABLKi rep2


title: epe1KOset1KO isolate D H3K9me2


title: scRCAT-seq_single_oocyteD4_2

description: applying single cell method to oocyte


title: wild type isolate C H3K4me3


title: 35.3.1


title: epe1KOset1KO isolate B H3K9me2


title: scRCAT-seq_single_oocyteD4_1

description: applying single cell method to oocyte


title: 34.1.2


title: wild type isolate C H3K9me2


title: epe1KOset1KO isolate A H3K9me2


title: epe1KOset1KO isolate C H3K9me2


title: wild type isolate D H3K4me3


title: scRCAT-seq_single_DRG_17

value: Dorsal root ganglion neuron


title: epe1KO isolate D H3K4me3


title: epe1KO isolate D H3K9me2


title: Xrcc4-/- ABLKi rep1

source_name: Xrcc4-/- ABLKi

value: Xrcc4-/-  v-abl/Bcl2 transformed mouse pro-B cells


title: Xrcc4-/- ABLKi rep2


title: 24 OVAR 4

value: primary


title: WT Released rep5

source_name: WT Released

value: Wild type from v-abl/Bcl2 transformed mouse pro-B cells


title: 49 OVAR 2.1


title: ovar 39.1.2


title: scRCAT-seq_single_DRG_16


title: p53-/- ABLKi rep1


title: scRCAT-seq_single_oocyteD4_4

description: applying single cell method to oocyte


title: ovar 20.1.2


title: 36.1.3


title: Xrcc4-/- ABLKi rep4


title: scRCAT-seq_single_oocyteD4_3

description: applying single cell method to oocyte


title: scRCAT-seq_single_DRG_15


title: epe1KO isolate C H3K9me2


title: 25 OVAR 1.2 re


title: WT Released rep4

value: Wild type v-abl/Bcl2 transformed mouse pro-B cells


title: Xrcc4-/- ABLKi rep3

value: Xrcc4-/- v-abl/Bcl2 transformed mouse pro-B cells


title: scRCAT-seq_single_DRG_18


title: scRCAT-seq_single_DRG_14


title: epe1KO isolate C H3K4me3


title: 13.16


title: scRCAT-seq_single_DRG_13


title: epe1KO isolate A H3K9me2


title: WT Released rep3


title: 5.16


title: 4.4


title: WT Released rep2


title: WT Released rep1


title: WT ABLKi rep4

source_name: WT ABLKi


title: pkg_T2

city: Wuhan

first: Qingwen

last: Shen

state: Hubei

address: Huazhong Agriculture University

department: Lipid metabolism

institute: National Key Laboratory of Crop Genetic Improvement

description: T, Treated with 10 μM Br-cGMP

data_processing:
Illumina Casava 1.8 software used for basecalling.
Three types reads were filtered: reads with adapter; contain N (no exact base information) reads; low-quality reads.
Based on HISAT2 software.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Oryza sativa

source_name: T, Treated with 10 μM Br-cGMP

growth_protocol: Growth on 1/2 MS medium for 14 days in growth chamber, under 12 h light/12 h dark photoperiods (30/24°C), with the light intensity of 30,000 lx and 60% humidity.

extract_protocol:
Total RNA was extracted using a Trizol reagent (TransGene Biotech, Beijing, China) following the manufacturer’s instruction, and DNA contaminated was removed using RNase-free DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seedlings were treated with or without 10 μM Br-cGMP for 5 h.

tag: cultivar

value: Seedling

value: PKG-/-


title: epe1KO isolate A H3K4me3


title: pkg_T3

description: T, Treated with 10 μM Br-cGMP

tag: age


title: scRCAT-seq_single_DRG_11


title: 34-Mcln-1-T2-E4

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
Illumina RiboZero bacteria kit was used for rRNA depletion. Samples were sequenced on the NextSeq sequencing instrumetn in mid output 150 v2 flow cell. Paired-end 75 bp reads were checked for technical artifacts using FastQC following Illumina default quality filtering steps. Raw FASTQ read data were processed using the R package DuffyNGS.
Genome_build: Mycobacterium chelonae ASM163280v1
Supplementary_files_format_and_content: tab-delimited text file includes RPKM for each sample

organism: Mycobacteroides chelonae

source_name: bacterial culture

growth_protocol:
planktonic samples grown in 30 degrees C static incubator with tyloxapol
pellicle samples grown in 30 degrees C static incubator without tyloxapol

extract_protocol:
In four independent experiments, cultures of M. chelonae were diluted in Sauton's media to an OD of 0.03 and grown in a 75cm2 cap-vented culture flask, in a 30 degrees C static incubator for 5 (t1) or 10 (t2) days. After harvesting at 5 or 10 days, cells pellets were spun down and immediately frozen at -80 degrees C until RNA isolation . Cell pellets in TRIzol were transferred to a tube containing Lysing Matrix B, and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer three times. This mixture was centrifuged at max speed for 1 min and the supernatant was transferred to a fresh tube. RNA was isolated using phenol-chloroform extraction method, followed by DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 10 days

tag: culture


title: pkg_T1

description: T, Treated with 10 μM Br-cGMP


title: scRCAT_seq_single_DRG_10


title: scRCAT_seq_single_DRG_9


title: WT ABLKi rep2


title: 33-Mcln-1-T1-E4

value: 5 days


title: WT_T3

description: T, Treated with 10 μM Br-cGMP

value: Wild-type


title: WT ABLKi rep3


title: WT ABLKi rep1


title: scRCAT-seq_single_DRG_8


title: WT_T2

description: T, Treated with 10 μM Br-cGMP


title: 30-Mcln-1-T2-E3


title: scRCAT-seq_single_DRG_7


title: Xrcc4-/- p53-/- non-treatment rep2

source_name: Xrcc4-/- p53-/- non-treatment

value: Xrcc4-/- p53-/- v-abl/Bcl2 transformed mouse pro-B cells

value: cycling cells without treatment


title: scRCAT_seq_single_DRG_6


title: Xrcc4-/- p53-/- non-treatment rep1


title: 31-Mcln-2-T1-E3

value: PlanktonicEarly


title: pkg_CK3

description: CK, Control

source_name: CK, Control


title: WT_T1

description: T, Treated with 10 μM Br-cGMP


title: 27-Mcln-2-T1-E2


title: 35-Mcln-2-T1-E4


title: WT non-treatment rep2

source_name: WT non-treatment


title: scRCAT-seq_single_DRG_12


title: pkg_CK2

description: CK, Control


title: 26-Mcln-1-T2-E2


title: WT non-treatment rep1


title: pkg_CK1

description: CK, Control


title: scRCAT_seq_single_DRG_4


title: 25-Mcln-1-T1-E2


title: scRCAT_seq_single_DRG_3


title: Xrcc4-/- p53-/- Released

description: Igk locus capture-based target enrichment  sequencing

data_processing:
For data analysis of Igk pull-down libraries, 2 x 250 bps paired-end reads were firstly assembled by FLASH tool by at least 10 nts overlapping. Both assembled and un-assembled reads were mapped to mouse mm9 reference genome using BWA mem using default settings.
Reads with mapping quality less than 10 and multiple mapping were filtered out. Reads containing Igk sequence were disentangled by Bedtools through intersection with Igk locus coordinate. These reads were further dissected into V-J joins and germlines by costumed perl scripts.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files contain all captured prey sequence with cis-rearrangement in Igk locus

source_name: v-abl/Bcl2 transformed pro-B cells

extract_protocol:
Genomic DNA was extracted with proteinase K digestion overnight and phenol/chloroforme extraction.
Briefly, 3 ug gDNA was sonicated to 150 to 200 bps size. Sheared DNA was end repaired, dA tailed, ligated with provided paired-end adaptor and amplified. The prepared DNA was hybridized to customized probes and captured by Dynabeads MyOne Streptavidin T1 (Life Technologies). The pull-downed DNA was amplified with provided indexing primers of Illumina MiSeq for 250 bps paired-end sequencing.

value: Released cells from 3 days v-abl kinease inhibitor treatment


title: WT_CK3

description: CK, Control


title: 23-Mcln-2-T1-E1


title: scRCAT_seq_single_DRG_2


title: Xrcc4-/- p53-/- ABLKi


title: 22-Mcln-1-T2-E1


title: WT_CK2

description: CK, Control


title: 21-Mcln-1-T1-E1


title: scRCAT_seq_single_DRG_1


title: Xrcc4-/- p53-/- non-treatment


title: WT_CK1

description: CK, Control


title: 29-Mcln-1-T1-E3


title: scRCAT_seq_single_DRG_5


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D8_AD004_indexed

status: Public on Aug 23 2020

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

source_name: C57BL/6J Male P56 Mouse Brain

tag: brain region

value: AON

tag: Sex

value: male


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D9_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D8_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D8_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D7_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D9_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D7_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D9_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_E10_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D9_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D9_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D9_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D7_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D6_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D7_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D7_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D8_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D9_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180212_1C_1_CEMBA180212_1C_2_D8_AD012_indexed


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