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Dataset results
222 results for “BCR”
PRJNA638224 - BCR repertoire sequencing from COVID-19 patients
<p><strong>Description</strong></p> <p>These are the processed BCR repertoire sequence data that accompany the following manuscript: “Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures”. The manuscript preprint is available at doi: <a href="https://doi.org/10.1101/2020.05.20.106294">https://doi.org/10.1101/2020.05.20.106294</a>. The raw sequence data are available on SRA under the BioProject PRJNA638224</p> <p> </p> <p><strong>Sequence processing</strong></p> <p>The Immcantation framework (docker container v3.0.0) was used for sequence processing. Briefly, paired-end reads were joined based on a minimum overlap of 20 nt, and a max error of 0.2, and reads with a mean phred score below 20 were removed. Primer regions, including UMIs and sample barcodes, were then identified within each read, and trimmed. Together, the sample barcode, UMI, and constant region primer were used to assign molecular groupings for each read. Within each grouping, usearch, was used to subdivide the grouping, with a cutoff of 80% nucleotide identity, to account for randomly overlapping UMIs. Each of the resulting groupings is assumed to represent reads arising from a single RNA. Reads within each grouping were then aligned, and a consensus sequence determined. For each processed sequence, IgBlast was used to determine V, D and J gene segments, and locations of the CDRs and FWRs. Isotype was determined based on comparison to germline constant region sequences. Sequences annotated as unproductive by IgBlast were removed.</p> <p> </p> <p><strong>Sequence data column description</strong></p> <ul> <li><strong>sample_id </strong>Unique identifier for each sequencing library</li> <li><strong>sequence_id </strong>Unique identifier for a sequence within a sample_id</li> <li><strong>sequence_alignment </strong>IMGT gapped nucleotide sequence</li> <li><strong>germline_alignment </strong>IMGT gapped germline sequence</li> <li><strong>v_call </strong>IGHV gene segment(s) and allele</li> <li><strong>d_call </strong>IGHD gene segment(s) and allele</li> <li><strong>j_call </strong>IGHJ gene segment(s) and allele</li> <li><strong>c_call </strong>Isotype subclass</li> <li><strong>junction </strong>Junction nucleotide sequence</li> <li><strong>junction_aa </strong>Junction amino acid sequence</li> <li><strong>duplicate_count </strong>UMI count for the given unique sequence</li> <li><strong>consensus_count </strong>Raw read count for the given unique sequence</li> </ul> <p> </p> <p><strong>Sequence metadata column description</strong></p> <ul> <li><strong>sample_id </strong>Unique identifier for each sequencing library</li> <li><strong>bioproject_accession </strong>NCBI BioProject accession number</li> <li><strong>biosample_accession </strong>NCBI BioSample accession number</li> <li><strong>sra_accession </strong>NCBI SRA accession number</li> <li><strong>sex </strong>Sex of patient</li> <li><strong>age </strong>Age of patient at time of sampling</li> <li><strong>ethnicity </strong>Ethnicity of patient</li> <li><strong>health_state </strong>One of worsening, stable, or improving</li> </ul>
BCR simulated data
<p>Simulated bulk BCR sequencing data for benchmarking BCRseq pipelines</p>
Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser
<p>In our publication, we created simulations of paired heavy and light chain BCR sequences. Uploaded here is all the data needed to rerun the simulations, as well as the output of the simulations we ran. The output of BCR phylo included here are the lineage trees, unpickled and put into one file (true_trees.tsv), and the fasta files ('starting_fastas' folder). The naive BCR sequences we used as a starting point are found in the 'naive_data' folder. The post-simulation data for all 20 iterations (combined heavy and light chain data through both simulation frameworks) can be found in the 'simulation_data' folder.</p>
Study of Diagnostic Performance of [18F]CTT1057 in BCR
ClinicalTrials.gov study NCT04838613. IPD Sharing: YES. Countries: 4. Publications: 0.
scRNA-seq revealed the rules for CDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains
<p>The scRNAseq datasets of CDR3 length pairing in TCR beta and alpha chains which come from human cental and peripheral samples and mouse peripheral samples.</p> <p>The scRNAseq datasets of CDR3 length pairing in BCR heavy and light chainsCDR3 length pairing in TCR beta and alpha chains and BCR heavy and light chains human cental and peripheral samples and mouse cental and peripheral samples.</p> <p> </p>
Homoharringtonine (Omacetaxine Mepesuccinate) in Treating Patients With Chronic Myeloid Leukemia (CML) With the T315I BCR-ABL Gene Mutation
ClinicalTrials.gov study NCT00375219. IPD Sharing: Not stated. Countries: 10. Publications: 1.
Nilotinib in Newly Diagnosed Adult Philadelphia Chromosome & /or BCR-ABL Positive Chronic Myeloid Leukaemia in Chronic Phase
ClinicalTrials.gov study NCT01061177. IPD Sharing: Not stated. Countries: 26. Publications: 2.
Combination Chemotherapy and Dasatinib in Treating Participants With Philadelphia Positive or BCR-ABL Positive Acute Lymphoblastic Leukemia.
ClinicalTrials.gov study NCT00390793. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Combination Chemotherapy With or Without Blinatumomab in Treating Patients With Newly Diagnosed BCR-ABL-Negative B Lineage Acute Lymphoblastic Leukemia
ClinicalTrials.gov study NCT02003222. IPD Sharing: Not stated. Countries: 4. Publications: 2.
Bulk RNA sequencing analysis of Lin- leukemia BCR-ABL and BCR-ABL/MSI2-HOXA9 cells (post-transplantation)
Open the record for dataset details and reuse information.
Table S3. Univariate analyses of early BCR in high-risk and very high-risk patients after propensity score matching.
<p>Table S3. Univariate analyses of early BCR in high-risk and very high-risk patients after propensity score matching.</p>
Blinatumomab, Methotrexate, Cytarabine, and Ponatinib in Treating Patients With Philadelphia Chromosome-Positive, or BCR-ABL Positive, or Relapsed/Refractory, Acute Lymphoblastic Leukemia
ClinicalTrials.gov study NCT03263572. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Testing the Use of Steroids and Tyrosine Kinase Inhibitors With Blinatumomab or Chemotherapy for Newly Diagnosed BCR-ABL-Positive Acute Lymphoblastic Leukemia in Adults
ClinicalTrials.gov study NCT04530565. IPD Sharing: YES. Countries: 3. Publications: 0.
Philadelphia Chromosome Positive CML Patients Without Optimal Response or Tolerance to Bcr-Abl TKI
ClinicalTrials.gov study NCT01602952. IPD Sharing: Not stated. Countries: 3. Publications: 1.
Autoimmune Cytopenia and BcR Inhibitors
ClinicalTrials.gov study NCT03469895. IPD Sharing: NO. Countries: 1. Publications: 16.
Treatment of Acute Lymphoblastic Leukemia Ph '(BCR / ABL) Positive Patients Aged > 55 Years
ClinicalTrials.gov study NCT01376427. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Treatment of Breakpoint Cluster Region-Abelson (BCR-ABL) Negative ALL in Adults
ClinicalTrials.gov study NCT04179929. IPD Sharing: NO. Countries: 1. Publications: 0.
Nilotinib in PH+, BCR-, ABL+ CML Patients
ClinicalTrials.gov study NCT01535391. IPD Sharing: NO. Countries: 1. Publications: 1.
Chemotherapy and Imatinib in Young Adults With Acute Lymphoblastic Leukemia Ph (BCR-ABL) POSITIVE
ClinicalTrials.gov study NCT01491763. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Dasatinib and Venetoclax in Treating Patients With Philadelphia Chromosome Positive or BCR-ABL1 Positive Early Chronic Phase Chronic Myelogenous Leukemia
ClinicalTrials.gov study NCT02689440. IPD Sharing: Not stated. Countries: 1. Publications: 3.
ScienceDex guides
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International Brain Laboratory public data
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OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.