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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...). (F) Flow cytometry analysis of shRNA-infected cells after 3 days culture, stained with the erythroid-specific cell surface marker LY76 (also known as TER-119). (G) Quantitative RT-PCR of Jun mRNA expression in LIN− cells isolated from spleens of PHZ-treated mice and cultured for 3 days, followed...
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LETTER: Cloning and Functional Analysis of cDNAs with Open Reading Frames for 300 Previously Undefined Genes Expressed in CD34+ Hematopoietic Stem/Progenitor Cells
- Qing-Hua Zhang,
- Min Ye,
- Xin-Yan Wu,
- Shuang-Xi Ren,
- Meng Zhao,
- Chun-Jun Zhao,
- Gang Fu,
- Yu Shen,
- Hui-Yong Fan,
- Gang Lu,
- Ming Zhong,
- Xiang-Ru Xu,
- Ze-Guang Han,
- Ji-Wang Zhang,
- Jiong Tao,
- Qiu-Hua Huang,
- Jun Zhou,
- Geng-Xi Hu,
- Jian Gu,
- Sai-Juan Chen,
- and Zhu Chen
Genome Res. October 1, 2000 10: 1546-1560; doi:10.1101/gr.140200
...genomics facing the completion of the human genomic sequences in the coming 1 or 2 years. RESULTS Primary Gene Expression Profiles of CD34+ HSPCs RT/PCR-based Capfinder cDNA libraries were constructed using mRNA from highly purified CD34+ HSPCs of cord blood and adult bone marrow, using methods described...
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Research: Pluripotent stem cells escape from senescence-associated DNA methylation changes
- Carmen M. Koch,
- Kristina Reck,
- Kaifeng Shao,
- Qiong Lin,
- Sylvia Joussen,
- Patrick Ziegler,
- Gudrun Walenda,
- Wolf Drescher,
- Bertram Opalka,
- Tobias May,
- Tim Brümmendorf,
- Martin Zenke,
- Tomo Šarić,
- and Wolfgang Wagner
Genome Res. February 2013 23: 248-259; Published in Advance October 18, 2012, doi:10.1101/gr.141945.112
..., surface-marker expression (CD14#2;, CD29+, CD31#2;, CD34#2;, CD45#2;, CD73+, CD90+, and CD105+), and differentiation potential toward osteogenic, adipogenic, and chondrogenic lineages (Dominici et al. 2006). Senescent MSC acquired large and flat morphology and expressed senescence...
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Resource: MicroRNA programs in normal and aberrant stem and progenitor cells
- Christopher P. Arnold,
- Ruoying Tan,
- Baiyu Zhou,
- Si-Biao Yue,
- Steven Schaffert,
- Joseph R. Biggs,
- Regis Doyonnas,
- Miao-Chia Lo,
- John M. Perry,
- Valérie M. Renault,
- Alessandra Sacco,
- Tim Somervaille,
- Patrick Viatour,
- Anne Brunet,
- Michael L. Cleary,
- Linheng Li,
- Julien Sage,
- Dong-Er Zhang,
- Helen M. Blau,
- Caifu Chen,
- and Chang-Zheng Chen
Genome Res. May 2011 21: 798-810; Published in Advance March 30, 2011, doi:10.1101/gr.111385.110
...marrow cells Viatour (et al. 2008) Splenic hematopoietic stem/ progenitor cells (KSL-Sp) HSPCs localized in the spleen Kit+Sca-1+Lin– cells from spleen from poly:IC-treated PTEN control mice Zhang et al. (2006) Muscle MuSCs Quiescent, self-renewing MuSCs CD45–CD11b–CD31–Sca1 –CD34+integrin-7+ from...
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Methods: Customized Molecular Phenotyping by Quantitative Gene Expression and Pattern Recognition Analysis
- Shreeram Akilesh,
- Daniel J. Shaffer,
- and Derry Roopenian
Genome Res. July 2003 13: 1719-1727; doi:10.1101/gr.533003
...and cellular effectors. J. Hematother. Stem Cell Res. 9 : 299 -306. ↵ Gibson, U.E., Heid, C.A., and Williams, P.M. 1996 . A novel method for real time quantitative RT-PCR. Genome Res. 6 : 995 -1001. ↵ Giulietti, A., Overbergh, L., Valckx, D., Decallonne, B., Bouillon, R., and Mathieu, C. 2001 . An overview...
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Research: Engineered LINE-1 retrotransposition in nondividing human neurons
- Angela Macia,
- Thomas J. Widmann,
- Sara R. Heras,
- Veronica Ayllon,
- Laura Sanchez,
- Meriem Benkaddour-Boumzaouad,
- Martin Muñoz-Lopez,
- Alejandro Rubio,
- Suyapa Amador-Cubero,
- Eva Blanco-Jimenez,
- Javier Garcia-Castro,
- Pablo Menendez,
- Philip Ng,
- Alysson R. Muotri,
- John L. Goodier,
- and Jose L. Garcia-Perez
Genome Res. March 2017 27: 335-348; Published in Advance December 13, 2016, doi:10.1101/gr.206805.116
...,E). These data were confirmed by semiquantitative RT-PCR (Supplemental Fig. S5C). Additionally, when we analyzed Ad-L1 retrotransposition, we reproducibly detected a very low level of L1 retrotransposition (Fig. 4C), despite efficient Ad-L1 transduction (Supplemental Fig. S11G). Thus, CD34+-HSCs express low...
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LETTER: Transcriptional Regulation of the Stem Cell Leukemia Gene (SCL) — Comparative Analysis of Five Vertebrate SCL Loci
- Berthold Göttgens,
- Linda M. Barton,
- Michael A. Chapman,
- Angus M. Sinclair,
- Bjarne Knudsen,
- Darren Grafham,
- James G.R. Gilbert,
- Jane Rogers,
- David R. Bentley,
- and Anthony R. Green
Genome Res. May 1, 2002 12: 749-759; doi:10.1101/gr.45502
...DNA to the genomic sequence. The position of noncoding exons was determined by RT–PCR using total RNA derived from whole adult zebrafish. A forward primer was designed from a putative first exon immediately downstream of a sequence highly homologous to mouse promoter 1a, and a reverse primer was designed from...
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RESOURCE: In Situ-Synthesized Novel Microarray Optimized for Mouse Stem Cell and Early Developmental Expression Profiling
- Mark G. Carter,
- Toshio Hamatani,
- Alexei A. Sharov,
- Condie E. Carmack,
- Yong Qian,
- Kazuhiro Aiba,
- Naomi T. Ko,
- Dawood B. Dudekula,
- Pius M. Brzoska,
- S. Stuart Hwang,
- and Minoru S.H. Ko
Genome Res. May 1, 2003 13: 1011-1021; doi:10.1101/gr.878903
...by decreasing t -value, and P is estimated using the z -distribution ( Benjamini and Hochberg 1995 ). Real-Time Quantitative RT-PCR For E12.5 embryo and placenta, 10-μg RNA aliquots were DNAse-treated using a DNA-Free Kit (Ambion), and annealed with random hexamers. cDNA synthesis was performed using Super...
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Method: Iterative epigenomic analyses in the same single cell
- Hidetaka Ohnuki,
- David J. Venzon,
- Alexei Lobanov,
- and Giovanna Tosato
Genome Res. October 2021 31: 1819-1830; Published in Advance February 24, 2021, doi:10.1101/gr.269068.120
...the erythroid, myeloid, and megakaryocytic lineages (Klein et al. 1976; Andersson et al. 1979; Lozzio et al. 1981). CD34 is expressed in CMP and GMP, but not in MEP (Warren et al. 2006). Stem-like chronic myeloid leukemia cells are marked by CD33 and CD47 (Valent et al. 2014). The epigenetic status of the CD34...
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Method: Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac
- Fei Xie,
- Lin Ye,
- Judy C. Chang,
- Ashley I. Beyer,
- Jiaming Wang,
- Marcus O. Muench,
- and Yuet Wai Kan
Genome Res. September 2014 24: 1526-1533; Published in Advance August 5, 2014, doi:10.1101/gr.173427.114
...) Colony-forming assay for differentiated cells at day 10 revealed various types of hematopoietic colonies as well as nucleated cells, including erythroblasts. Blue arrows indicate erythroid cells. (E) HBB and HBG gene expression (normalized to GAPDH) were measured by quantitative RT-PCR in hematopoietic...

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