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Blood, Vol. 110, Issue 12, 3881-3890, December 1, 2007
Smad1 and Smad5 differentially regulate embryonic hematopoiesis
Blood McReynolds et al.
110: 3881
Supplemental materials for McReynolds et al
Files in this Data Supplement:
- Document 1. Supplemental methods (PDF, 22.6 KB)
- Table S1. Primers used for quantitative real-time PCR assays (XLS, 13.5 KB)
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Forward and reverse primers are listed 5′ to 3′ for the various zebrafish genes evaluated by qPCR. Primers were designed using the Primer 3 software program (http://frodo.wi.mit.edu/). Each primer is 19-21 bp, has approximately a 50% G/C content, a Tm=60 C and amplifies ∼100 bp product. actin was used for normalization.
- Table S2. Smad-dependent genes revealed by microarray analysis (XLS, 3.06 MB)
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This and the subsequent four tables contain all the normalized data obtained from 18 microarray experiments. To obtain these values raw data received from Nimblegen was processed by the NimbleScan software for normalization. The first column is the SEQ_ID as designated by Nimblegen for each target. These identifiers were used to link to the gene names for analysis. The following columns in the Table contain the normalized data for each individual experiment (three for each morphant class and nine wild-type samples). In each experiment the wild-type and morphant samples were differentially labeled with Cy3 or Cy5 and co-hybridized, so the data is listed in two column sets and labeled with a letter, i.e. wildtypeA and Smad1MOA were analyzed using the same microarray.
- Table S3. Continuation of Smad-dependent genes revealed by microarray analysis (XLS, 3.06 MB)
- Table S4. Continuation of Smad-dependent genes revealed by microarray analysis (XLS, 3.06 MB)
- Table S5. Continuation of Smad-dependent genes revealed by microarray analysis (XLS, 3.06 MB)
- Table S6. Continuation of Smad-dependent genes revealed by microarray analysis (XLS, 3.05 MB)
- Table S7. Unique subsets deregulated in specific morphant classes (XLS, 34.5 KB)
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(A-F) Microarray analysis was performed using cDNA derived from one-somite stage morphant and sibling wild-type control embryos. Morphant classes that were compared with control wild-type cDNA include Smad1 alone, Smad5 alone, and Smad1+5 morphant embryos. Three independent sets of RNA were obtained and used to generate probes for hybridization to Nimblegen gene expression arrays. The results were processed by NimbleScan software for normalization. The mean intensities from the three experiments were determined and log2 ratios calculated by comparison to wild-type using the R statistical analysis program. The genes that show a two-fold or greater change were compiled. For the purpose of clarity, duplicated targets and those for entirely non-annotated genes were removed from the lists. Each list contains genes that are specifically 2.38 fold or greater changed in gene expression for that morphant class (they are unique) along with the matching TIGR oligo identifier and the log2 ratio for each gene.
(A) List of unique genes that are upregulated when Smad1 is knocked down.
(B) List of unique genes that are down-regulated when Smad1 is knocked down.
(C) List of unique genes that are upregulated when Smad5 is knocked down.
(D) List of unique genes that are down-regulated when Smad5 is knocked down.
(E) List of unique genes that are upregulated only when Smad1 and Smad5 are both knocked down.
(F) List of unique genes that are down-regulated only when Smad1 and Smad5 are both knocked down.
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