.arc/validation_packages.yml

+arc_specification: 2.0.0-draft
+validation_packages:
+  - name: invenio
+    version: 2.1.0
+  - name: pride
+    version: 1.0.3

.gitattributes

 **/dataset/** filter=lfs diff=lfs merge=lfs -text
+/assays/Transcriptomics/dataset/fastq/35C/recovery_24h/35C_C_(SRR15481355)/35C_C_14_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/Transcriptomics/dataset/fastq/35C/recovery_24h/35C_C_(SRR15481355)/35C_C_14_2.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/Transcriptomics/dataset/fastq/40C/heat_00.5h/40C_A_(SRR15481365)/40C_A_3_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/Transcriptomics/dataset/fastq/40C/heat_00.5h/40C_A_(SRR15481365)/40C_A_3_2.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/Transcriptomics/dataset/fastq/40C/heat_16h/40C_C_(SRR15481382)/40C_C_8_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
+/assays/Transcriptomics/dataset/fastq/40C/heat_16h/40C_C_(SRR15481382)/40C_C_8_2.fastq.gz filter=lfs diff=lfs merge=lfs -text

.gitignore

+# ----- macos rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/macOS.gitignore
+
+
+# General
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+.LSOverride
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+._*
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+.DocumentRevisions-V100
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+# Directories potentially created on remote AFP share
+.AppleDB
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+# ----- windows rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/Windows.gitignore
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\ No newline at end of file

README.md

 # Chlamydomonas reinhardtii heat stress time course experiment
 
+[![DOI](https://archive.nfdi4plants.org/badge/DOI/10.60534/9e5jx-75d83.svg)](https://doi.org/10.60534/9e5jx-75d83)
+
 ## Experimental design
-<img src="https://git.nfdi4plants.org/venn/Ru_ChlamyHeatstress/-/raw/main/studies/HeatstressExperiment/protocols/2022-07-12_121059.png" alt="Overview_HS40" width="80%"/>
+<img src="https://git.nfdi4plants.org/venn/Ru_ChlamyHeatstress/-/raw/main/studies/Growth/protocols/2022-07-12_121059.png" alt="Overview_HS40" width="70%"/>
 
-**Figure 1:** Experimental design of the heat treatment experiments (Zhang et al.)
+**Figure 1:** Experimental design of the heat treatment experiments (Zhang et al. 2022).
 
 ## Publication
 
-Title: Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. 
+#### Title
+Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. 
+
+#### Citation
 
-Authors: Zhang N, Mattoon EM, McHargue W, Venn B, Zimmer D, Pecani K, Jeong J, Anderson CM, Chen C, Berry JC, Xia M, Tzeng SC, Becker E, Pazouki L, Evans B, Cross F, Cheng J, Czymmek KJ, Schroda M, Mühlhaus T, Zhang R. 
+Zhang N, Mattoon EM, McHargue W, Venn B, Zimmer D, Pecani K, Jeong J, Anderson CM, Chen C, Berry JC, Xia M, Tzeng SC, Becker E, Pazouki L, Evans B, Cross F, Cheng J, Czymmek KJ, Schroda M, Mühlhaus T, Zhang R. Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. Commun Biol. 2022 May 13;5(1):460. doi: 10.1038/s42003-022-03359-z   . PMID: 35562408  ; PMCID: PMC9106746.  
 
-Journal: Commun Biol. 2022 May 13;5(1):460. doi: 10.1038/s42003-022-03359-z. PMID: 35562408; PMCID: PMC9106746.
 
 ## Sampling schema
 
-|time point [h]|condition |temperature [°C]|
-|---|--|--|
-|-24|control|25|
-|-2|control|25|
-|0|start heat treatment|25 -> 35/40|
-|0.5|heat treatment|35/40|
-|1|heat treatment|35/40|
-|2|heat treatment|35/40|
-|4|heat treatment|35/40|
-|8|heat treatment|35/40|
-|16|heat treatment|35/40|
-|24|end treatment|35/40 -> 25|
-|24|start recovery|25|
-|26|recovery|25|
-|28|recovery|25|
-|32|recovery|25|
-|48|recovery|25|
-|72|recovery|25|
+|time point [h]|condition |temperature [°C]|sample name|description|sample taken Proteomics =16|sample taken Transcriptomics =15|
+|---|--|--|--|--|--|--|
+|-20|control|25|pre1||x||
+|-18|control|25|pre2|preheat|x|x|
+|0|start heat treatment|25 -> 35/40|HS_T00h|RHT (reach high temperature)|x|x|
+|0.5|heat treatment|35/40|HS_T00.5h|-|x|x|
+|1|heat treatment|35/40|HS_T01h|-|x|x|
+|2|heat treatment|35/40|HS_T02h|-|x|x|
+|4|heat treatment|35/40|HS_T04h|-|x|x|
+|8|heat treatment|35/40|HS_T08h|-|x|x|
+|16|heat treatment|35/40|HS_T16h|-|x|x|
+|24|end treatment|35/40 -> 25|HS_T24h|end heat treatment|x|x|
+|24|start recovery|25|RE_T00h|RCT (reach control temperature)|x|x|
+|26|recovery|25|RE_T02h|-|x|x|
+|28|recovery|25|RE_T04h|-|x|x|
+|32|recovery|25|RE_T08h|-|x|x|
+|48|recovery|25|RE_T24h|-|x|x|
+|72|recovery|25|RE_T48h|-|x|x|
+
+|Technology|temperature treatments|timepoints|replicates|sample count|
+|--|--|--|--|--|
+|Proteomics|2|16|3|**96**|
+|Transcriptomics|2|15|3|**90**|