.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/40C/heat_01h/SRR15481368/SRR15481368_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
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-/assays/Transcriptomics/dataset/fastq/40C/heat_02h/SRR15481371/SRR15481371_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/assays/Transcriptomics/dataset/fastq/40C/heat_02h/SRR15481371/SRR15481371_2.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/assays/Transcriptomics/dataset/fastq/40C/heat_02h/SRR15481372/SRR15481372_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/assays/Transcriptomics/dataset/fastq/40C/heat_02h/SRR15481372/SRR15481372_2.fastq.gz filter=lfs diff=lfs merge=lfs -text
-/assays/Transcriptomics/dataset/fastq/40C/heat_02h/SRR15481373/SRR15481373_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
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-/assays/Transcriptomics/dataset/fastq/40C/heat_04h/SRR15481374/SRR15481374_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
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-/assays/Transcriptomics/dataset/fastq/40C/heat_04h/SRR15481375/SRR15481375_1.fastq.gz filter=lfs diff=lfs merge=lfs -text
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-/assays/Transcriptomics/dataset/fastq/40C/heat_04h/SRR15481376/SRR15481376_2.fastq.gz 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
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+/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
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+
+
+
+
+
+# ----- windows rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/Windows.gitignore
+
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
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+
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+
+# ----- linux rules -----
+# taken from https://github.com/github/gitignore/blob/main/Global/Linux.gitignore
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+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
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+.directory
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+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
\ 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]|sample name|description|
-|---|--|--|--|--|
-|-20|control|25|pre1||
-|-18|control|25|pre2||
-|0|start heat treatment|25 -> 35/40|HS_T00h|reach treatment temperature|
-|0.5|heat treatment|35/40|HS_T00.5h|-|
-|1|heat treatment|35/40|HS_T01h|-|
-|2|heat treatment|35/40|HS_T02h|-|
-|4|heat treatment|35/40|HS_T04h|-|
-|8|heat treatment|35/40|HS_T08h|-|
-|16|heat treatment|35/40|HS_T16h|-|
-|24|end treatment|35/40 -> 25|HS_T24h|end heat treatment|
-|24|start recovery|25|RE_T00h|RCT (reach control temperature)|
-|26|recovery|25|RE_T02h|-|
-|28|recovery|25|RE_T04h|-|
-|32|recovery|25|RE_T08h|-|
-|48|recovery|25|RE_T24h|-|
-|72|recovery|25|RE_T48h|-|
+|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**|