title: pachynema.LSD1

status: Public on Mar 26 2013

data_processing:
Trimmed sequences in 3' to 36 nts
mapped to hg19 (HeLa S3 data) or mm9 (germ cell data) with BOWTIE -m4 -v2
duplicates were removed with SAMTOOLS RMDUP (except  cell cycle ChIP-seq)
WIGs were generated with IGVtools count extending fragments to 200 nts
WIGs were normalized to 10,000,000 mapped reads (RP10M) using a shell script
normalized WIGs were converted to bigWigs with wigToBigWig
for the cell cycle data, the IgG bigWig profiles were subtracted from each IP profile using a custom script, IgG and input are provided before subtraction
Genome_build: hg19 (HeLaS3) or mm9 (germ cells)
Supplementary_files_format_and_content: RP10M-normalized bigWigs

source_name: pachynema cells

extract_protocol:
Isolated nuclei (HeLaS3) or whole cells (germ cells) were sonicated using a Diagenode Bioruptor to an average size of 200 bp. Chromatin was pre-cleared with BSA-blocked protein G sepharose (Roche) and incubated with antibodies at 4C overnight. The chromatin immunocomplexes were recovered with BSA-blocked protein G beads. After 5 washes in RIPA buffer, immunocomplexes were eluted in 1% SDS and DNA was decrosslinked at 65C for 16h.
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

value: pachynema cells

tag: antibody information

value: custom  protein A purified

tag: internal reference


title: spermatids.SFMBT1

type: SRA

city: Philadelphia

first: Roberto

last: Bonasio

state: PA

address: 3400 Civic Center Blvd - SCTR 9-111

department: Cell and Developmental Biology

country: USA

institute: University of Pennsylvania

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: spermatids

tag: cell type

value: spermatids

tag: antibody


title: pachynema.SFMBT1


title: spermatids.input

value: none (input)


title: HeLaS3.H3K4me1

organism: Homo sapiens

source_name: HeLa S3

value: HeLa S3

tag: cell cycle phase

value: asynchronous population


title: pachynema.POL2


title: pachynema.input


title: HeLaS3.SFMBT1


title: spermatids.POL2


title: HeLaS3.LSD1


title: HeLaS3.CoREST

value: CoREST


title: HeLaS3.input


title: HeLaS3.S.CoREST

description: Harvested 5 hours after release (double thymidine)

value: S


title: HeLaS3.siSFMBT1-1_siLSD1-2_siCoREST-1.R

description: depleted of polyA+ and rRNA

library_source: transcriptomic

data_processing:
Trimmed sequences in 3' to 36 nts
mapped to hg19 with BOWTIE -m40 -v2
assigned counts to gene models in ENS65 with DEGseq
Genome_build: hg19 (HeLaS3) or mm9 (germ cells)
Supplementary_files_format_and_content: RPKM and count table for ENS65

molecule: total RNA

extract_protocol:
RNA was isolated with TRIzol, depleted of polyA+ transcripts with oligo-dT beads, and depleted of rRNA with the Ribominus kit
libraries were prepared with the dUTP strand-specific protocol. After RT and second-strand synthesis, cDNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 ligase (Enzymatics). Fragments of 200±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530) after removal of the 2nd strand with heat-labile UDG (Roche).

tag: cell line

tag: treatment

value: siRNA against SFMBT1 (#1) + LSD1 (#2) + CoREST (#1)


title: HeLaS3.siCtrl.R

description: depleted of polyA+ and rRNA

value: siRNA control


title: HeLaS3.S.IgG

value: IgG control


title: HeLaS3.S.input

description: Harvested 13 hours after release (double thymidine)


title: HeLaS3.S.SFMBT1


title: HeLaS3.G1.SFMBT1


title: HeLaS3.G1.LSD1


title: HeLaS3.S.LSD1


title: HeLaS3.G1.IgG


title: HeLaS3.G1.CoREST


title: spermatids.LSD1


title: HeLaS3.G1.input


title: U2OS.KD.input

status: Public on Oct 16 2012

data_processing:
Trimmed (3') sequences to 36 nts
Mapped to hg19 using bowtie -v2 -m1
Duplicates were removed with samtools rmdup
Wig coverage was calculated with IGVtools extending the reads to 200 nts
Wigs were normalized to 10,000,000 sequenced reads using a shell script
BigWigs were generated with the wigToBigWig script from UCSC
Genome_build: hg19
Supplementary_files_format_and_content: normalized bigWigs

growth_protocol: U2OS cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum

extract_protocol: Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with T4 DNA ligase (Enzymatics). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

value: human osteosarcoma cells

tag: genotype/variation

value: stable SIRT3 knockdown (KD); retroviral expression of shRNAs against SIRT3

tag: chip antibody


title: U2OS.UV.input

treatment_protocol: UV: cells were irradiated with 400 J/m2 and harvested 2h later

value: UV-irradiated


title: U2OS.KD.SIRT3.r2

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: U2OS.UV.SIRT3


title: U2OS.NT.SIRT3


title: U2OS.KD.SIRT3.r1


title: U2OS.NT.input


title: U2OS.NT.IgG

value: control IgG


title: H3K27me3

status: Public on Feb 09 2012

data_processing:
293Trex_FH.H3K27me3.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.H3K27me3.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, H3K27me3 ChIP

growth_protocol: 293T-REx stable lines transfected with HA-tagged PRC1 subunits or an empty vector were grown in standard conditions (DMEM 10% FBS) and kept in selection with zeocin.

extract_protocol: Libraries were prepared according to the manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 300±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

treatment_protocol: Expression of the transgenes was induced by doxycycline treatment for 24 hours.

tag: transgene

value: Flag-HA (empty vector)

value: Millipore

tag: chip antibody catalog #

tag: chip antibody lot


title: RYBP

data_processing:
293Trex_FH.RYBP.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.RYBP.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, RYBP ChIP

value: RYBP

value: Sigma


title: CBX2

data_processing:
293Trex_FH.CBX2.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.CBX2.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, CBX2 ChIP

value: Abcam


title: FH-CBX2.HA

data_processing:
293Trex_FH-CBX2.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-CBX2.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-CBX2.HA ChIP

value: HA


title: PCGF4

data_processing:
293Trex_FH.PCGF4.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.PCGF4.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, PCGF4 ChIP

value: Bethyl


title: FH-PCGF6.HA

data_processing:
293Trex_FH-PCGF6.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-PCGF6.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-PCGF6.HA ChIP


title: RING1B

data_processing:
293Trex_FH.RING1B_be.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.RING1B_be.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, RING1B ChIP


title: H2AK119Ub1

data_processing:
293Trex_FH.H2AUb_cs.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.H2AUb_cs.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, H2AK119Ub1 ChIP

value: Cell Signaling


title: FH-PCGF5.HA

data_processing:
293Trex_FH-PCGF5.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-PCGF5.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-PCGF5.HA ChIP


title: FH-PCGF1.HA

data_processing:
293Trex_FH-PCGF1.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-PCGF1.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-PCGF1.HA ChIP


title: FH-RYBP.HA

data_processing:
293Trex_FH-RYBP.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-RYBP.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-RYBP.HA ChIP

value: Flag-HA-RYBP


title: FH-PCGF4.HA

data_processing:
293Trex_FH-PCGF4.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-PCGF4.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-PCGF4.HA ChIP


title: FH-PCGF2.HA

data_processing:
293Trex_FH-PCGF2.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-PCGF2.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-PCGF2.HA ChIP


title: input

data_processing:
293Trex_FH.input.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH.input.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, input


title: epfl4 epfl6 inflorescence tips 33 d post germination biological replicate 2

status: Public on Mar 28 2012

type: RNA

city: Austin

first: Keiko

middle: U

last: Torii

address: 2506 SPEEDWAY

institute: University of Texas at Austin

description: gene expression data from epfl4 epfl6 flower buds

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 h at 45C on GeneChip Arabidopsis ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were analyzed with the limma package embedded in the Robin software using RMA normalization. P-values were corrected using Benjamini Hochberg multiple testing correction.

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana epfl4 epfl6 inflorescence tips 33 d post germination

label_protocol: Biotinylated cRNA was prepared from 100 ng total RNA with GeneChip 3' IVT Express Kit (Affymetrix).

growth_protocol: Plants were grown on soil at 23C under continuous light

extract_protocol: total RNA was extracted using the plant RNeasy mini kit (Qiagen)

treatment_protocol: No treatment

tag: tissue

value: developing inflorescence tips

tag: age

value: 33 d post germination

tag: genotype

value: epfl4 epfl6

tag: genetic background


title: epfl4 epfl6 inflorescence tips 33 d post germination biological replicate 3


title: Col-0 WT inflorescence tips 33 d post germination biological replicate 2

description: gene expression data from Col-0 WT flower buds

source_name: Arabidopsis thaliana Col-0 WT inflorescence tips 33 d post germination

value: WT


title: R1810A Mutant - Replicate 1

status: Public on Apr 01 2011

description:
Raji is an Epstein-Barr-virus-positive Burkitt’s lymphoma cell line
Cells expressing R->A mutant CTD

data_processing:
Fastq file were generated with the Illumina pipeline
For processed data files, rRNA, tRNA, and mtRNA were removed with BOWTIE using a custom index. Remaining reads were mapped to hg19 with BOWTIE settings -v2 -m1 -51 -30. Mapped reads were assigned to the exon union gene set from ENSEMBL v. 59 using the DEGseq bioconductor package for R. Read densities were normalized against the gene size and total mapped reads into RPKM values.

source_name: Raji cells

growth_protocol: Raji cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 1% penicillin streptomycin (GIBCO, Invitrogen) and 2 mM L-glutamine (GIBCO, Invitrogen) at densities between 2x105 to 106 cells/ml.

extract_protocol: RNA was extracted using peqGOLD Total RNA Kit (PEQLAB Biotechnologie, Erlangen, Germany). Ribosomal RNA was removed using RiboMinusTM Eukaryote Kit for RNA-Seq from Invitrogen (Cat# A10837), starting from 5 µg of total RNA. rRNA-depleted libraries were constructed following Illumina guidelines. Sequences were obtained from an Illumina GAII

treatment_protocol: Cells were transfected with the wild-type and (R1810A) Rpb1 expression vectors by electroporation (10 mg of plasmid DNA/107 cells; 960 mF, 250 V). Polyclonal cell batches were established after selection with G418 (1mg/ml) for 6 - 12 days, and subsequently for 10 days with 2 mg/ml a-amanitin (Sigma).

value: Raji

tag: vector

value: LS*mock, expressing recombinant, HA-tagged R1810->A RPB1 (amanitin resistant)


title: R1810A Mutant - Replicate 2


title: FH-RING1B.HA

data_processing:
293Trex_FH-RING1B.HA.v2m1hg19f.bed.gz; genome build: hg19
293Trex_FH-RING1B.HA.v2m1hg19f.wig.gz; genome build: hg19
Sequenced reads from each ChIP-seq experiment were aligned to the human reference genome (assembly hg19) using Bowtie. Duplicated reads were removed with samtools rdup. ChIP-seq read density files were generated using igvtools by extending reads to 200bp.

Two types of processed files are provided for each ChIP-seq track:
BED files: 6-column files of the reads mapped to hg19 using Bowtie -m1 -v2.
WIG files: Variable-step files calculated on hg19 using the "igvtools count" command with window size of 25.

source_name: 293T-Rex, FH-RING1B.HA ChIP


title: er-2 inflorescence tips 33 d post germination biological replicate 3

description: gene expression data from er-2 flower buds

source_name: Arabidopsis thaliana er-2 inflorescence tips 33 d post germination


title: epfl4 epfl6 inflorescence tips 33 d post germination biological replicate 1


title: er-2 inflorescence tips 33 d post germination biological replicate 1


title: WT - Replicate 1

description:
Raji is an Epstein-Barr-virus-positive Burkitt’s lymphoma cell line
Cells expressing WT CTD

value: LS*mock, expressing recombinant, HA-tagged wild-type RPB1 (amanitin resistant)


title: er-2 inflorescence tips 33 d post germination biological replicate 2


title: WT - Replicate 2


title: Col-0 WT inflorescence tips 33 d post germination biological replicate 3


title: Col-0 WT inflorescence tips 33 d post germination biological replicate 1


title: scrm-D;mute seedling at 5 dpg, biological rep3

status: Public on Nov 08 2011

description: gene expression data from scrm-D;mute seedlings that have an epidermis solely composed almost entirely of meristemoids

hyb_protocol: Biotin-labeled RNA was fragmented and added to standard cocktail of salts, blocking agents and bacterial RNA spikes. The cocktail was hybridized with the ATH1 Genechip at 45 degrees Celsius for 16 hours. After hybridization, the chip was stained with the biotin binding agent, streptavidin-phycoerythrin. Staining signal amplification was amplified using an anti-Streptavidin antibody (goat) and biotinylated goat IgG antibody.

scan_protocol: Arrays were scanned using the Affy 3000 7G scanner, and data extracted from the scan using Affymetrix GeneChip Expression Console with standard settings. Images processed using GeneChip Operating Software (GCOS) (Affymetrix).

source_name: scrm-D;mute seedling at 5 dpg

label_protocol: cDNA was produced from RNA samples using  an oligo-dT primer. cDNA served as a template to produce amplified amounts of biotin-labeled antisense mRNA using in vitro transcription.

growth_protocol: Arabidopsis seeds were surface sterilized, stratified for 2 d at 4deg C and plated onto MS plates. Seedlings were grown for 5 days at 21 deg C and a 18 h light 6 h dark light cycle.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy kit according to the manufacturers protocol

treatment_protocol: Whole seedlings were harvested at 1 pm 5 days post germination and immediately shock frozen in liquid nitrogen.

tag: ecotype

value: whole seedling

value: 5 days post germination

value: scrm-D;mute


title: scrm-D seedling at 5 dpg, biological rep4

description: gene expression data from scrm-D;mute seedlings that have an epidermis solely composed solely of guard cells

source_name: scrm-D seedling at 5 dpg

value: scrm-D


title: spch seedling at 5 dpg, biological rep4

description: gene expression data from spch seedlings that have an epidermis solely composed of pavement cells

source_name: spch seedling at 5 dpg

value: spch


title: Col-0 WT seedling at 5 dpg, biological rep2

description: gene expression data from Col-0 WT seedlings

source_name: Col-0 WT seedling at 5 dpg

value: wild-type


title: scrm-D seedling at 5 dpg, biological rep2


title: scrm-D seedling at 5 dpg, biological rep3


title: scrm-D;mute seedling at 5 dpg, biological rep2


title: spch seedling at 5 dpg, biological rep2


title: Col-0 WT seedling at 5 dpg, biological rep3


title: scrm-D;mute seedling at 5 dpg, biological rep4


title: Col-0 WT seedling at 5 dpg, biological rep4


title: spch seedling at 5 dpg, biological rep3