title: x05_sid2_01_mock_06h_rep02


title: oocyte_A-_4h

status: Public on Dec 12 2017

type: SRA

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

description:
total mRNA of MPRA reporters
Mature oocytes were collected at 28C by squeezing the belly of adult female zebrafish under anesthesia with tricaine solution (0.15  mg/ml).
processed data file: seq0514.00A.txt

library_source: transcriptomic

data_processing:
Library strategy: UTR-Seq
data (160nt reads) was filtered to retain only sequences that contained both terminal adapter sequences (with up to 10 mismatches) and an insert of 90nt or longer.
data (100nt reads) was filtered to retain only sequences that contained the 5’ terminal adapter sequence (with up to 10 mismatches) and an insert of 62nt or longer.
Bowtie2 was used to align retained reads to a reference set of all 90,000 synthetic oligonucleotide sequences
The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample.
A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2-fold increments (highest 50fg, lowest 3.125fg), and the resulting linear transformation was used to normalize UMI counts.
Genome_build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record.
Supplementary_files_format_and_content: tab delimited files of normalized mRNA levels

molecule: total RNA

organism: Danio rerio

source_name: zebrafish oocyte

growth_protocol: Fertilized zebrafish eggs or oocytes were collected at 28C, and kept in culture medium (5.03mM NaCl, 0.17mM KCl, 0.33mM CaCl2, 0.33mM MgSo4, 0.1% Methylene blue).  A total of 20-40 injected embryos/oocytes were randomly collected per sample after ensuring that all embryos were at the same expected developmental stage.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen), after adding 120fg of mRNA with 5 known 3’UTR control sequences into each RNA sample during the initial TRIzol lysis step.
In the first step, total-RNA was reverse-transcribed with Maxima RT (Thermo Fisher) and a gene-specific primer that matched the constant 3’UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step, resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3’UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors

treatment_protocol: Embryos/oocytes were removed from their chorion and injected with 50-80pg of reporter mRNAs at the one-cell stage.

tag: developmental stage

tag: tissue

value: oocyte


title: Sperm_H3K4me3_ChIP-Seq_Rep1

city: Rochester

first: Patrick

last: Murphy

state: NY

address: 601 Elmwood Ave

country: USA

institute: University of Rochester

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K4me3_Sperm_Log10FE_over_Input_Lambda.bw; H3K4me3_Sperm_Peaks_Log10FE_3fold.bed

library_source: genomic

data_processing:
Reads were aligned to the Zv10 genome using Novoalign (v2.8, Novocraft) using the following options: -r Random -k -Q 13 -o SAM
Sam files were then combined due to high correlation between technical and biological replicates.
Macs2 was then used to generate read count normalized genome wide pileup tracks and lambda tracks for precipitated samples and input. (callpeak --nomodel --extsize 150 --SPMR)
Pileup tracks were then Input corrected using the Macs2 subtract function (bdgcmp -m subtract).
Log10 Fold enrichment was then calculated for each sample comparing input corrected pileups to input lambda. (bdgcmp -m logFE).
Peaks were then called as regions with greater than 3 fold enrichment over lambda using the Macs2 bdgpeakcall function. (bdgpeakcall -c 0.477 -l 100 -g 100)
Genome_build: Zv10
Supplementary_files_format_and_content: bed and bigWig files

molecule: genomic DNA

source_name: Sperm

growth_protocol: Standard zebrafish growth conditions.

extract_protocol:
Whole embryos were cross-linked with 2.2% formaldehyde, then nuclei were extracted as described in Potok et al. Cell 2013. Nuclei preps were then combined and sonicated using a Branson Sonicator. Antibodies were then added to each lysate to bind overnight. The following day protein A/G dynabeads were then used to precipitate antibody bound chromatin (bead binding was for 4 hours at 4C). Bead bound chromatin was then washed and eluted using standard ChIP techniques.
NEBNext ChIP-Seq Library Prep Reagents

value: Sperm

tag: strain

value: Tu

tag: injection

tag: mutation

value: Wild Type


title: Sperm_H3K4me1_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K4me1_Sperm_Log10FE_over_Input_Lambda.bw; H3K4me1_Sperm_Peaks_Log10FE_3fold.bed


title: CF13

city: Corvallis

first: Jay

middle: R

last: Reichman

state: OR

address: 200 SW 35th St.

department: Office of Research and Development

institute: US Environmental Protection Agency

description: DECe

data_processing:
Base calls were made with Illumina Casava version 1.8.2
Illumina reads were auto trimmed and aligned to the psme_transcriptome_v203 template using SeqMan NGen v13.1 (DNASTAR, Inc., Madison, WI)
Gene expression levels were quantified using QSeq/ArrayStar v13.1 (DNASTAR, Inc.) with Reads Assigned per Kilobase of target per Million mapped reads (RPKM) normalization. All values were capped to an auto-calculated minimum value. The averaging method for biological replicates was Mean. Sets of regulated transcripts in treated samples were identified by filtering for those with means ≥2-fold change and 95% confidence across biological replicates compared to Air Controls. The confidence was based on Student’s t-test (P ≤ 0.05) with Benjamini & Hochberg Multiple Testing Correction (FDR ≤ 0.05).
Mapping, annotation and gene ontology enrichment analyses were performed with Blast2Go v3.3 (BioBam, Inc. Valencia, Spain).
Pathway enrichment analyses of regulated transcripts were performed with MapMan v3.5.1R2.
Genome_build: TSA: Pseudotsuga menziesii, transcriptome shotgun assembly; GenBank: GFFY00000000.1
Supplementary_files_format_and_content: Text files of raw counts and linear total RPKM generated with Qseq/ArrayStar v13.1

molecule: polyA RNA

organism: Pseudotsuga menziesii

source_name: DECe

growth_protocol: Half-sibling Douglas-fir seedlings were planted in square 4-inch pots and the pots were placed in shared trays. Trays were positioned in Hazelton 1000 (984 L) exposure chambers (one each for DE, DECe, DECe Gas Phase, and Air Control) outfitted with two LED grow lights that supplied 280 µmol/s/m2 photosynthetically active radiation (PAR) at tray level to plants during the exposures. LED Grow Light banks were set on a 16-hour light:8-hour dark cycle.  Seedlings were re-distributed within the exposure chambers mid-way through the exposure period to minimize potential edge effects. Chamber experiments were run during the month of December when needle growth was dormant.

extract_protocol:
Total RNA was extracted from needles using PureLink Plant RNA Reagent per the manufacturer’s protocol (Ambion, Life Technologies, Inc. Austin, TX).  Messenger RNA was purified from total RNA samples with FastTrack MAG mRNA Isolation Kits (Ambion, Inc.).
RNA-sequencing libraries were prepared with PrepX RNA-Seq for Illumina Library Kits using an Apollo 324 automated system (Wafergen Biosystems, Inc, Freemont, CA). Clusters were amplified from pooled libraries with TruSeq PE Cluster Kit v3-cBot-HS kits on a cBot System (Illumina Inc., San Diego, CA).

treatment_protocol: Douglas-fir seedlings were randomly assigned to one of four groups: 1) Charcoal / Purafil HEPA filtered air (Air Control); 2) Emissions released from combustion of diesel fuel containing engineered CeO2 nanoparticle catalysts (DECe); 3) Emissions released from combustion of diesel fuel (DE); or 4) HEPA filtered DECe (DECe Gas Phase). The overall exposure regime was 6 hours/day X 5 days/week X 2 weeks. Filtered air was pumped through all chambers during the times between the exposures.

tag: growth year

tag: sampling year

value: needles

tag: needle location

value: on lateral stem

tag: stem position

value: proximal to most recent bud scar


title: CF15

description: DECe


title: Sperm_H3K4me1_ChIP-Seq_Rep1


title: rep_A-_10h

description:
total mRNA of MPRA reporters
processed data file: seq0417.00A.txt

source_name: zebrafish embryos

value: embryo


title: oocyte_A-_1h


title: CF10

description: DECe


title: x01_Col_03_AvrRpt2_06h_rep01

city: Kyoto

first: Akira

last: Mine

state: Kyoto

address: Kitashirakawaoiwake-cho

department: Graduate School of Agriculture

country: Japan

institute: Kyoto university

data_processing:
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the Arabidopsis genome using splice-aware read aligner TopHat (version 2.0.10) with the parameters -p 10 -a 10 -g 10 --library-type fr-firststrand -G TAIR10_GFF3_genes.gff and transformed into a count per gene per library by using HTSeq (version 0.6.1) with the parameters -s reverse -f bam -t exon.
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each of 348 samples (ReadCountTable_M001_348.txt).

organism: Arabidopsis thaliana

source_name: Fully-expanded leaves of 30 to 33 day-old plants

growth_protocol: Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.

extract_protocol:
Total RNAs were extracted using TRIzol (Invitrogen), followed by Dnase I (Roche) treatment.
RNA libraries were prepared from 1 μg of total RNA. Poly A enrichment and library preparation were performed with NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Fully-expanded leaves were syringe-infiltrated with mock (water) or bacterial suspensions at the OD600 of 0.001.

tag: genotype

tag: treatment

value: Pto AvrRpt2

tag: replicate

tag: time

value: 6 hpi

value: Leaves


title: Sperm_H3K27me3_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K27me3_Sperm_Log10FE_over_Input_Lambda.bw; H3K27me3_Sperm_Peaks_Log10FE_3fold.bed


title: rep_A-_8h


title: Sperm_H3K27me3_ChIP-Seq_Rep1


title: rep_A-_6h.3


title: AF5

description: Air Control

source_name: Air Control


title: x01_Col_02_EV_06h_rep01

value: Pto DC3000


title: P0,CD-1,Immature-Pyr-6

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Processing was performed with the 10X Chromium cellranger pipline version 1.3 using default settings
The Unique Molecular Identifier and cellular barcode corresponding to each read have been appended to the read id separated by an underscore.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited file of mRNA molecules per gene in each cell

organism: Mus musculus

source_name: dentate gyrus

extract_protocol:
Mice were sacrificed by an overdose of Isoflurane or Ketamin/Xylazine, followed by perfusion through the left ventricle with artificial cerebrospinal fluid (aCSF), equilibrated in 95%O2/5%CO2 on ice or 4°C. The dentate gyrus was then microdissected from 300 μm vibratome brain sections. Single-cell suspensions were prepared using the Papain kit (Worthington) with 25-35min enzymatic digestion followed by manual trituration using a BSA-coated p1000 pipette or fire-polished Pasteur pipettes. For hGFAP-GFP mice, GFP-positive cells were sorted on a BD FACSAria II  into oxygenated aCSF at 4°C.
1000 cells/  μl were resuspended in artificial cerebrospinal fluid and added to the   Reverse transcription mix to aim for sampling of around 3500 cells. All downstream cDNA synthesis (13 PCR   cycles), library preparation and sequencing were carried   out as instructed by the manufacturer   (10X Genomics Chromium Single Cell Kit Version 2).

tag: age

tag: cell cluster

value: Immature


title: rep_A-_6h.2


title: AF15

description: Air Control


title: x05_sid2_01_mock_06h_rep01

value: Mock


title: Sperm_H3K27ac_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K27ac_Sperm_Log10FE_over_Input_Lambda.bw; H3K27ac_Sperm_Peaks_Log10FE_3fold.bed


title: rep_A-_6h.1


title: x01_Col_01_mock_06h_rep02


title: Sperm_H3K27ac_ChIP-Seq_Rep1


title: AF3

description: Air Control


title: AF14

description: Air Control


title: x05_sid2_03_AvrRpt2_06h_rep01


title: Sperm_H3K27ac_ChIP-Seq_Rep3


title: Sperm_H3K14ac_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K14ac_Sperm_Log10FE_over_Input_Lambda.bw; H3K14ac_Sperm_Peaks_Log10FE_3fold.bed


title: AF11

description: Air Control


title: x01_Col_03_AvrRpt2_04h_rep03

value: 4 hpi


title: x01_Col_02_EV_04h_rep03


title: x01_Col_01_mock_06h_rep01


title: rep_A-_2h


title: rep_A-_4h


title: rep_A-_3h


title: AF8

description: Air Control


title: x01_Col_01_mock_04h_rep03


title: Sperm_H2AFV_ChIP-Seq_Rep3

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H2AZ_Sperm_Log10FE_over_Input_Lambda.bw; H2AZ_Sperm_Peaks_Log10FE_3fold.bed


title: rep_A-_1h


title: x05_sid2_02_EV_06h_rep01


title: Sperm_H2AFV_ChIP-Seq_Rep2


title: rep_A-_uninjected


title: Sperm_H2AFV_ChIP-Seq_Rep1


title: x01_Col_02_EV_04h_rep02


title: x01_Col_03_AvrRpt2_04h_rep01


title: techrep_A+_10h.2

description:
total mRNA of MPRA reporters
processed data file: seq0714.40A.2.txt


title: PreZGA_H3K4me1_ChIP-Seq_Rep1

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K4me1_preZGA_Log10FE_over_Input_Lambda.bw; H3K4me1_preZGA_Peaks_Log10FE_3fold.bed

source_name: 2.5hpf embryos

value: 2.5hpf embryos


title: x01_Col_01_mock_04h_rep02


title: PreZGA_H3K4me1_ChIP-Seq_Rep2


title: techrep_A+_8h.2


title: x01_Col_02_EV_04h_rep01


title: Sperm_H3K14ac_ChIP-Seq_Rep1


title: techrep_A+_7h.2


title: PreZGA_H3K27ac_ChIP-Seq_Rep1

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K27ac_preZGA_Log10FE_over_Input_Lambda.bw; H3K27ac_preZGA_Peaks_Log10FE_3fold.bed


title: x01_Col_01_mock_04h_rep01


title: PreZGA_H3K14ac_ChIP-Seq_Rep3

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K14ac_preZGA_Log10FE_over_Input_Lambda.bw; H3K14ac_preZGA_Peaks_Log10FE_3fold.bed


title: PreZGA_H3K27ac_ChIP-Seq_Rep2


title: techrep_A+_6h.2.2


title: x01_Col_03_AvrRpt2_03h_rep03

value: 3 hpi


title: x01_Col_01_mock_03h_rep03


title: techrep_A+_6h.2.1


title: x01_Col_02_EV_03h_rep03


title: techrep_A+_4h.2


title: x01_Col_03_AvrRpt2_04h_rep02


title: x01_Col_03_AvrRpt2_03h_rep02


title: PreZGA_H3K14ac_ChIP-Seq_Rep1


title: techrep_A+_3h.2


title: x01_Col_02_EV_03h_rep02


title: techrep_A+_5h.2


title: PreZGA_H2AFV_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H2AZ_preZGA_Log10FE_over_Input_Lambda.bw; H2AZ_preZGA_Peaks_Log10FE_3fold.bed


title: PreZGA_H2AFV_ChIP-Seq_Rep1


title: techrep_A+_2h.2


title: techrep_A+_9h.2


title: techrep_A+_1h.2


title: x01_Col_03_AvrRpt2_03h_rep01


title: techrep_A+_uninjected.2


title: x01_Col_01_mock_03h_rep02


title: PostZGA_H2AFV_ChIP-Seq_Rep3

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H2AZ_postZGA_Log10FE_over_Input_Lambda.bw; H2AZ_postZGA_Peaks_Log10FE_3fold.bed

source_name: Sphere Stage

value: Sphere Stage


title: PostZGA_H3K14ac_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: H3K14ac_postZGA_Log10FE_over_Input_Lambda.bw; H3K14ac_postZGA_Peaks_Log10FE_3fold.bed


title: PostZGA_H3K14ac_ChIP-Seq_Rep1


title: x01_Col_02_EV_03h_rep01


title: PreZGA_H3K14ac_ChIP-Seq_Rep2


title: techrep_A+_10h.1

description:
total mRNA of MPRA reporters
processed data file: seq0714.40A.1.txt


title: PostZGA_H2AFV_ChIP-Seq_Rep2


title: x01_Col_03_AvrRpt2_01h_rep03

value: 1 hpi


title: PostZGA_H2AFV_ChIP-Seq_Rep1

value: Tu


title: techrep_A+_8h.1


title: x01_Col_02_EV_01h_rep03


title: techrep_A+_7h.1


title: Mixed_Embryo_Input_ChIP-Seq

description:
Precipitated Genomic DNA from Chromatin
Processed data file: none

source_name: Mixed preZGA and postZGA chromin

value: Mixed preZGA and postZGA chromin

value: Wild Type


title: techrep_A+_6h.1.2


title: Anp32e_Sperm_Input_ChIP-Seq

value: Sperm

value: NHGRI

value: Anp32e Null


title: techrep_A+_6h.1.1

value: embryo


title: x01_Col_01_mock_01h_rep03


title: Anp32e_Sperm_H3K4me1_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: Anp32e_Sperm_H3K4me1_Log10FE_over_Input_Lambda.bw; Anp32e_Sperm_H3K4me1_Peaks_Log10FE_3fold.bed


title: x01_Col_02_EV_01h_rep02


title: Anp32e_Sperm_H3K4me1_ChIP-Seq_Rep1


title: techrep_A+_5h.1


title: Anp32e_Sperm_H2AFV_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: Anp32e_Sperm_H2AZ_Log10FE_over_Input_Lambda.bw; Anp32e_Sperm_H2AZ_Peaks_Log10FE_3fold.bed


title: x01_Col_01_mock_01h_rep02


title: x01_Col_03_AvrRpt2_01h_rep01

value: Pto AvrRpt2


title: x01_Col_02_EV_01h_rep01

value: Leaves


title: Anp32e_PostZGA_H2AFV_ChIP-Seq_Rep3

description:
Precipitated Genomic DNA from Chromatin
Processed data file: Anp32e_Sphere_H2AZ_Log10FE_over_Input_Lambda.bw; Anp32e_Sphere_H2AZ_Peaks_Log10FE_3fold.bed


title: x01_Col_01_mock_03h_rep01


title: techrep_A+_2h.1


title: techrep_A+_3h.1


title: techrep_A+_9h.1


title: x01_Col_01_mock_01h_rep01


title: techrep_A+_1h.1


title: Anp32e_PostZGA_H2AFV_ChIP-Seq_Rep2


title: techrep_A+_4h.1


title: techrep_A+_uninjected.1


title: Anp32e_Pat-Null_H2AFV_ChIP-Seq_Rep3

description:
Precipitated Genomic DNA from Chromatin
Processed data file: Anp32e_Pat_Null_H2AZ_Sphere_Log10FE_over_Input_Lambda.bw; Anp32e_Pat_Null_H2AZ_Sphere_Peaks_Log10FE_3fold.bed

value: Tu X NHGRI

value: Anp32e Paternal Null


title: Anp32e_PostZGA_H2AFV_ChIP-Seq_Rep1


title: x01_Col_03_AvrRpt2_01h_rep02


title: biorep_A+_10h.2

description:
total mRNA of MPRA reporters
processed data file: seq0312.40A.2.txt


title: Anp32e_Pat-Null_H2AFV_ChIP-Seq_Rep1


title: biorep_A+_4h.2


title: Anp32e_Mat-Null_H2AFV_ChIP-Seq_Rep2

description:
Precipitated Genomic DNA from Chromatin
Processed data file: Anp32e_Mat_Null_H2AZ_Sphere_Log10FE_over_Input_Lambda.bw; Anp32e_Mat_Null_H2AZ_Sphere_Peaks_Log10FE_3fold.bed

value: Anp32e Maternal Null


title: biorep_A+_6h.2


title: Anp32e_Pat-Null_H2AFV_ChIP-Seq_Rep2


title: Anp32e_Mat-Null_H2AFV_ChIP-Seq_Rep1


title: biorep_A+_1h.2


title: Flg22_wildtype_2

status: Public on Dec 11 2017

city: Cologne

first: Barbara

last: Kracher

address: Carl-von-Linné-Weg 10

department: Plant-Microbe Interactions

country: Germany

institute: Max Planck Institute for Plant Breeding Research

description: polyA-enriched RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using tophat v2.0.10 with parameters -a 10  -g 10 --library-type fr-firststrand
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10 (Arabidopsis)
Supplementary_files_format_and_content: tab-delimited text files including read counts per gene per sample

source_name: Arabidopsis leaves

growth_protocol: The plants were initially grown on MS-agar plates for 2 weeks under sterile conditions and subsequently transferred to Jiffy pots supplemented with a fertilizer, Wuxal TopN (Aglukon Spezialdünger), and grown for an additional 2 weeks under short day conditions. Four week-old plants were used for the PAMP and bacterial treatments.

extract_protocol:
RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen) according to the manufacurer's instruction, including an on-column DNA digestion.
RNA-seq libraries were prepared from total RNA by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).

treatment_protocol: Leaves were syringe-infiltrated with the indicated solution. For each sample, six leaf discs were taken at the specified time point from six independent plants and used for RNA extraction.

value: 100 nM of flg22


title: Rpm1_camta3D_2

description: polyA-enriched RNA

value: camta3-D (sr1-4d)


title: Rpm1_wildtype_2

description: polyA-enriched RNA


title: Rps4_camta3D_1

description: polyA-enriched RNA


title: Flg22_camta3D_1

description: polyA-enriched RNA


title: Rpm1_wildtype_1

description: polyA-enriched RNA


title: Rps4_wildtype_1

description: polyA-enriched RNA


title: Rps4_wildtype_2

description: polyA-enriched RNA


title: Anp32e_Sperm_H2AFV_ChIP-Seq_Rep1


title: biorep_A+_8h.2


title: 35S:RPS4, 2h, rep3

description: polyA-enriched RNA

growth_protocol: Plants were grown for 3,5 weeks at 28°C

treatment_protocol: Plants were shifted from 28°C to 19°C for 2h before collecting and freezing the samples.

value: leaf

value: Col-0 35S:RPS4-HS

value: 2 h


title: 35S:RPS4, 2h, rep2

description: polyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 24hpi, replicate 4

description: PolyA-enriched RNA

source_name: Arabidopsis lower leaf epidermis

growth_protocol: The plants were initially grown on MS-agar plates for 2 weeks under sterile conditions and subsequently transferred to Jiffy pots supplemented with a fertilizer, Wuxal TopN (Aglukon Spezialdünger), and grown for an additional 2 weeks under short day conditions. Four week-old plants were used for pathogen inoculation.

extract_protocol:
Lower leaf epidermis was isolated following the Tape-Sandwich method described in Wu et al. (2009) Plant Methods. RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer's instructions, including an on-column DNA digestion.
RNA-seq libraries were prepared from total RNA by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).

treatment_protocol: Inoculation of the fungal spores was described in Lipka, et al., Science 310, 1180 (2005). The spores were inoculated onto the abaxial leaf surface of detached leaves placed on agar plates. The leaves were kept on agar plates until sample collections.

value: lower leaf epidermis

tag: plant genotype

value: Col-0 pen2-1 pad4-1 sag101-2 dde2-2 ein2-1 sid2-2 (ppsdes) 35S:MLA1-HA

tag: fungal isolate

value: Blumeria graminis f. sp. hordei isolate A6

tag: virulence

value: virulent


title: Col-0, 2h, rep1

description: polyA-enriched RNA

tag: tissue


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 12hpi, replicate 4

description: PolyA-enriched RNA

value: Blumeria graminis f. sp. hordei isolate K1

value: avirulent


title: 35S:RPS4, 2h, rep1

description: polyA-enriched RNA


title: Col-0, 2h, rep2

description: polyA-enriched RNA


title: Rps4_camta3D_2

description: polyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 24hpi, replicate 3

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 18hpi, replicate 3

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 12hpi, replicate 3

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 24hpi, replicate 2

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 18hpi, replicate 2

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants unchallenged at 18hpi, replicate 3

description: PolyA-enriched RNA

value: uninfected


title: Flg22_wildtype_1

description: polyA-enriched RNA


title: Flg22_camta3D_2

description: polyA-enriched RNA


title: Rpm1_camta3D_1

description: polyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 12hpi, replicate 2

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants unchallenged at 18hpi, replicate 2

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 24hpi, replicate 2

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 18hpi, replicate 2

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 24hpi, replicate 1

description: PolyA-enriched RNA


title: Col-0, 2h, rep3

description: polyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 24hpi, replicate 1

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 18hpi, replicate 1

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 18hpi, replicate 1

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 12hpi, replicate 1

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 12hpi, replicate 3

description: PolyA-enriched RNA


title: MLA1 expressing ppsdes plants challenged with Bgh K1 isolate at 18hpi, replicate 3

description: PolyA-enriched RNA


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 6 h, rep1

description:
polyA-enriched RNA
CountTable_At_1725_raw.txt

growth_protocol: The plants were initially grown on MS-agar plates for 2 weeks under sterile conditions and subsequently transferred to Jiffy pots supplemented with a fertilizer, Wuxal TopN (Aglukon Spezialdünger), and grown for an additional 2 weeks under short day conditions. Four week-old plants were used for dexamethasone treatment.

treatment_protocol: Leaves were syringe-infiltrated with 1 µM dexamethasone. For each sample, six leaf discs were taken at the specified time point from six independent plants and used for RNA extraction.

value: Col-0 pen2-1 pad4-1 sag101-2 dde2-2 ein2-1 sid2-2 (ppsdes) DEXp:MLACC-mYFP

value: 6 h


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 8 h, rep3

value: 8 h


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 8 h, rep2


title: MLA1 expressing ppsdes plants unchallenged at 18hpi, replicate 1

description: PolyA-enriched RNA


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 6 h, rep2


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 6 h, rep3


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 4 h, rep3

value: 4 h


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 2 h, rep1


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 0 h, rep3

value: 0 h


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 2 h, rep2


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 4 h, rep1


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 2 h, rep3


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 4 h, rep2


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 0 h, rep2


title: ppsdes plants infiltrated with dexamethasone, 8 h, rep3

value: Col-0 pen2-1 pad4-1 sag101-2 dde2-2 ein2-1 sid2-2 (ppsdes)


title: MLA1 expressing ppsdes plants challenged with Bgh A6 isolate at 12hpi, replicate 1

description: PolyA-enriched RNA


title: ppsdes plants infiltrated with dexamethasone, 8 h, rep1


title: ppsdes plants infiltrated with dexamethasone, 6 h, rep1


title: ppsdes plants infiltrated with dexamethasone, 6 h, rep2


title: ppsdes plants infiltrated with dexamethasone, 4 h, rep3


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 0 h, rep1


title: ppsdes plants infiltrated with dexamethasone, 2 h, rep2


title: ppsdes plants infiltrated with dexamethasone, 4 h, rep1


title: ppsdes plants infiltrated with dexamethasone, 6 h, rep3


title: ppsdes plants infiltrated with dexamethasone, 2 h, rep3


title: ppsdes plants infiltrated with dexamethasone, 0 h, rep3


title: DEXp:MLACC-mYFP ppsdes plants infiltrated with dexamethasone, 8 h, rep1


title: ppsdes plants infiltrated with dexamethasone, 4 h, rep2


title: ppsdes plants infiltrated with dexamethasone, 0 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 6 h, rep3

description:
polyA-enriched RNA
CountTable_At_1493_raw.txt

value: Col-0 DEXp:MLACC-mYFP


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 8 h, rep1

value: leaf


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 8 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 8 h, rep3


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 6 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 4 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 2 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 2 h, rep3


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 2 h, rep1


title: ppsdes plants infiltrated with dexamethasone, 0 h, rep1


title: ppsdes plants infiltrated with dexamethasone, 8 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 4 h, rep3


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 0 h, rep3


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 0 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 0 h, rep1


title: DEXp:mYFP plants infiltrated with dexamethasone, 8 h, rep2

value: Col-0 DEXp:mYFP


title: DEXp:mYFP plants infiltrated with dexamethasone, 8 h, rep3


title: ppsdes plants infiltrated with dexamethasone, 2 h, rep1

value: 2 h


title: DEXp:mYFP plants infiltrated with dexamethasone, 8 h, rep1


title: DEXp:mYFP plants infiltrated with dexamethasone, 6 h, rep3


title: DEXp:mYFP plants infiltrated with dexamethasone, 4 h, rep1


title: DEXp:mYFP plants infiltrated with dexamethasone, 4 h, rep2


title: DEXp:mYFP plants infiltrated with dexamethasone, 6 h, rep1


title: DEXp:mYFP plants infiltrated with dexamethasone, 4 h, rep3


title: DEXp:mYFP plants infiltrated with dexamethasone, 6 h, rep2


title: DEXp:mYFP plants infiltrated with dexamethasone, 2 h, rep3


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 6 h, rep1


title: DEXp:mYFP plants infiltrated with dexamethasone, 2 h, rep2


title: DEXp:MLACC-mYFP plants infiltrated with dexamethasone, 4 h, rep1


title: DEXp:mYFP plants infiltrated with dexamethasone, 0 h, rep2


title: DEXp:mYFP plants infiltrated with dexamethasone, 0 h, rep3


title: DEXp:mYFP plants infiltrated with dexamethasone, 2 h, rep1


title: Pln+/+

city: Nashville

first: Daniel

last: DeLaughter

state: TN

address: Preston Research Building Room 460

department: Cell and Developmental Biology

institute: Vanderbilt University Medical School

data_processing:
Illumina base calling, alignment of reads to mm10 genome to create FASTq files, and generation of transcript counts per gene per cell were performed using Cell Ranger (version 1.2, 10x Genomics) with the default parameters for "mkfastq" (base calling) and "count" (alignment and transcript counting) commands.
The output of the "count" command which contains only detected cellular barcodes (the filtered gene matrices PLN++.csv and PLNr9c.csv) were aggregated to compare the 2 samples using the aggr Cell Ranger (version 1.2, 10x Genomics) command.
Genome_build: mm10
Supplementary_files_format_and_content: PLN++.csv and PLNr9c.csv are comma delimited matrices of cell barcodes (columns) which represent individual cells and genes (rows) with transcript counts.

source_name: Left Ventricle

extract_protocol:
A standard Langendorf preperation was performed on the hearts of two 18 week old male mice, PlnR9C/+ or Pln+/+. The left ventricle was harvested from the hearts and non-cardiomyocytes were seperated from cardiomyocytes using gravity seperation. Cells were rinsed 3 times in cold PBS, counted using a hemacytometer, and loaded onto a Genomics 10x chip following the manufacturer's protocol to capture single cells.
RNA libraries were prepared for sequencing using the standard protocol for the Genomics 10x Chromium Single-Cell 3' v2 Reagent Kits.

tag: strain

value: FVB

value: Wild Type

value: 18 Weeks


title: PlnR9C/+


title: 4-99-11

city: Boston

first: Mark

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

description: polyA RNA captured via SMART-seq library preparation kit instructions

data_processing:
Bulk RNA-seq processing: Samples were sequenced on the NextSeq 500 (Illumina) and paired end reads of lengths 38,38 were obtained. Reads were trimmed with Trimmmomatic-0.33 using the following parameters: ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:3072. A reference transcriptome was built with Tophat 2.1.1 and Bowtie 1.1.1 against the GRCm38.dna_sm.primary_assembly genome with the GTF file constructed above for inDrops mapping. Reads were mapped against this transcriptome with Tophat using the following options: --mate-inner-dist 500 --no-mixed --transcriptome-index [CUSTOM_TRANSCRIPTOME] --bowtie1 --no-novel-juncs. All samples showed ≥90% concordant pair alignment rate. The featureCounts package was used to obtain gene counts with the following command options: -p -B -C -g gene_name -a [GTF] -s 1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: [SAMPLE_ID]_counts.txt.gz: Raw count tables by sample obtained via featureCounts; TMM_norm_cpm.csv: Gene Expression Matrix of TMM-normalized CPM values as calculated by EdgeR from counts.txt files

source_name: visual cortex

extract_protocol:
For bulk RNA-seq experiments, RNA was extraacted using the Rneasy Mini kit (QIAGEN) with the DNase I digestion step included.
For bulk RNA-seq, libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit and Nextera XT DNA sample prep kit according to manufacturer's instructions.

tag: stimulus

value: 1 hour light exposure

value: inhibitor cocktail

tag: Sex

value: male


title: 4-99-8

value: unstimulated


title: 4-99-9


title: 4-99-10


title: 4-99-7


title: 4-99-6


title: 4-99-5


title: 4-99-4

value: control


title: 4-99-3


title: 4-99-2


title: 4-99-1


title: DEXp:mYFP plants infiltrated with dexamethasone, 0 h, rep1


title: B5_15_0h

description: polyA RNA captured via inDrop platform

data_processing:
Base-calling, filtering, trimming, read assignment to cell, alignment, UMI processing of reads to counts: Previously published pipeline (Klein et al., 2015) run with default parameters against custom transciptome also built with same pipeline (Ensembl GRCm38 genome and GRCm38.84 annotation, filtering the annotation gtf file gencode.v17.annotation.gtf for feature_type=”gene”, gene_type="protein_coding" and gene_status="KNOWN").
Removal of low quality cells: All mitochondrially-encoded genes were removed from the dataset. Cell that contained fewer than 700 or more that 15,000 UMI counts were excluded. This resulted in 65,639 cells isolated from 23 animals. All cells were merged into a single matrix
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: MATRIX.csv: Gene Expression Matrix of count data normalized by total counts in each cell; [SAMPLE_ID]_counts.txt.gz: Raw cell/counts tables by sample; merged_all_raw.csv: Gene Expression Matrix of raw count data; cell_type_assignments.csv: Metadata for individual cells: sample name, assigned cell type.

extract_protocol:
RNA was isolated within droplets according to the inDrops protocol (Klein et al Cell 2015)(Zilionis et al Nature Protocols 2017)
1 to 2 libraries of approximately 3000 cells was collected from each animal. inDrops library preparation was performed as previously described (Klein et al., 2015)(Zilionis et al., 2017) Libraries were sequenced on the Illumina NextSeq system.
custom inDrops single-cell RNA-Seq


title: B6_17_1h_B

description: polyA RNA captured via inDrop platform


title: B5_16_0h

description: polyA RNA captured via inDrop platform


title: B6_18_1h

description: polyA RNA captured via inDrop platform


title: B6_19_4h_B

description: polyA RNA captured via inDrop platform

value: 4 hour light exposure


title: B7_21_1h

description: polyA RNA captured via inDrop platform


title: 4-99-12


title: B7_22_4h_B

description: polyA RNA captured via inDrop platform


title: B6_20_4h_B

description: polyA RNA captured via inDrop platform


title: B7_22_4h_A

description: polyA RNA captured via inDrop platform


title: B7_23_4h_A

description: polyA RNA captured via inDrop platform


title: B5_14_0h

description: polyA RNA captured via inDrop platform


title: B6_19_4h_A

description: polyA RNA captured via inDrop platform


title: B6_20_4h_A

description: polyA RNA captured via inDrop platform


title: B7_23_4h_B

description: polyA RNA captured via inDrop platform


title: B5_13_0h

description: polyA RNA captured via inDrop platform


title: B6_17_1h_A

description: polyA RNA captured via inDrop platform


title: B3_10_4h

description: polyA RNA captured via inDrop platform


title: B4_12_0h

description: polyA RNA captured via inDrop platform


title: B3_8_1h

description: polyA RNA captured via inDrop platform


title: Hemocyte_negative control

city: Pasadena

first: Young-Kyung

last: Bae

state: CA

address: 1200 E California Blvd

institute: Caltech

data_processing:
Base calling was performed by Illumina CAVASA (2012)
Reads were aligned with BowTie 0.12.7
Spliced maps were generated by TopHat 1.3.3
Normalized abudance measurement was performed by CuffDiff via Cufflinks(v.1.3.0) that compared the accepted hits (.bam files) from a migrating cell type and the corresponding negative control.
Genome_build: drosophila_melanogaster.BDGP5.62.gtf
Supplementary_files_format_and_content: tab-delimited text files include comparing RPKM values between each migrating cell types and the negative cells sorted by FACS.

organism: Drosophila melanogaster

source_name: Non-hemocytes (HC) sorted by FACS

extract_protocol:
The total RNA from each population was extracted using Qiagen RNeasy Mini Kit (Cat. #74104) with on column DNase treatment as suggested in the protocol.
Libraries were prepared according to Illumina's instructions.

tag: developmental stage

value: embryonic stage 12-16

tag: cell type

value: Non-hemocytes (HC)


title: B3_9_4h

description: polyA RNA captured via inDrop platform


title: B3_7_1h

description: polyA RNA captured via inDrop platform


title: B4_11_0h

description: polyA RNA captured via inDrop platform


title: Hemocyte_migrating

source_name: Hemocytes (HC) sorted by FACS

value: Hemocytes (HC)


title: CVM_negative control

source_name: Non-caudal visceral mesoderm (CVM) cells sorted by FACS

value: embryonic stage 10-13


title: CVM_migrating

source_name: caudal visceral mesoderm (CVM) cells sorted by FACS

value: caudal visceral mesoderm (CVM) cells


title: B3_6_0h

description: polyA RNA captured via inDrop platform


title: B2_4_1h

description: polyA RNA captured via inDrop platform


title: Cbm8

city: La Jolla

first: Kun

last: Zhang

state: California

address: 9500 Gilman Drive

institute: UCSD

description:
processed data file:
CerebellarHem_snDrop-seq_UMI_Count_Matrix_08-01-2017.txt

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
First, paired-end reads were filtered out if read 1 had more than 4 non-T bases in the last 10 bases (to remove all non poly T-captured contaminated reads), or had one or more bases with poor quality score (less than 10). And cell barcode and UMI information were then inferred from the first 12 bases and the next 8 bases of read 1 respectively. The right mate of each read pair was trimmed to remove any portion of the SMART adaptor sequence or large stretches of polyA tails (6 consecutive bp or greater).
The trimmed reads were then aligned to the human genome (GENCODE GRCH38) using STAR v2.5 with the default parameter settings
Reads mapping to intronic or exonic regions of genes as per the GENCODE gene annotation were both recorded. One further correction step to fix barcode synthesis errors was performed by inserting N at last base of the cell barcode for reads which had identical first 11 bases of the cell barcode and same last T base of UMI.
Digital expression matrix was then generated with genes as rows and cells as columns. UMI counts were assigned for each gene of each cell by collapsing UMI reads which had only 1 edit distance
Genome_build: GENCODE GRCH38
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each sample passing QC filtering. The README file on the series record contains where the adaptor information can be found and the script needed to generate the count matrices by cell barcode.

organism: Homo sapiens

source_name: snDrop-seq_Cerebellar Hemisphere

extract_protocol:
Cryofrozen post-mortem brain tissue was treated with nuclear extraction buffer, isolated nuclei was stained with DAPI and FACS purified.
Nuclei were loaded at the concentration of 100 nuclei/ml, and co-encapsulated in droplets with barcoded beads purchased from ChemGenes Corporation, Wilmington MA (Cat. # Macosko201110). When encapsulation was complete, droplets were heated to lyze the nuclei membrane, and were then broken by perfluorooctanol, following which beads were harvested, and hybridized RNA was reverse transcribed. Beads hybridized with RNA from individual nuclei was harvested, pooled and reverse transcribed. cDNA was then PCR amplified for 16 cycles with primer, buffer and cycle conditions identical to original Dropseq protocol and libraries were prepared by Nextera XT tagmentation according to Illumina's instructions and indexed with different Nextera index 1 primers

tag: patient id

value: 49 years

value: Male

tag: race

value: Caucasian

tag: histology

value: Not specified

value: postmortem adult human brain

tag: region

value: Lateral

tag: brodmann area

value: Cerebellar Hemisphere

tag: experiment


title: B1_3_4h

description: polyA RNA captured via inDrop platform

tag: age


title: B1_2_1h

description: polyA RNA captured via inDrop platform

value: 1 hour light exposure


title: 4903: WT islet mRNA

city: Toronto

first: Chi Kin

last: Wong

address: 600 University Avenue

country: Canada

institute: LTRI

data_processing:
Quality filtered reads were aligned to reference mouse genome mm10 with TopHat2
Count tables for the aligned reads were generated and batch effects were corrected using SVA (15), followed by calling of differentially expressed genes using DESeq2 with default settings in R
Downregulated gene lists were uploaded to Webgestalt for gene ontology (GO) terms and transcription factor targets analyses.
Genome_build: mm10
Supplementary_files_format_and_content: count tables

source_name: Crebbpfl/fl mouse islet

extract_protocol:
Total RNA was extracted from islets using TRIzol (ThemoFisher, MA, USA) and RNeasy Micro Kit (QIAgen, Germany)
RNA samples with RIN higher than 8.5 as measured on Bioanalyzer 2100 (Agilent, CA, USA) were prepared into sequencing libraries on NeoPrep using TruSeq Stranded mRNA Library Prep kit (Illumina, CA, USA).

value: islets

tag: genotype/variation

value: Crebbpfl/fl


title: Cbm6

value: 35 years

value: Female


title: 5054: WT islet mRNA


title: 5051: WT islet mRNA


title: Cbm3

value: 48 years

value: African American


title: 5252: CBP KO islet mRNA

source_name: Neurog3-Cre; Crebbpfl/fl mouse islet

value: Neurog3-Cre; Crebbpfl/fl


title: B1_1_0h

description: polyA RNA captured via inDrop platform

value: unstimulated

value: male


title: Cbm7


title: 4851: Triallelic islet mRNA

source_name: Neurog3-Cre; Crebbpfl/WT; Ep300fl/fl mouse islet

value: Neurog3-Cre; Crebbpfl/WT; Ep300fl/fl


title: 4902: CBP KO islet mRNA


title: Cbm4

value: Male


title: Cbm9

value: 49 years

value: Caucasian


title: Cbm1

value: Not specified

value: postmortem adult human brain


title: 2503: WT islet mRNA

source_name: Ep300fl/fl mouse islet


title: 2591: p300 KO islet mRNA

source_name: Neurog3-Cre; Ep300fl/fl mouse islet

value: Neurog3-Cre; Ep300fl/fl


title: Cbm5

value: Lateral

value: Cerebellar Hemisphere


title: 4652: Triallelic islet mRNA

value: islets


title: 2504: WT islet mRNA


title: 4905: CBP KO islet mRNA


title: B3_5_0h

description: polyA RNA captured via inDrop platform


title: 2431: p300 KO islet mRNA


title: 2365: WT islet mRNA


title: Cbm2


title: ASF00617_ELA

city: Madrid

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
Image analysis and per-cycle base-calling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina). These files contain only reads that passed "chastity" filtering (flagged with a ‘N’, for *NOT filtered* in the sequence identifier line). "Chastity" parameter measures signal contamination in raw data and allows to flag unreliable reads. Quality check was done via fastqc (v0.9.4, Babraham Bioinformatics).
Raw reads were aligned to the build version GRCm38/mm10 of the mouse genome where the sequence of the ERCC synthetic spike-in RNAs (http://tools.invitrogen.com/downloads/ERCC92.fa) had been added. Tophat (version 2.0.4) was used for alignment with the following parameters: --bowtie1, --max-multihits 5, --genome-read-mismatches 1 --segment-mismatches 1 --segment-length 19 --splice-mismatches 0 --library-type fr-firststrand. Furthermore, reads were directionally extended to 300 bp and, for each base pair in the genome, the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a wig file to visualize the data in the University of California Santa Cruz (UCSC) genome browser.
Gene expression levels and synthetic spike-in RNA (Fragments Per Kilobase of exon per Million fragments mapped, FPKM) were quantified with cufflinks (version 2.0.2), with the following parameters: -N, --library-type fr-firststrand, --max-bundle-frags 10000000000000, -u
Further, we used a loess regression to renormalize the FPKM values by using only the spike-in values to fit the loess following the strategy described in Lovén et al. 2012 (doi: 10.1016/j.cell.2012.10.012). The affy package in R provides a function, loess.normalize, performing loess regression on a matrix of values and allowing to specify which subset of data to use when fitting the loess (see the affy package for further details (Gautier et al. 2004)).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: The result was a matrix of FPKM values normalized to the control ERCC spike-ins.
Supplementary_files_format_and_content: Wig files to visualize the data in the University of California Santa Cruz (UCSC) genome browser.

source_name: pancreas

extract_protocol:
Pancreas was lysated in Buffer GC and RNA isolated using Pheno-Chloroform
Total RNA (1µg) was spiked with ERCC ExFold RNA spike-In mixes (Life Technologies). RNA quality was assessed on an Agilent 2100 Bioanalyzer and samples with a RNA Integrity Number > 8.5 were used. PolyA+ fractions were purified, randomly fragmented, converted to double stranded cDNA, and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters following Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated libraries were generated by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA libraries were applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: pancreas

tag: genotype

value: 8 week-old

tag: sample


title: ASF00618_ELA


title: 4974: Triallelic islet mRNA


title: ASF00613_ELA


title: 2505: p300 KO islet mRNA


title: Ptf1a_ChIP-Seq

description: DNA from one mouse (ASF414)

data_processing:
Image analysis and per-cycle base-calling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format with the ELAND algorithm (v2e) was performed with CASAVA-1.8 (Illumina). Quality check was done via fastqc (v0.9.4, Babraham Bioinformatics).
ChIP-seq reads were aligned to the human reference genome (NCBI37/mm9, July 2007) with Burrows-Wheeler Aligner (bwa, v0.5.9-r16) allowing 0-1 mismatches (Li and Durbin 2009). Unique aligned reads were converted to BED format. All ChIP and input samples were normalized randomly to the same number of reads (13,235.265).
Furthermore, reads were directionally extended to 300 bp and, for each base pair in the genome, the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a wig file to visualize the data in the University of California Santa Cruz (UCSC) genome browser.
Identification of the binding sites (peak calling) were performed using MACS (version 1.4.1 20110622) with parameters: -g 1.87e9; -m 10,30; -p 0.05 and the input DNA experiment as control (Feng et al. 2011).
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: A BED file with the MACS peaks is provided
Supplementary_files_format_and_content: Wig files to visualize the data in the University of California Santa Cruz (UCSC) genome browser.

extract_protocol:
Tissue were cut into small pieces, washed with cold PBS, and fixed with 1% formaldehyde for 20 min at room temperature; fixation was stopped by addition of glycine (0.125 M, final concentration) with an additional incubation of 5 min. Cells were collected by centrifugation and washed twice with cold PBS. After centrifugation, the cells were pelleted and lysed for 30 min in 700ml of SDS buffer (50mM Tris pH 8.1, 100mM NaCl, 5mM EDTA, 0.5% SDS) supplemented with protease inhibitors (Roche #11873580001). Chromatin was disrupted using a Covaris instrument during 40 min (20% duty cycle; 10% intensity; 200 cycle), yielding DNA fragments with a bulk size of 300–500 bp. Samples were centrifuged to pellet cell debris. The amount of chromatin isolated was quantified in a Nanodrop; an aliquot of this material was used as input for sequencing. To each sample (500mg of chromatin for ChIP or 1mg for ChIP-seq) Triton dilution buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) was added to a total of 1 mL and the sample was pre-cleared during 2h with a mix of protein G/A (previously blocked with 5% BSA) at 4 ºC. We used 10μg of anti-c-Myc antibody (N262, Santa Cruz) pre-bound overnight to 100μl of G protein in PBS with 0.5% BSA. Beads were added to samples and incubated overnight at 4 °C in a rotating platform. After washing and elution, crosslinks were reversed as described by (Aparicio et al. 2005). This included successive washes in 1 mL of Mixed Micelle Buffer (20mM Tris at pH 8.1,150 mM NaCl, 5mM EDTA, 5% w/v sucrose, 1% Triton X-100, and 0.2% SDS), Buffer 500 (50mM HEPES at pH 7.5, 0.1% w/v deoxycholic acid, 1% Triton X-100, 500mM NaCl, and 1mM EDTA), LiCl Detergent Wash Buffer (10mM Tris at pH 8.0, 0.5% deoxycholic acid, 0.5% NP-40, 250mM LiCl, and 1mM EDTA), and TE (pH 7.5). Crosslinks were reversed by incubation overnight at 65 °C in Elution Buffer (1% SDS, 0.1M NaHCO3). The eluted DNA was treated with proteinase K solution (10mM EDTA, 40mM Tris-HCl pH 6.5 and 40mg/ml proteinase K) and purified by phenol-chloroform extraction; the DNA pellet was resuspended in 40ml.
DNA (20ng) was quantified by fluorometry, resolved by electrophoresis, and fractions of 50-250 bp were extracted. Input samples correspond to balanced blends of inputs from selected samples. Fractions were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters following Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were amplified by limited-cycle PCR with Illumina PE primers (12 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents following manufacturer's protocols.

tag: origin

tag: chip antibody

value: Ptf1a antibody (kindly supplied by Bernardette Bréant)

value: Ela1-myc mice

value: 8 weeks-old


title: ASF00615_WT

tag: tissue

value: WT


title: c-Myc_ChIP-Seq

description: DNA pool of three mice (502-503-510)

value: c-Myc antibody (N262, Santa Cruz)


title: ASF00611_WT


title: 4mo_SC_rep3

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

description: from astrocyte ribome pulldown

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the mm10 genome was performed using the STAR aligner version 2.4.0k using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite and differential gene expression was carried out using the edgeR package v3.6.8 using duplicates to copute within-group dispersion. FDR < 0.05 and log2 fold change greater than 0.5
Genome_build: mm10
Supplementary_files_format_and_content: raw counts (text file)
Supplementary_files_format_and_content: fpkm normalized table (text file)

source_name: somatosensory cortex

growth_protocol: 12 hour light/dark cycle with ad lib access to standard mouse chow

extract_protocol:
1% PFA perfusion then brain microdissection in cold physiological buffer, then RNA extracted (input) or ribosomal pulldown via Ribotag protocol (Sanz et al PNAS 2009): HA-tagged ribosome pulled down with Cst Rb anti-HA antibody, isolated via Pierce IgG beads. All RNA extracted with Qiagen RNeasy Micro kit.
standard Illumina protocol (PolyA beads)

value: somatosensory cortex

tag: strain

value: adult (4 month old)


title: Input_DNA 2

description: Input DNA for c-myc ChIP-Seq (502-503-510)


title: Input_DNA 1

description: Input DNA for Ptf1a ChIP-Seq from five mice (ASF405, ASF407, ASF408, ASF414 and ASF420)


title: ASF00616_WT


title: 4mo_SC_rep2

description: from astrocyte ribome pulldown


title: Ctrl2-MSN-B

city: Saint Louis

first: Bo

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were aligned to the human genome (assembly hg38) with STAR version 2.4.2a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount, version 1.4.6, with GENCODE gene annotation (V23)
BigWig files were transfromed from BAM file by using igvtools.

source_name: Fibroblast

extract_protocol:
Total mRNA from reprogrammed neurons or their respective untransduced fibroblasts was collected and prepared for sequencing 32 days after viral transduction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human adult dermal fibroblasts obtained from the Coriell Institute for Medical Research Biorepository from patients with Huntington's disease or age- and gender-matched healthy controls were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124, with striatal enriched transcription factors BCL11B (Also known as CTIP2), DLX1, DLX2, and MYT1L to directly convert fibroblasts into striatal neurons as previously established (Victor et al., Neuron 2014; Richner et al., Nat. Prot. 2015).

tag: ethnicity

tag: age (years)

tag: disease

value: Healthy Patient


title: HD3-MSN-A

value: Caucasian

value: Hutington's Disease Patient


title: Ctrl4-MSC-A


title: HD3-Fib-A


title: Ctrl4-Fib-B


title: 4mo_SC_IN

description: whole ROI homogenate (input)


title: Ctrl2-MSN-A


title: Ctrl4-MSC-B


title: ZT8-WT-A_Kidney_RNASeq

city: Lausanne

first: Felix

last: Naef

address: AAB 040 Station 15

department: Bioengineering

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT8
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz

data_processing:
Genome_build: mm10
kallisto (version 0.42.4) was run using Mus musculus genome build GRCm38 reference using parameters --single -b 100 -t 20 -l 200 -s 12
Supplementary_files_format_and_content: Estimates of transcript abundance in TPM. Concatenated abundances.tsv from kallisto.

extract_protocol: RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium  thiocyanate lysis buffer.

value: Kidney

tag: feeding

value: Night-restricted feeding

value: post-natal 8-12 weeks

tag: time


title: ZT16-WT-B_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT16
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: ZT20-WT-B_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT20
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: HD3-Fib-B


title: Ctrl2-Fib-B


title: Ctrl4-Fib-A


title: 4mo_SC_rep1

description: from astrocyte ribome pulldown


title: ZT12-KO-A_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from KO mice at ZT12
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz

value: KO


title: Ctrl2-Fib-A


title: ZT16-KO-B_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from KO mice at ZT16
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: ZT8-KO-A_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from KO mice at ZT8
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: HD1-MSN-B


title: HD1-Fib-B


title: HD3-MSN-B


title: ZT12-WT-A_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT12
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: ZT20-KO-B_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from KO mice at ZT20
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: ZT8-WT-B_Kidney_RNASeq


title: ZT16-WT-A_Kidney_RNASeq


title: ZT20-WT-A_Kidney_RNASeq


title: ZT12-WT-B_Kidney_RNASeq


title: HD1-Fib-A


title: ZT8-KO-B_Kidney_RNASeq


title: D5RNA-R2

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: Day 5 regenerating trunk fragments

data_processing:
Alignment with bowtie2 (-k 100)
Genome_build: Combined transcriptome of GDAG01, GCZZ01 and genbank S. mediterranea transcripts

organism: Schmidtea mediterranea

source_name: trunk fragments

extract_protocol: RNA was extracted by standard TRIzol (Ambion) methods (Chomczynski, 1987). Libraries for sequencing were prepared with the TruSeq RNA Sample Preparation kit v2 (RS-122-2001).

tag: biotype

value: Sexual S2F2

tag: time point

value: day 5


title: Juv-R2

description: Whole Juvenile Animal

source_name: Whole Juvenile Animal


title: ZT12-KO-B_Kidney_RNASeq


title: D5RNA-R3

description: Day 5 regenerating trunk fragments


title: Juv-R1

description: Whole Juvenile Animal


title: D5RNA-R1

description: Day 5 regenerating trunk fragments


title: Juv-R3

description: Whole Juvenile Animal


title: D7RNA-R3

description: Day 7 regenerating trunk fragments

value: day 7


title: ZT20-KO-A_Kidney_RNASeq


title: ZT4-WT-A_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT4
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: D7RNA-R1

description: Day 7 regenerating trunk fragments


title: D3RNA-R3

description: Day 3 regenerating trunk fragments

value: day 3


title: ZT0-WT-B_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from WT mice at ZT0
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: D3RNA-R2

description: Day 3 regenerating trunk fragments


title: HD1-MSN-A


title: D3RNA-R1

description: Day 3 regenerating trunk fragments


title: ZT4-KO-A_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from KO mice at ZT4
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: ZT4-WT-B_Kidney_RNASeq


title: D0RNA-R2

description: Day 0 trunk fragments

value: day 0


title: ZT0-KO-B_Kidney_RNASeq

description:
Kidney PolyA-selected RNA
RNA-Seq of Kidney extracted from KO mice at ZT0
kidneyWT_vs_kidneyKO_kallisto_abundances.txt.gz


title: D0RNA-R3

description: Day 0 trunk fragments


title: ZT16-KO-A_Kidney_RNASeq


title: D0RNA-R1

description: Day 0 trunk fragments


title: 28a

data_processing:
RNA-seq reads were aligned to the human genome (assembly hg38) with STAR version 2.4.2a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount, version 1.4.6, with GENCODE gene annotation (V23)
BigWig files were transfromed from BAM file by using igvtools.
Genome_build: hg38

growth_protocol: Human adult dermal fibroblasts obtained from the Coriell Institute for Medical Research Biorepository from patients with Huntington's disease or age- and gender-matched healthy controls were transduced with lentivirus to express the brain enriched microRNAs, miR-9/9* and miR-124, with striatal enriched transcription factors BCL11B (Also known as CTIP2), DLX1, DLX2, and MYT1L to directly convert fibroblasts into striatal neurons as previously established (Victor et al., Neuron 2014; Richner et al., Nat. Prot. 2015).

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total mRNA from reprogrammed neurons or their respective untransduced fibroblasts was collected and prepared for sequencing 32 days after viral transduction.

tag: disease state


title: Day 31 leaf 12 basal rep2

city: Newcastle

first: Yuzhou

last: Wu

state: NSW

address: University Drive

country: Australia

institute: University of Newcastle

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and v2.2.70 and Real Time Analysis (RTA) v1.18.66.3 and v1.18.66.4, running on the instrument computer.
Basecalls performed using CASAVA version 1.8.2
Then the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Raw reads from each sample were reloaded and analyzed in CLC Genomics Workbench 8.0 (Qiagen) installed on an Intel® Xeon® workstation with 64 Gb RAM
The first 10 nucleotides from the 5ʹ end of each read was removed, and reads with quality scores lower than 0.05 and with more than two ambiguous nucleotides were trimmed according to CLC procedures. Subsequently, adapter sequences were removed according to the Illumina Adapter List.
RNA-Seq analysis was performed in CLC Genomics Workbench 8.0 by mapping the trimmed reads to the TAIR10 Arabidopsis reference genome sequence, under default settings. Reads Per Kilobase (of exon) per Million (RPKM) mapped reads were calculated as expression values describing expression per gene.
Statistical analysis identifying differentially expressed genes (DEGs) was conducted using the tool Empirical analysis of DGE in CLC Genomics Workbench, with original total exon counts from each sample used as input.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include Gene ID, total exon reads and RPKM values for each Sample.

source_name: basal thirds of leaf 12 minus mid vein

growth_protocol: Seeds of Arabidopsis (Col-0) were germinated in moistened potting mix (Debco Seed Raising Mix) in small square pots (85 mm2), with 24 pots held in a single tray. After stratification in darkness at 4°C for three days, each tray of pots werewas transferred to an Adaptis A1000 growth chamber (16/8 h (day/night), 22°C /18°C (day/night), 90-120 μmol photons m-2 s-1 at the surface of the seeds). Plants were fertilized immediately upon removal from cold (Day 0) by adding 500 mL of 0.4% (v/v) Ionic Grow Plant Nutrient (pH ~6.0; Growth Technology) into each tray and weekly thereafter. At Day 5, excess seedlings were removed with fine tweezers to leave one seedling per pot. The plants were then watered by adding 500 mL water to each tray every two or three days except the day when plants were fertilized.

extract_protocol:
Entire cotyledons and juvenile leaves were harvested with sterile scissors and collected into RNase-free microfuge tubes, immediately snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. For each biological replicate (n = 3), a total of 30 and 20 pairs of cotyledons at Day 5 and Day 10, respectively, and 10 and two pairs of Leaf 1 and 2 at Day 10 and Day 16, respectively, were collected. Mature adult leaves (n = 3) were dissected to harvest the apical and basal thirds of the blade from the same Leaf 12 at Day 31, with the main vein in the basal section of leaves removed. These samples were also snap frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from samples using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions, including two rounds of on-column gDNA elimination using DNase I digestion (Qiagen). The yield and purity of the extracted RNA was determined by Nanodrop (Thermo Fisher Scientific). At least 2.5 μg of total RNA from a single biological replicate was aliquoted into at least four technical replicates, to ensure at least three biological replicates from each single tissue type were processed for RNA-Seq. Total RNA samples were assessed and sequencing was performed by the Australian Genome Research Facility (AGRF, Melbourne).
Sequencing libraries were constructed by Australian Genome Research Facility using the Illumina TruSeq stranded mRNA sample preparation protocol.

value: basal thirds of leaf 12 minus mid vein

tag: developmental stage

value: Day 31


title: 27b

tag: age


title: Day 31 leaf 12 basal rep3


title: HeLa GFP

data_processing:
The image files generated by the Genome Analyzer were processed to extract DNA sequence data. Sequences were aligned to the human reference genome (GRCh37/hg19, Feb 2009) with Burrows-Wheeler Aligner (bwa,v0.5.9-r16) allowing one mismatch. Uniquely aligned reads were converted to BED format. All ChIP and control samples were normalized randomly to the same number of reads (10543138)
Furthermore, reads were directionally extended to 300 bp, and for each base pair in the  genome the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a Wiggle (WIG) file to visualize the data in the University of California Santa Cruz  (UCSC) Genome Browser
Identification of the binding sites (peak calling) was performed using MACS (version 2.0.9 20111102, tag:alpha) with parameters: -g 2.7e9; -m 10,30; -q 0.05. HeLa GFP was used as control
In addition, genomic binding sites overlapping to the peaks in the negative control (GFP ChIP-Seq on wild type HeLa cells) were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: BED files: for binding sites (chromosome, start, end, MACS_peak and -log10(qvalue)) and WIG files: to visualize binding sites in UCSC browser

source_name: HeLa GFP

growth_protocol: To generate mammalian cells expressing proteins of the EMSY/KDM5A complex at near endogenous levels bacterial artificial chromosomes containing EMSY, GATAD1, PHF12 or KDM5A respectively were obtained from the BACPAC Resources Center and a GFP cassette was inserted as a C-terminal in-frame fusion using BAC recombineering. HeLa cells were transfected with the recombineered BAC using Lipofectamine 2000PEImax (for EMSY) and selected with 400μg/ml geneticin (G418). Expression of the recombineered ZNF131 BAC HeLa cells proved unsuccessful hence a full length mouse ZNF131 construct that was a gift from Juliet Daniel was cloned into the plasmid pBabePuro-C-GFP by gateway cloning that was used to generate retrovirus particles using the Phoenix ecotropic packaging cells. Short hairpin knockdown of ZNF131 in the EMSY GFP expressing HeLa cells was mediated lentiviral transduction. A set of 5 short hairpins purchased from Sigma were transfected into Cos7 cells in combination with lentiviral packaging vectors using PEImax. After 24 hours, virus generated into the media was aspirated, filtered and concentrated. The target cells (EMSY GFP HeLa) were transduced with the virus in the presence of polybrene. shRNA integrated cells were subjected to puromycin selection, 24 hours after transduction. Single cells were grown into monoclonals and the knockdown status was assessed by RT-qPCR and western blotting (AntiZNF131, mouse polyclonal #H0000 7690-B0IP, Abnova). The monoclonals selected for this study were shZNF131#1 (TRCN0000254328) and shZNF131#2 (TRCN0000254331).

extract_protocol:
ChIP-Seq HeLa Kyoto wild type (WT), HeLa EMSY GFP, HeLa GATAD1 GFP and HeLa EMSY GFP with knockdown of ZNF131 were seeded in 15 cm dishes and 24 hours later were formaldehyde crosslinked for 10 minutes. Chromatin obtained from the cells after sonication was subjected to overnight IP using a GFP custom antibody (Michiel Vermeulen's lab) followed by extensive washes and decrosslinking. DNA was purified using the Qiagen PCR clean-up kit and the bound DNA was analysed by qPCR using the desired primers.
ChIP-Seq was carried out by conventional ChIP followed by end repair of 15 ng (for protein-GFP fusions) or 30 ng (for the histone modifications) enriched DNA as measured by Qubit fluorometer using the Quant-iT dsDNA HS Assay Kit from (Invitrogen, Q32851). Adaptors were ligated to DNA fragments, which were subsequently size selected (∼300 base pair [bp]). The adaptor-modified DNA fragments were subjected to limited PCR amplification (14 cycles) and quality control was made by qPCR (primers sequences are available upon request), as well as by running the PCR products on a Bioanalyzer (BioRad). Cluster generation and sequencing-by-synthesis (36 bp) was performed using the Illumina Genome Analyzer IIx (GAIIx) according to standard protocols of the manufacturer (Illumina).

tag: cell line

value: cervical adenocarcinoma epithelial cell line, HeLa

tag: expressing

value: GFP


title: 27a


title: 18b


title: ZT4-KO-B_Kidney_RNASeq

tag: genotype


title: 2yo_CB_rep3

description: from astrocyte ribome pulldown

source_name: cerebellum

value: cerebellum

value: aged (2 year old)


title: 19a

value: Caucasian

value: Healthy Patient


title: 2yo_CB_rep2

description: from astrocyte ribome pulldown


title: 19b


title: HeLa GFP EMSY with Znf131 KD

source_name: HeLa GFP EMSY with Znf131 KD

value: EMSY GFP with knockdown of Znf131

value: GFP custom antibody (Michiel Vermeulen's lab)


title: 18a


title: ZT0-KO-A_Kidney_RNASeq

value: Kidney

value: Night-restricted feeding

value: post-natal 8-12 weeks


title: HeLa GFP EMSY

source_name: HeLa GFP EMSY

value: EMSY GFP


title: ZT0-WT-A_Kidney_RNASeq

value: WT


title: Day 31 leaf 12 apical rep3

source_name: apical thirds of leaf 12 minus mid vein

value: apical thirds of leaf 12 minus mid vein


title: Day 31 leaf 12 apical rep2


title: 15b

value: Hutington's Disease Patient


title: D7RNA-R2

description: Day 7 regenerating trunk fragments

value: Sexual S2F2

value: day 7


title: 4mo_CB_IN

description: whole ROI homogenate (input)

value: adult (4 month old)


title: 15a


title: 2yo_CB_IN

description: whole ROI homogenate (input)


title: Day 31 leaf 12 basal rep1

value: basal thirds of leaf 12 minus mid vein

value: Day 31


title: Day 31 leaf 12 apical rep1


title: 4mo_CB_rep3

description: from astrocyte ribome pulldown

value: cerebellum


title: Slc45a3long-Liver-EF-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Liver of mice
Slc45a3long_processed_4cseq_counts_plusminus2MB.txt.gz

data_processing:
Library strategy: 4CSeq
Genome_build: mm9
See Supplemental methods of paper for details. In brief, read counts were normalized by total counts on the cis chromosome. For each fragment, we fit a weighted linear model with a Gaussian window of 2.5kb in order to incorporate signal from neighboring fragments.
Supplementary_files_format_and_content: We fit a weighted linear regression for each fragment in the genome to obtain 4CSeq signal (value A with variance Avar). Processed formats show fragments within +/- 2MB of the bait. Zscore and p-value represent differential contacts between liver and kidney. Log10 4CSeq signal.

extract_protocol: Liver and kidney nuclei were prepared as previously described (Ripperger and Schibler 2006) with some minor changes. In brief, liver and kidneys from individual animals were homogenized and fixed in 4ml of PBS including 1.5percent formaldehyde for 10 minutes at room temperature. Cross-linking reaction was stopped by adding 25 ml of ice-cold stop reaction buffer (2.2 M sucrose; 150 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF) to the homogenates and kept 5 minutes on ice. Homogenates were then loaded on top of 10 ml cushion buffer (2.05 M sucrose; 10 % glycerol; 125 mM glycine; 10 mM HEPES pH 7.6; 15 mM KCl; 2 mM EDTA; 0.15 mM spermine; 0.5 mM spermidine; 0.5 mM DTT; 0.5 mM PMSF) and centrifuged for 45 minutes at 105g at  4degC. Nuclei were washed twice in PBS and immediately frozen.

value: Liver

value: Ad libitum


title: HeLa GFP GATAD1

source_name: HeLa GFP GATAD1

value: cervical adenocarcinoma epithelial cell line, HeLa

value: GATAD1 GFP


title: 14b

value: Caucasian


title: Day 16 leaf 1+2 rep3

source_name: first pair leaves

value: first pair leaves

value: Day 16


title: 4mo_CB_rep2

description: from astrocyte ribome pulldown


title: Slc45a3short-Liver-EF-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Liver of mice
Slc45a3short_processed_4cseq_counts_plusminus2MB.txt.gz

value: post-natal 8-12 weeks


title: Pi3kap1-Liver-AB-ZT08-WT

description:
Crosslinked genomic DNA
4CSeq of Liver of mice
Pi3kap1_processed_4cseq_counts_plusminus2MB.txt.gz

value: WT


title: 14a


title: Day 16 leaf 1+2 rep2


title: 4mo_CB_rep1

description: from astrocyte ribome pulldown


title: 13b


title: 2yo_HTH_IN

description: whole ROI homogenate (input)

source_name: hypothalamus

value: hypothalamus

value: aged (2 year old)


title: Slc44a1-Kidney-EF-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Kidney of mice
Slc44a1_processed_4cseq_counts_plusminus2MB.txt.gz

value: Kidney


title: Day 16 leaf 1+2 rep1


title: 2yo_CB_rep1

description: from astrocyte ribome pulldown


title: 28b

value: Healthy Patient


title: Slc45a3short-Kidney-EF-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Kidney of mice
Slc45a3short_processed_4cseq_counts_plusminus2MB.txt.gz


title: Day 10 leaf 1+2 rep3

value: Day 10


title: 2yo_HTH_rep3

description: from astrocyte ribome pulldown


title: Mreg-Liver-EF-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Liver of mice
Mreg_processed_4cseq_counts_plusminus2MB.txt.gz


title: 13a

value: Hutington's Disease Patient


title: Pi3kap1-Kidney-CD-ZT08-WT

description:
Crosslinked genomic DNA
4CSeq of Kidney of mice
Pi3kap1_processed_4cseq_counts_plusminus2MB.txt.gz


title: 2yo_HTH_rep2

description: from astrocyte ribome pulldown


title: 11b


title: 2yo_HTH_rep1

description: from astrocyte ribome pulldown


title: Day 10 leaf 1+2 rep1


title: Day 10 cotyledons rep3

source_name: cotyledons

value: cotyledons


title: 4mo_HTH_IN

description: whole ROI homogenate (input)

value: adult (4 month old)


title: 11a


title: 4mo_HTH_rep2

description: from astrocyte ribome pulldown


title: Slc45a3short-Kidney-GH-ZT20-WT


title: Pi3kap1-Liver-CD-ZT08-WT

value: Liver


title: Day 10 cotyledons rep1


title: Pi3kap1-Kidney-AB-ZT08-WT

value: Ad libitum


title: Slc44a1-Liver-EF-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Liver of mice
Slc44a1_processed_4cseq_counts_plusminus2MB.txt.gz


title: Day 10 cotyledons rep2


title: EGKVIII_S4

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
Adaptor sequences and low quality bases with PHERD scores (Q) ≤ 30 were removed. And we employed Trimmomatic for removal of adapter sequences.
The read mapping into assembled transcriptome was performed using tophat2
Finally, HTSeq-count was employed for quantification.
Genome_build: We used watermelon reference genome (97103) version 1 in Curcurbit Genomics Database.
Supplementary_files_format_and_content: TSV file for each sample

organism: Gallus gallus

source_name: Embryonic cell

extract_protocol:
Total RNA was prepared from the samples and Total RNA was extracted using TRIzol reagent (MRC).
Libraries were prepared based on Illimina instruction

value: EGKVIII


title: Day 5 cotyledons rep3

value: Day 5


title: 4mo_HTH_rep1

description: from astrocyte ribome pulldown


title: Mreg-Kidney-GH-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Kidney of mice
Mreg_processed_4cseq_counts_plusminus2MB.txt.gz


title: Day 5 cotyledons rep2


title: Slc44a1-Kidney-GH-ZT20-WT


title: Day 5 cotyledons rep1


title: EGKVIII_S2


title: EGKVIII_S3


title: 2yo_MC_rep3

description: from astrocyte ribome pulldown

source_name: motor cortex

value: motor cortex


title: Day 10 leaf 1+2 rep2

value: first pair leaves


title: Slc45a3long-Kidney-EF-ZT20-WT

description:
Crosslinked genomic DNA
4CSeq of Kidney of mice
Slc45a3long_processed_4cseq_counts_plusminus2MB.txt.gz


title: 2yo_MC_IN

description: whole ROI homogenate (input)


title: 2yo_MC_rep2

description: from astrocyte ribome pulldown


title: EGKVI_S6

value: EGKVI


title: Col-0, 8h, rep3

description: polyA-enriched and rRNA-depleted RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using tophat v2.0.10 with parameters -a 10  -g 10 - r 160  --mate-std-dev 160 --library-type fr-unstranded
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

source_name: Arabidopsis leaves

extract_protocol:
Total RNA were extracted using the Qiagen Rneasy kit. RNA were DNaseI-treated and a purification was done using the Qiagen Rneasy MinElute kit. Ribosomal RNAs were depleted from 2.5 µg RNA using the RiboMinus Plant Kit for RNA-seq (Life Technologies).
For library preparation, oligodT-primed cDNA synthesis was done using the TruSeq RNA preparation kit (Life Technologies).  All proceadures were performed according to the manufacturer's instructions.
paired-end RNA-seq

treatment_protocol: Plants were shifted from 28°C to 19°C for 4 and 8h before collecting and freezing the samples. T0 samples were not shifted.

value: leaves

value: Col-0 WT

value: 8 h


title: Mreg-Liver-GH-ZT20-WT

value: post-natal 8-12 weeks

value: WT


title: 4mo_HTH_rep3

description: from astrocyte ribome pulldown

value: hypothalamus


title: EGKVI_S5


title: Col-0, 8h, rep2

description: polyA-enriched and rRNA-depleted RNA


title: Slc45a3short-Liver-GH-ZT20-WT


title: Col-0, 8h, rep1

description: polyA-enriched and rRNA-depleted RNA


title: EGKVI_S1


title: Slc45a3long-Liver-GH-ZT20-WT


title: EGKIII_S5

value: EGKIII


title: 4mo_MC_rep3

description: from astrocyte ribome pulldown


title: Col-0, 4h, rep3

description: polyA-enriched and rRNA-depleted RNA

value: 4 h


title: 4mo_MC_rep2

description: from astrocyte ribome pulldown


title: 4mo_MC_rep1

description: from astrocyte ribome pulldown


title: Slc45a3long-Kidney-GH-ZT20-WT

value: Kidney


title: EGKIII_S3


title: Col-0, 4h, rep1

description: polyA-enriched and rRNA-depleted RNA


title: Col-0, T0, rep3

description: polyA-enriched and rRNA-depleted RNA

value: 0 h


title: Col-0, T0, rep2

description: polyA-enriched and rRNA-depleted RNA


title: 2yo_VC_IN

description: whole ROI homogenate (input)

source_name: visual cortex

value: visual cortex

value: aged (2 year old)


title: Cbh1

address: 9500 Gilman Drive, MC0412, PFBH402

institute: University of California San Diego

description: scTHS-seq data

data_processing:
Library strategy: scTHS-seq and Nextera
Basecalls performed using bcl2fastq v2.17.1.14
Sequencing data from the same samples was concatenated together and then as input to deindexder (https://github.com/ws6/deindexer) with 0 mismatch barcode demultiplexing.
Barcode combinations associated with each read were appended to each reads header with in house perl scripts and all fastq’s were combined and mapped to a hg38 no alternative loci plus decoy reference genome (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) and mm10 no alternative loci reference genome (GCA_000001635.5_GRCm38.p3_no_alt_analysis_set) using BWA 0.7.12-r1039. Mapped sam outputs were redemultiplexed by barcodes, converted to bam files and clonal reads removed with samtools 1.3.1
multimapping reads MAPQ<5 were removed from each single cell dataset to remove reads in repeat regions
Joint peak calling was performed on pooled bam files using SPP (v1.13; https://github.com/hms-dbmi/spp). Reads mapping within 100bps of known repeat regions according to annotations from Repeat Masker (http://www.repeatmasker.org) were removed. A smoothed density of pooled reads was generated using window tag counts with a window size of 500bps and a window step of 100bps. DNA accessible regions (peaks) were called based on the smoothed density with a minimum threshold of 5 reads and minimum span of 5 steps between each peak. Peaks were filtered using a permutation based FDR of 10e-8 and filtered for presence in at least 40 cells from the visual cortex. Called peaks were then assessed for reads in each individual cell to generate a matrix of peaks versus cells for downstream clustering and analysis.
Genome_build: GENCODE GRCh38, GENCODE GRCm38
Supplementary_files_format_and_content: combined tab-delimited accessibilty peaks file for occ1, fcx1 and cbh1
Supplementary_files_format_and_content: differential accessiblity peaks between cell types. MAINSPLITS are differential accessibility between the main cell types. EXONLY are only differential peaks between the excitatoy sub clusters. INONLY are only differential peaks between the inhibitory sub clusters.
Supplementary_files_format_and_content: count matrices for occ1, fcx1 and cbh1. Matrices have been exported column by column from R and tar gzipped, where each barcode labeled text file is data for 1 cell. Column is the cell, rows are reads in accessibility peaks in the combined tab-delimited accessibilty peaks file for occ1, fcx1 and cbh1

source_name: Brain

extract_protocol:
Cryofrozen post-mortem brain tissue was treated with nuclear extraction buffer, isolated nuclei was stained with DAPI and FACS purified.
To the 384 well plate of freshly generated uniquely barcoded Tn5059 r5 transposome complexes, 4 µL of human/mouse mixed cell sample was added for a total of ~960 nuclei/well and final concentration of 0.7 µM Tn5059 r5 transposome complex. Each sample was mixed gently 5X by the electronic pipettor. Optimally ~2000 nuclei/well are wanted, however nuclei yields were low. The 384 well plate was then incubated at 37ºC for 30 minutes. To stop the reaction, 4.0 µL of 50 mM EDTA was added to each well and mixed gently 5X by the electronic pipettor for a final concentration of 20 mM EDTA in 10 uL, followed by incubating the 384 well plate at 37ºC for 15 minutes. The 384 well plate of samples was then frozen at -20ºC overnight. The next day, the 384 well plate of samples was thawed, and one volume of cold 2X FACS buffer (1X FACS buffer: 2 mM EDTA, 1% BSA in PBS) was added to each well. Samples are then mixed gently 3X by the electronic pipettor and pooled into one tube on ice, which was spun down at 500xg for 5 minutes at 4ºC. Supernatant was removed, and tagmented nuclei resuspended in 1.5 mL cold 1X FACS buffer. Next, 75 µL eBioscience Propidium Iodide (PI) was added to the tube, and gently mixed. Nuclei were then sorted by flow cytometry into 96 well plates containing 10 µL PBS/well at 100 nuclei/well, and put on ice. Doublets were removed based on forward and side scatter plots, and PI stained events selected. Nuclei were now ready for RNA amplification and processing.
Each 96 well plate of nuclei was processed individually. First, 11 µL guanidine hydrochloride was added to each well and mixed by lightly vortexing. Reactions were purified by addition of 40 µL (1.8X) AMPure SPRI beads and lightly vortexed, then bead pelleting and 80% ethanol washes were performed with the “flick and blot” method and magnetic plate from V&P Scientific. After 80% ethanol washes were complete the plate was quickly spun down at 500xg and leftover 80% ethanol removed by pipetting. 10 µL 1X NEB Taq polymerase was added to each reaction and the plate was lightly vortexed to resuspend the beads (SPRI beads left in reaction), followed by running the reactions at 72ºC for 3 minutes for end fill in and put on ice. For in vitro transcription (IVT) amplification the NEB HiScribe T7 high yield synthesis kit was used. To each reaction a mastermix of 2 µL of 10X transcription buffer, 2 µL ATP, 2 µL CTP, 2 µL GTP, 2 µL UTP was directly added to the end fill in reactions, lightly vortexed, and incubated at 37ºC for 19 hours. To check IVT amplification, two full reactions were purified with SPRI binding buffer, run on a 6% Tris-Borate-Urea (TBU) gel for 20 minutes at 250 volts followed by SYBR gold staining and visualization on a UV-transilluminator. Next, reactions were purified by addition of 44 µL (2.0X) SPRI binding buffer (20% PEG 8000, 2.5 M NaCl, 10 mM Tris–HCl, 1 mM EDTA) to each reaction and the plate vortexed thoroughly. 80% ethanol washes and leftover 80% ethanol removal were performed as describe above, and SPRI beads were resuspended in 9 µL nuclease free water. For reverse transcription, first 2.5 µL of 20 µM random hexamers was added to each reaction, the plate vortexed lightly and then heated to 70ºC for 3 minutes, and immediately cooled on ice. Then Clontech SMART® MMLV Reverse Transcriptase kit was used with addition of 4 µL 5X first strand synthesis, 2 µL dNTP mix, 2 µL 100 mM DTT, 0.5 µL SMART MMLV RT in a mastermix to each reaction and the plate vortexed lightly. Reactions were incubated at 22ºC for 10 minutes, then 42ºC for 60 minutes, and terminated at 70ºC for 10 minutes. To degrade RNA in cDNA-RNA hybrids 1 µL of 0.5 units Enzymatics RNase H was added to each reaction, the plate was vortexed lightly and incubated at 37ºC for 20 minutes. For second strand synthesis first 2.5 µL of 20 µM sss_scnXTv2 (Table S12) was added to each reaction and lightly vortexed, then incubated for 2 minutes at 65ºC and immediately cooled on ice. Then 5.9 µL of NEB taq5X was added to each reaction and incubated at 72ºC for 8 minutes. After cooling on ice, 60 µL (2.0X) SPRI binding buffer was added to each sample. The plate was vortexed thoroughly and 80% ethanol washes and leftover 80% ethanol removal performed as described previously, and SPRI beads resuspended by light vortexing in 7 µL of nuclease free water. Double stranded cDNA fragments then undergo simultaneous fragmentation and 3’ adaptor addition with a custom nXTv2_i7 Tn5059 transposome (Table S12). To 7 µL of sample, 2 µL of 5X tagmentation buffer was added to each sample, followed by addition of 2 µL of prepared 0.7 µM custom nXTv2_i7 Tn5059 transposomes (final transposome concentration of 0.14 µM), vortexed lightly, then incubated at 55ºC for 6 minutes, and cooled briefly on ice. Immediately after cooling, 19 µL of 6.32M guanidine hydrochloride, for a final guanidine hydrochloride concentration of 4M was added to each reaction and briefly vortexed. Then 60 µL (2.0X) SPRI binding buffer was added to each sample. The plate was vortexed thoroughly and 80% ethanol washes and leftover 80% ethanol removal was performed as described previously. However, for this purification SPRI beads were resuspended in 16 µL nuclease free water and the plate was placed back onto the magnetic plate. Sample was eluted off SPRI beads held by the magnetic plate, and transferred to a qPCR plate. Standard Illumina Nextera XT v2 barcoding in an 8x12 (i5xi7) format was performed with qPCR, using custom scTHS-seq i5 indexes and standard Illumina i7 indexes (Table S12). In total, 20 µL of KAPA SYBR Fast, 2 µL of 10 µM scT7_S5XX index primer and 2 µL of 10 µM nXTv2_i7XX index primer were added to each reaction for a total volume of 40 µL, and mixed well. qPCR was run at 72ºC for 3 minutes, 95ºC for 30 seconds, followed by cycling for (95ºC for 10 seconds, 63ºC for 30 seconds, 72ºC for 1 minute) until curves reach saturation, typically 9-12 cycles. Plates were stored at -20ºC.

tag: experiment

tag: patient

tag: region

value: Cerebellular Hemisphere

tag: brodmann area

value: CBL

tag: histology

value: Not Specified

value: 27 years

tag: Sex

value: Male

tag: race

tag: source

value: U Miami School of Medicine Brain Bank


title: EGKI_S4

value: EGKI


title: Col-0, T0, rep1

description: polyA-enriched and rRNA-depleted RNA

tag: tissue

value: leaves

value: Col-0 WT

tag: time


title: EGKI_S2


title: 2yo_MC _rep1

description: from astrocyte ribome pulldown

value: motor cortex

tag: strain


title: 2yo_VC_rep3

description: from astrocyte ribome pulldown


title: EGKI_S1


title: 4mo_MC_IN

description: whole ROI homogenate (input)

value: adult (4 month old)


title: 35S:RPS4, 8h, rep3

description: polyA-enriched and rRNA-depleted RNA

value: Col-0 35S:RPS4-HS

value: 8 h


title: 2yo_VC_rep2

description: from astrocyte ribome pulldown


title: Zygote_S6

value: Zygote


title: 4mo_VC_IN

description: whole ROI homogenate (input)


title: 2yo_VC_rep1

description: from astrocyte ribome pulldown


title: Mreg-Kidney-EF-ZT20-WT

value: Kidney

tag: feeding

value: Ad libitum

value: post-natal 8-12 weeks

value: WT


title: 35S:RPS4, 8h, rep2

description: polyA-enriched and rRNA-depleted RNA


title: Zygote_S5

tag: developmental stage


title: EGKIII_S4

value: EGKIII


title: Col-0, 4h, rep2

description: polyA-enriched and rRNA-depleted RNA

value: 4 h


title: 35S:RPS4, 8h, rep1

description: polyA-enriched and rRNA-depleted RNA


title: Zygote_S4


title: 35S:RPS4, 4h, rep3

description: polyA-enriched and rRNA-depleted RNA


title: 4mo_VC_rep3

description: from astrocyte ribome pulldown

value: visual cortex

tag: age


title: Slc44a1-Liver-GH-ZT20-WT

value: Liver


title: Oocyte_S3

value: Oocyte


title: 4mo_VC_rep2

description: from astrocyte ribome pulldown


title: Oocyte_S2


title: 35S:RPS4, 4h, rep1

description: polyA-enriched and rRNA-depleted RNA


title: 4mo_VC_rep1

description: from astrocyte ribome pulldown