title: R1_LIM [II]

description:
R1 ES cells differentiated to rosette-like pluripotency.
processed data file: normcounts_R1_IB10_L2I_LIM_Prim.txt

data_processing:
During sequencing, Read 1 was assigned 26 base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60 base pairs and used to map to the reference transcriptome of mm10 with BWA. Data demultiplexing and statistical UMI poisson counting correction was done as described in Grun, D., Kester, L. & van Oudenaarden, A. Validation of noise models for single-cell transcriptomics. Nat Methods 11, 637-640 (2014).
Mapping and generation of count tables were done using the MapAndGo script https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo . The empty wells (167, 168, 191 and 192) were removed from the normalized count matrix.
Single-cell transcriptomics analysis was done using the RaceID3 algorithm, following an adapted version of the RaceID manual (https://cran.r-project.org/web/packages/RaceID/vignettes/RaceID.html). In total, 1152 cells were sequenced.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: normcounts_R1_IB10_L2I_LIM_Prim.txt: Tab-delimited text file containing a matrix of normalized read counts.

source_name: R1 embryonic stem cells

growth_protocol: Cells were grown in serum-free N2B27 medium on tissue culture plastic plates coated with 0.1% gelatin and fetal calf serum.

extract_protocol:
Cells were heat-lysed at 65° C for 5 min.
Following lysis, cDNA was synthesized using the CEL-Seq2 protocol (Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77 (2016)) and robotic liquid handling platforms. After second strand cDNA synthesis, the barcoded material was pooled into libraries of 384 cells and amplified using IVT. Following amplification, the rest of the CEL-seq2 protocol was followed for preparation of the amplified cDNA library, using TruSeq small RNA primers (Illumina).
The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles).

treatment_protocol:
Cells were cultured in the presence of LIF and the indicated supplements for the indicated duration. 2i is CHIR99021+PD325901. Concentrations: CHIR99021 3 uM; PD325901 0.1 uM; IWP2 2 uM; FGF2 12 ng/ml; human Activin A 20 ng/ml.
After culture, the cells were trypsinized and FACS sorted into 384-wells plates containing 384 primers, dNTPs and Mineral oil (Sigma). For each sample, 192 wells were used. Wells 167, 168, 191 and 192 for each sample were left empty. After sorting, plates were snap-frozen on dry ice and stored at -80° C.

value: LIF+IWP2+PD325901 for 6 passages

tag: passage number


title: zebrafish_123s_E7

status: Public on Apr 28 2020

type: SRA

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

library_source: transcriptomic

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the zebrafish reference genome (danRer11) using TapHat2, Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the three sample-plates (plate_123, plate_989, plate_990) were combined into one expression matrix file
counts data was processed and analyzed using velocyto, SingleCellExperiment and pagoda2 packages in R-software
Genome_build: GRCz11 (danRer11)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

molecule: total RNA

organism: Danio rerio

source_name: zebrafish

extract_protocol:
FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin-EDTA and 10U Dnase I for 30min at 30°C
RNA libraries were prepared using standard SmartSeq2 protocol

tag: tissue

value: embryo trunk

tag: starin

tag: age

value: 48 hpf


title: CD4-4096

city: Hefei

first: Bin

last: Li

address: NO. 96 Jinzhai Road

country: China

institute: University of Science and Technology of China

description: ftATAC-seq data of mouse thymoctyes

library_source: genomic

data_processing:
We used BOWTIE2 to map the trimmed sequencing data to the corresponding genome index and used PICARD for the sorting, duplicate removal, and fragment length counting of the aligned data.
We calls peaks from the merged single-cell profiles of all cells using MACS2 to ensure that the entire analysis is unsupervised. We then ranked and filtered out the low quality peaks based on the false discovery rate (Q-value).
Genomic locations of the peaks were annotated by HOMER, and motifs searched by FIMO.
We calculates the number of fragments and the percent of reads mapped to the TSS region (±2000 BP) for each cell, and filters out high quality cells for downstream analysis.
We integrate all processing steps as a pre-process script of APEC.
Genome_build: mm9
Supplementary_files_format_and_content: The cell.csv file is a CSV format file containing the information of filtered cells; the features.bed file is a BED format file containing the information of filtered peaks; the matrix.mtx file is the fragment count matrix stored in MTX format.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse thymoctyes

extract_protocol:
Thymus tissues isolated from 6- to 8-week-old male mice were gently ground in 1 mL of RPMI-1640. Thymocytes in a single-cell suspension were counted after passing through a 40 μm nylon mesh. A total of 1 × 106 thymocytes were stained with PerCP-Cy5.5-anti-CD45, PE-anti-CD8a and APC-Cy7-anti-CD4 antibodies (Biolegend) and then fixed in 1× PBS containing 1% methanal at room temperature for 5 min. After washing twice with 1× PBS, the cells were counted again. A total of 1 × 105 fixed cells were resuspended in 40 μL of 1× TD buffer (5 mM Tris-HCl, pH 8.0, 5 mM MgCl2 , and 10% DMF) containing 0.1% NP-40. Then, 10 μL of fluorescent transposomes were added and mixed gently. Fluorescent tagmentation was conducted at 55 °C for 30 min and stopped by adding 200 µL of 100 mM EDTA directly to the reaction mixture. The cells were loaded on a Sony SH800S sorter, and single cells of the CD45+/AF488-Tn5hi population were index-sorted into each well of 384-well plates. The 384-well plates used to acquire sorted cells were loaded with 2 µL of release buffer (50 mM EDTA, 0.02% SDS) before use. After sorting, the cells in the wells were incubated for 1 min. Plates that were not processed immediately were preserved at -80 °C.
To prepare a single-cell ATAC-seq library, plates containing fluorescently tagmented cells were incubated at 55 °C for 30 min. Then, 4.2 μL of PCR round 1 buffer (1 μL of 100 μM MgCl2, 3 μL of 2× I-5 PCR mix [MCLAB], and 0.1 μL each of 10 μM R1 and R2 primers) were added to each well, followed by PCR: 72 °C for 10 min; 98 °C for 3 min; 10 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Thereafter, each well received 4 µL of PCR round 2 buffer (2 μL of I-5 PCR Mix, 0.5 μL each of Ad1 and barcoded Ad2 primers, and 1 μL of ddH2O), and final PCR amplification was carried out: 98 °C for 3 min; 12 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Wells containing different Ad2 barcodes were collected together and purified with a QIAquick PCR purification kit (Qiagen).

tag: strain

value: thymocytes

value: 6-8 weeks


title: zebrafish_123s_E23


title: CD4-4093

description: ftATAC-seq data of mouse thymoctyes


title: IB10_L2I [II]

city: Rotterdam

first: Derk

last: ten Berge

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: ErasmusMC

description:
IB10 ES cells in Lif/2i.
processed data file: normcounts_R1_IB10_L2I_LIM_Prim.txt

source_name: IB10 embryonic stem cells

tag: cell line

tag: treatment


title: THP0 3

city: Muenster

first: Maria

middle: V

last: Yusenko

address: Wilhelm-Klemm-Str. 2

department: Institute of Biochemistry

country: Germany

institute: University of Muenster

data_processing:
The sequences were demultiplexed (bcl2fastq2) to fastq data and quality controlled.
Trimmomatic (v. 038) was used for adapter trimming and read filtering.  (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
The resulted reads were aligned to the  hg38 using Hisat2 (v.2.1.0; Parameter: default) and sorted using SAM tools (v. 1.9)
The sorted and aligned reads were counted into genes using HTSeq (v.0.11.1;  Parameter: --minaqual 0,  --stranded reverse)
Testing for differential expression was performed using DESeq2 r-package (v. 1.22.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files

organism: Homo sapiens

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium containing 10% FBS and 5% L-Glut

extract_protocol:
Total RNA was harvested using Trizol reagent.
NEBNext Ultra Directional RNA II Library Prep kit  was used for the construction of sequencing libraries, which were then sequenced with the Illumina NextSeq 500 System and NextSeq v2 sequencing reagent kit in a single read-mode with a read-length of 75 bp.

treatment_protocol: The cells were left untreated or treated with 1 µM Monensin for 16 hours. All experiments were done in triplicate.

tag: cell type

value: acute monocytic leukemia

value: no exposure


title: zebrafish_123s_E3


title: zebrafish_123s_E22


title: R1_4Dprimed [II]

description:
R1 ES cells differentiated to primed pluripotency.
processed data file: normcounts_R1_IB10_L2I_LIM_Prim.txt

value: LIF+FGF2+Activin A+IWP2 for 4 days


title: IB10_LIM [II]

description:
IB10 ES cells differentiated to rosette-like pluripotency.
processed data file: normcounts_R1_IB10_L2I_LIM_Prim.txt

value: LIF+IWP2+PD325901 for 5 passages


title: zebrafish_123s_E4


title: CD4-4094

description: ftATAC-seq data of mouse thymoctyes


title: IB10_4Dprimed [II]

description:
IB10 ES cells differentiated to primed pluripotency.
processed data file: normcounts_R1_IB10_L2I_LIM_Prim.txt


title: CD8-4097

description: ftATAC-seq data of mouse thymoctyes


title: R1_L2I [II]

description:
R1 ES cells in Lif/2i.
processed data file: normcounts_R1_IB10_L2I_LIM_Prim.txt


title: CD4-4092

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E21


title: CD4-4091

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E5


title: CD4-4095

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E24


title: CD4-4090

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E2


title: CD4-4088

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E19


title: zebrafish_123s_E20


title: CD4-4089

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E18


title: zebrafish_123s_E17


title: CD4-4086

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E13


title: zebrafish_123s_E15


title: CD4-4083

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4085

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E16


title: zebrafish_123s_E14


title: CD4-4080

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4082

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E12


title: CD4-4081

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4084

description: ftATAC-seq data of mouse thymoctyes


title: AD_M704_7.3m

city: Jerusalem

first: Naomi

last: Habib

address: Safra Campus

department: Center for brain sciences

country: Israel

institute: Hebrew University of Jerusalem

description: Admouse_Hippocampus_3TimeCourses_Astrocytes_WT_AD_Aging.csv

data_processing:
De-multiplexing, alignment to the mm10 transcriptome and unique molecular identifier (UMI)-collapsing were performed using the Cellranger toolkit (version 2.1.1, chemistry V2, or version 3.0.2, chemistry V3) provided by 10X Genomics for chemistry Single Cell 3’, and run using cloud computing on the Terra platform (https://Terra.bio).
Filtering of cells with less than 400 detected genes,  filtering of genes that were detected in fewer than 10 nuclei, in R
Selecting astrocyte cells and merging datasets with Seurat software version 3.0
Genome_build: mm10
Supplementary_files_format_and_content: Unique mulecule identifiers (UMIs, or transcripts) counts per gene (rows) across cell (columns)

source_name: Brain

extract_protocol:
Brain tissue was frozen after dissociation until nuclei isolation. Tissue was transferred into a dounce homogenizer with 2mL of EZ Lysis Buffer or NP40 Lysis Buffer. Tissue was carefully dounced while on ice, then transferred to a 15mL conical tube. with 3mL of additional lysis buffer. When using EZ, the lysis homogenate was incubated on ice for 5 mins, for NP40 buffer no incubation was done. The samples were centrifuged with a swinging bucket rotor at 500g for 5 mins at 4C. Supernatant was removed and the pellet was resuspended in PBS (for EZ lysis) or Tris buffer (for NP40 lysis). Resuspended nuclei were gently filtered through 40um FlowMi cell strainers into 1.5mL Eppendorf tubes.
10,000 nuclei were used as input to 10X Genomics single-cell 3’ Gene Expression v2 assay (22 samples) or v3 assay (10 samples). Libraries were prepared following the manufacturer’s protocol.

tag: region

value: Hippocampus


title: WT_M766_13.3m


title: zebrafish_123s_E10


title: WT_M721_4.7m


title: CD4-4079

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4078

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4077

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E1


title: CD4-4087

description: ftATAC-seq data of mouse thymoctyes


title: WT_M768_13.3m


title: WT_M680_8.1m


title: WT_M208_19.6m


title: zebrafish_123s_D8


title: zebrafish_123s_D7


title: WT_M206_19.6m


title: CD4-4076

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D6


title: zebrafish_123s_E11


title: zebrafish_123s_D4


title: HipR-AD-G2-14m


title: zebrafish_123s_D5


title: HipR-WT-G2-14m


title: zebrafish_123s_D3


title: HipR-WT-G2-2m


title: CD4-4073

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D24


title: CD4-4071

description: ftATAC-seq data of mouse thymoctyes


title: HipR-AD-G2-2m


title: zebrafish_123s_D23


title: HipR-AD-G1-13m


title: zebrafish_123s_D22


title: CD4-4070

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D21


title: CD4-4068

description: ftATAC-seq data of mouse thymoctyes


title: HipR-AD-G1-2m


title: CD4-4069

description: ftATAC-seq data of mouse thymoctyes


title: HipR-WT-G1-13m


title: CD4-4067

description: ftATAC-seq data of mouse thymoctyes


title: HipR-WT-G1-2m


title: CD4-4074

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4075

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4066

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D19


title: KO_RPF_2

city: Boston

first: Yang

last: Shi

state: Massachusetts

address: 320 LONGWOOD AVE

department: NEWBORN MEDICINE

country: USA

institute: BOSTON CHILDREN'S HOSPITAL

description:
RiboZero mRNA
KO_RPF_2

data_processing:
Library strategy: Ribo-Seq
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to mouse rRNA and tRNA sequence which were retrieved from Ensembl (Release 91) (https://useast.ensembl.org/Mus_musculus/Info/Index) and GtRNAdb databases (Chan and Lowe, 2016), respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the mouse canonical known gene models (UCSC, mm10) using Bowtie with a maximum one mismatch allowed (Langmead et al., 2009). The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx

molecule: polyA RNA

growth_protocol: Mouse melanoma B16 cells were grown in standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were treated by cyclohexamide to pause translation and lyzed in Mammalian Polysome Buffer. Input mRNAs and RPFs were isolated, ribosomal RNAs were depleted and cDNA libraries were prepared using NEBNext® Small RNA Library Prep Set for Illumina® as described before(Han,D et al, Nature 2019).
NEBNext® Small RNA Library Prep Set for Illumina®

treatment_protocol: Mettl5 knockout B16 cells were generated by CRISPR/Cas9-mediated gene editing

value: melanoma

tag: genotype

value: Mettl5 KO

tag: sample type

value: RPF


title: CD4-4072

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D2


title: zebrafish_123s_D18


title: zebrafish_123s_D17


title: CD4-4065

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4062

description: ftATAC-seq data of mouse thymoctyes


title: KO_RPF_1

description:
RiboZero mRNA
KO_RPF_1


title: CD4-4063

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D16


title: zebrafish_123s_D20


title: zebrafish_123s_D15


title: CD4-4061

description: ftATAC-seq data of mouse thymoctyes


title: KO_input_1

description:
RiboZero mRNA
KO_input_1

value: Input


title: WT_input_2

description:
RiboZero mRNA
WT_input_2

value: WT


title: KO_input_2

description:
RiboZero mRNA
KO_input_2


title: CD4-4060

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D13


title: zebrafish_123s_D14


title: zebrafish_123s_D12


title: WT_input_1

description:
RiboZero mRNA
WT_input_1


title: AD_M15_4.7m


title: CD4-4058

description: ftATAC-seq data of mouse thymoctyes


title: WT_RPF_1

description:
RiboZero mRNA
WT_RPF_1


title: RSC-ChIP-R1-H3K27me3

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

institute: Radboud University Nijmegen, RIMLS

data_processing:
Bowtie2 v2.0.2 (single end) --sensitive-local --end-to-end
Removal of duplicates and reads with MAPQ < 15
Peak calling with SICER v1.1 1 200 180 0.8 600(H3K27me3)/200(H3K4me3) 0.1
The data was mapped against the mm9 reference genome using bowtie v2.0.2. Duplicate and low confidence mapping reads (mapq<15) were removed. Peak calling was performed using SICER v1.1 with window size 200, gap size 200 (for H3K4me3) or 600 (for H3K27me3) at an E-value of 0.1. Bivalency was demarcated using bedtools v2.20.1 by intersection of H3K4me3 and H3K27me3 replicate consistent peak-calls. Bedtools was used to collect read counts within peaks. DESeq2 v1.16.1 was used for rlog transformation and normalization of the read counts. The data was clustered and visualized using R v3.1.1, ngsplot v2.61, bam2bw v1.21 and the UCSC genome browser.
Genome_build: mm9
BigWigs generated using bam2bw -c -e 180; Bed files contain peak location and quantification

source_name: Rosette stem cell

growth_protocol: R1 and CGR8 ESCs were cultured on gelatin and fetal calf serum-coated plates in N2B27 supplemented with LIF, 2 µM IWP2 and 1 µM PD325901 for 8 days.

extract_protocol:
Confluent cultures were fixed in PBS with 1% formaldehyde (Sigma) for 8 minutes and quenched using 100 mM fresh glycine for 15 minutes at room temperature. Fixed cell preparations were harvested by scraping, then washed and sonicated in 1% SDS, 30 mM Tris pH 8.0, 150 mM NaCl using a Diagenode Bioruptor UCD-300 to a size range with a median of 200 base pairs. 1 million cell equivalent chromatin was diluted 7x to 15 mM Tris pH 8.0, 1 mM EDTA, 150 mM NaCl, 1% Triton X-100 with fresh protease inhibitor cocktail (Roche) and 0.5 µg H3K27me3 or 1 µg H3K4me3 antibody (Diagenode) and incubated overnight at 4°C with rotation. Protein A/G magnetic beads were washed in the same dilution buffer with 0.15% SDS and 0.1% BSA, added to the chromatin/antibody mix and rotated for 60 min at 4°C. Beads were washed with 400 μl buffer for 5 min at 4°C using (i) first a 150 mM NaCl wash buffer; (ii) then twice a 500 mM NaCl buffer; and (iii) finally a 10 mM Tris buffer. DNA was eluted from the beads using 150 mM NaCl, 30 mM Tris, 1% SDS, 0.1 µg/µl Proteinase K buffer for 30 minutes at 55°C followed by 2 hours shaking at 65°C. The beads were removed after which the DNA was purified using QIAGEN Qiaquick MinElute PCR purification Kit according to manufacturer’s protocol and eluted in 20 μl EB.
Illumina library preparation was performed using the Kapa Hyper Prep Kit using 5 ng of ChIPped DNA: For end repair and A-tailing double stranded DNA was incubated with end repair and A-tailing buffer and enzyme and incubated first for 30 min at 20°C and then for 30 min at 65°C. Adapters were ligated by adding 30 μl ligation buffer, 10ul Kapa DNA ligase, 5 μl 600 nM adaptor in a total volume of 110 μl and incubated for 15 min at 15°C. Post-ligation cleanup was performed using Agencourt AMPure XP reagent and products were eluted in 20 μl elution buffer. Libraries were amplified by adding 25 μl 2x KAPA HiFi Hotstart ReadyMix and 5 μl 10x Library Amplification Primer Mix using 10 PCR cycles. Samples were purified using the QIAquick MinElute PCR purification kit. Libraries were size selected to ~300bp size using Agencourt Ampure XP beads. Correct size selection was confirmed by Agilent BioAnalyzer. Sequencing was performed using Illumina NextSeq500 with 42bp read lengths.

tag: antibody

value: Millipore 04-779 (H3K27me3)


title: zebrafish_123s_D10


title: CD4-4064

description: ftATAC-seq data of mouse thymoctyes


title: WT_RPF_2

description:
RiboZero mRNA
WT_RPF_2


title: CD4-4055

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_D1


title: RSC-ChIP-CGR8-H3K27me3


title: CD4-4057

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4054

description: ftATAC-seq data of mouse thymoctyes


title: RSC-ChIP-CGR8-H3K4me3


title: zebrafish_123s_C9


title: zebrafish_123s_C7


title: CD4-4059

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4052

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4053

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_C6


title: RSC-ChIP-R1-H3K4me3


title: zebrafish_123s_D11


title: CD4-4051

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4050

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_C5


title: CD4-4056

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_C4


title: zebrafish_123s_C3


title: zebrafish_123s_C8


title: CD4-4049

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4048

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4047

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4046

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_C24


title: zebrafish_123s_C23


title: CD4-4045

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_C22


title: zebrafish_123s_C21


title: CD4-4044

description: ftATAC-seq data of mouse thymoctyes


title: ECO-FCE Ileum 440

type: RNA

city: Dummerstorf

first: Henry

last: Reyer

address: Wilhelm-Stahl-Allee 2

institute: Leibniz Institute for Farm Animal Biology (FBN)

hyb_protocol: Labelled DNA was hybridized for 16 hr at 42°C on Snowball Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing:
Snowball arrays (Freeman et al. in BMC Biol 2012, 10:90), see the ArrayExpress database, accession no. A-AFFY-189
Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and R environment.

label: biotin

organism: Sus scrofa

source_name: Ileum

label_protocol: Each RNA sample was transcribed to DNA using the Ambion WT Expression Kit (Ambion, Austin, TX, USA). DNA preparations were fragmented and labelled with the WT Terminal Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Animals differing in feed efficiency traits

tag: feed efficiency

value: high

tag: gender

value: female

tag: sow

value: ileal mucosa


title: zebrafish_123s_C20

value: embryo trunk

value: 48 hpf


title: ECO-FCE Ileum 436


title: ECO-FCE Ileum 435

value: low


title: ECO-FCE Ileum 438

value: male


title: ECO-FCE Ileum 428


title: ECO-FCE Ileum 434


title: ECO-FCE Ileum 432


title: ECO-FCE Ileum 425


title: CD4-4043

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes

value: 6-8 weeks


title: CD4-4042

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_C2


title: zebrafish_123s_C19


title: CD4-4041

description: ftATAC-seq data of mouse thymoctyes


title: ECO-FCE Ileum 420


title: zebrafish_123s_C17


title: zebrafish_123s_C18


title: CD4-4039

description: ftATAC-seq data of mouse thymoctyes


title: G121_M10

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using Bowtie
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadhsee showing MACS2 output, including peaks discovered and statistics per peak

source_name: K27ac marks_male mouse liver 3 h TCPOBOP_liver1_G121_M10

extract_protocol:
ChIP was performed using antibodies against K4me1 (ab8895), K4me3 (ab8580), and K27ac (ab4729).
NEBNext Ultra DNA library prep kit for Illumina

treatment_protocol: Male and female CD1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA) at 7 weeks of age. Mice were injected with 3 mg/kg TCPOBOP or vehicle alone (1% DMSO in corn oil) between 8:00-8:45 AM on Day 1 and tissue was collected between 11:00-11:45 AM on Day 1 (3 h samples) or between 11:00-11:45 AM on Day 2 (27 h samples). For the 3 h samples, liver nuclei were isolated and then crosslinked for 9 minutes by incubation with 0.8% formaldehyde at 30°C (crosslinked nuclei).  For the 27 h samples, livers were flash frozen in liquid nitrogen. A portion was subsequently homogenized and then crosslinked by incubation with 1% formaldehyde for 10 minutes at 22°C (crosslinked frozen whole tissue). All samples were sonicated to yield genomic DNA fragments approximately 100-300 bp in length, and then used for ChIP.

value: CD-1 (Charles River)

value: 3 mg/kg TCPOBOP_ 3 h

value: liver

tag: Sex

value: 7 weeks

tag: crosslinking method

value: Crosslinked nuclei

tag: mouse id number


title: zebrafish_123s_C16

tag: tissue


title: CD4-4038

description: ftATAC-seq data of mouse thymoctyes


title: CD4-4040

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_C15

tag: starin


title: zebrafish_123s_C14

tag: age


title: ECO-FCE Ileum 417


title: CD4-4037

description: ftATAC-seq data of mouse thymoctyes

tag: strain


title: CD4-4036

description: ftATAC-seq data of mouse thymoctyes


title: ECO-FCE Ileum 412


title: zebrafish_123s_C13


title: ECO-FCE Ileum 415


title: CD4-4035

description: ftATAC-seq data of mouse thymoctyes


title: ECO-FCE Ileum 405


title: ECO-FCE Ileum 408


title: ECO-FCE Ileum 406


title: HCT116_CDK11_RNA_seq_CDK11_KD

city: Brno

first: Dalibor

last: Blazek

address: Studentska 1, Building A35

department: Molecular Medicine

country: Czech Republic

institute: Central European Institute of Technology (CEITEC), Masaryk University

description: synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).

data_processing:
iCLIP reads were analysed on iCount web server (http://icount.biolab.si), following the latest protein-RNA interaction developments (Chakrabarti et. al., 2018). Briefly, reads were align to human genome (ENSEMB v.59 GRCh37) using Bowtie 0.12.7 with parameters: ‘-v 2 -m 2 -a --best -strata’ (Langmead et al., 2009). Oligonucleotides used for reverse transcription include Unique Molecular Identifiers (UMIs) to distinguish and remove PCR duplicates (Huppertz et al., 2014). First nucleotide after the UMI was assigned as the cross link site defined by the truncated cDNA. Significant cross link sites were assessed based on false discovery rate (FDR) < 0.05 comparing specific sites with randomised data (100 permutations). Clusters of significant cross links were calculated with iCount function (https://github.com/tomazc/iCount): ‘-random_perm 100 -flank 15 -fdr_th 0.05’.
We aligned RNA-seq data against the human genome (ENSEMB v.59 GRCh37) with STAR aligner v.2.5.2a with parameters: ‘-winAnchorMultimapNmax 20 -outFilterMultimapNmax 20 -twopassMode Basic’ (Dobin et al. 2013). Aligned reads were quantified at gene level using HTseq with parameters: ‘-q --stranded=reverse -i gene_id’ (Anders et al. 2015). RNA-seq differential expressed genes (-1>log2FoldChange>1,  p.adj<0.05) were assess with DeSeq2, discarding genes with less than one read (Love et al. 2014).
ChIP-seq data were aligned to human (ENSEMB v.59 GRCh37) using STAR v.2.5.2a defaults parameters and ‘--alignIntronMax 1 --alignEndsType EndToEnd’ (Dobin et al. 2013). Pooled bam files, to create a single data set for each sample condition (Samtools v.0.1.19; Handsaker et al., 2009), summited to MACS2 significant peaks comparing no antibody input and corresponding samples: ‘callpeak -g hs -B -q 0.05 --fe-cutoff 1.5 --broad --keep-dup all’ (Zhang et al., 2008). Differential peak between the control and knock down mutant were called with MACS2 parameters: ‘bdgdiff --max-gap 100 --min-len 120’, normalising using sequencing deep of each library (Zhang et al., 2008). To plot Fig. 6H, we calculated the reads per million inside differential peaks with DiffBind v.2.8.0: ‘dba.count score=DBA_SCORE_RPKM’ (Stark et al, 2011).
Combined coverage tracks generated using deeptools (Ramírez, Fidel et al., 2014). They were normalised by sequencing deep and mappable genome size (reads per genomic content, RPGC) and binned per nucleotide to produce final bigwig coverage tracks.
Then we normalised RNAPII ChIP-seq RPGC siCDK11 log2 fold change after CDK11 depletion and P-Ser2/RNAPII normalised ChIP RPGC siCDK11 log2 fold change after CDK11 depletion and binned in 10 nucleotide to produce final bigwig coverage tracks (ChIP-seq_P-Ser2_RNAPII_RPGC_log2_FC_bin10.bigwig and ChIP-seq_RNAPII_RPGC_log2_FC_bin10.bigwig).
Genome_build: hg19 (ENSEMB v.59 GRCh37)

growth_protocol: Human colorectal HCT116 Flp-in cell line (gift from Dr. B. G. Wouters, Toronto, Canada, Rouschop et al., 2011), HEK293 Flp-in cell line (Thermo Fisher Scientific, R75007) and HCT116 cell line were all maintained in DMEM/high glucose media supplemented with L-glutamine, sodium pyruvate and 5% FBS at 37°C and 5% CO2. To prepare cell lines stably expressing CDK11 proteins corresponding CDK11 plasmids were transfected into the HEK293 Flp-in or HCT116 Flp-in cells.

extract_protocol: siRNA mediated-CDK11 knockdown (Sigma, SASI_WI_00000026) was performed in HCT116 cells growing in 6-well plate using Lipofectamine RNAiMax (Thermo Fisher Scientific, 13778-150). The cells from one well were washed twice with ice-cold PBS 36h post-transfection, scraped, pelleted at 500g for 3min and treated for 5 min with 150 µl of cytoplasmic lysis buffer (10 mM Tris-Cl, pH 8, 0.32 M Sucrose, 3 mM CaCl2, 2 mM MgCl2, 0.1 mM EDTA, 0.5% TritonX-100, supplemented with 40 U/ml RNase inhibitor, Roche, 3335402001). Cytoplasmic RNAs in the supernatant were removed by centrifugation (500g for 3 min). Nuclear pellet was treated again with 90 µl of cytoplasmic lysis buffer and supernatant was completely removed after centrifugation (500g for 3 min). Nuclear RNAs were isolated from the remaining nuclear pellet using Tri-Reagent (MRC, #TR118). 500 ng of RNA were treated with 1ul of DNase (Sigma, AMPD1). Ribosomal RNA was depleted using NEBNext rRNA Depletion Kit (E6310S). Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760) and sequenced on Illumina HiSeq 2500 (50bp single-end).

treatment_protocol: Cells were usually plated at 30% confluency 6-10 h before transfection. siRNA was transfected at a final concentration of 10 nM using Lipofectamine RNAiMax (Thermo Fisher Scientific, 13778-150) according to the manufacturer´s instruction. Control samples were transfected with non-targeting control siRNA-A (Santa Cruz, sc-37007). CDK11 knock-down was performed with siRNAs (Sigma, SASI_WI_00000026, SASI_WI_00000027).

value: HCT116 cells

tag: method

value: RNA-seq

tag: condition

value: HCT116 Flp-in


title: HCT116_CDK11_RNA_seq_CDK11_KD_1


title: zebrafish_123s_C12


title: zebrafish_123s_C11


title: zebrafish_123s_C1


title: HCT116_CDK11_RNA_seq_2


title: ECO-FCE Ileum 413

tag: cell type


title: CD4-4033

description: ftATAC-seq data of mouse thymoctyes


title: HCT116_CDK11_RNA_seq_1


title: HCT116_CDK11_RNA_seq


title: HCT116_CDK11_RNA_seq_CDK11_KD_2


title: CD4-4034

description: ftATAC-seq data of mouse thymoctyes


title: ECO-FCE Ileum 402

value: high


title: CD45+ mononuclear cells, 18w (10x scRNA)

first: Xiaolei

last: Hao

state: Anhui

address: huangshan Road 443

institute: Institute of Immunology, USTC

description: 10x scRNA

data_processing:
*R1_001.fastq.gz: contains the cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 150  nt RNA sequence.
*I1_001.fastq.gz: contains the 8 nt sample index.
Sequenced reads were mapped to mm10 using Cellranger (v2.1.1) with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: filtered feature bc matrix

source_name: CD45+ mononuclear cells

extract_protocol:
Single-cell barcoded scRNA-seq libraries using Chromium Single Cell 3′ Library V2 (10x Genomics) and sc-RNA-libraries were sequenced on HiSeq X Ten (Illumina).
scRNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: CD45+ mononuclear cells

tag: time

tag: treatment

value: HBs-HepR mice adoptively transferred with HBsAg+ hepatocytes from HBs-Tg mice


title: ECO-FCE Ileum 403

value: ileal mucosa


title: ECO-FCE Ileum 401

value: female


title: HCT116_RNAPol2_ChIP_60h_CDK11_KD

extract_protocol: ChIP was performed with Santa Cruz RNAPII antibody (sc-899). Protein G Dynabeads (Thermo Fisher Scientific, 10009D) were pre-blocked with BSA for 4 h, washed 3 times with RIPA buffer (50 mM Tris-Cl, pH 8, 150 mM NaCl, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, supplemented with protease inhibitors, Sigma, P8340), followed by the incubation with specific antibody for at least 4 h at 4°C. Cells were crosslinked with 1% formaldehyde for 10 min, reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed twice with ice-cold PBS, scraped, and pelleted. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20 x 7s (amp 0.85) using 5/64 probe (QSonica Q55A). Clarified extracts (13,000g for 10 min) were precleared with protein G Dynabeads rotating for 2-4 h at 4°C and then incubated overnight with antibody pre-bound to protein G Dynabeads. For each ChIP-seq experiment we performed 3 technical replicates, dissolved each replicate in 17 µl of water and pooled them together to get at least 2.5 ng of immunoprecipitated DNA before library preparation (measured by Qubit). ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2 (NEB E7335S, E7500S). Libraries were sequenced (50-bp single-end reads) using an Illumina HiSeq 2500 (VBCF Vienna).

value: ChIP-seq RNAPolII

value: Santa Cruz RNAPII (sc-899)


title: ECO-FCE Caecum 438

source_name: Caecum

value: male

value: caecal mucosa


title: zebrafish_123s_B9

value: embryo trunk

value: 48 hpf


title: zebrafish_123s_B7


title: ECO-FCE Ileum 419

value: low


title: CD45+ mononuclear cells, 12w (10x scRNA)

description: 10x scRNA


title: ECO-FCE Caecum 436


title: zebrafish_123s_B6


title: CD45+ mononuclear cells, 0w (10x scRNA)

description: 10x scRNA


title: zebrafish_123s_B5


title: HCT116_RNAPol2_ChIP_CDK11_KD_1


title: Paeruginosa_PAO1_PA08051_4

city: Vancouver

first: Shannon

last: Coleman

state: BC

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

description: Bacteria were grown on swarm plates, and the swarm fronts were harvested and suspended in RNA-Protect Bacteria Reagent

data_processing:
Illumina software used for basecalling.
Sequence reads were mapped to the pseudomonas aeruginosa genome using STAR v2.6.
Count data was generated from STAR produced BAM files using HTSeq v0.61p1.

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial culture

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

tag: genotype/variation

value: PA0805.1 over-expression

value: bacterial culture


title: HCT116_RNAPol2_ChIP_CDK11_KD_2

value: HCT116 cells

tag: antibody


title: HCT116_RNAPol2_ChIP_CDK11_KD

value: HCT116 Flp-in


title: Paeruginosa_PAO1_PA08051_5


title: HCT116_RNAPol2_ChIP_60h


title: zebrafish_123s_B3


title: Paeruginosa_PAO1_PA08051_3


title: HCT116_RNAPol2_ChIP_2


title: zebrafish_123s_B4


title: ECO-FCE Caecum 435

tag: feed efficiency


title: ECO-FCE Caecum 434

tag: gender


title: ECO-FCE Caecum 428

tag: sow


title: HCT116_RNAPol2_ChIP_1


title: zebrafish_123s_B24


title: Paeruginosa_PAO1_PA08051_1


title: HCT116_RNAPol2_ChIP


title: Paeruginosa_PAO1_EmptyVector_5

value: Empty vector


title: zebrafish_123s_B22


title: HCT116_P_Ser2_ChIP_60h_CDK11_KD

extract_protocol: ChIP was performed with Active Motif Phospho-Ser2 antibody (61083). Protein G Dynabeads (Thermo Fisher Scientific, 10009D) were pre-blocked with BSA for 4 h, washed 3 times with RIPA buffer (50 mM Tris-Cl, pH 8, 150 mM NaCl, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, supplemented with protease inhibitors, Sigma, P8340), followed by the incubation with specific antibody for at least 4 h at 4°C. Cells were crosslinked with 1% formaldehyde for 10 min, reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed twice with ice-cold PBS, scraped, and pelleted. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20 x 7s (amp 0.85) using 5/64 probe (QSonica Q55A). Clarified extracts (13,000g for 10 min) were precleared with protein G Dynabeads rotating for 2-4 h at 4°C and then incubated overnight with antibody pre-bound to protein G Dynabeads. For each ChIP-seq experiment we performed 3 technical replicates, dissolved each replicate in 17 µl of water and pooled them together to get at least 2.5 ng of immunoprecipitated DNA before library preparation (measured by Qubit). ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2 (NEB E7335S, E7500S). Libraries were sequenced (50-bp single-end reads) using an Illumina HiSeq 2500 (VBCF Vienna).

value: ChIP-seq P-Ser2

value: Active Motif Phospho-Ser2 (61083)


title: Paeruginosa_PAO1_EmptyVector_4


title: zebrafish_123s_B21


title: HCT116_P_Ser2_ChIP_CDK11_KD_2


title: Paeruginosa_PAO1_EmptyVector_3


title: Paeruginosa_PAO1_PA08051_2


title: Paeruginosa_PAO1_EmptyVector_2


title: ECO-FCE Caecum 432


title: ECO-FCE Caecum 420

value: high


title: HCT116_P_Ser2_ChIP_CDK11_KD_1

data_processing:
iCLIP reads were analysed on iCount web server (http://icount.biolab.si), following the latest protein-RNA interaction developments (Chakrabarti et. al., 2018). Briefly, reads were align to human genome (ENSEMB v.59 GRCh37) using Bowtie 0.12.7 with parameters: ‘-v 2 -m 2 -a --best -strata’ (Langmead et al., 2009). Oligonucleotides used for reverse transcription include Unique Molecular Identifiers (UMIs) to distinguish and remove PCR duplicates (Huppertz et al., 2014). First nucleotide after the UMI was assigned as the cross link site defined by the truncated cDNA. Significant cross link sites were assessed based on false discovery rate (FDR) < 0.05 comparing specific sites with randomised data (100 permutations). Clusters of significant cross links were calculated with iCount function (https://github.com/tomazc/iCount): ‘-random_perm 100 -flank 15 -fdr_th 0.05’.
We aligned RNA-seq data against the human genome (ENSEMB v.59 GRCh37) with STAR aligner v.2.5.2a with parameters: ‘-winAnchorMultimapNmax 20 -outFilterMultimapNmax 20 -twopassMode Basic’ (Dobin et al. 2013). Aligned reads were quantified at gene level using HTseq with parameters: ‘-q --stranded=reverse -i gene_id’ (Anders et al. 2015). RNA-seq differential expressed genes (-1>log2FoldChange>1,  p.adj<0.05) were assess with DeSeq2, discarding genes with less than one read (Love et al. 2014).
ChIP-seq data were aligned to human (ENSEMB v.59 GRCh37) using STAR v.2.5.2a defaults parameters and ‘--alignIntronMax 1 --alignEndsType EndToEnd’ (Dobin et al. 2013). Pooled bam files, to create a single data set for each sample condition (Samtools v.0.1.19; Handsaker et al., 2009), summited to MACS2 significant peaks comparing no antibody input and corresponding samples: ‘callpeak -g hs -B -q 0.05 --fe-cutoff 1.5 --broad --keep-dup all’ (Zhang et al., 2008). Differential peak between the control and knock down mutant were called with MACS2 parameters: ‘bdgdiff --max-gap 100 --min-len 120’, normalising using sequencing deep of each library (Zhang et al., 2008). To plot Fig. 6H, we calculated the reads per million inside differential peaks with DiffBind v.2.8.0: ‘dba.count score=DBA_SCORE_RPKM’ (Stark et al, 2011).
Combined coverage tracks generated using deeptools (Ramírez, Fidel et al., 2014). They were normalised by sequencing deep and mappable genome size (reads per genomic content, RPGC) and binned per nucleotide to produce final bigwig coverage tracks.
Genome_build: hg19 (ENSEMB v.59 GRCh37)


title: zebrafish_123s_B20


title: zebrafish_123s_B2


title: HCT116_P_Ser2_ChIP_CDK11_KD


title: Paeruginosa_PAO1_EmptyVector_1


title: zebrafish_123s_B19


title: ECO-FCE Caecum 425


title: ECO-FCE Caecum 419


title: Chicken_heart_spatial_RNAseq_D14

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

description:
chicken_heart_spatial_RNAseq_D14
Spatial RNA sequencing of 10um thick tissue sections from fetal chicken hearts at day 14

data_processing:
Sequencing data was aligned to chicken reference genome (assembly: GRCg6a) using the 10X Genomics Space Ranger 1.0.0 pipeline.
Genome_build: GRCg6a
Supplementary_files_format_and_content: HDF5 file containing filtered feature barcode expression matrix (UMI counts)

organism: Gallus gallus

source_name: Fetal chicken hearts

growth_protocol: Fertilized wildtype chicken eggs were purchased from a local farm and incubated in a standard humidity and temperature regulating egg incubator until day of interest.

extract_protocol:
Whole hearts were isolated using aseptic technique and placed in ice cold sterile Hank’s Balanced Salt Solution and then blood was carefully removed by perfusing the hearts through the apex. Fresh tissues were immediately embedded in Optimal Cutting Compound (OCT) media and frozen in liquid-nitrogen-cooled isopentane bath, cut into 10µm sections using Thermo Scientific™ CryoStar NX50 cryostat, mounted on 10x Visium slides (pre-cooled to -20°C), and used for library construction.
10x Genomics Visium Spatial Gene Expression 3’ Library Construction V1 Kit

value: Whole hearts

tag: developmental stage

tag: sample pooling size

value: One heart


title: HCT116_P_Ser2_ChIP_2


title: zebrafish_123s_B18


title: Chicken_heart_spatial_RNAseq_D10

description:
chicken_heart_spatial_RNAseq_D10
Spatial RNA sequencing of 10um thick tissue sections from fetal chicken hearts at day 10

value: Two hearts


title: ECO-FCE Caecum 417

value: female


title: HCT116_P_Ser2_ChIP_1


title: zebrafish_123s_B17


title: HCT116_P_Ser2_ChIP


title: zebrafish_123s_B15


title: Chicken_heart_spatial_RNAseq_D7

description:
chicken_heart_spatial_RNAseq_D7
Spatial RNA sequencing of 10um thick tissue sections from fetal chicken hearts at day 7

value: Four hearts


title: Chicken_heart_spatial_RNAseq_D4

description:
chicken_heart_spatial_RNAseq_D4
Spatial RNA sequencing of 10um thick tissue sections from fetal chicken hearts at day 4

value: Three hearts


title: zebrafish_123s_B16

value: embryo trunk


title: HCT116_ChIP_noAb_2

extract_protocol: ChIP was performed with Abcam CDK11 antibody (ab19393). Protein G Dynabeads (Thermo Fisher Scientific, 10009D) were pre-blocked with BSA for 4 h, washed 3 times with RIPA buffer (50 mM Tris-Cl, pH 8, 150 mM NaCl, 5 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, supplemented with protease inhibitors, Sigma, P8340), followed by the incubation with specific antibody for at least 4 h at 4°C. Cells were crosslinked with 1% formaldehyde for 10 min, reaction was quenched with glycine (final concentration 125 mM) for 5 min. Cells were washed twice with ice-cold PBS, scraped, and pelleted. Each 20 µl packed cell pellet was lysed in 650 µl of RIPA buffer and sonicated 20 x 7s (amp 0.85) using 5/64 probe (QSonica Q55A). Clarified extracts (13,000g for 10 min) were precleared with protein G Dynabeads rotating for 2-4 h at 4°C and then incubated overnight with antibody pre-bound to protein G Dynabeads. For each ChIP-seq experiment (CDK11) we performed 3 technical replicates, dissolved each replicate in 17 µl of water and pooled them together to get at least 2.5 ng of immunoprecipitated DNA before library preparation (measured by Qubit). ChIP-seq libraries were generated using the KAPA Biosystems Hyper Prep Kit (KK8502) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and Set 2 (NEB E7335S, E7500S). Libraries were sequenced (50-bp single-end reads) using an Illumina HiSeq 2500 (VBCF Vienna).

value: ChIP-seq noAb

value: noAb


title: ECO-FCE Caecum 415

value: low

value: caecal mucosa


title: ECO-FCE Caecum 412

value: male


title: ECO-FCE Caecum 406


title: ECO-FCE Caecum 408


title: HCT116_P_Ser2_ChIP_60h

value: HCT116 cells

value: HCT116 Flp-in


title: HCT116_ChIP_noAb_1


title: Chicken_heart_scRNAseq_D14_LV

description:
chicken_heart_scRNAseq_D14_LV
Single cell RNA sequecning of left ventricles from fetal chicken heart at day 14

data_processing:
Sequencing data was aligned to chicken reference genome (assembly: GRCg6a) using the 10X Genomics Cell Ranger 3.0.2 pipeline.
Genome_build: GRCg6a
Supplementary_files_format_and_content: HDF5 file containing filtered feature barcode expression matrix (UMI counts)

extract_protocol:
Embryos and hearts were isolated aseptically and placed in ice cold Hank's Balanced Salt Solution. To extract ventricular chicken cells, day 10 and day 14 stage samples were digested for four cycles of 10 minutes in 300U/mL collagenase type II at 37 degrees Celsius while Day 4 and day 7 stage samples were digested for one cycle of 20 minutes and once cycle of 10 minutes in 1.5mg/mL collagenase type II/dispase at 37 degrees Celsius. Samples were then passed through a 40 um cell filter, centrifuged, resuspended in ammonium chloride potassium red blood cell lysis buffer, centrifuged again, resuspended in phosphate buffered saline with 0.04% bovine serum albumin at 1 x10^6 cells/mL, and used for library constrction.
10x Genomics Chromium Next GEM Single Cell 3’ RNA-seq Library Construction V2 Kit

value: Heart left ventricles

value: One dozen


title: Expt_B: prmt5 mutant control rep 3-1

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

data_processing:
Basecalling done with Bustard Illumina Pipelline
Sequence reads were mapped to Arabidopsis thaliana TAIR10 genome using STAR  with default parameters, except of maximum intron length set in 5000
Count tables for different feature levels were obtained from bam files using Aspli v 1.13

organism: Arabidopsis thaliana

source_name: pool of tissues

growth_protocol: WT (Col) and prmt5 mutants seeds were grown on Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4 °C, and then grown for nine days under continuous white light at 22ºC.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate the concentration and quality of samples, NanoDrop 2000c (Thermo Scientific) and gel electrophoresis were used, respectively.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, and first-strand cDNA synthesized by reverse transcriptase (SuperScript II; Invitrogen) and random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies)

treatment_protocol: Whole plants were harvested after 9 d.

tag: ecotype

tag: genotype

value: prmt5 mutant


title: zebrafish_123s_B13

extract_protocol:
FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin-EDTA and 10U Dnase I for 30min at 30°C
RNA libraries were prepared using standard SmartSeq2 protocol

tag: tissue

tag: starin

value: 48 hpf


title: HCT116_ChIP_noAb

tag: strain


title: ECO-FCE Caecum 403


title: Chicken_heart_scRNAseq_D10_RV

description:
chicken_heart_scRNAseq_D10_RV
Single cell RNA sequecning of right ventricles from fetal chicken heart at day 10

value: Heart right ventricles

value: Three dozen


title: zebrafish_123s_B14

tag: age


title: ECO-FCE Caecum 402

value: high


title: ECO-FCE Caecum 413


title: ECO-FCE Caecum 405

value: female


title: HCT116_CDK11_ChIP_S_phase_1

tag: method

value: ChIP-seq CDK11

tag: condition

value: Abcam CDK11 (ab19393)


title: ECO-FCE Caecum 401

tag: cell type


title: Expt_B: prmt5 mutant control rep 1-1


title: Chicken_heart_scRNAseq_D10_LV

description:
chicken_heart_scRNAseq_D10_LV
Single cell RNA sequecning of left ventricles from fetal chicken heart at day 10


title: zebrafish_123s_B11

value: embryo trunk


title: Chicken_heart_scRNAseq_D14_RV

description:
chicken_heart_scRNAseq_D14_RV
Single cell RNA sequecning of right ventricles from fetal chicken heart at day 14


title: Chicken_heart_scRNAseq_D7_RV

description:
chicken_heart_scRNAseq_D7_RV
Single cell RNA sequecning of right ventricles from fetal chicken heart at day 7

extract_protocol:
Embryos and hearts were isolated aseptically and placed in ice cold Hank's Balanced Salt Solution. To extract ventricular chicken cells, day 10 and day 14 stage samples were digested for four cycles of 10 minutes in 300U/mL collagenase type II at 37 degrees Celsius while Day 4 and day 7 stage samples were digested for one cycle of 20 minutes and once cycle of 10 minutes in 1.5mg/mL collagenase type II/dispase at 37 degrees Celsius. Samples were then passed through a 40 um cell filter, centrifuged, resuspended in ammonium chloride potassium red blood cell lysis buffer, centrifuged again, resuspended in phosphate buffered saline with 0.04% bovine serum albumin at 1 x10^6 cells/mL, and used for library constrction.
10x Genomics Chromium Next GEM Single Cell 3’ RNA-seq Library Construction V3 Kit

value: Four dozen


title: zebrafish_123s_B10


title: HCT116_CDK11_ChIP_G2_M_phase_1


title: Expt_B: WT Col control rep 3-1

value: Wild type


title: Chicken_heart_scRNAseq_D7_LV

description:
chicken_heart_scRNAseq_D7_LV
Single cell RNA sequecning of left ventricles from fetal chicken heart at day 7


title: zebrafish_123s_B1


title: Expt_B: WT Col control rep 1-1


title: zebrafish_123s_A9


title: zebrafish_123s_B12


title: HCT116_CDK11_ChIP_G2_M_phase


title: HCT116_CDK11_ChIP_3


title: HCT116_CDK11_ChIP_2


title: Differentiated NHU cells (Y1108)

city: York

first: Simon

middle: Charles

last: Baker

address: Wentworth Way, Heslington

department: Biology Department

country: United Kingdom

institute: University of York

data_processing:
Reads quality was checked using FastQC
Retained adapter sequences were removed and reads were trimmed using trimmomatic v0.36 when the 4bp-sliding-window average base quality dropped below 20, and reads dropped if over half the original read was trimmed
Remaining reads were ‘pseudoaligned’ to the Ensembl GRCh38.p10 reference transcriptome using kallisto v0.46.0, and expression expressed at gene level using tximport v1.14.0 in R v3.6.0
Data was expressed as transcripts per million (TPM)
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: text (Tab-delimited) file with TPMs for each of the three cell cultures.

source_name: Normal human urothelial (NHU) cells

growth_protocol: Cells were expanded to confluence in KSFMc, pre-treated in KSFMc + 5% (v/v) adult bovine serum for 3-5 days before passage onto permeable PET membranes (Corning Snapwell). 24h after seeding onto membranes, the calcium in the medium was raised to near physiological (2mM). Cells were cultured for a further 7 days and trans-epithelial electrical resistances were recorded immediately before RNA harvest.

extract_protocol:
Total RNA was extracted in Trizol reagent according to manufacturer's instructions
cDNA libraries were prepared for sequencing using standard Illumina TruSeq protocols that prime polyadenylated mRNA

treatment_protocol: No treatments were applied

value: M

tag: trans-epithelial electrical resistance (ω.cm²)

tag: rin


title: zebrafish_123s_A8


title: Differentiated NHU cells (Y1077)


title: HCT116_CDK11_ChIP_S_phase

tag: antibody


title: zebrafish_123s_A7


title: HCT116_CDK11_ChIP_1


title: Differentiated NHU cells (Y1026)


title: HCT116_CDK11_ChIP


title: Expt_A: prmt5 mutant control rep 3-1

growth_protocol: WT (Col) and prmt5 mutants seeds were grown on Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4 °C, and then grown for fifteen days under continuous white light at 22ºC

treatment_protocol: Whole plants were harvested after 15 d.


title: Expt_B: WT Col control rep 2-1


title: Expt_B: prmt5 mutant control rep 2-1


title: zebrafish_123s_A6


title: Chicken_heart_scRNAseq_D4

description:
chicken_heart_scRNAseq_D4
Single cell RNA sequecning of whole ventricles from fetal chicken heart at day 4

value: Heart whole ventricles

value: Six dozen


title: zebrafish_123s_A4


title: Expt_A: prmt5 mutant control rep 1-1


title: zebrafish_123s_A3


title: K562_shRPS14 641 Translatome biological rep2

city: Paris

first: Ismael

last: Boussaid

address: 22 Rue Mechain

country: France

institute: Inserm

hyb_protocol: cDNA was hybridized to HTA2.0 affymetrix microarrays following standard

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA) and custom brainarray CDFv20   ID= EntrezGene

source_name: shRPS14 641 Translatome

label_protocol: Briefly, linear amplification of 20 ng of total RNA was performed using the Ovation Biotin RNA Amplification and Labelling System (NuGEN, San Carlos, CA).

growth_protocol: The K562 cell line was cultured in αMinimum Essential Medium (αMEM) containing 10% fetal calf serum (FCS), 1mM glutamine, 100UI/mL penicillin-streptomycin

extract_protocol: RNA was extracted using the Kit QIAamp® RNA Blood MiniKit. RNA from ribosomal fractions was purified using Trizol (Invitrogen).

treatment_protocol: A scramble (SCR) control shRNA and RPS14 shRNA (640 and 641) were cloned in pLKO.1 Tet-On vector. Cells were selected with puromycine (1 mg/mL). shRNA expression was induced by doxycycline (0.2 μg/mL) for 3 days

tag: cell line

tag: genotype/variation

value: lentivirus expressing RPS14 shRNA

tag: time post induction

value: 5 days after induction

tag: molecule subtype

value: RNA extracted from heavy polysomes


title: HEK293_CDK11_nFLAG_iCLIP_4SU_365_noAb

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNTTGTNN
3' adapter: AGATCGGAAGAGCGGTTCAG

data_processing:
Library strategy: iCLIP
iCLIP reads were analysed on iCount web server (http://icount.biolab.si), following the latest protein-RNA interaction developments (Chakrabarti et. al., 2018). Briefly, reads were align to human genome (ENSEMB v.59 GRCh37) using Bowtie 0.12.7 with parameters: ‘-v 2 -m 2 -a --best -strata’ (Langmead et al., 2009). Oligonucleotides used for reverse transcription include Unique Molecular Identifiers (UMIs) to distinguish and remove PCR duplicates (Huppertz et al., 2014). First nucleotide after the UMI was assigned as the cross link site defined by the truncated cDNA. Significant cross link sites were assessed based on false discovery rate (FDR) < 0.05 comparing specific sites with randomised data (100 permutations). Clusters of significant cross links were calculated with iCount function (https://github.com/tomazc/iCount): ‘-random_perm 100 -flank 15 -fdr_th 0.05’.
We aligned RNA-seq data against the human genome (ENSEMB v.59 GRCh37) with STAR aligner v.2.5.2a with parameters: ‘-winAnchorMultimapNmax 20 -outFilterMultimapNmax 20 -twopassMode Basic’ (Dobin et al. 2013). Aligned reads were quantified at gene level using HTseq with parameters: ‘-q --stranded=reverse -i gene_id’ (Anders et al. 2015). RNA-seq differential expressed genes (-1>log2FoldChange>1,  p.adj<0.05) were assess with DeSeq2, discarding genes with less than one read (Love et al. 2014).
ChIP-seq data were aligned to human (ENSEMB v.59 GRCh37) using STAR v.2.5.2a defaults parameters and ‘--alignIntronMax 1 --alignEndsType EndToEnd’ (Dobin et al. 2013). Pooled bam files, to create a single data set for each sample condition (Samtools v.0.1.19; Handsaker et al., 2009), summited to MACS2 significant peaks comparing no antibody input and corresponding samples: ‘callpeak -g hs -B -q 0.05 --fe-cutoff 1.5 --broad --keep-dup all’ (Zhang et al., 2008). Differential peak between the control and knock down mutant were called with MACS2 parameters: ‘bdgdiff --max-gap 100 --min-len 120’, normalising using sequencing deep of each library (Zhang et al., 2008). To plot Fig. 6H, we calculated the reads per million inside differential peaks with DiffBind v.2.8.0: ‘dba.count score=DBA_SCORE_RPKM’ (Stark et al, 2011).
Combined coverage tracks generated using deeptools (Ramírez, Fidel et al., 2014). They were normalised by sequencing deep and mappable genome size (reads per genomic content, RPGC) and binned per nucleotide to produce final bigwig coverage tracks.
Then we normalised RNAPII ChIP-seq RPGC siCDK11 log2 fold change after CDK11 depletion and P-Ser2/RNAPII normalised ChIP RPGC siCDK11 log2 fold change after CDK11 depletion and binned in 10 nucleotide to produce final bigwig coverage tracks (ChIP-seq_P-Ser2_RNAPII_RPGC_log2_FC_bin10.bigwig and ChIP-seq_RNAPII_RPGC_log2_FC_bin10.bigwig).
Genome_build: hg19 (ENSEMB v.59 GRCh37)

extract_protocol: iCLIP was performed as previously described (Huppertz et al., 2014) with only minor modifications described below. Briefly, F-CDK11 HEK293 Flp-in cells as well as F-CDK11 (226-783) HEK293 Flp-in cells were plated onto 150 cm2 plates to reach 75% confluency at the day of crosslinking. CDK11 was induced with 1 µg/ml of doxycycline 24 h before crosslinking. We used two methods to crosslink RNA and proteins: either by UV-C (254 nm, 200 mJ/cm2) or by UV-A (365 nm, 200 mJ/cm2) after 100 µM final concentration of 4-thiouridine (Sigma, T4509) was added to the cells 6-8 h prior to the crosslinking. Cells from one 150 cm2 plate were used per one immunoprecipitation and two technical replicates were performed for each condition, both of them were mixed together after reverse transcription step. Composition of all buffers was the same as described in Huppertz et. al., 2014. Each cell pellet (originally from one 150 cm2 plate) was lysed in 1 ml of lysis buffer and the lysate was homogenized by passing three-times through an insulin syringe. Lysate was treated with 4 U/ml Turbo DNase (Thermo Fisher Scientific, AM2238), 12 U/ml RNase I (Thermo Fisher Scientific, AM2295) shaking at 1100 rpm and 37°C for 3 min. Clarified extracts (21000g for 30 min) were incubated for 2 h with 2 µg of flag antibody (Sigma, F1804) pre-bound to 50 µl of protein G Dynabeads. After series of stringent washes, adenylated L3 RNA adapter was ligated to the 3’end of crosslinked RNAs. Proteins and crosslinked RNAs were resolved by SDS-PAGE (NuPAGE 4-12% Bis-Tris Protein Gel, Thermo Fisher Scientific, NP0322) and transferred to nitrocellulose membrane. The region of the membrane containing the radioactively labeled crosslinked protein–RNA complexes was excised, RNA was isolated and reverse transcribed to cDNA (technical replicates were mixed together after this step). cDNA was fractionated using urea denaturing gel electrophoresis and three fractions running between 70-85 nt (L-low), 85-120 nt (M-medium) and 120-200 nt (H-high) were isolated. Each fraction was independently circularized by single-stranded DNA ligase, annealed to an oligonucleotide complementary to the restriction site and cut between the two adapter regions by BamHI. After final PCR amplification using P3 and P5 Solexa primers all three fractions were pooled together in ratio 1:5:5 (L:M:H). Multiplexed libraries were sequenced as 50bp single-end reads on Illumina sequencer (EMBL, Heidelberg).

value: HEK293 cells

value: iCLIP

value: F-CDK11-nFLAG 4SU_365

value: HEK293 Flp-in

value: Sigma FLAG M2 (F1804)


title: Expt_A: WT Col control rep 3-1


title: HEK293_CDK11_226del783FLAG_iCLIP_4SU_365_1

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNCTTGNN
3' adapter: AGATCGGAAGAGCGGTTCAG


title: Expt_A: WT Col control rep 2-1


title: zebrafish_123s_A24

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the zebrafish reference genome (danRer11) using TapHat2, Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the three sample-plates (plate_123, plate_989, plate_990) were combined into one expression matrix file
counts data was processed and analyzed using velocyto, SingleCellExperiment and pagoda2 packages in R-software
Genome_build: GRCz11 (danRer11)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

value: 48 hpf


title: HEK293_CDK11_nFLAG_iCLIP_4SU_365_noAb_1


title: zebrafish_123s_A5


title: zebrafish_123s_A23


title: Expt_A: WT Col control rep 1-1


title: Expt_A: prmt5 mutant control rep 2-1

value: prmt5 mutant


title: HEK293_CDK11_nFLAG_iCLIP_noUV

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNGGTTNN
3' adapter: AGATCGGAAGAGCGGTTCAG

value: F-CDK11-nFLAG noUV


title: HEK293_CDK11_nFLAG_iCLIP_noUV_1


title: zebrafish_123s_A21

value: embryo trunk


title: HEK293_CDK11_226del783FLAG_iCLIP_4SU_365

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNGCGTNN
3' adapter: AGATCGGAAGAGCGGTTCAG


title: zebrafish_123s_A20


title: K562_shRPS14 640 Translatome biological rep1

scan_protocol: affymetrix microarrays following standard

source_name: shRPS14 640 Translatome


title: HEK293_CDK11_1del226_nFLAG_iCLIP_4SU_365

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNGGCGNN
3' adapter: AGATCGGAAGAGCGGTTCAG

value: F-CDK11_1del226-nFLAG 4SU_365


title: K562_shRPS14 641 Translatome biological rep1


title: lasR_coculture_WT_rep3

city: Farmington

first: Mark

last: Adams

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Basecalls - Illumina native app
Trimming - Illumina native app to trim adapter sequences
Quality Control CLC Genomics Workbench: quality score = 0.05, ambiguous bases = 2, auto adapter trim = NO, trim bases 5' and 3', filter length above =  NO,  filter length below = NO
Alingment to Pseudomonas aeruginosa strain PA14  genome - CLC Workbench: mismatched cost = 2, insertion cost = 2, deletion cost = 3, length fraction = 0.8, similarity fraction = 0.8, strands = both, max # hits per read = 10, global allignment = NO
Reporting - CLC Workbench export raw counts, TPM, CPM and RPKM
Genome_build: UCBPP-PA14
Supplementary_files_format_and_content: csv including TPM

organism: Pseudomonas aeruginosa

source_name: colony biofilm

growth_protocol: P. aeruginosa strains used for initial inoculum were grown for 16 h overnight in 5 mL LB on roller drum at 37 ℃.  A 200 µL aliquot of optical density normalized (OD 600 = 1) cultures of PA14 or PA14 ∆lasR were evenly spread on an LB plate with sterile glass beads and briefly allowed to dry. Two isopore 0.2 µm PC membrane filters were stacked on the lawn  (37 mm diameter filter directly on lawn then 25 mm diameter filter on top), and 15 µL of normalized (OD 600 = 1) ∆lasR cultures were spotted on the top-most filter. After 16 h incubation at 37 ℃, the top filter was collected and ∆lasR cells were resuspended in 1 mL LB by 5 min of vigorous shaking using a Genie Disruptor (Zymo) for collection of cells.

extract_protocol:
RNA was extracted according to manufacturer’s protocol with the QIAGEN RNeasy Mini kit
RNA was treated with Invitrogen Turbo DNA-Free kit and ribo-depletion performed using RiboZero (bacteria). Library prep was done as the Illumina TrueSeq Stranded RNAseq.

treatment_protocol: P. aerguinosa PA14 ∆lasR was grown above either ∆lasR or WT.

tag: taxonomy id


title: HEK293_CDK11_1del226_nFLAG_iCLIP_4SU_365_1


title: K562_shSCR Translatome biological rep2

source_name: shSCR Translatome

value: lentivirus expressing scramble (SCR) control shRNA


title: K562_shRPS14 640 Translatome biological rep2


title: zebrafish_123s_A22

first: Lars

last: Muhl

address: Blickagången 6

institute: Karolinska Institutet

source_name: zebrafish


title: lasR_coculture_WT_rep1


title: shRPS14 641 Translatome biological rep2

description:
UT7/EPO cells infected with lentivirus expressing RPS14 641 shRNA, harvested 72 hours after induction
RNA extracted from heavy polysomes

growth_protocol: The UT-7/EPO erythro-megakaryocytic cell line was cultured in αMinimum Essential Medium (αMEM) containing 10% fetal calf serum (FCS), 1mM glutamine, 100UI/mL penicillin-streptomycin and 1 UI/mL EPO

value: UT7/EPO cells

tag: shRNA

value: lentivirus expressing RPS14 641 shRNA


title: ECO-FCE Caecum 440

extract_protocol: Total RNA was isolated using Qiazol reagent (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was column-purified using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: feed efficiency

value: high

tag: gender

value: female

tag: sow

value: caecal mucosa


title: shRPS14 641 Translatome biological rep1

source_name: UT7/EPO cells infected with lentivirus expressing RPS14 641 shRNA, harvested 72 hours after induction


title: lasR_monoculture_rep3

tag: strain


title: zebrafish_123s_A18

tag: tissue

tag: starin

tag: age


title: HEK293_CDK11_1del226_nFLAG_iCLIP_254_1

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNCCACNN
3' adapter: AGATCGGAAGAGCGGTTCAG

tag: method

tag: condition

value: F-CDK11_1del226-nFLAG 254


title: HEK293_CDK11_1del226_nFLAG_iCLIP_254

value: HEK293 cells


title: lasR_monoculture_rep2


title: K562_shSCR Translatome biological rep1

value: 5 days after induction

value: RNA extracted from heavy polysomes


title: shRPS14 640 Translatome biological rep2

description:
UT7/EPO cells infected with lentivirus expressing RPS14 640 shRNA, harvested 72 hours after induction
RNA extracted from heavy polysomes

value: lentivirus expressing RPS14 640 shRNA


title: zebrafish_123s_B23


title: lasR_coculture_WT_rep2


title: shRPS14 640 Translatome biological rep1

source_name: UT7/EPO cells infected with lentivirus expressing RPS14 640 shRNA, harvested 72 hours after induction


title: lasR_monoculture_rep1


title: HEK293_CDK11_nFLAG_iCLIP_4SU_365

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNTGGCNN
3' adapter: AGATCGGAAGAGCGGTTCAG

value: iCLIP

value: F-CDK11-nFLAG 4SU_365

value: HEK293 Flp-in

value: Sigma FLAG M2 (F1804)


title: HEK293_CDK11_nFLAG_4SU_365_1


title: shRPS14 641 Transcriptome biological rep3

data_processing: Raw expression values were normalized using Robust Multiarray Averaging (RMA) and custom brainarray CDFv20    ID = EntrezGene

value: lentivirus expressing shRPS14 641


title: 48 h

city: Beijing

first: Xuncheng

last: Wang

address: 5 Yiheyuan Road

institute: Peiking University

data_processing:
FastQC analysis was performed to estimate the quality of raw reads (http://www.plob.org/2013/07/16/5987.html). After trimming adapter sequences and filtering low-quality reads with Q < 20 from the 5' and 3' ends of the remaining reads, the clean reads with 21 bp to 49 bp length were mapped onto the Nipponbare reference genome (IRGSP build 5.0) using RSEM version 1.1.11 (Li and Dewey, 2011). The levels of gene expression were quantified in terms of FPKM (fragments per kilo base of exon per million) using RSEM version 1.1.11 (Li and Dewey, 2011), and then the gene expressions were estimated and normalized with the software package edgeR version 2.3.52 (McCarthy et al., 2012). The log2 fold changes of gene FPKM were tested between 0 h and 24 h imbibed seeds (0 vs. 24 h) and between 24 h and 48 h imbibed seeds (24 vs. 48 h) respectively.
Genome_build: IRGSP build 5.0
Supplementary_files_format_and_content: *txt: Tab-delimited text files include FPKM values for each Sample.

organism: Oryza sativa Japonica Group

source_name: seed, germinated

growth_protocol: Seeds were imbibed in Petri dishes (d = 9 cm) with 10 mL distilled water and incubated in a growth chamber at 30 ± 1 ºC for 10 days.

extract_protocol:
Total RNA was extracted from approximately 80~100 mg powder of each sample using the RNeasy plant mini kit (Qiagen, www.qiagen.com) according to the manufacturer’s protocol.
The complementary DNA (cDNA) libraries were prepared according to Zhang et al. (2016) by performing a series of procedures, including poly(A) enrichment, RNA fragmentation, cDNA synthesis, linker ligation, size selection and PCR amplification.

value: Jiucaiqing

value: seed

tag: imbibition time


title: zebrafish_123s_A16

value: embryo trunk

value: 48 hpf


title: shSCR Translatome biological rep2

description:
UT7/EPO cells infected with lentivirus expressing SCR shRNA, harvested 72 hours after induction
RNA extracted from heavy polysomes

value: UT7/EPO cells

value: lentivirus expressing SCR shRNA


title: shSCR Translatome biological rep1

source_name: UT7/EPO cells infected with lentivirus expressing SCR shRNA, harvested 72 hours after induction


title: zebrafish_123s_A15


title: zebrafish_123s_A2


title: 24 h

source_name: seed, imbibed


title: HEK293_CDK11_nFLAG_iCLIP_254_1

description:
synchronization protocol: HCT116 cells were synchronized with double thymidine block method. The cells were blocked with 2 mM thymidine (Sigma, T1895) for 16 h, washed twice with PBS, released into fresh media for 8 h and blocked again with 2 mM thymidine for 16 h. Finally, the cells were released into fresh media. G1/S, S and G2/M cells were collected at 0 h, 2 h and 8 h after the release from the second thymidine block, respectively. Progression into the different cell cycle phases was verified by flow cytometry (propidium iodide staining).
5' barcode: NNNAATANN
3' adapter: AGATCGGAAGAGCGGTTCAG

value: F-CDK11-nFLAG 254

tag: antibody


title: zebrafish_123s_A14


title: zebrafish_123s_A17


title: H3K27me3_muBeaf_exp2

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

institute: CNRS

data_processing:
Raw reads quality control perfomed with Fastqc (version 0.11.5)
Reads were first trimmed with bbduk.sh script from BBtools (38.00) and with standard parameters.
The alignments were performed with Bowtie2 (2.3.3.1) on dm3 genome version with -q 10 parameter.
Samtools rmdup (1.4.1) was then used on sorted BAM files to filter out potential PCR duplicates.
Bigwig files were generated with deeptools BamCoverage (3.0.1-2-2) RPKM normalized and using a bin size of 50bp with a smoothing window of 150 bp.
Genome_build: Dm3
Supplementary_files_format_and_content: Bigwig files containing ChIP-seq coverage for each sample in RPKM.

organism: Drosophila melanogaster

source_name: S2 cells

growth_protocol: S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO, Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/streptomycin (GIBCO, Invitrogen)

extract_protocol:
S2 cells were treated with formaldehyde followed by standard sonication and extraction procedures of chromatin for ChIP analysis  ChIP samples were prepared for sequencing using standard Illumina protocols of TruSeq ChIP sample prep kits from 100 ng of starting precipitated DNA to generate sequencing libraries
As performed by BGI plateform (BGISEQ-500 sequencing system)

treatment_protocol: S2 cells were stably transfected after precipitation with calcium of serial vectors (pUWG) carrying the neomycin resistance gene together with mutant-Beaf gene as compared to WT. G418 resistant colonies were taken after about 10 days under selection and then grown under normal conditions. For RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for beaf32 were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 5 days and cells were then harvested.

tag: cell type

value: Late embryonic derived S2 cells

value: S2 Schneider cells

tag: treatment

tag: passages


title: zebrafish_123s_A13

city: Huddinge


title: 0 h

source_name: seed, dry

value: 0 h


title: tetTKO_24hpf_RRBS_rep2

city: darlinghurst

first: Samuel

middle: Ernest

last: Ross

state: NSW

address: 384 victoria st

country: Australia

institute: Garvan Institute of Medical Research

description: CRISPR/Cas9 injected F0 zebrafish with a mosaic tet1/2/3 KO

data_processing:
RRBS sequence reads were trimmed with Trim Galore (--illumina --rrbs --paired) (https://github.com/FelixKrueger/TrimGalore),and mapped using WALT (-t 12) (Chen et al. 2016) onto the bisulfite-converted GRCz10 reference (UCSC) containing λ  sequence  added as a separate chromosome. The resulting alignments in BAM format were processed with MethylDackel (--mergeContext --maxVariantFrac 0.25 --minOppositeDepth 2 --OB 10,140,10,140 --OT 10,140,10,140) (https://github.com/dpryan79/MethylDackel) to obtain methylation calls.
Genome_build: GRCz10
Supplementary_files_format_and_content: merged CG file: (1) chromosome, (2) start position, (3) end position, (4) methylation percentage rounded to an integer, (5) The number of alignments/pairs reporting methylated bases, (6) The number of alignments/pairs reporting unmethylated base.

source_name: 24hpf embryos

growth_protocol: Adult wild type (AB/Tubingen) Danio rerio (zebrafish) were bred in a 1 male:1 female ratio. Embryos were collected 0 hours post-fertilisation (hpf) and incubated in 1X E3 medium (0.03% NaCl, 0.005% CaCl2, 0.0013% KCl, 99.9557% H2O, 0.008% H14MgO11S) for 24 hours at 28.5°C.

extract_protocol:
24hpf embryos were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted from 24hpf embryos using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.
RRBS library construction was performed using the restriction enzyme MspI (New England BioLabs, Ipswich, MA, USA) and 0.025ng of unmethylated lambda phage DNA (Promega, Madison, WI, USA) was used as a spike-in control to determine the efficiency of bisufite conversion. Briefly, 500ng of zebrafish gDNA was digested overnight with 20U MspI (New England BioLabs, Ipswich, MA, USA). The 5’ overhands of the digested DNA were filled in and A-tailed before ligation of adapters to DNA overnight using NEXTFLEX Bisulfite-Seq Barcodes (PerkinElmer, Waltham, MA, USA). DNA was bisulfite converted using EZ DNA Methylation Gold Kit (Zymo Research,Irvine,CA,USA ) according to manufacturer instructions. Library amplification was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems, Woburn, MA), using 13 cycles of amplification. Library concentration was quantified through qPCR using KAPA Library Quantification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to manufacturer instructions. The combined libraries with 15% PhiX spike-in was sequenced on the Illumina HiSeq 10X platform using 150bp paired-end sequencing (high output mode).

treatment_protocol: tet1/2/3 KO microinjection mixtures where made by combining 100 ng of each tet gRNA with 1 μl EnGene CAS9 NLS, S Pyogenes  (New England BioLabs, Ipswich, MA, USA) and 1.5 μl KCl (1M).  500pL of micoinejection mixtures were injected into single cell stage embryos.

value: whole embryos

value: Mixed AB and Tubingen

value: tet1/2/3 CRISPR/Cas9 injected

tag: genotype

value: tet1/2/3 KO


title: zebrafish_123s_A12


title: H3K27me3_muBeaf_exp1


title: tetTKO_24hpf_RRBS_rep1


title: zebrafish_123s_A11


title: shRPS14 641 Transcriptome biological rep2

tag: cell line

tag: time post induction


title: H3K27me3_CTL_exp2


title: shRPS14 641 Transcriptome biological rep1

tag: shRNA


title: shRPS14 640 Transcriptome biological rep3

value: lentivirus expressing shRPS14 640


title: WT_24hpf_RRBS_rep2

value: control

value: wild type


title: zebrafish_123s_A10


title: zebrafish_123s_A1


title: WT_24hpf_RRBS_rep1


title: SK68, mutant

city: Wuxi

first: Xuewei

last: Pan

address: 1800, Lihu Avenue

institute: Jiangnan University

data_processing:
Use software FastQC (v0.10.1) to control of raw data's quality
Use Cutadapt (version 1.9.1) to filtering low-quality data, removing contamination and joint sequence
Use bowtie2(v2.1.9) software to compare with reference sequence
Software (V 0.6.1) Htseq was used to calculate gene expression, the software used FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) method to calculate gene expression.
Differentially expressed genes between samples JNB5-1 and SK68 were screened based on differentially expressed genes. KEGG_B_Class function enrichment analysis were performed for significant difference genes
Genome_build: S. marcescens WW4 (NC_020211.1)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

organism: Serratia marcescens

source_name: Bacteria

growth_protocol: Bacterial cultures were routinely incubated in LB medium at 30℃

extract_protocol:
The collected cells were treated with RNAprep pure Kit (TIANGEN) to extract total bacterial RNA and delivered to GENEWIZ in dry ice for transcriptome resequencing analysis
The total RNA extracted from the bacterial were subjected to rRNA removing to obtain mRNA. The mRNA was used as templates for DNA synthesis. Illumina Hiseq platform was used for the cDNA libraries sequencing

treatment_protocol: S. marcescens JNB5-1 and SK68 cells were grown in LB medium for 4 h before harvesting

value: mutant


title: shRPS14 640 Transcriptome biological rep1


title: H3K27me3_CTL_exp1


title: input_ChIP

value: Input


title: shSCR Transcriptome biological rep3

description: shSCR Transcriptome biological rep3

source_name: shSCR Transcriptome biological rep3


title: shRPS14 640 Transcriptome biological rep2


title: JNB5-1, wildtype


title: HEK293_CDK11_nFLAG_iCLIP_254

value: HEK293 cells

value: iCLIP

value: HEK293 Flp-in

value: Sigma FLAG M2 (F1804)


title: shSCR Transcriptome biological rep1

description: shSCR Transcriptome biological rep1

source_name: shSCR Transcriptome biological rep1

value: UT7/EPO cells

value: lentivirus expressing SCR shRNA


title: Pig4_border

status: Public on Apr 27 2020

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

data_processing:
Fastq files were trimmed to remove adapter and loq quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the reference (Sscrofa11) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM and Counts
Genome_build: Sscrofa11
Supplementary_files_format_and_content: tab-delimited text files include TPM and COUNTS for all samples

source_name: Left ventricular myocardial tissue

growth_protocol: None- tissue was extracted when pigs were 4-weeks post surgery and rapidly frozen before RNA extracted.

extract_protocol:
Myocardial tissue was harvested 4-weeks following surgery and cut into zonal sections. Tissue was washed in PBS and rapidly frozen in liquid nitrogen, before transfer to a -80C freezer for storage. RNA was then extracted using a commercially available kit (NucleoSpin RNA kit (740955, Macherey-Nagel) and eluted in RNAse free H20 prior to submission to CCHMC DNA Core for processing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol

treatment_protocol: Ischemia/reperfusion= 1-hour occlusion of the left anterior descending artery, just below the second diagonal branch, following by reperfusion. Sham= same procedure but no occlusion of artery.

tag: surgery

value: Sham

tag: zone

value: Border

tag: Sex

value: Female


title: Pig12_scar

value: Scar

value: Male


title: Pig5_border


title: Pig4_scar


title: shMOB2

city: Dalian

first: Ke

last: Jiang

state: Liaoning

address: lvshun south road no.9

institute: Dalian Medical University

data_processing:
clean reads were retained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw fastq data using in-house perl scripts
RNASeq reads were aligned to the hg38 genome assembly using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to generate gene-level count matrix as input for edgeR’s statistical model
Differential expression analysis between shFKBP9 and shControl cells was performed using the edgeR package
Genome_build: hg38
Supplementary_files_format_and_content: Excel file include FPKM expression value and gene annotation

source_name: LN-229 cells

growth_protocol: Cells were routinely generated by re-plating with DMEM supplied with 5% FBS.

extract_protocol:
RNA was isolated from LN-229-shMOB2 or LN-229-shControl cells using TRIzol Reagent.
The sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's instructions.

treatment_protocol: LN-229 cells were infected with pGIPZ-CTRL and MOB2-shRNA lentiviruses, and stable clones were selected using puromycin.

value: epithelial glioma cells

tag: tissue

value: brain


title: shControl


title: E10.5 WT

city: Minato-ku

first: Satomi

last: Yogosawa

state: Tokyo

address: 3-25-8, Nishi-shinbasi

department: Department of Biochemistry

country: Japan

institute: Jikei University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.
quantile normalized signal (non-log scaled) and ABS CALL.

source_name: Wild type

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain

value: Wild type

value: whole embryo


title: M100R.X1

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

institute: Netherlands Cancer Institute

data_processing:
Read mapping was performed using TopHat version 2.0.9
Read counts per gene were quantified using HTSeq version 0.5.4
Read counts were normalised using DEseq2.
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Read count table

source_name: Melanoma PDX

growth_protocol: Tumor fragments of ~5mm3 were used for subcutaneous transplantation into NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mice, which was performed under anesthesia. Tumor outgrowth was measured twice a week with a caliper. Before reaching the maximum allowed tumor size of 1000 mm3, mice were sacrificed, tumors were removed and tumor pieces were snap-frozen and stored at -80°C for RNAseq analysis.

extract_protocol: RNA isolated by Trizol, according to manufacturers protocol.RNA libraries were prepared for sequencing using standard Illumina protocols

tag: origin

value: Patient derived xenograft (PDX) sample

tag: derived from

value: melanoma metastases

tag: host strain

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse


title: M099.X1


title: M098.X1


title: M103.X1


title: M097R.X1


title: E10.5 DYRK2-KO

source_name: Knockout

value: DYRK2 knockout

tag: age


title: E8.5 WT


title: M093.X1


title: M092.X1


title: M091.X1


title: M096.X1


title: M101.X1


title: shSCR Transcriptome biological rep2

description: shSCR Transcriptome biological rep2

source_name: shSCR Transcriptome biological rep2


title: FF_uninfected_3

city: Birmingham

first: Shinichi

last: Kano

state: AL

address: 1720 7th Ave South

department: Psychiatry

institute: University of Alabama at Birmingham

description:
5823049023_J
SAMPLE 11

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data were extracted using GenomeStutio v1.0 Expression Module and quantile-normalized at the gene level without background subtraction. Avg_Signal data were imported into GeneSpring GX 11.0.2 for statistical analysis among sample groups under the following conditions: Signal intensity threshold was set to 1 and data were log 2-transformed.
Illumina BeadStudio version 2 -generated_signal intensity

label_protocol: Biotinylated, amplified antisense complementary RNA (cRNA) was prepared from RNA by using the Illumina CustomPrep RNA amplification kit (Applied Biosystems/Ambion).

growth_protocol: EBV-lymphoblastoid cells were maintained in RPMI-1640 supplemented with 15% fetal bovine serum and penicillin/streptomycin.

extract_protocol: Total RNA extraction using Qiagen RNEasy kit

treatment_protocol: Tachyzoites were prepared from T. gondii strain 2F, which constitutively expresses cytoplasmic b-galactosidase and are derived from strain RH. Cells were infected with tachyzoites of T. gondii strain 2F at a multiplicity of infection (MOI) of 1, and then harvested for RNA collection at 48 h.

value: EBV-transformed human lymphoblastoid cells

tag: genotype/variation

value: DISC1 607 Phe/Phe

tag: cell source

value: blood

tag: gender (for cell source)

value: male

tag: age (cell source)

tag: infected with

value: none (uninfected control)


title: FF_uninfected_2

description:
5823049023_F
SAMPLE 9

tag: cell type


title: E8.5 DYRK2-KO

tag: genotype


title: M090.X1


title: M087_2.X1


title: M089.X1


title: LL_infected_3

description:
5823049023_K
SAMPLE 6

value: DISC1 607 Leu/Leu

value: T. gondii for 48 hrs


title: FF_uninfected_1

description:
5823049023_B
SAMPLE 7


title: LL_uninfected_3

description:
5823049023_I
SAMPLE 5


title: M085R.X1


title: M084.X1


title: FF_infected_1

description:
5823049023_D
SAMPLE 8


title: FF_infected_2

description:
5823049023_H
SAMPLE 10


title: M083.X1


title: LL_infected_2

description:
5823049023_G
SAMPLE 4


title: LL_uninfected_2

description:
5823049023_E
SAMPLE 3


title: FF_infected_3

description:
5823049023_L
SAMPLE 12


title: LL_infected_1

description:
5823049023_C
SAMPLE 2


title: M081.X1


title: M079.X1


title: M076.X1


title: M078R.X1


title: M080.X1


title: M075.X1


title: LL_uninfected_1

description:
5823049023_A
SAMPLE 1


title: M073.X1


title: M070.X1


title: M066R.X1


title: M066.X1


title: M063R.X1


title: M064R.X1


title: M062R.X1


title: M064.X1


title: M060R.X1


title: M056R.X1


title: M059.X1


title: M057.X1


title: M054R.X1


title: M052.X1


title: M050.X1


title: M049.X1


title: M061R.X1


title: M074R.X1


title: M048.X1


title: M048R2.X1


title: M044R.X1


title: Pig5_scar

value: Sham

value: Scar

value: Female


title: M041.X1


title: M043R.X1


title: M040.X1


title: M065.X1


title: M042R.X1


title: M039R.X1


title: M037.X1


title: M034R.X1


title: M032R1.X1


title: M032.X1


title: M046.X1


title: M036_2R.X1


title: M032R5.X1


title: M031R2.X1


title: M055.X1


title: M029.X1


title: M028.X1


title: M048R.X1


title: M029R.X1


title: M035.X1


title: M026R.X1


title: M026.X1


title: M022.X1


title: M082.X1


title: M024.X1


title: M021.X1


title: M019.X1


title: M019R.X1


title: M017.X1


title: M025.X1


title: M020R.X1


title: M033R.X1


title: M013R.X1


title: M011-5R.X1


title: M014R.X1


title: M011-4R.X1


title: M032R6.X1


title: M011-3R.X1


title: M027.X1


title: M006R.X1


title: M005R.X1


title: M005.X1


title: M010R.X1


title: M009R.X1


title: M009.X1


title: M004R.X1


title: M002.X1


title: M001R.X1


title: M003.X1


title: Seedling, BL_rep1

city: Chuncheon

first: Dong-Hoon

last: Jeong

state: Gangwon-do

address: Room #8306, Department of Life Science, 1 Hallymdaehak-gil

department: Dept. of Life Science

country: South Korea

institute: Hallym University

description: small RNA

data_processing:
miRNA expression analysis was conducted using CLC genome workbench small RNA pipeline (Quiagen, Denmark).
After pre-processing, miRNA reads were retrieved by mapping the small RNA reads to the know Arabidopsis miRNAs from miRBase Release 22.1 (Kozomara and Griffiths-Jones 2014a).
After normalization of miRNA reads with TP4M (Transcripts Per 4 Million reads), differentially expressed miRNAs were identified by a 2 –fold difference between control and epiBL-treated seedlings with statistic significance of p-value < 0.001.
Genome_build: Arabidopsis genome (TAIR10) , miRBase Release 22.1
Supplementary_files_format_and_content: Excel file with differentially expressed miRNAs

source_name: Seedling

growth_protocol: Plants expressing wild-type BRI1-Flag protein under its native promoter in the bri1-5 mutant were used at the plant material. Seeds were surface sterilized, kept at 4 °C for 2 days, and Arabidopsis thaliana plants were grown in shaking liquid culture as previously described (Oh et al. 2009)

extract_protocol:
Total RNAs, including small RNA fractions, were isolated using mirVanaTM miRNA isolation kit (ThermoFisher, Waltham, MA) from Arabidopsis seedlings treated with mock or epiBL for 90 minutes, with three biological replicates.
Small RNA library was prepared using the TruSeq small RNA sample preparation protocol (Illumina, San Diego, CA), barcoded, and sequenced on an Illumina GAxII platform.

treatment_protocol: plants were treated with 1 μM epibrassinolide (epiBL) or a solvent control for 90 min before harvest.

tag: treatment

value: treated with 1 μM epibrassinolide (epiBL) for 90 min

value: Seedling

tag: replicates

value: biological replicate #1


title: Seedling, BL_rep3

description: small RNA

value: Plants expressing wild-type BRI1-Flag protein under its native promoter in the bri1-5 mutant

value: biological replicate #3


title: Seedling, Control_rep1

description: small RNA

value: treated with a solvent control for 90 min


title: Seedling, Control_rep3

description: small RNA


title: M011-1R.X1

value: Patient derived xenograft (PDX) sample

value: melanoma metastases

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ mouse


title: Seedling, Control_rep2

description: small RNA

value: biological replicate #2


title: M011-2R.X1


title: Seedling, BL_rep2

description: small RNA