title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 20) treated with DMSO, Biological Replicate 1

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description:
20DMSO_RPF_1
20DMSO_L002
TSC2-treatment_RPF.txt

data_processing:
Linker tags were removed from RNA sequencing and ribosome profiling reads by the FASTX Toolkit, v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/)
All reads that mapped to rRNAs, tRNAs or mitochondrial rRNAs were removed, and the remaining reads were mapped to RefSeq (v38) by TopHat v2.0.13.
Finally all read counts that mapped uniquely to genes were extracted for expression analysis with the help of samtools, v1.1.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: .txt files report raw read counts that mapped uniquely to genes

source_name: TSC2-/- cells (number 20) treated with DMSO, RPF

growth_protocol: NSCs were cultured according to standard methods. All used tissue culture dishes were coated with poly-L-ornithine (Sigma Aldrich) and laminin (Roche) and undifferentiated cultures were maintained in a basic medium composed of a 1:1 mix of DMEM:F12 Glutamax medium and Neurobasal medium (both Gibco, Invitrogen) that was supplemented with 1x B27, 1x N2 and 0.1 mM beta-mercaptoethanol (all Gibco, Invitrogen). For self-renewing conditions the following growth factors were added: 10 ng/mL FGF2, 20 ng/mL BDNF (both Peprotech) and 10 ng/mL EGF (R&D Systems). Ventralization was induced for a period of seven days by replating the cells at a density of 12000 cells/cm2 and changing the supplementing growth factors to 200 ng/mL Shh, 100 ng/mL FGF8 (both Peprotech) and 100 μM ascorbic acid phosphate (Sigma Aldrich). Neuronal differentiation was initiated by replating the cells at a density of 40000 cells/cm2 in basic medium supplemented with 20 ng/mL BDNF, 10 ng/mL GDNF (both Peprotech), 0.5 mM cAMP (BIOLOG Life Science) and 100 μM ascorbic acid phosphate (Sigma Aldrich). Medium was changed twice per week until the day of analysis.

extract_protocol:
Cells for each biological replicate of heterozygous and homozygous cells with or without drug treatment were washed with ice cold PBS and lysed on ice in the presence of 100 μg/mL cycloheximide (Sigma). The cleared lysate was flash frozen and stored at -80° C until further processing. For ribosomal RNA depletion the RiboZero magnetic Gold kit (Illumina) was used. Quality of amplified libraries was accessed by capillary electrophoresis with a high sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified by quantitative PCR with a sequencing library quantification kit (KAPA Biosystems) on a Roche Light Cycler 480. Multiplexed libraries with 1 % spiked in PhiX control were sequenced on a HiSeq2500 instrument for 50 cycles using version 4 chemistry reagents (Illumina).
Ribosome profiling and RNA sequencing libraries were prepared using the TruSeq Ribo Profile kit (Illumina, #RPHMR12126) as detailed in the manufacturer’s protocol.

treatment_protocol: Cells were treated with DMSO, AZD-8055, and Rapamycin for 3 hours, respectively. After 3 hours cells are washed and harvested.

value: Embryonic stem cell-derived neurons

tag: genotype/variation

value: DMSO

tag: cell line id

tag: assayed molecule

value: Ribosome protected fragments


title: Total RNA of TSC2-/- cells (number 20) treated with Rapamycin, Biological Replicate 1

status: Public on Jul 25 2016

type: SRA

description:
20Rapamycin_mRNA_1
20Rapamycin_L006
TSC2-treatment_RNA.txt

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: TSC2-/- cells (number 20) treated with Rapamycin, total RNA

tag: cell type

tag: treatment

value: Rapamycin

value: mRNA


title: Total RNA of TSC2-/- cells (number 20) treated with Rapamycin, Biological Replicate 2

description:
20Rapamycin_mRNA_2
20Rapamycin_L007
TSC2-treatment_RNA.txt


title: Total RNA of TSC2-/- cells (number 20) treated with AZD-8055, Biological Replicate 2

description:
20AZD_mRNA_2
20AZD_L008
TSC2-treatment_RNA.txt

source_name: TSC2-/- cells (number 20) treated with AZD-8055, total RNA


title: Ss rep 1

city: Winnipeg

first: Kelly

last: Duke

address: 410 Buller Bldg, 100 Chancellors Circle

department: Microbiology

country: Canada

institute: University of Manitoba

description:
Processed data files:
gene_exp.diff
genes.fpkm_tracking
cuffdiff_genes_nossl.txt

data_processing:
Sequenced reads were analyzed to remove barcode adapters and low quality reads using the Trimmomatic tool. The parameters for Trimmomatic which maximized mapping efficiency to the B. napus genome [B. napus: v.4.1, Chalhoub et al. was determined using FastQC reports for quality control (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) followed by alignment using Tophat2 v.2.1.0.
Alignment was completed using Tophat2 v.2.1.0. Alignment of reads to these genomes was performed in high-sensitivity mode using B. napus reference annotation v5 from Chalhoub et al. as guides.
The cufflinks and cuffmerge tools within the Cufflinks v.2.2.1 suite were used construct a transcriptome from the reads and identify novel transcripts.
Transdecoder was used to identify open reading frames (ORFs) within transcript sequences. Genes were identified by aligning translated ORF sequences with proteins in the Arabidopsis TAIR10, NCBI and Uniprot databases using BLAST.
Read counts were normalized to FPKM values using the cuffquant and cuffdiff tools in the Cufflinks package with default settings.
Genome_build: B. napus: v.4.1, Chalhoub et al.
Supplementary_files_format_and_content: Cuffdiff output files (gene_exp.diff; genes.fpkm_tracking) were used for FPKM values and significant log2 fold change values. Cuffdiff_genes_nossl.txt matches mapped sequence XLOC identifiers to corresponding Bna gene identifiers determined via BLAST search.

organism: Brassica napus

source_name: Ss, leaf

growth_protocol: Brassica napus cv. Westar plants were grown in Sunshine Mix #1 soil in growth chambers at 21ºC with a light/dark photoperiod of 16h/8h and 0% humidity

extract_protocol:
Total RNA was extracted using PureLink® Plant RNA Reagent (Invitrogen). DNA contamination was removed using Turbo DNA-freeTM kit (Ambion), following the manufacturer’s instructions. RNA concentration was verified using a NanoVue spectrophotometer (GE Healthcare), and quality was measured using an Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico and Nano Chips (Agilent Technologies; Santa Clara, CA, USA).
RNA-seq libraries were prepared according to the alternative HTR protocol (C2) described by Kumar with the exception of PCR enrichment of the libraries, where the number of cycles was adjusted to 11. Libraries were validated using the Agilent Bioanalyzer High Sensitivity DNA Assay with DNA chips (Agilent Technologies). The desired fragment sizes of sheared cDNA with ligated adapters were isolated using the E-Gel® electrophoresis system (Invitrogen). 100 bp single-end RNA sequencing was carried out at Génome Québec (Montreal, Canada) on the Illumina HiSeq 2000 platform.

treatment_protocol: One day prior to fungal pathogen exposure, B. napus plants at the 30% flowering stage were sprayed until dripping with a 2x108 cfu/mL solution of PA23 resuspended in sterile water supplemented with 0.02% Tween 20 as a surfactant. Plants not receiving biocontrol treatment (water control and Ss only groups) were sprayed with sterile water (0.02% Tween 20). Plants were sealed in clear bags to preserve relative humidity and returned to the growth chamber for 24 hours. The following day, bags were removed and plants receiving the pathogen treatment were sprayed with an 8x104 spores/mL solution of S. sclerotiorum ascospores resuspended in sterile water (0.02% Tween 20). Control plants and plants to be exposed only to PA23 were sprayed with sterile water (0.02% Tween 20). Plants were transferred to a humidity chamber with humidity levels of 70-90% for 72 hours. During this time, plants were gently shaken at the base twice to encourage petals to detach and fall into the plant canopy. Three leaves per plant and three plants per treatment group were used for each biological replicate. Leaves upon which petals had landed were used for collection, as these are sites of potential infection. The petal was removed from the leaf and approximately 1cm2 area of leaf tissue surrounding the site was collected with a scalpel. For S. sclerotiorum-infected leaves, green tissue immediately surrounding the lesion was collected. Cuttings were flash frozen in liquid nitrogen, and stored at -80℃ for no more than 2 days before processing.

tag: tissue

value: leaf

tag: developmental stage

value: 30% flowering

value: S. sclerotiorum ascospores


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 20) treated with AZD-8055, Biological Replicate 2

description:
20AZD_RPF_2
20AZD_L004
TSC2-treatment_RPF.txt

source_name: TSC2-/- cells (number 20) treated with AZD-8055, RPF


title: Total RNA of TSC2-/- cells (number 20) treated with AZD-8055, Biological Replicate 1

description:
20AZD_mRNA_1
20AZD_L007
TSC2-treatment_RNA.txt


title: Total RNA of TSC2-/- cells (number 20) treated with DMSO, Biological Replicate 1

description:
20DMSO_mRNA_1
20DMSO_L006
TSC2-treatment_RNA.txt

source_name: TSC2-/- cells (number 20) treated with DMSO, total RNA


title: Total RNA of TSC2-/- cells (number 20) treated with DMSO, Biological Replicate 2

description:
20DMSO_mRNA_2
20DMSO_L007
TSC2-treatment_RNA.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 20) treated with DMSO, Biological Replicate 2

description:
20DMSO_RPF_2
20DMSO_L004
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 20) treated with Rapamycin, Biological Replicate 2

description:
20Rapamycin_RPF_2
20Rapamycin_L004
TSC2-treatment_RPF.txt

source_name: TSC2-/- cells (number 20) treated with Rapamycin, RPF


title: Total RNA of TSC2-/- cells (number 19) treated with Rapamycin, Biological Replicate 1

description:
19Rapamycin_mRNA_1
19Rapamycin_L006
TSC2-treatment_RNA.txt

source_name: TSC2-/- cells (number 19) treated with Rapamycin, total RNA


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 19) treated with Rapamycin, Biological Replicate 2

description:
19Rapamycin_RPF_2
19Rapamycin_L003
TSC2-treatment_RPF.txt

source_name: TSC2-/- cells (number 19) treated with Rapamycin, RPF


title: Total RNA of TSC2-/- cells (number 19) treated with Rapamycin, Biological Replicate 2

description:
19Rapamycin_mRNA_2
19Rapamycin_L008
TSC2-treatment_RNA.txt


title: CCR6–Foxp3EGFP+ Il4raR576 Treg 1

city: Los Angeles

first: Matteo

last: Pellegrini

state: CA

address: 610 Charles Young Drive East

country: USA

institute: UCLA

data_processing:
Reads aligned with STAR (version 2.5.1b)
Raw counts quantified with htseq-count (version 0.6.1p1)
Normalized counts generated with DESeq2 (version 1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of normalized counts

organism: Mus musculus

source_name: CCR6–Foxp3EGFP+ Il4raR576 Treg

extract_protocol:
We purified CCR6+Foxp3EGFP+ Il4raR576 and CCR6–Foxp3EGFP+ Il4raR576 Treg cells from total lung digests of OVA-sensitized and challenged mice, using FACS (Fluorescence Activated Cell Sorting).
RNA was first converted to cDNA using ClonetechÕs SMART-Seq v4 Ultra Low Input RNA kit following standard procedure. After cDNA was measured with Nanodrop, 250 ng in a 50 ul volume was then fragmented to 200-300 bp size using the Covaris M220. All the fragmented DNA was then used with the KAPA Hyper Prep Kit (Illumina platform) to make cDNA libraries. Libraries were quantified using HS DNA Qubit and Agilent HS DNA Bioanalyzer.

treatment_protocol: 5- 5-7 week-old female mice were sensitized to ovalbumin (OVA) by intraperitoneal injection of 100 μg of OVA in 100 μL of PBS and then boosted 2 weeks later with a second intraperitoneal injection of OVA in PBS. Starting on day 29, OVA-sensitized mice were challenged with aerosolized OVA at 1% delivered through a Schuco 2000 nebulizer (Allied Health Care Products) for 30 minutes daily for 3 days. Mice were euthanized on day 32 post sensitization and analyzed.

tag: age

value: 5-7 weeks

tag: gender

value: female

tag: sensitized and challenged with

value: ovalbumin (OVA)

value: lung; total lung digest

tag: genotype

value: CCR6-Foxp3EGFP+ Il4raR576

value: regulatory T (Treg) cells


title: Total RNA of TSC2-/- cells (number 19) treated with DMSO, Biological Replicate 2

description:
19DMSO_mRNA_2
19DMSO_L008
TSC2-treatment_RNA.txt

source_name: TSC2-/- cells (number 19) treated with DMSO, total RNA


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 19) treated with Rapamycin, Biological Replicate 1

description:
19Rapamycin_RPF_1
19Rapamycin_L001
TSC2-treatment_RPF.txt


title: Water rep 1

source_name: Water, leaf

value: water


title: Total RNA of TSC2-/- cells (number 19) treated with DMSO, Biological Replicate 1

description:
19DMSO_mRNA_1
19DMSO_L006
TSC2-treatment_RNA.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 19) treated with DMSO, Biological Replicate 2

description:
19DMSO_RPF_2
19DMSO_L003
TSC2-treatment_RPF.txt

source_name: TSC2-/- cells (number 19) treated with DMSO, RPF


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 19) treated with AZD-8055, Biological Replicate 2

description:
19AZD_RPF_2
19AZD_L003
TSC2-treatment_RPF.txt

source_name: TSC2-/- cells (number 19) treated with AZD-8055, RPF


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 19) treated with AZD-8055, Biological Replicate 1

description:
19AZD_RPF_1
19AZD_L002
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 19) treated with DMSO, Biological Replicate 1

description:
19DMSO_RPF_1
19DMSO_L001
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 20) treated with Rapamycin, Biological Replicate 1

description:
20Rapamycin_RPF_1
20Rapamycin_L003
TSC2-treatment_RPF.txt


title: Total RNA of TSC2-/- cells (number 19) treated with AZD-8055, Biological Replicate 2

description:
19AZD_mRNA_2
19AZD_L008
TSC2-treatment_RNA.txt

source_name: TSC2-/- cells (number 19) treated with AZD-8055, total RNA


title: Total RNA of TSC2+/+ cells (number 16) treated with Rapamycin, Biological Replicate 2

description:
16Rapamycin_mRNA_2
16Rapamycin_L008
TSC2-treatment_RNA.txt

source_name: TSC2+/+ cells (number 16) treated with Rapamycin, total RNA


title: Total RNA of TSC2+/+ cells (number 16) treated with Rapamycin, Biological Replicate 1

description:
16Rapamycin_mRNA_1
16Rapamycin_L007
TSC2-treatment_RNA.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cells (number 20) treated with AZD-8055, Biological Replicate 1

description:
20AZD_RPF_1
20AZD_L003
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 16) treated with Rapamycin, Biological Replicate 2

description:
16Rapamycin_RPF_2
16Rapamycin_L005
TSC2-treatment_RPF.txt

source_name: TSC2+/+ cells (number 16) treated with Rapamycin, RPF


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 16) treated with Rapamycin, Biological Replicate 1

description:
16Rapamycin_RPF_1
16Rapamycin_L002
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 16) treated with DMSO, Biological Replicate 1

description:
16DMSO_RPF_1
16DMSO_L002
TSC2-treatment_RPF.txt

source_name: TSC2+/+ cells (number 16) treated with DMSO, RPF


title: Total RNA of TSC2+/+ cells (number 16) treated with DMSO, Biological Replicate 1

description:
16DMSO_mRNA_1
16DMSO_L007
TSC2-treatment_RNA.txt

source_name: TSC2+/+ cells (number 16) treated with DMSO, total RNA


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 16) treated with AZD-8055, Biological Replicate 1

description:
16AZD_RPF_1
16AZD_L002
TSC2-treatment_RPF.txt

source_name: TSC2+/+ cells (number 16) treated with AZD-8055, RPF


title: Total RNA of TSC2+/+ cells (number 16) treated with AZD-8055, Biological Replicate 1

description:
16AZD_mRNA_1
16AZD_L007
TSC2-treatment_RNA.txt

source_name: TSC2+/+ cells (number 16) treated with AZD-8055, total RNA


title: Total RNA of TSC2+/+ cells (number 15) treated with Rapamycin, Biological Replicate 2

description:
15Rapamycin_mRNA_2
15Rapamycin_L007
TSC2-treatment_RNA.txt

source_name: TSC2+/+ cells (number 15) treated with Rapamycin, total RNA


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 15) treated with Rapamycin, Biological Replicate 1

description:
15Rapamycin_RPF_1
15Rapamycin_L001
TSC2-treatment_RPF.txt

source_name: TSC2+/+ cells (number 15) treated with Rapamycin, RPF


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 16) treated with DMSO, Biological Replicate 2

description:
16DMSO_RPF_2
16DMSO_L005
TSC2-treatment_RPF.txt


title: Total RNA of TSC2-/- cells (number 19) treated with AZD-8055, Biological Replicate 1

description:
19AZD_mRNA_1
19AZD_L006
TSC2-treatment_RNA.txt


title: Total RNA of TSC2+/+ cells (number 15) treated with DMSO, Biological Replicate 1

description:
15DMSO_mRNA_1
15DMSO_L006
TSC2-treatment_RNA.txt

source_name: TSC2+/+ cells (number 15) treated with DMSO, total RNA


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 15) treated with DMSO, Biological Replicate 2

description:
15DMSO_RPF_2
15DMSO_L004
TSC2-treatment_RPF.txt

source_name: TSC2+/+ cells (number 15) treated with DMSO, RPF


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 15) treated with Rapamycin, Biological Replicate 2

description:
15Rapamycin_RPF_2
15Rapamycin_L004
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 15) treated with DMSO, Biological Replicate 1

description:
15DMSO_RPF_1
15DMSO_L001
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 15) treated with AZD-8055, Biological Replicate 2

description:
15AZD_RPF_2
15AZD_L005
TSC2-treatment_RPF.txt

source_name: TSC2+/+ cells (number 15) treated with AZD-8055, RPF


title: Total RNA of TSC2+/+ cells (number 15) treated with AZD-8055, Biological Replicate 1

description:
15AZD_mRNA_1
15AZD_L006
TSC2-treatment_RNA.txt

source_name: TSC2+/+ cells (number 15) treated with AZD-8055, total RNA


title: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 1

description:
3R19
TSC2-cellModel_RPF.txt

source_name: TSC2-/- cell line generated from hESC cell line 3, RPF

extract_protocol:
Cells for each biological replicate of control, heterozygous and homozygous cells were washed with ice cold PBS and lysed on ice in the presence of 100 μg/mL cycloheximide (Sigma). The cleared lysate was flash frozen and stored at -80° C until further processing. For ribosomal RNA depletion the RiboZero magnetic Gold kit (Illumina) was used. Quality of amplified libraries was accessed by capillary electrophoresis with a high sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified by quantitative PCR with a sequencing library quantification kit (KAPA Biosystems) on a Roche Light Cycler 480. Multiplexed libraries with 1 % spiked in PhiX control were sequenced on a HiSeq2500 instrument for 50 cycles using version 4 chemistry reagents (Illumina).
Ribosome profiling and RNA sequencing libraries were prepared using the TruSeq Ribo Profile kit (Illumina, #RPHMR12126) as detailed in the manufacturer’s protocol.

tag: parental cell line id


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 15) treated with AZD-8055, Biological Replicate 1

description:
15AZD_RPF_1
15AZD_L001
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 1

description:
3R15
TSC2-cellModel_RPF.txt

source_name: TSC2+/+ control generated from hESC cell line 3, RPF


title: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 2

description:
3R20
TSC2-cellModel_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 1

description:
3R17
TSC2-cellModel_RPF.txt

source_name: TSC2+/- cell line generated from hESC cell line 3, RPF


title: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 2

description:
3R18
TSC2-cellModel_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 2

description:
3R16
TSC2-cellModel_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 2

description:
2R20
TSC2-cellModel_RPF.txt

source_name: TSC2-/- cell line generated from hESC cell line 2, RPF


title: Total RNA of TSC2+/+ cells (number 16) treated with AZD-8055, Biological Replicate 2

description:
16AZD_mRNA_2
16AZD_L008
TSC2-treatment_RNA.txt


title: Total RNA of TSC2+/+ cells (number 16) treated with DMSO, Biological Replicate 2

description:
16DMSO_mRNA_2
16DMSO_L008
TSC2-treatment_RNA.txt


title: Total RNA of TSC2+/+ cells (number 15) treated with Rapamycin, Biological Replicate 1

description:
15Rapamycin_mRNA_1
15Rapamycin_L006
TSC2-treatment_RNA.txt


title: Ribosome protected fragments (RPF) of TSC2+/+ cells (number 16) treated with AZD-8055, Biological Replicate 2

description:
16AZD_RPF_2
16AZD_L005
TSC2-treatment_RPF.txt


title: Ribosome protected fragments (RPF) of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 1

description:
2R19
TSC2-cellModel_RPF.txt


title: Super_DAL9.rep3

city: Shanghai

first: Renyi

last: Liu

state: Shanghai

address: 3888 Chenhua Road

department: Bioinformatics

country: China

institute: Shanghai Center for Plant Stress Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Cucumber genome sequence (http://cucumber.genomics.org.cn, v2i) using TopHat. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 RPM (readss per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM (Reads per Million) values for 33 Samples .

organism: Cucumis sativus

source_name: corolla

growth_protocol: The cucumber inbred line '6457' (parthenocarpic rate≥95%) was grown in a greenhouse with a 12h photoperiod, a mean daily air temperature of 29/20℃(day/night), a relative humidity of 85% and a photosynthetic photo flux density of 800μmolm-2s-1at Hebei Normal University of Science and Technology. Pest control was performed according to standard management practices. The female flowers at the top node of the main stem, were treated prior to bagging in order to prevent pollination.

extract_protocol:
As described above, 11 kinds of corolla samples were collected for RNA-seq analysis. For each sample, 5 individual corollas were ground into powder and mixed in liquid nitrogen (three replicates). Total RNAs were isolated using the RNA extraction kit (Huayueyang, China). RNA was checked on 1% agarose gels to avoid possible degradation and contamination, and was then examined by a Nano Photometer spectrophotometer (IMPLEN, CA, USA) for RNA purity. Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA) was used to measure RNA concentration, and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was used to evaluate RNA integrity.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: This was followed by two kinds of treatments during the full bearing period:(1) super ovary induction treatment, fertilizer and water adequacy , only one fruit (the first female flower near the growing point) was set per plant to limit interfruit competition effects on fruit development and yield super ovary; (2) normal ovary induction treatment, fertilizer and water deficiency, one or two fruits (exceptthe first female flower near the growing point) were set per plant to promote the yield of normal ovary.

value: corolla

value: inbred line 6457

tag: phenotype

value: super ovary bloom


title: Super_DAL9.rep1


title: Super_DAL9.rep2


title: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 2

description:
2R18
TSC2-cellModel_RPF.txt

source_name: TSC2+/- cell line generated from hESC cell line 2, RPF

value: Embryonic stem cell-derived neurons


title: Total RNA of TSC2+/+ cells (number 15) treated with DMSO, Biological Replicate 2

description:
15DMSO_mRNA_2
15DMSO_L007
TSC2-treatment_RNA.txt

value: DMSO


title: Ribosome protected fragments (RPF) of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 1

description:
2R17
TSC2-cellModel_RPF.txt

value: Ribosome protected fragments


title: Total RNA of TSC2+/+ cells (number 15) treated with AZD-8055, Biological Replicate 2

description:
15AZD_mRNA_2
15AZD_L008
TSC2-treatment_RNA.txt

value: mRNA


title: Super_DAL8.rep2


title: Total RNA of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 1

description:
3T19
TSC2-cellModel_RNA.txt

source_name: TSC2-/- cell line generated from hESC cell line 3, total RNA


title: Super_DAL7.rep2


title: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 1

description:
2R15
TSC2-cellModel_RPF.txt

source_name: TSC2+/+ control generated from hESC cell line 2, RPF


title: Super_DAL7.rep3


title: Super_DAL8.rep3


title: Total RNA of TSC2-/- cell line generated from hESC cell line 3, Biological Replicate 2

description:
3T20
TSC2-cellModel_RNA.txt


title: Super_DAL8.rep1


title: Super_DAL7.rep1


title: Total RNA of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 2

description:
3T16
TSC2-cellModel_RNA.txt

source_name: TSC2+/+ control generated from hESC cell line 3, total RNA


title: Total RNA of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 1

description:
3T17
TSC2-cellModel_RNA.txt

source_name: TSC2+/- cell line generated from hESC cell line 3, total RNA


title: Super_DAL5.rep3


title: Super_DAL5.rep2


title: Ribosome protected fragments (RPF) of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 2

description:
2R16
TSC2-cellModel_RPF.txt


title: Super_DAL4.rep3


title: Super_DAL5.rep1


title: Total RNA of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 2

description:
2T20
TSC2-cellModel_RNA.txt

source_name: TSC2-/- cell line generated from hESC cell line 2, total RNA


title: Total RNA of TSC2+/+ control generated from hESC cell line 3, Biological Replicate 1

description:
3T15
TSC2-cellModel_RNA.txt


title: Super_DAL4.rep2


title: Super_DAL4.rep1


title: Super_DAL3.rep3


title: Total RNA of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 2

description:
2T16
TSC2-cellModel_RNA.txt

source_name: TSC2+/+ control generated from hESC cell line 2, total RNA


title: Total RNA of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 1

description:
2T17
TSC2-cellModel_RNA.txt

source_name: TSC2+/- cell line generated from hESC cell line 2, total RNA


title: Total RNA of TSC2+/+ control generated from hESC cell line 2, Biological Replicate 1

description:
2T15
TSC2-cellModel_RNA.txt


title: Super_DAL3.rep2


title: Super_DAL1.rep3


title: Total RNA of TSC2+/- cell line generated from hESC cell line 2, Biological Replicate 2

description:
2T18
TSC2-cellModel_RNA.txt


title: Super_DAL3.rep1


title: Normal_DAL5.rep3

value: normal ovary bloom


title: 293T_TET2_Mut_K27me3

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

library_source: genomic

data_processing:
base_calling: CASAVA package (Illumina v1.6)
ChIP-seq reads were aligned to the hg19 or mm9 genome assembly using bowtie-1.0.0
peaks were called using macs14 with the following setting:--pvalue=1e-5
normalized abundance on gene features is generated using home-made softwares
Genome_build: Genome_build: hg19,mm9
Supplementary_files_format_and_content: *peaks.bed: peaks bed files generated by Macs14, monoExt*.bed:mapped reads files in bed format, monoExt*.bg:ChIP-seq density files in bedgraph format.

molecule: genomic DNA

source_name: 293T cells

growth_protocol:
Cells were maintained in Dulbecco’s modified Eagle’s medium (Hyclone) containing 10% FBS (Hyclone).
Mouse embryonic stem cells (mESCs) were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% Glutamine, 1% NEAA and LIF. For ES cell maintenance dishes were coated with 0.2% gelantin and irradiated CF1 mouse embryonic fibroblasts (MEFs) were plated as confluent layer of feeder cells. ESCs were seeded in a density of 50000 cells/ 6well and were splitted every 2-3 days.

extract_protocol:
293T cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 108 cells and fragmented to 200 to 400 bp by sonication.Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.3% SDS) overnight at 4℃. The antibody-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
Mouse embryonic stem cells were crosslinked with formaldehyde treatment. The chromatin were isolated from 1 × 108 cells and fragmented to 200 to 400 bp by sonication.Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.3% SDS) overnight at 4℃. The antibody-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol:
Tet2,Tet2-mutant protein stably expressing HeLa cell lines were established using a retroviral expressing system.we also have a stable mock 293T cell line with empty vector using same retroviral expressing system.
Tet1\Tet2 double were knocked out in Mouse embryonic stem cells.

tag: cell line/type

value: Catalytic mutant TET2 stably expressed

tag: chip antibody


title: Super_DAL1.rep1


title: Total RNA of TSC2+/- cell line generated from hESC cell line 3, Biological Replicate 2

description:
3T18
TSC2-cellModel_RNA.txt


title: 293T_TET2_Mut_K4me3


title: 293T_TET2_WT_K4me3

value: WT TET2 stably expressed


title: 293T_TET2_Mut_Histone_Input


title: Total RNA of TSC2-/- cell line generated from hESC cell line 2, Biological Replicate 1

description:
2T19
TSC2-cellModel_RNA.txt


title: Normal_DAL5.rep2


title: Super_DAL1.rep2


title: Normal_DAL5.rep1


title: 293T_TET2_WT_Histone_Input


title: Normal_DAL4.rep3


title: 293T_mock_K4me3

value: Empty vector


title: 293T_TET2_WT_K27me3


title: 293T_mock_K27me3


title: Normal_DAL4.rep1


title: Normal_DAL3.rep2


title: 293T_TET2_Mut_MeDIP

value: 5mC Active Motif, #39649


title: Normal_DAL3.rep1


title: HeLa-S3_LATS2-/-_H3K4me3_ChIPSeq

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
The MACS software (ver. 1.4.1) was used for peak detection of each histone mark. The parameters for MACS were ‘--nomodel --extsize 146 --broad --to-large --pvalue 1e-3’, and the other parameters were the software defaults.
Genes were called in association with a given chromatin mark only when peaks were called within ±5 kb of the TSS.
To calculate normalized depth around TSSs of all RefSeq genes, and to perform GO analysis of the called genes, the Homer software was used with the default settings.
To visualize normalized ChIP profiles in genome browser, BigWig files were generated using our custom scripts and visualized using the IGV software from the Broad Institute.
Genome_build: Sequence reads for H3K27me3, H3K4me3, and input were aligned to the human genome (hg19) using the Bowtie software (parameter: -v 3 –m 1)
Supplementary_files_format_and_content: bigWig files were generated for processed data containing chromosome, regions

source_name: LATS2-knockout HeLa-S3 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP DNA and input DNA ends were repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase (PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3′-end. After ligation of the Genomic Adaptor Oligo Mix (Illumina) using TaKaRa Ligation Mix (TaKaRa), the adaptor-ligated DNA fragments were amplified with Paired-End Sample Prep Oligo primers (Illumina) for 18 cycles. The amplified library was separated on a 2.0% agarose gel, and the samples were purified using the QIAquick MinElute kit (Qiagen) after each preparation step. The purified library was used for cluster generation and sequencing analysis on a HiSeq 2000 (Illumina)

tag: cell line

value: cervix


title: HeLa-S3_LATS2-/-_H3K27ac_ChIPSeq


title: Normal_DAL1.rep3


title: 293T_TET2_Mut_DNA_Input


title: HeLa-S3_LATS2-/-_H3K27me3_ChIPSeq


title: Normal_DAL1.rep2


title: HeLa-S3_LATS2+/+_H3K4me3_ChIPSeq

source_name: parental wild-type HeLa-S3 cells


title: HeLa-S3_LATS2+/+_input DNA

description: WT_input DNA


title: 293T_TET2_WT_MeDIP


title: Normal_DAL1.rep1


title: HeLa-S3_LATS2+/+_H3K27me3_ChIPSeq


title: 293T_TET2_WT_hMeDIP

value: 5hmC Active Motif, #39769


title: Normal_DAL4.rep2


title: HeLa-S3_LATS2+/+_H3K27ac_ChIPSeq


title: 293T_mock_Histone_Input


title: fip37-4 LEC1:FIP37 2

city: Singapore

first: Hao

last: Yu

address: Science Drive 4

country: Singapore

institute: National University of Singapore

description: mRNA and LncRNA

data_processing:
Alignment: TopHat v2.0.9 using default settings; expression levels: Cufflinks v2.1.1 using default settings
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: Arabidopsis thaliana plants were grown on MS plates in growth chambers under long day conditions (16 hr light/8 hr dark) at 23°C ± 2°C.

extract_protocol:
Five-day-old wild-type and fip37-4 LEC1:FIP37 seedlings grown on MS plates were harvested for total RNA extraction using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. The amount and quality of RNA were tested by Qubit RNA Assay Kit (Life Technologies), gel electrophoresis and Agilent Bioanalyzer 2100 system. Ribosomal RNA was removed by Ribo-ZeroTM rRNA Removal Kit (Epicentre).
NEBNext® UltraTM Directional RNA Library Prep Kit for illumina® (NEB) was used to construct the library and sequencing was done on Illumina Hiseq 2500 platform.

tag: ecotype

value: Five-day-old

value: fip37-4 LEC1:FIP37

value: whole plant


title: 293T_TET2_WT_DNA_Input

tag: genotype/variation


title: 293T_mock_DNA_Input


title: fip37-4 LEC1:FIP37 1

description: mRNA and LncRNA


title: fip37-4 LEC1:FIP37 3

description: mRNA and LncRNA


title: Normal_DAL3.rep3

value: corolla


title: Wild-type 3

description: mRNA and LncRNA

value: Wild-type


title: 293T_mock_MeDIP


title: 293T_mock_hMeDIP


title: 293T_TET2_Mut_hMeDIP


title: Wild-type 2

description: mRNA and LncRNA


title: HeLa-S3_LATS2_KO+KD

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The low quality regions of raw reads were trimed with Btrim (http://graphics.med.yale.edu/trim/readme)
The trimmed reads were mapped onto the reference human genome hg19 using TopHat ver.2.0.11 in combination with Bowtie ver. 2.2.2 and SAMtools ver. 0.1.19
Gene expression was quantified with Cufflinks ver. 2.2.1
Genome_build: hg19

source_name: HeLa-S3 cell, LATS2 KO, rescued by kinase-dead LATS2, clone#21

growth_protocol: Add-back rescued LATS2 KO HeLa-S3 cells were cultured in DMEM + 10% fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).
120 ng of each DNA was sheared to about 400 bp fragments using the Covaris S220 (Covaris) with following condition; peak incident power 140 W; duty factor 10%; cycles per burst 200; and treatment time 55 seconds. The resulting DNA fragments were purified using 0.7× volume Agencourt AMPureXP beads (Beckman Coulter). Illumina libraries were prepared using KAPA Library Preparation Kit (Kapa Biosystems) and TruSeq adaptors (Illumina) according to manufacturer’s instructions.

treatment_protocol: no treatment

tag: trans-gene

value: LATS2 kinase-dead


title: HeLa-S3_LATS2_KO+WT

source_name: HeLa-S3 cell, LATS2 KO, rescued by wild-type LATS2, clone#21

value: LATS2 wild-type


title: HeLa-S3_LATS2_KO+EV

source_name: HeLa-S3 cell, LATS2 KO, rescued by empty vector, clone#3

value: empty vector


title: Wild-type 1

description: mRNA and LncRNA


title: fip37-4 LEC1:FIP37 IP2

data_processing:
Library strategy: m6A-seq
Sequence data were analyzed according to the procedure previously described (Dominissini et al., 2013). Briefly, BWA was run to align read sequences of the input and IP samples to the Columbia reference genome and annotation file (TAIR10). Non-unique reads with MAPQ less than 13 were discarded from downstream analysis. The peak-caller MACS (Feng et al., 2011; Dominissini et al., 2013) was used for peak detection, and the parameter of ‘effective genome size’ was adjusted to the calculated transcriptome size (65084215). Peaks were considered if their MACS-assigned false discovery rate (FDR) value is less than 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files were generated using the MACS2. Scores represent pileup normalized to 1M reads.

extract_protocol:
Five-day-old wild-type and fip37-4 LEC1:FIP37 seedlings grown on MS plates were collected. fip37-4 LEC1:FIP37 were identified in the segregated progenies from fip37-4/+ LEC1:FIP37 under microscope. Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s instructions. m6A sequencing was performed as previously described  (Dominissini et al., 2013). RNA samples were fragmented into ~100-nucleotide-long fragments by RNA fragmentation buffer (10 mM Tris-HCl, pH 7.0, 10 mM ZnCl2). Fragmented RNA was incubated for 2 h at 4 °C with 0.5 mg/ml anti-m6A polyclonal antibody (Synaptic Systems) in IP buffer (150 mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl, pH 7.4) supplemented with RNasin® Plus RNase inhibitor (Promega). The mixture was then immunoprecipitated by incubation with Protein A/G Plus-Agarose (Santa Cruz) that was pre-bound with bovine serum albumin (BSA) at 4 °C for an additional 2 h. After extensive washing, bound RNA was eluted from the beads with 6.7 mM N6-methyladenosine (Sigma-Aldrich) in IP buffer, and precipitated by ethanol.
NEBNext® UltraTM Directional RNA Library Prep Kit for illumina® (NEB) was used to construct the libraries from immunoprecipitated RNA and input RNA. Sequencing was done on Illumina Hiseq 2500 platform.

tag: antibody


title: HeLa-S3_LATS2-/-_input DNA

description: KO_input DNA


title: HeLa-S3_parental_WT_RNA-seq

description: HeLa-S3 cell, wild type

molecule: polyA RNA

source_name: HeLa-S3 cell, wild type

growth_protocol: LATS2 KO HeLa-S3 cells and parental wild type cells were cultured in DMEM + 10% fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA). After then,  polyA RNA was isolated from the total RNA with Nucleo-Trap mRNA kit (Macherey-Nagel) and prepare the double-stranded cDNA using SuperScript Double-Stranded cDNA Synthesis kit (Life Technologies) according to manufacturer's instructions.
120 ng of each double-stranded cDNA was sheared to about 400 bp fragments using the Covaris S220 (Covaris) with following condition; peak incident power 140 W; duty factor 10%; cycles per burst 200; and treatment time 55 seconds. The resulting DNA fragments were purified using 0.7× volume Agencourt AMPureXP beads (Beckman Coulter). Illumina libraries were prepared using KAPA Library Preparation Kit (Kapa Biosystems) and TruSeq adaptors (Illumina) according to manufacturer’s instructions.


title: HeLa-S3_LATS2_KO_RNA-seq

description: HeLa-S3 cell, LATS2 KO

source_name: HeLa-S3 cell, LATS2 KO


title: fip37-4 LEC1:FIP37 Input1


title: fip37-4 LEC1:FIP37 IP1


title: Wild-type Input2


title: Wild-type IP2


title: Wild-type Input1


title: BB cycling 28 rep 2

city: La Jolla

first: Thiago

middle: Ghirello

last: Lima

state: California

address: 9500 Gilman Drive #0202

institute: Scripps Institution of Oceanography

description:
SRX1538851
SAMN04431676
BB2028-20_2028-28_batch_DE.txt

data_processing:
Illumina reads were trimmed for adaptor sequence and for quality in CLC Genomics Workbench (v.7)
Trimmed reads from each population (all treatments combined) were mapped to the annotated Tigriopus californicus genome, and population specific consensus references were extracted
A de nono transcriptome form Pereira et al 2016 was used to complement our set of genes, as the annotated T californicus assembly is not complete
Genes from these reference genes were  annotated in Blast2GO
Trimmed reads (each treatment separate) were mapped to their respective assemblies in CLC Genomics Workbench (v.7)
Differential expression between treatment within each population was determined with the program EdgeR
Genome_build: The annotated T. californicus genome is published at https://i5k.nal.usda.gov/Tigriopus_californicus. De nono references from Pereira et al 2016 can be found in Dryad doi: 10.5061/ dryad.23s61
Supplementary_files_format_and_content: Processed files are the output of differential expression analyses for pairwise comparisons between two treatments. Files are tab delimited, with Gene ID (Name), log fold-change (logFC), log of counts per million (logCPM), likelihood ratio test (LR), p-value for the test (PValue), false discovery rate at 5% for multiple comparisons (FDR), and the last four columns are the normalized expression values for each replicate and treatment.

organism: Tigriopus californicus

source_name: Pooled whole animals

extract_protocol:
Pools of 100 adults individuals per populations per treatment were place in Tri-reagent following their respective treatment, extraction was done using manufacture's protocol
Libraries were prepared using the TruSeq mRNA unstranded prep kit

tag: location

value: Bodega Bay, California, USA

tag: region

value: northern CA

value: cycling 28


title: ESC_WT_K27me3

source_name: Mouse embryonic stem cells

value: Mouse embryonic stem cells (mES)

value: WT


title: BB cycling 20 rep 1

description:
SRX1538839
SAMN04431672
BB2028-20_2028-28_batch_DE.txt
BB20-20_2028-20_batch_DE.txt

tag: treatment

value: cycling 20


title: BB stress 28 rep 2

description:
SRX1538838
SAMN04431671
BB20-20_20-28_DE_desc.txt

value: stress 28


title: CNT1-G283E rep2

first: Sheng-Bo

last: He

address: 800 Rd Dongchuan

institute: Shanghai Jiao Tong University

description: replicate 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  primaryTranscript dataset obtained from primaryTranscript of  Arabidopsis thaliana TAIR10 gene set  using Bowtie 2 version 2.2.2  with parameters --very-fast-local
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

growth_protocol: seeds were germinated in 1/2 MS plus 1% sucrose and placed at 4 degree centigrade for 3 days and then tranferred to white light for 12 h before placed in darkness or blue light for another 4 days

extract_protocol:
RNA was extracted with RNAprep plant kit from TIANGEN, followed by DNase I (Takara) treatment. Quality control was performed with Agilent Bioanalyser. mRNA was purifed with Dynabeads® Oligo (dT)25（Life).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: light condition

value: 15 μmol/m2/s blue light

tag: growth time

value: 4.5 days


title: CNT1 rep1

description: replicate 1


title: ESC_WT_Histone_Input


title: CNT1 rep2

description: replicate 2


title: BB cycling 28 rep 1

description:
SRX1538846
SAMN04431675
BB2028-20_2028-28_batch_DE.txt


title: CNT1-G283E rep1

description: replicate 1


title: ESC_DKO_K4me3

value: Tet1 and Tet2 double knock


title: BB constant 20 rep 2

description:
SRX1538733
SAMN04431669
BB20-20_20-28_DE_desc.txt
BB20-20_2028-20_batch_DE.txt

value: constant 20


title: ESC_WT_K4me3


title: fip37-4 LEC1:FIP37 Input2

tag: age

value: Five-day-old

value: fip37-4 LEC1:FIP37

tag: tissue

value: whole plant


title: ESC_WT_MeDIP

value: 5mC Active Motif, #39649


title: BB stress 28 rep 1

description:
SRX1538755
SAMN04431670
BB20-20_20-28_DE_desc.txt


title: BB cycling 20 rep 2

description:
SRX1538840
SAMN04431673
BB2028-20_2028-28_batch_DE.txt
BB20-20_2028-20_batch_DE.txt


title: ESC_DKO_K27me3


title: BR cycling 28 rep 2

description:
SRX1538448
SAMN04422993
BR2028-20_2028-28_batch_DE.txt

value: La Jolla, California, USA

value: southern CA


title: SC stress 28 rep 1

description:
SRX1538586
SAMN04431661
SC20-20_20-28_batch_DE.txt

value: Santa Cruz, California, USA


title: SC constant 20 rep 1

description:
SRX1538449
SAMN04423024
SC20-20_20-28_batch_DE.txt
SC20-20_2028-20_batch_DE.txt

value: northern CA


title: ESC_DKO_hMeDIP

value: 5hmC Active Motif, #39769


title: ESC_WT_DNA_Input

value: Mouse embryonic stem cells (mES)


title: ESC_DKO_MeDIP


title: ESC_WT_hMeDIP

value: WT


title: Wild-type IP1

tag: genotype

value: Wild-type


title: BR cycling 20 rep 1

description:
SRX1538443
SAMN04422452
BR2028-20_2028-28_batch_DE.txt
BR20-20_2028-20_batch_DE.txt

value: cycling 20


title: BR stress 28 rep 2

description:
SRX1538387
SAMN04422447
BR20-20_20-28_batch_DE.txt

value: stress 28


title: NC-siRNA

city: Nanjing

first: lifan

last: zhang

state: Jiangsu

address: No.6 Tongwei road

department: College of Animal Science and Technology

institute: Nanjing agricultural university

description: NC-siRNA treated cells from three individuals pooled

data_processing:
Raw sequencing data was evaluated by FAST-QC
Raw reads after quality control testing were mapped to the reference pig genome version 10.2 (Sscrofa 10.2) using MapSplice program (v.2.1.8)
The normalized expression level of each gene was measured by Upper Quartile of Reads Per Kilobase per Million mapped reads (UQRPKM)
Genome_build: Sscrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files include UQRPKM values for each gene

organism: Sus scrofa

source_name: follicular granulosa cell

extract_protocol:
Follicular granulosa cells were subjected to total RNA extraction using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA from NC-siRNA and SMAD4-siRNA treatment groups (three individuals/group) was pooled in equal amounts to generate mixed sample respectively. Sequencing libraries were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Ion protocols

treatment_protocol: Two groups of follicular granulosa cells treated of NC-siRNA and SMAD4-siRNA

tag: strain

value: Chinese Erhualian pigs

value: ovary

tag: Sex

value: female


title: BB constant 20 rep 1

description:
SRX1538729
SAMN04431668
BB20-20_20-28_DE_desc.txt
BB20-20_2028-20_batch_DE.txt

value: Bodega Bay, California, USA

value: constant 20


title: SMAD4-siRNA

description: SMAD4-siRNA treated cells from three individuals pooled


title: BR stress 28 rep 1

description:
SRX1538386
SAMN04422446
BR20-20_20-28_batch_DE.txt


title: KO_DH

city: Leeds

first: Andrew

last: Cuming

address: Faculty of Biological Sciences

department: Centre for Plant Sciences

country: United Kingdom

institute: University of Leeds

data_processing:
Illumina basecall software
Raw reads were trimmed for low quality bases, adapters as well as first 10-12bp of each read which showed some bias according to fastqc using trimmomatic.
Reads were mapped to the V3.0 Physcomitrella patens genome assembly and to the V3.0 gff3 gene models using tophat2 using the --b2-very-sensitive option.
Mapped reads were sorted and indexed using samtools.
Bedtools was used to extract count data against a gene model gff file of V3.0 gene models for use in Trinity Differential Gene Expression package after TMM normalisation.
Genome_build: Physcomitrella patens V3.0
Supplementary_files_format_and_content: Normalised_abundance.txt data file contains the tab-delimited TMM normalised count values matrix for all libraries with columns in order: WT_C, WT_ABA, WT_DH, WT_man, KO_C, KO_ABA, KO_DH, KO_Man. Pp_genemodels.gff contains a modified version of the full V3.0 gff3 file which contains all gene features. These were stripped out to leave only the gene start and finish coordinates.

organism: Physcomitrium patens

source_name: 6-day subcultured chloronemata

growth_protocol: Chloronemal homogenate cultures were grown on BCDAT agar medium overlaid with cellophanes at 25 C, under continuous illumination (50W.m2.cm2) and subcultured every 6 days.

extract_protocol:
Tissue was squeezed dry between two sheets of 3MM paper and frozen in liquig N2. Tissue was powdered in liquid N2 and  RNA was extracted in 0.1M Tris-Cl, pH9.0-0.5% (w/v) SDS – 2% (w/v) PVP-40 – 5mM beta-mercaptoethanol and emulsified with phenol-chloroform-isoamyl alcohol (25:24:1). Total nucleic acids were recovered by ethanol precipitation and RNA purified by selective precipitation in 2.5M NaCl at 4 C. Residual DNA was removed by digestion with RQ DNase1 at room temperature for 15 minutes, and the RNA recovered by phenol-chloroform extraction and ethanol precipitation.
cDNA libraries were constructed and sequenced by GATC Biotech (Konstanz, Germany). cDNA was synthesised from poly(A)-containing RNA by random primed reverse transcription.

treatment_protocol: For hormone and mannitol treatment, cellophanes were transferred into Petri dishes containing a 3MM paper disc soaked with liquid BCDAT medium containing ABA (10-5M) or mannitol (10% (w/v)) for 1 hour. For dehydration, tissue was transferred from cellophane into empty 9cm Petri dishes and the open dishes were placed in a desiccator over a saturated solution of NaCl, and allowed to slowly dehydrate. Tissue was harvested after 70% of the original fresh weight had been lost.

value: Gransden

value: PpanrKO


title: SC cycling 20 rep 2

description:
SRX1538713
SAMN04431664
SC2028-20_2028-28_batch_DE.txt
SC20-20_2028-20_batch_DE.txt


title: SC cycling 28 rep 2

description:
SRX1538720
SAMN04431667
SC2028-20_2028-28_batch_DE.txt

value: cycling 28


title: SC cycling 20 rep 1

description:
SRX1538641
SAMN04431663
SC2028-20_2028-28_batch_DE.txt
SC20-20_2028-20_batch_DE.txt


title: BR cycling 28 rep 1

description:
SRX1538447
SAMN04422987
BR2028-20_2028-28_batch_DE.txt

value: La Jolla, California, USA

value: southern CA


title: KO_C


title: ESC_DKO_DNA_Input

tag: cell line/type

value: Tet1 and Tet2 double knock


title: SC stress 28 rep 2

description:
SRX1538588
SAMN04431662
SC20-20_20-28_batch_DE.txt

value: Santa Cruz, California, USA

value: northern CA


title: KO_ABA


title: SC cycling 28 rep 1

description:
SRX1538716
SAMN04431665
SC2028-20_2028-28_batch_DE.txt


title: BR constant 20 rep 1

description:
SRX1538382
SAMN04422392
BR20-20_20-28_batch_DE.txt
BR20-20_2028-20_batch_DE.txt


title: ESC_DKO_Histone_Input

value: Mouse embryonic stem cells (mES)

tag: chip antibody


title: BR constant 20 rep 2

description:
SRX1538383
SAMN04422440
BR20-20_20-28_batch_DE.txt
BR20-20_2028-20_batch_DE.txt


title: SC constant 20 rep 2

description:
SRX1538450
SAMN04431660
SC20-20_20-28_batch_DE.txt
SC20-20_2028-20_batch_DE.txt


title: KO_Man


title: BR cycling 20 rep 2

description:
SRX1538444
SAMN04422986
BR2028-20_2028-28_batch_DE.txt
BR20-20_2028-20_batch_DE.txt


title: SD cycling 28 rep 2

description:
SRX1538365
SAMN04422348
SD2028-20_2028-28_batch_DE.txt

value: San Diego, California, USA


title: SD cycling 28 rep 1

description:
SRX1538360
SAMN04422288
SD2028-20_2028-28_batch_DE.txt


title: WT_Man

value: wild-type


title: SD cycling 20 rep 1

description:
SRX1538358
SAMN04422281
SD2028-20_2028-28_batch_DE.txt
SD20-20_2028-20_batch_DE.txt

value: cycling 20


title: WT_ABA


title: SD cycling 20 rep 2

description:
SRX1538359
SAMN04422286
SD2028-20_2028-28_batch_DE.txt
SD20-20_2028-20_batch_DE.txt


title: WT_C


title: SD stress 28 rep 1

description:
SRX1538356
SAMN04422190
SD20-20_20-28_batch_DE.txt

value: stress 28


title: SD constant 20 rep 1

description:
SRX1536404
SAMN04422048
SD20-20_20-28_batch_DE.txt
SD20-20_2028-20_batch_DE.txt


title: SD constant 20 rep 2

description:
SRX1538171
SAMN04422177
SD20-20_20-28_batch_DE.txt
SD20-20_2028-20_batch_DE.txt


title: SD stress 28 rep 2

description:
SRX1538357
SAMN04422277
SD20-20_20-28_batch_DE.txt


title: 3rd 12h JQ1(-) 0.2 µM

status: Public on Jul 24 2016

first: Guofeng

last: Meng

address: Jinke 3528

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
Sequencing was performed by HiSeq2000 sequencing platform
Quality control to raw data using “fastqc”
RNA-seq reads were aligned to mouse genome (mm9) using TopHat2
The gene expression was quantified using RPKM values from cufflink analysis using NCBI RefSeq gene annotation
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Neural progenitor cells

growth_protocol: NPCs from E12 mouse cortices were isolated and expanded in DMEM/F12 containing 2% of B27-supplement and 10 ng/ml of basic fibroblast growth factor (bFGF). NPCs of passage 3 were used in all assays.

extract_protocol:
RNA was isolated using  RNeasy Mini Kit (Qiagen, Valencia, CA). The samples were quantified and more than 2 μg of total RNA for each sample was sent to BGI for library construction.
i. DNase I digest: DNase I degrade double-stranded and single-stranded DNA in RNA samples.  ii. mRNA isolation: Poly (A)-containing mRNA molecules were purified from total RNA using poly (T) oligo-attached magnetic beads.  iii. mRNA fragment: mRNA were fragmented into small pieces using fragmentation reagent.  iv. cDNA synthesis: First-strand cDNA was generated using random hexamer-primed reverse transcription. This was followed by a second-strand cDNA synthesis and a cDNA purify using purification Kit.  v. End repair, add A and adaptor ligation: The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNA fragments. Ligation products were purified with the magnetic beads, and dissolved in the appropriate amount of Epstein-Barr solution.  vi. RCR: This process was to amplify those cDNA fragments with adaptors from previous step. PCR products were purified with the magnetic beads, and dissolved in the appropriate amount of Epstein-Barr solution.  vii. Library quality control: Library was validating on the Agilent Technologies 210
RNA-Seq. Single-end 50bp (SE50) sequencing was done on the HiSeq2000 sequencing platform (Illumina, Inc, CA, USA) according to the manufacturer’s protocol.

treatment_protocol: NPCs were treated with (+)-JQ-1 or inactive enantiomer (-)-JQ-1 at 0.2 μM or 0.5 μM for 12 and 24 hrs in differentiation medium. The experiments were carried out in  3 independent preparations of NPCs (triplicates).

tag: cell type

value: Brain cortices_E12_isolated neural progenitor cells


title: 3rd 12h JQ1(+) 0.5 µM


title: 3rd 12h JQ1(-) 0.5 µM


title: 2nd 12h JQ1(+) 0.2 µM


title: 3rd 12h JQ1(+) 0.2 µM


title: 2nd 12h JQ1(-) 0.2 µM


title: 2nd 12h JQ1(-) 0.5 µM


title: 1st 12h JQ1(-) 0.5 µM


title: 2nd 12h JQ1(+) 0.5 µM


title: 1st 12h JQ1(+) 0.5 µM


title: 1st 12h JQ1(+) 0.2 µM


title: 3rd 24h JQ1(-) 0.5 µM


title: 1st 12h JQ1(-) 0.2 µM


title: 3rd 24h JQ1(+) 0.2 µM


title: 3rd 24h JQ1(-) 0.2 µM


title: 2nd 24h JQ1(-) 0.5 µM


title: 3rd 24h JQ1(+) 0.5 µM


title: 2nd 24h JQ1(-) 0.2 µM


title: 2nd 24h JQ1(+) 0.2 µM


title: 2nd 24h JQ1(+) 0.5 µM


title: 1st 24h JQ1(-) 0.5 µM


title: WT_DH


title: 1st 24h JQ1(+) 0.5 µM


title: 1st 24h JQ1 (+) 0.2 µM


title: 1st 24h JQ1(-) 0.2 µM


title: BS-seq-hiEndoPC2

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

data_processing:
Paired-end BS-seq reads were  mapped against the reference by Bismark with stringent parameters: -n 2 -l 60 -e 100 -X 600. The overlapped part of paired reads is trimmed from one end to prevent counting twice from the same observation. For each CpG site, the number of CGs and the number of TGs were counted.
5mC level is calculated as the number of CGs divided by the sum of the number of CGs and the number of Tgs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include 5mC level for each sample. The file "README-BSseq.txt.gz" (available on the series record) contains column header information for the processed data files.

source_name: hiMEPs derived from GECs by reprogramming

growth_protocol: GECs were cultured in Kubota's medium. The hiMEPs were reprogrammed from GECs under advanced DMEM/F12 with 2μM Bay K 8644, 0.5μM Bix01294 , 0.04μM RG108, 2μM SB431542, with the support of feeder cells. The hiMEP-Heps were induced from hiMEPs under hepatic differentiation conditions and cultured in hepatocyte medium (Sciencell) with 25 ng/ml HGF (R&D), 1 μM Dexamethasone (Sigma), and 10 ng/ml OSM (R&D).Fetal-Heps were cultured in hepatocyte medium (Sciencell).

extract_protocol:
genomic DNA(Qiagen, Cat#: 51306) were extracted according to manufacturer’s instructions.
The DNA was directed to bisulfite conversion using the EZ DNA methylation-Gold kit (Zymo Research) according to the instruction manual. The library was sequenced using illumina Hiseq platform.

treatment_protocol: GECs, hiMEP-Heps and Fetal-Heps were collected after trypsinized with TrypLE. The hiMEPs were collected by manual picking.


title: BS-seq-hiEndoPC1

value: hiMEPs derived from GECs by reprogramming


title: BS-seq-hiEndoPC-Hep1

source_name: hepatoctes induced by differentiation of hiMEPs


title: BS-seq-hGEC1

source_name: gastric epthelial cells isolated from stomach

value: stomach


title: RNA-seq-hiEndoPC-Hep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were  mapped against the UCSC GRCh38 reference by Tophat with stringent parameters: --coverage-search --microexon-search --b2-very-sensitive. Only unique mapping reads were retained for normalization purposes. Read counts of each gene were summarized using HTSeq version 0.6.1p1. DESeq2 was used to normalize read counts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts of each gene for each sample. The "README.txt" file on the series record contains annotations for the processed data file.

extract_protocol:
total RNA (Qiagen, Cat#: 74004) were extracted according to manufacturer’s instructions.
mRNA was reverse transcribed and amplified by REPLI-g Single Cell Kit (cat#. 150063). The library was sequenced using Illumina HiSeq 2500.

value: hepatoctes induced by differentiation of hiMEPs


title: RNA-seq-hiEndoPC-Hep1


title: RNA-seq-PGT2

data_processing:
Illumina Casava1.7 software used for basecalling.
Paired-end reads were  mapped against the UCSC GRCh38 reference by Tophat with stringent parameters: --coverage-search --microexon-search --b2-very-sensitive. Only unique mapping reads were retained for normalization purposes. Read counts of each gene were summarized using HTSeq version 0.6.1p1. DESeq2 was used to normalize read counts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts of each gene for each sample

source_name: hESC-derived primitive gut tube

growth_protocol: GECs were cultured in Kubota's medium. The hiMEPs were reprogrammed from GECs under advanced DMEM/F12 with 2μM Bay K 8644, 0.5μM Bix01294 , 0.04μM RG108, 2μM SB431542, with the support of feeder cells. The hiMEP-Heps were induced from hiMEPs under hepatic differentiation conditions and cultured in hepatocyte medium (Sciencell) with 25 ng/ml HGF (R&D), 1 μM Dexamethasone (Sigma), and 10 ng/ml OSM (R&D).Fetal-Heps were cultured in hepatocyte medium (Sciencell).To induce ESCs differentiation to definitive endoderm (DE) cells, 80% confluent ESCs were cultured in RPMI 1640 with 3 μM CHIR99021 and 100 ng/ml Activin A for 1 day. The medium was then changed to RPMI 1640 with 0.2% FBS and 100 ng/ml Activin A for 2 days. To further differentiate to primitive gut endoderm (PGT) cells, the medium was changed to RPMI 1640 with 2% FBS, 50 ng/ml human FGF10, and 0.25 mM KAAD-cyclopamine (Stemgent) for 3 days. To differentiate to posterior foregut (PFG) cells, day3 DE was cultured in RPMI 1640 with 2 μM RA (Sigma) and 1.5 μM Dorsomorphin (Stemgent).

extract_protocol:
total RNA (Qiagen, Cat#: 74004) were extracted according to manufacturer’s instructions.
mRNA was reverse transcribed and amplified by REPLI-g Single Cell Kit (cat#. 150063). The library was sequenced using Illumina HiSeq X ten.

treatment_protocol: GECs, hiMEP-Heps, Fetal-Heps, DE, PGT and PFG were collected after trypsinized with TrypLE. The hiMEPs were collected by manual picking.

value: hESC-derived primitive gut tube


title: RNA-seq-PGT1


title: RNA-seq-PFG1

source_name: hESC-derived posterior foregut

value: hESC-derived posterior foregut


title: RNA-seq-hiEndoPC-Hep2


title: WT

city: Pasadena

first: Chun-Kan

last: Chen

address: 1200 E California Blvd

institute: California Institute of Technology

data_processing:
Library strategy: RAP-Seq
Sequencing reads were aligned to the Mus musculus genome (mm9)
using bowtie2 with the following parameters: -k 1 --very-sensitive --fr --no-discordant --no-mixed --maxins 2000. Reads were removed if they had mapping qualities less than 30. We calculated alignment statistics for each library using the Picard package. All calculations were performed using fragment counts, which were defined using the read-pairs.
We calculated the data by first scaling the number of reads in each sample to obtain the same total number of reads for all the samples in 1 kb windows. We then normalized each sample to its own input followed by a second normalization to the wild-type Xist sample to obtain the relative ratio of each window. We then plotted the log-ratio of these values 100 Kb upstream and downstream of each gene on X-chromosome along with the gene body region, which was scaled across genes to represent the same overall area.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig or bedgraph files showing relative Xist enrichment across X-chromosome of each sample in comparison to wild-type cells

source_name: mouse ES cells

extract_protocol:
10 million mouse ES cells were induced with  doxycycline for 6 hours and were prepared and Xist RNA was captured and purified with antisense 5’ biotinylated 90-mer DNA oligonucleotides that spanned the entire length of the Xist RNA.
We generated standard Illumina sequencing libraries using the ChIP Seq Library Prep Master Mix Set (New England Biolabs). We used barcoded adaptors to allow multiplexed sequencing, and amplified RAP libraries with 10-16 cycles of PCR.

tag: cell line


title: RNA-seq-hiEndoPC4


title: RNA-seq-hiEndoPC5


title: RNA-seq-hiEndoPC3


title: RNA-seq-hiEndoPC2


title: WTInput


title: RNA-seq-hiEndoPC1


title: RNA-seq-DE1

source_name: hESC-derived definitive endoderm

value: hESC-derived definitive endoderm


title: RNA-seq-GEC2

value: gastric epthelial cells isolated from stomach


title: LMNBRes


title: dLBS


title: BS-seq-hiEndoPC-Hep2


title: RNA-seq-Fetal-Hep2

source_name: fetal hepatocytes isolated from fetal liver

value: liver


title: BS-seq-hGEC2


title: RNA-seq-Fetal-Hep1

value: fetal hepatocytes isolated from fetal liver


title: LBRKD


title: Ctrl rep1

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2)
Sequence libraries were filtered for adapter contamination using cutadapt (v1.8.3)
Filtered reads were aligned to hg19 geneome assembly using Bowtie (v.2.2.5)
Counted the siBP3 and control samples mapped readsin the annotated transcripts regions using featurecounts(v1.4.6) module from subread package. Counts were normalized to library size
Differential expression analysis was performed using edgeR bioconductor package (v.3.8.6)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include count per million values for each Sample

source_name: HeLa cell lines

growth_protocol: Cells were grown until 70% confluency, and then transiently transfected with siRNAs   using Lipofectamine RNAiMax reagent according to manufacturer’s protocol (Thermofisher Scientic). Second siRNA transfection were done 48 hours later. Cells then were harvested after 48 hours

extract_protocol:
Total RNA was extracted using Trizol® reagent following the manufacturer’s protocol (Thermofisher Scientic)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Not applicable

value: Hela

value: cervical carcinoma

value: immortal

value: Ctrl


title: siBP3 rep1


title: siBP3 rep2


title: Ctrl rep2


title: RNA-seq-DE2


title: HP1BP3_ChIP

data_processing:
Basecalls were performed using CASAVA (v. 1.8.2)
ChIP-seq reads were aligned to hg19 geneome assembly using Bowtie (v.2.2.5)
Mapped reads were filtered to remove low quality, ambiguous and redundant reads
Peaks were called using the SICER (v. 1.1)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contains DROSHA, HP1BP3 and H1.5 peak coordinates in BED format

source_name: BAC transgenic Hela cell lines

growth_protocol: HeLa cells were cultured at 37 °C in 5% CO2 in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin /streptomycin.

extract_protocol:
BAC transgenic cells at 80% confluency (~1x107) were cross-linked with 1% formaldehyde for 10 minutes at 37°C, and quenched with 125 mM glycine at room temperature for 5 minutes. The fixed cells were washed twice with cold PBS, scraped, and transferred into 1 ml PBS containing protease inhibitors (Roche). After centrifugation at 700 g for 4 minutes at 4°C, the cell pellets were resuspended in 100 μl ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors) and sonicated at 4°C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 15 minutes). The sheared chromatin with a fragment length of ~200 – 600 bp) was centrifuged at 20,000 g for 15 minutes at 4°C). 100 μl of the supernatant was used for ChIP or as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4°C overnight with 6 μg/ml of a goat anti-GFP (raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP). Immunoprecipitation was carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4°C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65°C in 192 mM NaCl for 16 hours. DNA fragments were purified using QiaQuick PCR Purification kit (QIAGEN) and eluted into 30 μl H2O according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.
barcoded libraries of DROSHA-GFP, HP1BP3-GFP and H1.5-GFP ChIP and input DNA were generated with the TruSeq® ChIP Sample Preparation Kit (Illumina)

value: HeLa

value: Polyclonal (goat) against full length His-EGFP


title: HP1BP3_INPUT


title: RNA-seq-hGEC1


title: SHARPKD


title: H1_5_ChIP


title: DROSHA_ChIP


title: WT_SDA

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

description: Experiment of library WT

data_processing:
Illumina HiSeq™ 2000 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Screening of differentially expressed genes in paired library of WT_SDA/BbSNF1_SDA. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Data table including Gene ID, gene length, RPKM values, log2(fold change) and FDR-value  for the paired sample.

organism: Beauveria bassiana ARSEF 2860

source_name: WT mycelia

growth_protocol: Conidia suspension (100 ul,5X106 conidia ml-1) of WT and ΔBbSNF1 of Beauveria bassiana were inoculated on the SDA plates (Glucose 4%, Peptone 1%, and Yeast extract 1% plus 1.5% Agar), respectively, and incubated at 25 °C for 4 day with shaking.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were harvested from the culture plates.

value: ARSEF 2860

tag: genotype/variation

value: wild-type

tag: culture time

value: 4 days

value: mycelia


title: ddm1 dcl3 replicate A (sRNA seq)

status: Public on Jul 22 2016

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA-seq
Equivalent to GSM1376911 (same raw file, same processed file).

data_processing:
Illumina software was used for basecalling. Sequenced reads were de-multiplexed and trimmed for adaptor sequence. Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, tRNA and rRNA-matching reads were removed, and only small RNAs that perfectly match the genome are reported (UEA small RNA tool v 2.5.0 used).
Genome_build: TAIR10
Supplementary_files_format_and_content: First column: small RNA sequence. Second column: normalized abundance (Reads per million) of the small RNA.

source_name: ddm1-2 dcl3-1

growth_protocol: Plants were grown on soil in 18 hour long days at 22-23ºC (as indicated in Characteristics 'growth conditions').

extract_protocol: For the total RNA libraries, total RNA was extracted using Trizol reagent and enriched using the MirVana microRNA isolation kit. Cloning of small RNAs was performed using the Illumina TruSeq RNA Sample Preparation Kit.

tag: ecotype

value: Col

value: ddm1 dcl3 mutant

tag: developmental stage

value: stage 1-12

value: inflorescence


title: DROSHA_INPUT

tag: antibody


title: ddm1 replicate B (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1376907 (same raw file, same processed file).

value: ddm1 mutant


title: ddm1 pol IV rdr6 replicate B (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1376917 (same raw file, same processed file).

source_name: ddm1-2 nrpd1a-3 rdr6-15

value: ddm1 pol IV rdr6 mutant


title: pol IV (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1376902 (same raw file, same processed file).

value: pol IV mutant


title: ddm1 pol V (sRNA seq)

description: small RNA-seq

source_name: ddm1-2 pol V

value: ddm1 pol V mutant


title: H1_5_INPUT


title: ddm1 rdr6 replicate B (sRNA seq)

description: small RNA-seq

value: ddm1 rdr6 mutant


title: ddm1 dcl3 replicate B (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1376912 (same raw file, same processed file).


title: wt Col replicate B (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1376900 (same raw file, same processed file).

source_name: wild type Columbia

value: wild type


title: DBbSNF1_SDA

description: Experiment of library DBbSNF1

source_name: DBbSNF1 mycelia


title: ddm1 rdr2 (sRNA seq)

description: small RNA-seq

source_name: ddm1-2 rdr2-1

value: ddm1 rdr2 mutant


title: ddm1 pol IV rdr6 replicate A (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1376916 (same raw file, same processed file).


title: ddm1 pol IV replicate B (sRNA seq)

description: small RNA-seq

source_name: ddm1-2 nrpd1a-3

value: ddm1 pol IV mutant


title: ddm1 pol IV replicate A (sRNA seq)

description: small RNA-seq


title: pol IV rdr6 (sRNA seq)

description: small RNA-seq

source_name: nrpd1a-3 rdr6-15

value: pol IV rdr6 mutant


title: rdr6 replicate B (sRNA seq)

description: small RNA-seq

value: rdr6 mutant


title: dcl3 (sRNA seq)

description: small RNA-seq

value: dcl3 mutant


title: tel_ch9

city: New York

first: Neeman

last: Mohibullah

state: NY

address: 1275 York Avenue

department: Molecular Biology

institute: MSKCC

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

organism: Saccharomyces cerevisiae

source_name: tel1∆ (Chr IX insert)

growth_protocol: Synchronized meiotic cultures were prepared in 2% potassium acetate at 30°C by the SPS pre-growth method as described in Murakami et al. (2009) Methods Mol Biol 557: 117-142

extract_protocol:
Based on Thacker et al 2014 Nature, with modifications. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Protein A fusion with IgG-coated Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell, and Thacker et al. 2014 Nature. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: epitope tag

tag: artificial hotspot

value: arg4-URA3 insert on Chr IX

tag: time in meiosis

value: 4 hr in meiosis


title: wt_ch9

description: Spo11-associated DNA oligonucleotides

source_name: Wild type (Chr IX insert)


title: tel_ch3

description: Spo11-associated DNA oligonucleotides

source_name: tel1∆ (Chr III insert)

value: arg4-URA3 insert on Chr III


title: wt_ch3

description: Spo11-associated DNA oligonucleotides

source_name: Wild type (Chr III insert)


title: tel6_2

description: Spo11-associated DNA oligonucleotides

source_name: tel1∆ 6 h sample 2

value: 6 hr in meiosis


title: telzip_1

description: Spo11-associated DNA oligonucleotides

source_name: tel1∆ zip3∆ sample 1

value: tel1 zip3


title: tel4_2

description: Spo11-associated DNA oligonucleotides

source_name: tel1∆ 4 h sample 2


title: tel6_1

description: Spo11-associated DNA oligonucleotides

source_name: tel1∆ 6 h sample 1


title: wt6_2

description: Spo11-associated DNA oligonucleotides

source_name: Wild type 6 h sample 2


title: wt4_2

description: Spo11-associated DNA oligonucleotides

source_name: Wild type 4 h sample 2


title: wt5_1

description: Spo11-associated DNA oligonucleotides

source_name: Wild type 5h sample 1

value: 5 hr in meiosis


title: ddm1 dcl3

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: library strategy: MethylC-seq

data_processing:
Data were mapped to the TAIR10 reference genome
MethylC-seq analysis were performed as described in Schmtiz et al. Epigenome-wide inheritance of DNA methylation variants in a recombinant inbred population. Genome Research (2013).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab delimited text file, see metafile for column headers

source_name: stage 1-9 inflorescence tissue

growth_protocol: All mutants used in this study are in the Col-0 ecotype background of Arabidopsis thaliana. Plants were grown in long-day (18 hour light) conditions at 23℃ and stage 1-12 inflorescence tissue was used for all experiments and sequencing.

extract_protocol: DNA was isolated using fractional precipitation followed by phenol-chloroform extraction and RNase A treatment. 1ug of DNA was used to prepare libraries as previously described (Urich et al. 2015).

value: ddm1 dcl3


title: ddm1 pol V

description: library strategy: MethylC-seq

value: ddm1 pol V


title: ddm1 rdr6

description: library strategy: MethylC-seq

value: ddm1 rdr6


title: RNA-seq-PFG2

source_name: hESC-derived posterior foregut

value: hESC-derived posterior foregut


title: ddm1 rdr2

description: library strategy: MethylC-seq

value: ddm1 rdr2


title: ddm1 pol IV

description: library strategy: MethylC-seq

value: ddm1 pol IV


title: ddm1 drm2

description: library strategy: MethylC-seq

value: ddm1 drm2


title: ddm1

description: library strategy: MethylC-seq


title: rdr6

description: library strategy: MethylC-seq


title: rdr2

description: library strategy: MethylC-seq


title: telzip_2

description: Spo11-associated DNA oligonucleotides

source_name: tel1∆ zip3∆ sample 2


title: pol V

description: library strategy: MethylC-seq

value: pol V


title: pol IV

description: library strategy: MethylC-seq

value: pol IV


title: pol IV rdr6

description: library strategy: MethylC-seq

value: pol IV rdr6


title: drm2

description: library strategy: MethylC-seq


title: wt4_1

description: Spo11-associated DNA oligonucleotides

source_name: Wild type 4 h sample 1

value: wild type


title: wt6_1

description: Spo11-associated DNA oligonucleotides

source_name: Wild type 6 h sample 1


title: wt5_2

description: Spo11-associated DNA oligonucleotides

source_name: Wild type 5 h sample 2


title: cmt2

description: library strategy: MethylC-seq


title: wildtype Col-0

description: library strategy: MethylC-seq

value: wildtype Col-0


title: dcl3

description: library strategy: MethylC-seq


title: MN_Spombe_Drsc1_1

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Alignment: bowtie 0.12.7
The smoothed profiles at jBrowse available in http://genomics.usal.es/Materne2016 were generated by using a modified version of NUCwave (Quintales et al. 2015) to normalize signal against repeated sequences.
Genome_build: S. pombe 2007 (ASM294v2)

organism: Schizosaccharomyces pombe

growth_protocol: Yeast cultures were grown in YES medium

extract_protocol:
200 ml cultures at 0.8x10⁷ cells/ml were collected  for preparation of mononucleosomal DNA. Cells were treated with 8 mg of Zymolyase  20T during 30 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 200 units/ml of micrococcal nuclease (MNase) at 37 ºC during 45 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the 2x41 pair-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: molecule subtype

value: Mononucleosomal DNA


title: MN_Spombe_WT_2


title: ago1

description: library strategy: MethylC-seq


title: tel4_1

description: Spo11-associated DNA oligonucleotides

source_name: tel1∆ 4 h sample 1

tag: genotype

value: 4 hr in meiosis


title: ddm1 rdr6 replicate A (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1023593 (same raw file, same processed file).

value: Col

value: ddm1 rdr6 mutant

value: stage 1-12

tag: tissue

value: inflorescence


title: MN_Spombe_Drsc1_2


title: ddm1 replicate A (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1023592 (same raw file, same processed file).

value: ddm1 mutant


title: splB_mix_JK2_BL6

city: Boston

first: Jiazhi

last: Hu

state: MA

address: 300 Longwood Ave

department: PCMM

institute: Children's Hospital Boston

description:
Sample 56
Barcode: CA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

data_processing:
HTGTSrep pipeline was used for generating the processed files with "pass.xls" ends; Linear amplification-mediated (LAM)-HTGTS pipeline was used for generating processed files with "tlx" ends.
Paire-end sequenced reads were trimmed for barcode and adaptor sequence and joined
The trimmed reads then were searched against VDJ gene databases using igblast1.5 with default parameters and further processed by the HTGTSrep pipeline, or against LAM-HTGTS pipeline with default settings.
For HTGTSrep pipeline, reads can successfully aligned to V, D, J databases are reported and a statistic report including V gene usage and in-frame/non-productive information is created by the pipeline.
Genome_build: mm9, mm9_AJ851868ins (Based on the genome build of mm9, we replaced its chr12 between 114,493,850 and 115,696,909 with the reverse complement sequence of the GeneBank AJ851868.3)
Supplementary_files_format_and_content: tab-delimited text files include aligned V, D, J genes for each read and a V usage report for each sample.

growth_protocol: Mice were bought from Jackson labs and kept in our mouse facility

extract_protocol:
Tissues were extracted and treated with RBC lysis, resuspended in PBS, and stained for FACS. Bone marrow-derived pro-B (B220+IgM-CD43+) cells were purified from 129SVE or C57BL/6 mice by sorting and after the depletion of erythrocytes. Single cell suspensions were stained with B220-APC, CD43-PE, and IgM-FITC antibodies. Splenic resting B cells were purified using biotin/streptavidin bead methods (B220 positive selection) or EasySep CD43-negative B cell selection.  Cells were then processed for genomic DNA extraction.
Libraries were prepared via HTGTS-Rep-seq protocols

treatment_protocol: No immunization, but the food and water are not germ-free

tag: strain

value: wild-type

tag: bait locus

tag: growth protocol

value: No immunization

tag: age

value: 4-6 weeks

value: Splenic B

tag: primer strategy

value: Combined with Jk1, Jk4, Jk5 primers in one library preparation

tag: dna amount

value: 1 ug


title: GFP_ChIP-seq

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Raw data were analyzed by the Illumina CASAVA 1.8.2
Alignment : Reads were mapped to mm9 assembly of mouse genome using Bowtie aligner release<=1.0.0, with principle parameters: -m 1 --strata --best
Peak detection was performed using the MACS (version 1.4.2) software under settings where an anti-GFP ChIP was used as a negative control
Genome_build: mm9
Supplementary_files_format_and_content: MACS 1.4.2 peak calling file with the following collumns: chr, start,end,length,summit,tags,-10*LOG10(pvalue),fold_enrichment,FDR(%),peak name.

source_name: caudate putamen

growth_protocol: RARβ-null mutant male mice as well as their wild type (WT) control littermates were raised on a mixed genetic background (C57BL/6J and 129SvEms/j) from heterozygous crosses, and housed in groups of 4-5 mice per cage. All mice were housed in individually ventilated cages, type “MICE” (Charles River, France) in a 7am-7pm light/dark cycle. Food and water were freely available.

extract_protocol: ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881,Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads. Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 8pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Hiseq2500 as single-end 50 base reads following Illumina’s instructions.

value: brain

tag: brain region

value: caudate putamen

tag: Sex

value: male

value: C57BL/6J x 129SvEms/j

value: anti-GFP (ab290, Abcam)


title: MN_Spombe_WT_1

tag: genotype/variation

value: wild type

value: Mononucleosomal DNA


title: wt Col replicate A (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1023591 (same raw file, same processed file).

source_name: wild type Columbia

tag: ecotype

value: Col

tag: developmental stage


title: H3K4me3_ChIP-seq

tag: antibody

value: anti-H3K4me3 (ab8580, Abcam)


title: ddm1 ago1

description: library strategy: MethylC-seq

value: ddm1 ago1


title: RARbeta_ChIP-seq

value: anti-RARbeta (sc-552, Santa Cruz)


title: splB_mix_JK1_BL6

description:
Sample 55
Barcode: CA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: wild-type

tag: cell type

value: Combined with Jk2, Jk4, Jk5 primers in one library preparation


title: ago6

description: library strategy: MethylC-seq


title: splB_mix_JK4_BL6

description:
Sample 57
Barcode: CA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: No immunization

value: 4-6 weeks

value: Combined with Jk1, Jk2, Jk5 primers in one library preparation


title: splB_JK4_BL6

description:
Sample 54
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: Splenic B

value: Combined with JH1, JH2, JH3 primers in one library preparation

value: 2 ug


title: splB_JK2_BL6

description:
Sample 53
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: Combined with JH1, JH2, JH4 primers in one library preparation


title: splB_JK1_BL6

description:
Sample 52
Barcode: -
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: Combined with JH1, JH3, JH4 primers in one library preparation


title: splB_mix_JH4_129sve

description:
Sample 51
Barcode: GATCAG
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: Combined with JH2, JH3, JH4 primers in one library preparation


title: splB_mix_JH2_129sve

description:
Sample 49
Barcode: GCAT
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: Individual


title: splB_mix_JH3_129sve

description:
Sample 50
Barcode: GCCAAT
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH4_mouse3_129sve

description:
Sample 47
Barcode: GATCAG
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_mix_JH1_129sve

description:
Sample 48
Barcode: GCCAAT
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH4_mouse1_129sve

description:
Sample 45
Barcode: GCCAAT
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH4_mouse2_129sve

description:
Sample 46
Barcode: ACTTGA
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: rdr6 replicate A (sRNA seq)

description:
small RNA-seq
Equivalent to GSM1023594 (same raw file, same processed file).

value: rdr6 mutant

value: stage 1-12

value: inflorescence


title: splB_JH3_mouse2_129sve

description:
Sample 43
Barcode: GCCAAT
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH2_mouse2_129sve

description:
Sample 40
Barcode: GCAT
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH2_mouse3_129sve

description:
Sample 41
Barcode: CTGA
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH3_mouse1_129sve

description:
Sample 42
Barcode: -
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_mouse3_129sve

description:
Sample 35
Barcode: TGACCA
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH1_mouse2_129sve

description:
Sample 37
Barcode: GCCAAT
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH1_mouse1_129sve

description:
Sample 36
Barcode: -
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH2_mouse1_129sve

description:
Sample 39
Barcode: -
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: proB_mouse2_129sve

description:
Sample 31
Barcode: AGTG
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait

value: progenitor B


title: proB_mouse1_129sve

description:
Sample 30
Barcode: -
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_mouse2_129sve

description:
Sample 34
Barcode: GATCAG
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: proB_mouse3_129sve

description:
Sample 32
Barcode: GTAC
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_mouse1_129sve

description:
Sample 33
Barcode: ACTTGA
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_500ng_repeat3_BL6

description:
Sample 29
Barcode: TGACCA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: TS5-VM3

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequence reads were aligned to the mouse mm9 genome using Bowtie.
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that the molecule counting by unique molecule identifiers was omitted.
The data was further analyzed using Qlucore omics explorer.
Genome_build: mm9
Supplementary_files_format_and_content: TAB-delimited file of RPKM values

source_name: ventral midbrain

growth_protocol: E12.5 embryos were obtained from C57bl/6 mice expressing GFP under the Th promoter.

extract_protocol:
Tissues were dissected under microscope. RNA was extracted from the collected tissue according to a Trizol RNA isolation protocol (Life Technology).
cDNA libraries were prepared from 200 ng RNA according to Illumina's TruSeq DNA sample preparation guide.


title: TS2-L3

source_name: Alar plate


title: TS10-VM1


title: TS23-VM2


title: splB_500ng_repeat2_BL6

description:
Sample 28
Barcode: GATCAG
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: TS8-L1


title: TS4-HB3

source_name: hindbrain


title: TS21-L2


title: splB_JH3_mouse3_129sve

description:
Sample 44
Barcode: CTTGTA
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_500ng_repeat1_BL6

description:
Sample 27
Barcode: ACTTGA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: TS22-HB2


title: TS9-HB1


title: splB_2ug_repeat3_BL6

description:
Sample 26
Barcode: CAGATC
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_JH1_mouse3_129sve

description:
Sample 38
Barcode: CTTGTA
aligned to mm9_AJ851868ins
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: TS25-FB3

source_name: forebrain


title: TS11-FB2


title: TS1-FB1


title: TS20-DM2

source_name: dorsal midbrain


title: TS27-DM3


title: TS3-DM1


title: splB_2ug_repeat2_BL6

description:
Sample 25
Barcode: CTTGTA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_2ug_repeat1_BL6

description:
Sample 24
Barcode: GCCAAT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_100ng_repeat2_BL6

description:
Sample 22
Barcode: AGT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_100ng_repeat3_BL6

description:
Sample 23
Barcode: GACT
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait


title: splB_100ng_repeat1_BL6

description:
Sample 21
Barcode: CAA
aligned to mm9
Library strategy: HTGTS-Rep-seq with individual or combined J segment coding ends as bait