title: 2_Non_infectdde_CD45_P_MMP_P

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

institute: Weizmann Institute of Science

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
alignment: hisat 0.1.5  with deafult parameters
filter PCR amplification bias using alignment break site and UMI barcode (size 8).
create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/)
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna mm9 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: FACS sorted cells

extract_protocol:
Lungs from infected and control uninfected C57BL/6J mice were immersed in cold PBS, cut into small pieces in 5 ml DMEM containing 10% bovine fetal serum (FACS buffer). Cell suspensions were grinded using 1-ml syringe cup on a 70μm cell strainers (BD Falcon). Cells were washed with ice-cold PBS. Remaining red blood cells were lysed using ammonium chloride solution (Sigma). Cells were harvested and immersed in 1ml FACS buffer (PBS+2% FCS, 1mM EDTA). Lung cells were stained with antibodies against multiple surface antigens: PE-conjugated LEM 2/15 (anti-MT1-MMP Ab), PerCP/cy5.5-conjugated anti-mouse CD45 (clone –F11) or Pacific blue-conjugated anti-mouse CD45
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

tag: strain

value: Lung

tag: selection marker

value: CD45 positive

tag: cell population

value: MT1-MMP positive

value: Naïve


title: porcine epiblast day 10-11 embryos rep1

status: Public on Jan 01 2017

type: SRA

city: Frederiksberg

first: Kristine

middle: Karla

last: Freude

address: Groennegardsvej

country: Denmark

institute: University Copenhagen

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, poly A/T tails and low-quality then filtered for low-complexity and for minimum read length (50 bp).
Pre-processed reads were mapped to Sscrofa10.2 with STAR (setting default parameters and allowing for maximum 5 mismatches).
Reads mapped to each gene (Ensembl Sus Scrofa 10.2.75) were counted with HTSeq-count
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files includes read counts for each Ensembl gene ID

molecule: total RNA

organism: Sus scrofa

source_name: Epiblast from day 10-11 embryos

growth_protocol: piPSC were grown in DMEMF12, 20% KOSR, 2i with either LIF or FGF (Secher et al., 2016)

extract_protocol:
iPSC RNA was isolated with RNAeasy micro kits from Qiagen and
embryonic RNA was isolated using TriZol and the PureLink™ RNA Micro Kit (Invitrogen)
iPSC: After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes).  Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates.
embryonic material: RiboZero kit (EpiBio, Medison USA) was used to deplete for ribosomal RNA, and hexamers for priming the reverse transcription, followed by regular sample preparation for sequencing.

treatment_protocol: ICM for porcine embryos 7-8 were isolated by immunosurgery. Porcine embryo day 10-11 epiblast and day 12-13 embryonic disc were manually isolated.

tag: cell type

value: Epiblast from day 10-11 embryos


title: RPMI8226_Gapdh

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

country: USA

institute: Emory University

description:
mRNA-seq
Processed data file: diff.geneFpkm.exon.glm.LogFc.0.exc.Gapdh.RPMI8226_MCL1.txt

data_processing:
RNA-seq data was mapped back to the UCSC human genome hg19 using Tophat2 (v.2.0.13) with the following parameters "-p 8 -N2 -max-multihits 1 -read-gap-length 1" and the UCSC Known Genes hg19 transcript file as a guide.
PCR duplicates were determined using Picard (http://broadinstitute.github.io/picard/) and removed from subsequent analyses.
Reads that uniquely overlapped hg19 exons were determined in R (v.3.2.2) using the 'summarizeOverlaps' function in mode 'IntersectionNotEmpty' of the 'GenomicAlignments' package (v.1.6.3).
Reads per million (RPM) were calculated for each gene based on the number reads in all potential exons for a given gene and the total number of uniquely mappable reads per sample.
Fragments per kilobase per million (FPKM) were calculated based on RPM and the total size of non-overlapping exons for a gene.
Differentially expressed genes were determined with EdgeR (v.3.12.1) where an FDR less than 0.01 was considered significant.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: diff.geneFpkm.exon.glm.LogFc.0.exc.Gapdh.RPMI8226_MCL1.txt: Tab-delimited text file includes normalized read counts (that map to exons) expressed in fragments per kilobase per million (FPKM) for UCSC mm9 KnownGenes, and a summary of differential statistics, not including the RPMI8226 overexpressing Mcl1.

organism: Homo sapiens

source_name: RPMI8226 cells, Gapdh shRNA

extract_protocol:
RNA was isolated using the Qiagen RNeasy kit following the manufacturer's instructions.
1 mg of RNA was sent to Hudson Alpha for RNA-seq library construction using the Illumina TruSeq mRNA protocol.

treatment_protocol: The myeloma cell lines were transfected with short hairpin RNAs targeting CD28, CD86, Gapdh (control), or empty vector (pLK0.1)

tag: cell line

value: myeloma cell line

tag: shRNA

value: Gapdh

tag: overexpression


title: CDK9 ChIP on A771726-treated cells.

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

library_source: genomic

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph pileup from MACS 2.0 output

molecule: genomic DNA

source_name: A375 melanoma cell line

growth_protocol: Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).

extract_protocol:
DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam), CDK9 (Santa Cruz) or RNA Pol II (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp.  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: One hundred million A375 cells per condition were treated with DMSO or 25 μM A771726.  Drugs used were DMSO (Sigma) and A771726 (Enzo Life Sciences) After a 48 hr treatment, cells were washed, proteins and DNA were cross-linked with 11% formaldehyde and cell pellets were frozen down at -80C.

tag: treatment


title: porcine inner cell mass day 7-8 embryos rep1

source_name: Inner cell mass from day 7-8 embryos

value: Inner cell mass from day 7-8 embryos


title: 1_Non_infectded_CD45_P_MMP_P

department: Immunology

country: Israel

organism: Mus musculus

tag: tissue


title: porcine inner cell mass day 7-8 embryos rep2


title: CDK9 ChIP on DMSO-treated cells.

value: DMSO


title: parental neonatal fibroblasts rep3

source_name: Fibroblasts

value: Fibroblasts


title: Input ChIP on A771726-treated cells-2


title: porcine inner cell mass day 7-8 embryos rep3


title: Anti-TERT_VA13_Replicate 1

city: Singapore

first: Vinay

last: Tergaonkar

address: 61, Biopolis Drive

department: IMCB

country: Singapore

institute: A*STAR

description:
antibody: TERT (abcam, ab32020, Lot YI021602CR)
Chipped DNA

data_processing:
Reads from cell lines were mapped to the hg19 genome using bowtie (version. 2.2.3) keeping uniquely aligned reads
Replicate bam files were merged using Samtools
PCR duplicates were removed from merged file and sorted indexed files were used for peak calling using MACS (version 2.1.10) with default parameters using q value of 0.05 to identified significantly enriched region/ peaks compared to input control sample
Coverage file for read density visualization is created using deepTools software and normalize to 1x options for normalization of read coverage across the sequencing libraries
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig (.bw) for read density visualization is created using deepTools software and normalize to 1x options for normalization of read coverage across the sequencing libraries.

source_name: transformed lung fibroblasts, TERT negative

growth_protocol: VA13  cells were grown in DMEM medium.  All cells were cultured at 37 degree celcius with 5% Carbon dioxide.

extract_protocol:
Lysates were clarified from sonicated nuclei and TERT-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the NEB NEXT ULTRA ILLUMINA Library preparation kit (E7370L).

treatment_protocol: All the cells were fixed in medium  Cells were fixed directly in growth medium with 1% formaldehyde for 10 minutes at room temprature with shaking.


title: gastrulating epiblast day 12-13 embryos rep1

source_name: Gastrulating epiblast from day 12-13 embryos


title: parental neonatal fibroblasts rep1


title: LIF piPSC rep3

source_name: induced Pluripotent Stem Cells (iPSCs)

value: induced Pluripotent Stem Cells (iPSCs)


title: HEXIM1>CDK9 reChIP on A375 cells

description: DMSO HEXIM1>CDK9 reChIP

extract_protocol:
DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam) followed by CDK9 (Santa Cruz) antibodies sequentially and vice versa. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp.  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: One hundred million A375 cells per condition were washed, proteins and DNA were cross-linked with 11% formaldehyde and cell pellets were frozen down at -80C.


title: Input ChIP on DMSO-treated cells-2


title: parental neonatal fibroblasts rep2


title: LIF piPSC rep2


title: Input reChIP on A375 cells (DMSO HEXIM1-CDK9 reChIP Input)

description: DMSO HEXIM1>CDK9 reChIP Input


title: CDK9>HEXIM1 reChIP on A375 cells

description: DMSO CDK9>HEXIM1 reChIP


title: Input reChIP on A375 cells (DMSO CDK9-HEXIM1 reChIP Input)

description: DMSO CDK9>HEXIM1 reChIP Input


title: HEXIM1 ChIP on DMSO-treated cells.


title: FGF piPSC rep3


title: LIF piPSC rep1


title: FGF piPSC rep1


title: SP1 ChIP on DMSO-treated cells.

description: DMSO SP1 ChIP

extract_protocol:
DNA was sonicated and chromatin immunoprecipitation was performed with SP1 (Abcam) antibody. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp.  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.


title: Input ChIP on A771726-treated cells.

description: A771726 Input


title: SP1 ChIP on A771726-treated cells.

description: A771726 SP1 ChIP


title: FGF piPSC rep2


title: Input ChIP on DMSO-treated cells.

description: DMSO Input


title: RNA-seq on Dox-treated Tet-On HEXIM1-inducible A375 cells-2

description: HEXIM1-inducible Dox-2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using cutadapt, then mapped to hg19 whole genome using Tophat 2.0.11 without novel splicing form calls
Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts
Genome_build: hg19
Supplementary_files_format_and_content: excel files include RPKM values for each Sample ...

source_name: A375 melanoma cell line - HEXIM1-inducible

growth_protocol: Human HEXIM1-inducible A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).

extract_protocol:
After 48 hrs, RNA was isolated using the RNeasy Plus Kit (Qiagen) and treated with the RiboZero Gold Kit (EpiCentre) to remove rRNAs.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 15 cycles. The indexed libraries were size-selected for 300 bp fragments using Agencourt Ampure XP beads (Beckman Coulter).  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: One million HEXIM1-inducible A375 cells per condition were treated with DMSO or 1 μg/mL doxycycline.  Drugs used were DMSO (Sigma) and doxycycline (Sigma).


title: RNA-seq on Dox-treated Tet-On HEXIM1-inducible A375 cells-3

description: HEXIM1-inducible Dox-3


title: RNA-seq on DMSO-treated Tet-On HEXIM1-inducible A375 cells-3

description: HEXIM1-inducible DMSO-3


title: RNA-seq on Dox-treated Tet-On HEXIM1-inducible A375 cells-1

description: HEXIM1-inducible Dox-1


title: RNA-seq on A771726-treated cells treated for 72 hrs-2

description: A771726 72hr-2

treatment_protocol: One million A375 cells per condition were treated with DMSO or 25 μM A771726.  Drugs used were DMSO (Sigma) and A771726 (Enzo Life Sciences).

value: A771726-treated for 72 hrs


title: RNA-seq on A771726-treated cells treated for 72 hrs-1

description: A771726 72hr-1


title: RNA-seq on DMSO-treated cells treated for 72 hrs-2

description: DMSO 72hr-2

value: DMSO-treated for 72 hrs


title: RNA-seq on DMSO-treated Tet-On HEXIM1-inducible A375 cells-2

description: HEXIM1-inducible DMSO-2


title: RNA-seq on A771726-treated cells treated for 48 hrs-1

description: A771726 48hr-1

value: A771726-treated for 48 hrs


title: RNA-seq on A771726-treated cells treated for 48 hrs-2

description: A771726 48hr-2


title: RNA-seq on DMSO-treated cells treated for 72 hrs-1

description: DMSO 72hr-1


title: RNA-seq on A771726-treated cells treated for 24 hrs-2

description: A771726 24hr-2

value: A771726-treated for 24 hrs


title: RNA-seq on A771726-treated cells treated for 24 hrs-1

description: A771726 24hr-1


title: RNA-seq on A771726-treated cells treated for 12 hrs-1

description: A771726 12hr-1

value: A771726-treated for 12 hrs


title: RNA-seq on DMSO-treated Tet-On HEXIM1-inducible A375 cells-1

description: HEXIM1-inducible DMSO-1


title: RNA-seq on A771726-treated cells treated for 0 hrs-1

description: A771726 0hr-1

value: A771726-treated for 0 hrs


title: RNA-seq on A771726-treated cells treated for 12 hrs-2

description: A771726 12hr-2


title: RNA-seq on A771726-treated cells treated for 0 hrs-2

description: A771726 0hr-2


title: H3K27me3_ChIPSeq - mutant

city: Xi’an

first: Yiping

last: Qu

address: The First Affiliated Hospital of Xi’an Jiaotong University

department: Department of Endocrinology

country: China

description: ChIP antibody: H3K27me3 (CST,#9733)

data_processing:
Basecalls performed using  fastx (version:0.0.13)
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie (version: 0.12.8)
peaks were called using  MACS (version:1.4.2) with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using Bowtie (version: 0.12.8)

source_name: NIH3T3 cells

growth_protocol: NIH3T3 cells were cultured in DMED with bovine calf serum to a final concentration of 10% at 37°C. Atmosphere: air, 95%;

extract_protocol:
Wild and mutation cells were fixed with 1.0% formaldehyde at room temperature for 15 min, after which glycine was added to the medium. The cells were then lysed and the rabbit polyclonal antibodies against H3K27me3 (#9733, CST) was used for the ChIP assay using the Pierce™ Magnetic ChIP Kit (Thermo, Inc., MA, USA) according to the instructions of manufacturer. Immunoprecipitated DNA (20 ng) was subjected to size selection of fragments around 200-bp in length.
Sequencing libraries were consequently constructed by adaptor ligation and PCR. Sequencing was carried out with an Illumina HiSeq2500 system according to the manufacturer's protocol.

treatment_protocol: NIH3T3 cells were transfected with a pEFm6-BRAF and pEFm6-BRAFV600E plasmids

tag: transfection

tag: passages

value: NIH/Swiss


title: KO3_ATAC

city: London

first: Albert

last: Basson

address: Floor 27, Tower Wing, Guy's Hospital

department: Craniofacial Development and Stem Cell Biology

country: United Kingdom

institute: King's College London

description:
processed data file
master_sheet_atac_all_datav2.xlsx

data_processing:
ATAC-seq:
15bp was trimmed from the raw sequencing reads using trim_galore [version 0.4.1] with parameters as follows: trim_galore --nextera --paired --quality 20 --stringency 5 --gzip --clip_R1 15 --clip_R2 15 --length 25 -o [output_filename]
Reads were uniquely aligned to the mouse reference genome (mm10) using Bowtie [version 1.1.1]  with a maximum insert size for valid paired-end alignments of 2000 and a maximum number of attempts of 200 to match an alignment for one mate with an alignment for the opposite mate.
bam files were sorted and indexed using samtools [version 0.1.19-96b5f2294a]
Peaks were called in three WT replicates by comparing them to three KO samples and vice versa using MultiGPS [version 0.5] with the minimum q-value for reported peaks set at 0.05 and the mitochondrial genome excluded.
The bedtools window function from BEDTools [version 2.17.0] was used to identify ATAC-seq peaks within 1000bp of DEGs, and Dnase-seq peaks within 100bp of ATAC-seq peaks.
RNA-seq:
RNAseq reads were aligned to the mouse reference genome (mm10) using TopHat [version 2.0.14] with an expected inner distance between mate pairs of 150bp and standard deviation for the distribution on inner distances between mate pairs of 50bp.  The transcriptome index was created using ENSEMBL build 75
HTseq [version 0.6.1p1] was used to estimate the number of RNA sequencing reads supporting the expression of protein coding genes. For this, an intersection-strict mode was used and all reads with alignment quality lower than 3 skipped.
Differential expression was analyzed with DESeq2 1.8.1. Genes with an FDR<0.05 were considered differentially expressed.
ChIP-seq:
Reads were aligned to the mouse reference genome (mm10) using Bowtie [version 1.1.0] , only allowing uniquely mapping reads, with an insert size of 1000 bases. Default values were used for all other parameters
Following mapping, PCR duplicates were removed using the samtools 'rmdup' command
Identification of enriched regions was performed by comparing the ChIP to the input reads using macs2 [2.1.0.20140616], with a p-value cutoff of 0.0001 and 3,90 as the model building parameters. The bedGraph output generated by macs2 was used to visualise the ChIP and input signals.
Genome_build: mm10
Supplementary_files_format_and_content: master_sheet_atac_all_datav2.xlsx: Excel document with sheets containing coordinates of all identified peaks,i.e.   CTRL Vs. KO peaks  KO Vs. CTRL peaks  All ATAC peaks  All DNase Peaks  CTRL Vs. KO peaks within 1kb of a downregulated gene (incl. names of all unique genes)  CTRL Vs. KO peaks within 1kb of a upregulated gene (incl. names of all unique genes)  KO Vs. CTRL  peaks within 1kb of a downregulated gene (incl. names of all unique genes)  KO Vs. CTRL  peaks within 1kb of a upregulated gene (incl. names of all unique genes)
Supplementary_files_format_and_content: DEGs_Chd7.xls Excel file containing all differentially expressed genes as identified by DESeq2, including log2 fold change values and FDR.
Supplementary_files_format_and_content: WT_R1_htseq_strict_a3_s_counts.txt  WT_R2_htseq_strict_a3_s_counts.txt   KO_R1_htseq_strict_a3_s_counts.txt   KO_R2_htseq_strict_a3_s_counts.txt   → All text files containing raw  read counts for the corresponding fastq file
Supplementary_files_format_and_content: H3K4me1_WT.bw; Signal profile file showing the extent of H3K4me1-DNA binding genome wide

extract_protocol:
ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, with the excpetion that the Nuclei EZ Prep Nuclei Isolation Kit (Sigma, NUC-101) was used for nuclei isolation.
ATAC-seq: Protocol as described in Buenrostro et al (2015): doi:10.1002/0471142727.mb2129s109, using illumina barcoded primers for sequencing.
RNA-seq: The cerebella of post natal day 7 Chd7f/f (cn) and Math1cre;Chd7f/f (cko) pups were dissected in DPBS (Gibco) and lobules IX and X were removed. The cerebella of the individuals from each genotype were pooled. Cells were dissociated using Papain I (100U, Worthington) followed by trituration. Granule cell precursors were isolated by Percoll fractionation with a 35% and 65% Percoll gradient (Sigma) as described (Yu T, Meiners LC, Danielsen K, Wong MT, Bowler T, Reinberg D, Scambler PJ, van Ravenswaaij-Arts CM, and Basson MA. Deregulated FGF and homeotic gene expression underlies cerebellar vermis hypoplasia in CHARGE syndrome. eLife. 2013;2(e01305.). Total RNA was extracted from freshly isolated cells (5x106/cerebellum) with an Agilent Absolutely RNA miniprep kit (Agilent Technologies, Stockport, UK)
RNA-seq: RNA quality and integrity was assessed on a 2100 Bioanalyzer and 2200 Tapestation using an R6K screenTape (Agilent Technologies, Stockport, UK). After quantification on Qubit using Quant-iT RNA assay kit (Life Technologies, Paisley, UK), 2g total RNA was used from each sample for library preparation using an Illumina TruSeq kit (Illumina, Cambridge, UK). Libraries were resolved by agarose gel electrophoresis, 250-550bp DNA fragments isolated and gel purified with a Qiagen DNA gel extraction kit (Qiagen, Manchester, UK). Two libraries with unique barcodes were combined and sequenced per lane on a HiSeq2000 (Illumina, Cambridge, UK) at the Biomedical Research Centre, King’s Health Partners.
ChIP-seq: The cerebella of post natal day 7 Chd7f/f (cn) and Math1cre;Chd7f/f (cko) pups were dissected in DPBS (Gibco) and lobules IX and X were removed. The cerebella of the individuals from each genotype were pooled. Cells were dissociated using Papain I (100U, Worthington) followed by trituration. Granule cell precursors were isolated by Percoll fractionation with a 35% and 65% Percoll gradient (Sigma) as described (Yu T, Meiners LC, Danielsen K, Wong MT, Bowler T, Reinberg D, Scambler PJ, van Ravenswaaij-Arts CM, and Basson MA. Deregulated FGF and homeotic gene expression underlies cerebellar vermis hypoplasia in CHARGE syndrome. eLife. 2013;2(e01305.).
ChIP-seq: Freshly isolated cells (2-3x107) of each genotype were fixed, chromatin isolated, precipitated with an antibody to H3K4me1 (Abcam, Cambridge UK) and ChIP-seq libraries produced and sequenced as previously described (Tee WW, Shen SS, Oksuz O, Narendra V, and Reinberg D. Erk1/2 activity promotes chromatin features and RNAPII phosphorylation at developmental promoters in mouse ESCs. Cell. 2014;156(4):678-90.).

tag: strain background

tag: age

tag: genotype/variation

value: cerebellar granule cell precursors (GCps)


title: T0+2

city: Fuzhou

first: Yue

last: Zhicao

state: Fujian

address: Institute of Life Sciences, Fuzhou University

department: Institute of Life Sciences

institute: Fuzhou University

data_processing:
Image analysis and basecalling was performed using the Illumina Pipeline.
Raw sequences are transformed into Clean Tags after following steps of data-processing using customized workflow developed by Shenzhen Huada Gene Sci-Tech Company.
1. 3' adaptor sequence removal: since Tags are only 21nt long while the sequencing reads are 35nt long, raw sequences are with 3' adaptor sequences
2. Empty reads removal (reads with only 3' adaptor sequences but no tags)
3. Low quality tags removal (Tags with unknown sequences 'N')
4. Removal of tags which are too long or too short, leaving Tags of 21nt long
5. Removal of Tags with a copy number of 1 (probably be sequencing error)
6. Generate Clean Tags
A virtual libraries containing all the possible CATG+17 bases length sequences of the reference gene sequences (Mus musculus: UniGene Build #192). All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). (Morrissy, A. S., R. D. Morin, et al . 2009. "Next-generation tag sequencing for cancer gene expression profiling." Genome Res.)
Genome_build: Mus musculus: UniGene Build #192
Supplementary_files_format_and_content: text file with gene expression level

source_name: skin

extract_protocol:
Total RNAs were extracted by Trizol.
Beads of Oligo(dT) are used to enrich mRNA from the total RNA, and then are transferred into double-stranded cDNA through reverse transcription. 4 base recognition enzyme NlaIII is used to digest this cDNA, and Illumina adaptor 1 is ligated. Mmel is used to digest at 17bp downstream of CATG site; Illumina adaptor 2 is ligated at 3' end. Primer GX1 and Primer GX2 are added for PCR. Then, regain 95bp fragments through 6% TBE PAGE. The DNA was purified and followed by Illumina sequencing.

value: skin

tag: gender

value: male

tag: time

value: 2 day after treatment

value: 150mg/km Cyclophosphamide


title: T0+1

value: 1 day after treatment


title: KO2_ATAC


title: KO1 _ATAC


title: H2O2_3_60 - H2O2 after 60 min of the addtion, replica 3

city: Kgs. Lyngby

first: Klara

last: Bojanovic

address: Building 220, Kemitorvet

department: Novo Nordisk Foundation Center for Biosustainability

institute: Technical University of Denmark

data_processing:
Trimming: The RNA-seq data was trimmed using Trimmomatic
Data analysis by Rockhopper: The RNA-seq data was analyzed with the open source software Rockhopper with the default settings, choosing reverse complement reads and strand specific analysis (version 2.0.3). The reads were mapped to the sequenced reference P. putida KT2440 genome (GenBank accession no. NC_002947.3).
Differential expression analysis: Differential gene and sRNA expression analysis were carried out with the webserver T-REx using the RPKM values generated in the Rockhopper analysis, where all the tested conditions were compared to the control, a sample harvested just prior to addition of the compound. Differential expression of genes was considered significant with a fold change ≥ 2 and adjusted p-value ≤ 0.05.
Genome_build: GenBank accession no. NC_002947.3
Supplementary_files_format_and_content: One file with all the processed results in excel: Raw counts, Normalized counts, RPKM, Expression values, q-values

organism: Pseudomonas putida KT2440

growth_protocol: Cells are rutinelly grown in LB medium, 37°C, 250 rpm, usually inoculated on solid media from -80°C stock and incubated overnight proir to experiments. For this experiment they were grown in M9 minimal medium + glucose.

extract_protocol:
RNA extraction was performed as previously described (Gomez-Lozano et al. 2012. Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa. Environ Microbiol 14:2006–16.). Briefly, 20 mL of harvested culture was mixed with 0.2 volumes of STOP solution (95% [v/v] ethanol, 5% [v/v] phenol). Cells were centrifuged, snap frozen and stored at -80° C. Total RNA was extracted with Trizol (Invitrogen) and treated with DNase I (Fermentas) for DNA removal. Total RNA integrity and quality were validated by Agilent 2100 Bioanalyzer (Agilent Technologies).
Transcriptome libraries (LIB>100) were constructed as previously described (Gomez-Lozano et al. 2012. Genome-wide identification of novel small RNAs in Pseudomonas aeruginosa. Environ Microbiol 14:2006–16.) with some modifications. The total RNA sample was depleted of rRNA with the Ribo Zero Kit for Gram Negative Bacteria (Illumina). cDNA libraries were prepared with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following the Low Sample LS Protocol. Libraries were validated with a DNA 1000 chip on the Agilent 2100 Bioanalyzer and concentration was measured using a Qubit 2.0 Fluorometer (Invitrogen, Life Technologies). The concentration of each library was normalized to 10 nM in TE buffer and cDNA libraries were pooled together for sequencing on the Illumina HiSeq 2000 platform at Beckman Coulter Genomics. The transcriptome libraries were single-end sequenced with 100 bp reads.

treatment_protocol: Single colonies were grown overnight in 5 mL M9 medium and the cultures were diluted to a starting OD600 of 0.05 in 50 mL M9 medium in 250 mL shake flasks. At mid-exponential growth phase (OD600~0.6) different compounds were added at different concentrations. For RNA-seq experiments, the following compound concentrations were used:  3% NaCl, 0.05 mM H2O2 and 0.1 μg/mL of imipenem. The cultures grown in the same manner as described above were harvested 7 and 60 minutes after the addition of the stress compounds and the control was a sample harvested just prior to compound addition. All experiments were carried out in 3 biological replicates.

tag: stress

tag: time point

value: 60 min


title: WT 1_ATAC

value: wild type


title: WT 3_ATAC


title: WT 2_ATAC


title: H2O2_3_7 - H2O2 after 7 min of the addtion, replica 3

tag: strain

value: 7 min


title: H2O2_2_60 - H2O2 after 60 min of the addtion, replica 2


title: ubc9-1, untreated, rep1

city: Oslo

first: Håvard

last: Aanes

address: Sognsvannsveien 20

department: Dept of microbiology

country: Norway

institute: Oslo University Hospital

data_processing:
Reads were filtered and trimmed using a custom script (BGI)
Reads were mapped against the R64-1-1 genome assembly using Tophat2 (v. 2.0.13) with default settings.
The number of reads per gene in the Ensemble 75 gene build were counted using featureCounts (v. 1.4.6-p3) in paired-end mode and with -t gene and -M options.
Only features <200 nt were used for further analysis
Genome_build: R64-1-1.75
Supplementary_files_format_and_content: Tab-delimited text files include raw counts and the normalized CPM values for each Sample

organism: Saccharomyces cerevisiae

source_name: Cell

growth_protocol: YPD medium

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen) and RNAs between 50 and 100 nt were selected.
Library construction and sequencing were performed by BGI

treatment_protocol: 100 nM rapamycin for 30 min

value: No treatment


title: ubc9-1, untreated, rep2


title: H2O2_1_60 - H2O2 after 60 min of the addtion, replica 1


title: H2O2_2_7 - H2O2 after 7 min of the addtion, replica 2


title: ubc9-1, rapamycin treated, rep2

value: Rapamycin


title: IP_1_60 - Imipenem after 60 min of the addtion, replica 1

value: Imipenem


title: H3K27me3_ChIPSeq - wild type

institute: The First Affiliated Hospital of Xi’an Jiaotong University

description: ChIP antibody: H3K27me3 (CST,#9733)


title: IP_2_7 - Imipenem after 7 min of the addtion, replica 2


title: ubc9-1, rapamycin treated, rep1


title: NaCl_3_7 - NaCl after 7 min of the addtion, replica 3

value: NaCl


title: IP_3_7 - Imipenem after 7 min of the addtion, replica 3


title: H2O2_1_7 - H2O2 after 7 min of the addtion, replica 1


title: IP_3_60 -  - Imipenem after 60 min of the addtion, replica 3


title: IP_2_60 - Imipenem after 60 min of the addtion, replica 2


title: WT, rapamycin treated, rep2


title: IP_1_7 - Imipenem after 7 min of the addtion, replica 1


title: NaCl_3_60 - NaCl after 60 min of the addtion, replica 3


title: NaCl_2_60 - NaCl after 60 min of the addtion, replica 2


title: Time 0


title: WT, rapamycin treated, rep1


title: NaCl_2_7 - NaCl after 7 min of the addtion, replica 2


title: WT, untreated, rep2


title: C_2_0 - Control sample 2

source_name: C_2_0 - Control sample 2


title: C_3_0 - Control sample 3

source_name: C_3_0 - Control sample 3


title: NaCl_1_7 - NaCl after 7 min of the addtion, replica 1


title: Head RNAi male biological replicate 3

city: Raleigh

first: John

last: Shorter

state: NC

address: 112 Derieux Place 3510 Thomas Hall

department: Biological Sciences

institute: North Carolina State University

data_processing:
Demultiplexing: Barcoded sequence reads were demultiplexed using the Illumina pipeline v1.9.
Filtering Contaminant Sequences: Adapter sequences were trimmed using cutadapt v1.6 and trimmed sequences shorter than 50bp were discarded from further analysis. Trimmed sequences were then filtered for ribosomal RNA sequences by aligning against a database containing the complete 5S, 18S-5p8S-2S-28S, mt:lrRNA, and mt:srRNA sequences using BWA v0.7.10 (MEM algorithm with parameters ‘-v 2 –t 4’).
Alignment: The remaining sequences were aligned to the D. melanogaster genome (BDGP5) and known transcriptome (FlyBase v5.57) using STAR v2.4.0e.
Read Counting: Read counts were computed for known gene models using HTSeq-count with the ‘intersection-nonempty’ assignment method.
Genome_build: BDGP5/FlyBase5.57
Supplementary_files_format_and_content: Raw read counts for each gene feature in each sample provided as a single table (tab-delimited text). EXPRESSED column indicates whether gene feature met our minimum expression requirements for analysis.

organism: Drosophila melanogaster

source_name: Adult Head

growth_protocol: Flies were reared in vials on cornmeal/molasses/agar medium under standard culture conditions (25°C, 12:12 hour light/dark cycle).

extract_protocol:
We flash froze at -80 °C three-to-five day-old flies, with at least thirty flies per replicate and four replicates per sex per selected population per generation (32 samples) All flies were collected between 8 AM and 11 AM. Total RNA was extracted with Trizol using the RNAeasy Mini Kit (Qiagen, Inc.). rRNA was depleted using the Ribo-Zero™ Gold Kit (Epicentre, Inc.) with 5ug total RNA input.
Depleted mRNA was fragmented and converted to first strand cDNA. During the synthesis of second strand cDNA, dUTP instead of dTTP was incorporated to label the second strand cDNA. cDNA from each RNA sample was used to produce barcoded cDNA libraries using NEXTflex™ DNA Barcodes (Bioo Scientific, Inc.) with an Illumina TrueSeq compatible protocol. Library size was selected using Agencourt Ampure XP Beads (Beckman Coulter, Inc.) and centered around 250 bp with the insert size ~130 bp. Second strand DNA was digested with Uracil-DNA Glycosylase before amplification to produce directional cDNA libraries. Libraries were quantified using Qubit dsDNA HS Kits (Life Technologies, Inc.) and Bioanalyzer (Agilent Technologies, Inc.) to calculate molarity. Libraries were then diluted to equal molarity and re-quantified. Two pools of 16 libraries were made, one of the 16 libraries from replicate 1 high and low lines; and one of the 16 libraries from replicate 2 high and low lines. Pooled library samples were quantified again to calculate final molarity and then denatured and diluted to 14pM. Pooled library samples were clustered on Illumina cBot; each pool was sequenced on one lane of Illumina Hiseq2500 using 125 bp single-read v4 chemistry.

treatment_protocol: Flies from the progenitor/RNAi OBP56hKK111996 collection from were crossed to a Dll-GAL4 driver (P{w[+mW.hs]=GawB}Dllmd23/CyO). F1 individuals with CyO wings were discarded.

tag: tissue type

value: Head

tag: genotype

value: RNAi knockdown

tag: Sex

tag: biological replicate


title: Head RNAi male biological replicate 4


title: Head RNAi male biological replicate 1


title: Head progenitor male biological replicate 2

value: Progenitor


title: Head RNAi female biological replicate 2

value: female


title: Head RNAi male biological replicate 2


title: Body RNAi male biological replicate 2

source_name: Adult Body

value: Body


title: Head RNAi female biological replicate 1


title: Head progenitor male biological replicate 3


title: Body RNAi male biological replicate 1


title: Head progenitor male biological replicate 1


title: Head progenitor male biological replicate 4


title: Head progenitor female biological replicate 3


title: Head progenitor female biological replicate 4


title: NaCl_1_60 - NaCl after 60 min of the addtion, replica 1


title: WT, untreated, rep1


title: Body RNAi male biological replicate 3


title: Head progenitor female biological replicate 2


title: Body RNAi female biological replicate 4


title: Body RNAi female biological replicate 2


title: Body RNAi female biological replicate 1


title: Body RNAi female biological replicate 3


title: C_1_0 - Control sample 1

source_name: C_1_0 - Control sample 1


title: Body progenitor male biological replicate 3


title: Body progenitor male biological replicate 4


title: Head progenitor female biological replicate 1


title: Head RNAi female biological replicate 4


title: Head RNAi female biological replicate 3


title: Body progenitor male biological replicate 1


title: S2_GROseq_r2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: GRO-Seq (nascent RNA)

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the Drosophila melanogaster genome (dm3) using bowtie2 (v2.1.0), keeping only reads that mapped to a unique genomic location (MAPQ > 10).
HOMER (v4.7) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser and TSS using modified version of ChIP-Seq peak finding. HOMER finds TSS from 5'GRO-Seq by looking for strand-specific clusters of initiation sites within 150 bp that have more than 4x the normalized read counts relative to non-5' enriched signal (from traditional GRO-Seq).
Genome_build: dm3
Supplementary_files_format_and_content: bed format (centered on TSS)
Supplementary_files_format_and_content: FPKM for the non-TSS samples: Columns: (1) RefSeq ID (2) chromosome (3) Start (4) End (5) Strand (6) Annotation (7) Sample3 FPKM (8) Sample4 FPKM

source_name: S2 Cells

growth_protocol: Drosophila Schneider S2 cells were grown at 25°C in Shields & Sang M3 media (Sigma; St. Louis, MO) prepared with yeast extract (Sigma; St. Louis, MO) and Bacto Peptone (BD Biosciences; San Jose, CA) supplemented with 10% heat-inactivated FBS.

extract_protocol:
5’GRO-seq was performed as described previously (Lam et al., 2013). About 10^7 Drosophila S2 nuclei were used for run-on with BrU-labeled NTPs. Fragmented transcripts were incubated with polynucleotide kinase (PNK, NEB) to remove 3’ phosphates. BrU-labeled nascent transcripts were subsequently immunoprecipitated with anti-BrdU agarose beads (Santa Cruz Biotech). For 5’GRO-seq, immunoprecipitated RNA was dephosphorylated with calf intestinal phosphatase (NEB). Then 5’ capped fragments were de-capped with tobacco acid pyrophosphatase (Epicenter). Illumina TruSeq adapters were ligated to the RNA 3’ and 5’ ends with truncated mutant RNA ligase 2 (K227Q) and RNA ligase 1 (NEB), respectively. Reverse transcription was performed with Superscript III (Invitrogen) followed by PCR amplification for 12 cycles. Final libraries were size selected on PAGE/TBE gels to 175–225 bp. GRO-seq was essentially performed as 5’GRO-seq, but the immunoprecipitated RNA was directly de-capped with tobacco acid pyrophosphatase (Epicenter) and subsequently kinased with PNK (NEB) prior to adaptor ligation. 5’GRO-seq was performed as described previously (Lam et al., 2013). About 10^& Drosophila S2 nuclei were used for run-on with BrU-labeled NTPs. Fragmented transcripts were incubated with polynucleotide kinase (PNK, NEB) to remove 3’ phosphates. BrU-labeled nascent transcripts were subsequently immunoprecipitated with anti-BrdU agarose beads (Santa Cruz Biotech). For 5’GRO-seq, immunoprecipitated RNA was dephosphorylated with calf intestinal phosphatase (NEB). Then 5’ capped fragments were de-capped with tobacco acid pyrophosphatase (Epicenter). Illumina TruSeq adapters were ligated to the RNA 3’ and 5’ ends with truncated mutant RNA ligase 2 (K227Q) and RNA ligase 1 (NEB), respectively. Reverse transcription was performed with Superscript III (Invitrogen) followed by PCR amplification for 12 cycles. Final libraries were size selected on PAGE/TBE gels to 175–225 bp. GRO-seq was essentially performed as 5’GRO-seq, but the immunoprecipitated RNA was directly de-capped with tobacco acid pyrophosphatase (Epicenter) and subsequently kinased with PNK (NEB) prior to adaptor ligation.
Illumina HiSeq 2500 system and associated protocol was used. Run type: SE50; Run mode: High Output

tag: cell type

value: S2 (Schneider 2 cells)

value: Embryo 20-24h

tag: sample type

value: Nascent RNA


title: Body progenitor female biological replicate 4


title: Body RNAi male biological replicate 4

value: male


title: S2_GROseq_r1

description: GRO-Seq (nascent RNA)

tag: tissue


title: Body progenitor female biological replicate 1


title: S2_GRO5_r1

description: 5'GRO-Seq (nascent RNA TSS)

value: 5' Capped Nascent RNA


title: Body progenitor female biological replicate 3


title: Body progenitor female biological replicate 2


title: DAT1

city: Yangling

first: Chengyu

last: Yu

state: Shaanxi

address: 3 Taicheng Road

department: College of Agronomy

institute: Northwest A&F University

description: replicate of amidosulfuron  treatment

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to our previously assembled transcriptome dataset (Trinity_rapeseed.fa.gz attatchment of gene expression Omnibus GSE69638) using Bowtie V2-2.1.0, with Brassica rapa genome FPsc v1.3 (DOE-JGI, http://phytozome.jgi.doe.gov/) as reference.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Brassica rapa FPsc v1.3
Supplementary_files_format_and_content: tab-delimited text files include count number and RPKM values for each Sample

organism: Brassica napus

source_name: young floral buds

growth_protocol: The seeds of CultivarQinyou3 was sown in field in September and the seedlings were transplanted into greenhouse in early December after vernalization under field condition.

extract_protocol:
Based on cytological observation, we knew that the key stage respond to gametocide amidosulfron was young floral buds before uninucleate microspore. Therefor, young floral buds from amidosulfuron-treated (DAT) and control plants (F) were dissected, put into RNAlater and stored at −80°C for later use. Total RNAs were extracted using the Trizol® Reagent (Invitrogen, USA) and purified using TRK1001 Kit (LC Science, Houston, TX). The total RNA quantity and purity were analyed by using of Bioanalyzer 2100 with RNA 6000 Nano LabChip Kit (Agilent, CA, USA). We used 10 µg total RNA from each sample to create normalized cDNAs. Three independent biological replicates were used for the herbicide or control treatment.
RNA libraries were prepared for sequencing using Illumina’s Digital Gene Expression Tag Profiling Kit according to the manufacturer’s protocol

treatment_protocol: The plants of Cultivar Qinyou3 at bolting stage were sprayed with 0.3mg/L Amidosulfuron. The contrast plants were sprayed with water.

tag: cultivar

value: young floral buds

tag: developmental stage

value: meiosis of pollen mother cell

tag: treatment

value: amidosulfuron


title: DAT2

description: replicate of amidosulfuron  treatment


title: T.S. BS-seq1

city: shenzhen

first: Guanyu

last: Ji

state: GuangDong

address: 14th of middle jinxiu road

department: R&D

institute: GENEDOHEALTH

description: T.S.meth.txt

data_processing:
BS-seq
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 taenia solium whole genome using BSMAP v2.74 with parameters -m 0 -x 1000
methylation information of CpG site was analysised using methratio.py
Genome_build: taenia solium (http://taenia.big.ac.cn/resources.html version 2)
Supplementary_files_format_and_content: tab-delimited text files include methylation level information of taenia solium.
RNA-seq
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 taenia solium whole genome using tophat v2.0.11 with parameters -r 200 -p 4 -N 7 --read-gap-langth 10
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: taenia solium (http://taenia.big.ac.cn/resources.html version 2)
Supplementary_files_format_and_content: tab-delimited text files include RPKM value information of taenia solium.

organism: Taenia solium

source_name: taenia solium

extract_protocol:
Genomic DNA was fragmented and libraries were constructed as the Illumina Pair-End protocol. Briefly, purified randomly fragmented DNA was treated with a mix of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair, blunt and phosphorylate ends. The blunt DNA fragments were subsequently 3’ adenylated using Klenow Fragment (3’-5’ exo-) and following with ligation to adaptors synthesized with 5’-methylcytosine instead of cytosine using T4 DNA Ligase. After that, ZYMO EZ DNA Methylation-Gold Kit was employed to convert unmethylated cytosine to uracil. Finally, PCR was carried out and the library was purified using QIAquick gel extraction kit (Qiagen).
BS libraries were prepared for sequencing using standard Illumina protocols

value: whole organism


title: Body progenitor male biological replicate 2


title: F3

description: replicate of the control

value: control


title: Oligodendrocyte 5 - 1

city: Stockholm

first: Kasper

last: Karlsson

address: Scheeles väg 2

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
Barcode: TACTAG Full barcode: TACTAGAGTAGCACTC
Short reads were created with P4C2 chemistry, long reads were created with P6C4 chemistry.

data_processing:
Demultiplexing, identification of viable reads and deconcatenation of concatenated reads: custom program
Commando used for one barcode:gmap -f 1 --split-output ACACGC --no-chimeras --min-identity=0.9 -d mouse_genome -n 1 ACACGC_short.fa  with GMAP version 2014-10-22.
Concatenate blocks smaller than 40 bp apart: custom program
Annotate reads according to RefSeq: custom program
Combine reads based on their UMI: custom program
Genome_build: mm10
Supplementary_files_format_and_content: Custom file format. Reads combined based on UMI and annotated to RefSeq for genes and exons

molecule: polyA RNA

source_name: Oligodendrocyte 5

extract_protocol:
Single cells were captured with fluidigms C1 single-cell capturing system and processed with a protocol described in Zeisel et al 2015 DOI: 10.1126/science.aaa1934
cDNA from the C1 system was diluted and then amplified 12-15 rounds of PCR using primers with a specific 16 bp barcode and sequenced with Pacific Biocience single molecule real time sequencing technoloy using P4/C2 chemistry or P6/C4 chemistry

value: Brain

value: Oligodendrocyte

value: Embryo


title: Oligodendrocyte 5 - 2

description:
Barcode: TGTGTA Full barcode: TGTGTATCAGTACATG
Short reads were created with P4C2 chemistry, long reads were created with P6C4 chemistry.


title: T.S. RNA-seq

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Oligodendrocyte 1 - 1

description:
Barcode: CTATAC Full barcode: CTATACATGACTCTGC
Short reads were created with P4C2 chemistry, long reads were created with P6C4 chemistry.

source_name: Oligodendrocyte 1


title: F1

description: replicate of the control


title: DAT3

description: replicate of amidosulfuron  treatment


title: Oligodendrocyte 1 - 2

description:
Barcode: TCAGAC Full barcode: TCAGACGATGCGTCAT
Short reads were created with P4C2 chemistry, long reads were created with P6C4 chemistry.


title: T.S. BS-seq2

description: T.S.meth.txt


title: Oligodendrocyte progenitor cell 2

description:
Barcode: GATCTC Full barcode: GATCTCTACTATATGC
Short reads were created with P4C2 chemistry, long reads were created with P6C4 chemistry.

source_name: Oligodendrocyte progenitor cell

value: Oligodendrocyte progenitor cell


title: Oligodendrocyte progenitor cell 1

description:
Barcode: ACACGC Full barcode: ACACGCATGACACACT
Short reads were created with P4C2 chemistry, long reads were created with P6C4 chemistry.


title: K2_St

description: The hfq gene of was C-terminally tagged with 3xFLAG epitopes on the chromosome. DNA fragments were amplified by PCR using the PfuX7 polymerase (Nørholm, 2010) and the primers listed in Table S1. The 3xFLAG sequence (Uzzau et al., 2001) was inserted with primers containing long tails carrying a sequence for 3xFLAG. Plasmid pKB1 was constructed with the Uracil excision-based cloning system (USER). The backbone pSIJ218 and two homologous regions of about 800 bp of P. putida KT2440 genome (upstream and downstream of the insertion – stop codon of hfq gene) were amplified with primers containing uracil, forming single-stranded overhangs compatible among each other to form the plasmid pKB1 in USER reaction as described previously (Cavaleiro et al., 2015). The plasmid was transformed into chemically competent E. coli DH5α λpir for plasmid replication. The correct assembly of pKB1 was checked by colony PCR and sequencing. pKB1 was further transformed into P. putida KT2440 by electroporation as previously described (Choi et al., 2006). The hfq gene was replaced with the hfq::3xFLAG allele forcing two recombination events by conditionally expressing a homing endonuclease I-SceI introduced in plasmid pSW-I, as previously described (Martínez-García and de Lorenzo, 2011). Correct genomic insertions were confirmed by sequencing and the resulting strain with the 3xFLAG tag on the hfq gene was named KL3.

data_processing:
RNA-seq data was analysed with open source software Rockhopper (version 2.0.3) (McClure et al., 2013)
Differential gene and sRNA expression analysis were carried out with the webserver T-REx (de Jong et al., 2015) using the RPKM values generated in the Rockhopper analysis. Differential expression of genes was considered significant with a fold change ≥ 2 and adjusted p-value ≤ 0.05
Genome_build: GenBank accession no. NC_002947.3
Supplementary_files_format_and_content: One file with all the processed results in excel: Raw counts, Normalized counts, RPKM, Expression values, q-values

organism: Pseudomonas putida

source_name: Bacteria

growth_protocol: P. putida KT2440 was grown at 30 °C, 250 rpm and routinely cultured in LB medium according to standard protocols

extract_protocol:
Cell pellets were resuspended in 0.8 mL of lysis buffer, supplemented with 200 U of RiboLock RNase inhibitor (Thermo Scientific) and cOmplete mini protease inhibitor (Roche). Cells were lysed by vortexing with the glass beads (diameter 150-212 μm, Sigma) for two times 20 s burst, with a chill on ice for one min in between. Lysis buffer (0.4 mL) was added, followed by centrifugation at 16.000 x g at 4 °C for 30 min. Cleared lysate (0.9 mL) was used for immunoprecipitation with Hfq combined with 80 μL of ANTI-FLAG M2 Magnetic Beads (Sigma, M8823) for 4 h on 4 °C with rotation. Beads with precipitated antibody-protein-RNA complexes were washed five times with TBS and finally resuspended in 0.5 mL of TBS. RNA was extracted by phenol:chlorophorm:isoamyl alcohol and ethanol-precipitated. Followed by DNaseI treatment (Fermentas), RNA was analysed with a Bioanalyzer (RNA 6000 Pico Kit, Agilent). During the immunoprecipitation assay aliquots were saved and used for Western blot analysis.
For KB4 cDNA library, coIP RNA was treated with RNA 5’ Polyphosphatase (Epicentre). The fragmentation was omitted and cDNA libraries were prepared using using TruSeq Small RNA Sample Preparation Kit (Illumina). Illumina NextSeq 500 and NextSeq 550 used.

treatment_protocol: For coIP experiments wt and KL3 strains were used. Equivalent number of cells to OD600 = 50 was harvested in three points on the curve by centrifugation at 4000 x g at 4 °C for 10 min. Pellets were washed with 1 mL of ice-cold lysis buffer (20 mM Tris pH 8, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), snap frozen and stored on -80 °C.

tag: strain/genotype

value: KL3 (KT2440 hfq::3xFLAG)

tag: growth phase

value: stationary


title: S3_S

data_processing:
Illumina Casava1.8+ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to a previous assembled unigene dataset using Bowtie V2-2.1.0 with Brassica rapa genome in JGI (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV10) as reference.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: Brapa_1.0 [GCF_000309985.1] and Trinity_rapeseed.fa [FASTA file assembled by us based on our de novo RNA-seq data of the flower transcriptome of rapeseed]
Supplementary_files_format_and_content: tab-delimited text files include count number and RPKM values for each Sample

growth_protocol: The seeds of SP2S and SP2F were sown in field in September and the seedlings were transplanted into greenhouse in early December after vernalization under field condition.

extract_protocol:
Total RNAs were extracted using the Trizol® Reagent (Invitrogen), and purified using TRK1001 Kit (LC Science, Houston, TX). The total RNA quantity and purity were analyzed by using of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA).
RNA libraries were prepared for sequencing using standard protocol for Illumina digital gene expression tag profiling  (Directional mRNA-Seq Sample-PreparationPart#150184 60Rev.A)

treatment_protocol: The plants were grown in a greenhouse woth average temperature at 22°C and photoperiod longer than 14h. This conditions would keep the SP2S line to be male sterile.


title: S2_S


title: S2_GRO5_r2

description: 5'GRO-Seq (nascent RNA TSS)


title: S1_S


title: K1_St


title: F2

description: replicate of the control


title: F2_F


title: F3_F


title: K2_Tr

value: transition


title: F1_F


title: K1_Tr


title: K2_Ex

value: exponential


title: K1_Ex

description: The hfq gene of was C-terminally tagged with 3xFLAG epitopes on the chromosome. DNA fragments were amplified by PCR using the PfuX7 polymerase (Nørholm, 2010). The 3xFLAG sequence (Uzzau et al., 2001) was inserted with primers containing long tails carrying a sequence for 3xFLAG. Plasmid pKB1 was constructed with the Uracil excision-based cloning system (USER). The backbone pSIJ218 and two homologous regions of about 800 bp of P. putida KT2440 genome (upstream and downstream of the insertion – stop codon of hfq gene) were amplified with primers containing uracil, forming single-stranded overhangs compatible among each other to form the plasmid pKB1 in USER reaction as described previously (Cavaleiro et al., 2015). The plasmid was transformed into chemically competent E. coli DH5α λpir for plasmid replication. The correct assembly of pKB1 was checked by colony PCR and sequencing. pKB1 was further transformed into P. putida KT2440 by electroporation as previously described (Choi et al., 2006). The hfq gene was replaced with the hfq::3xFLAG allele forcing two recombination events by conditionally expressing a homing endonuclease I-SceI introduced in plasmid pSW-I, as previously described (Martínez-García and de Lorenzo, 2011). Correct genomic insertions were confirmed by sequencing and the resulting strain with the 3xFLAG tag on the hfq gene was named KL3.


title: siSHARPIN_N3

city: Shenzhen

first: Qiangzu

last: Zhang

address: Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province

institute: Lemondata BioTechnology Limited

data_processing:
Illumina HiSeq 4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software.
Mapping QC by SAMtools and Picard software.
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs).
Genome_build: GRCh37
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited text files include FPKM values for each Sample.

source_name: MCF-7 breast cancer cells, siSHARPIN

growth_protocol: MCF-7 cells were cultured in DMEM with 10% FBS.

extract_protocol:
The total RNA was extracted from cells by the Qiagen RNA extraction kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).

treatment_protocol: Cells were treated with 50nM siSHARPIN or siControl for 48hrs.

tag: cell line

value: breast cancer cell line

tag: sirna

value: SHARPIN


title: siSHARPIN_N2


title: siSHARPIN_N1


title: Wt2_Tr

description: wild-type


title: Wt1_St

description: wild-type


title: Wt2_St

description: wild-type


title: siControlN2

source_name: MCF-7 breast cancer cells, siControl

value: scramble


title: Wt1_Tr

description: wild-type


title: miRNAs_LDCV_biological replicate_1

city: Izmir

first: Yongsoo

last: Park

address: Balcova

country: Turkey

institute: Izmir International Biomedicine and Genome Institute (iBG-izmir)

description: small RNA library

data_processing:
All libraries have been pooled equimolar and been sequenced 51 bp plus one 7 bp Index read on a Hiseq 2500 using Illumina v3 SBS (sequencing by synthesis) chemistry.
Mapper utility of miRDeep2 v2.0.0.7 was employed for removing 3’ adapter sequences (AAGATCGGAAGAGCACACGTCT) of Illumina reads. Trimmed reads were then aligned using mapper utility to Bos taurus  (UMD3.1 assembly, Ensembl release 84) reference genome with default parameters, except that the reads shorter than 17 nucleotides were discarded.
miRBase (release 21) and miRDeep2.pl script were utilized to quantify expression levels of known microRNA species and to discover novel microRNA transcripts as well.
The output of microRNA counts from miRDeep2.pl script were converted to library size normalized Count Per Million (CPM) values using cpm function of edgeR Bioconductor package.
MicroRNAs, which were expressed ≥ 1 CPM at all samples, were utilized for further analysis.
Genome_build: UMD3.1
Supplementary_files_format_and_content: raw.count.values.csv file represent the output of miRDeep2 analysis pipeline, which includes raw and normalized count expression values of samples. log2CPM.value.csvs file represent CPM value filtered, library size normalized log2 CPM values of microRNA expression levels.

organism: Bos taurus

source_name: Cow from local slaughter

extract_protocol:
Large dense-core vesicles were purified from bovine chromaffin cells and total RNA was extracted from of purified vesicles using miRNeasy Mini Kit (Qiagen, Cat: 217004).
The small RNA libraries have been prepared starting with 500 ng of RNA using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Set 1) (NEB, Cat: E7300S/L).

value: Adrenal gland medulla

value: Chromaffin cell


title: siControlN1


title: Wt2_Ex

description: wild-type


title: Wt1_Ex

description: wild-type


title: miRNAs_LDCV_technical replicate_2

description: small RNA library


title: C1TLV30_26MPa_rep1

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

data_processing:
The obtained reads were mapped to the D. piezophilus C1TLV30 genome sequences (MicroScope accession number: BN4v2_DESPIv2) using the Life Technologies Bioscope™ Genomic Analysis Software.
Genome_build: Desulfovibrio piezophilus C1TLV30 (MicroScope accession number: BN4v2_DESPIv2; GCF_000341895.1)
Supplementary_files_format_and_content: bedgraph coverage files were obtained using the UCSC genomeCoverageBed tools.

organism: Pseudodesulfovibrio piezophilus C1TLV30

growth_protocol: Desulfovibrio piezophilus C1TLV30 was grown anaerobically at the optimal temperature of 30 °C, under either 0.1 MPa (atmospheric pressure, low hydrostatic pressure), 26 or 10 MPa (high hydrostatic pressures), for 40 h in 20 mL of the medium described by Kheilafia et al. (2011). These cultures were used to inoculate fresh medium (100 mL) for RNA preparation and biochemical experiments at each corresponding hydrostatic pressure. These large-scale cultures were inoculated at a 1:10 ratio and the cells were grown until the OD600 nm = 0.2. All cultures were carried out in duplicate. Cells were treated as indicated below for either RNA preparation or intracellular metabolites extractions.

extract_protocol:
For mRNA enrichment, 23S and 16S rRNA were depleted using a Ribo-ZeroTM Magnetic Kit (Gram-Negative Bacteria by Epicentre, Illumina®, Cat. No. MRZGN126), according to the manufacturer’s instructions. Briefly, 5 µg of total RNA of each sample was treated by Ribo-Zero rRNA Removal Solution; rRNA was then removed using magnetic beads from Ribo-ZeroTM Magnetic Core Kit (Cat. No. MRZ116C). The ribo-depleted samples were purified by ethanol precipitation and eluted in 13 µl of RNase Free water. The concentration of resulted RNA was determined using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), between 8-16 % of the input RNA was recovered after purification. RNA integrity was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico chip Kit.
Strand-specific libraries constructions were carried out using the SOLiD Total RNA-Seq Kit (Life Technologies) as describes in the manufacturer’s instructions. About 0.35 µg of ribo-depleted RNA was subjected to the enzymatic mRNA fragmentation using RNaseIII from the SOLiD Total RNA-Seq Kit. The fragmented RNA was then concentrated using the Invitrogen RiboMinusTM Concentration Module according to the manufacturer’s protocol. The quantity and quality of resulted RNA were assessed using a Qubit Fluorometer (Life Technologies) and Agilent 2100 Bioanalyzer with the RNA 6000 Pico chip Kit.  Fragmented RNA (0.1 µg) was subjected to cDNA synthesis. After hybridization, ligation of the SOLiDTM Adaptator, RNA was reversed transcripted at 42 °C for 30 min. The resulted cDNA was purified using the Agencourt AMPure XP Reagent performing two rounds. The eluted cDNA was then amplified by PCR reaction (10 cycles: 95 °C 5 min, 95 °C 30 sec, 62 °C 30 sec, 72 °C 30 sec, 72 °C 7 min) using a SOLiDTM 5’ primer and a SOLiDTM 3’ primer specific for each sample (barcode allowing us to pool the samples for sequencing), the resulted product was then purified using the same technique used for the cDNA purification (Agencourt AMPure XP Reagent). The quality and integrity of this DNA was confirmed using a NanoDrop ND-1000 Spectrophotometer and Agilent 2100 Bioanalyzer with DNA 1000 Kit. cDNA libraries were constructed from two independent experiments, for each pressure growth condition. The libraries were amplified with the SOLiD EZ Bead Amplifier, before that the samples were prepared using the SOLiD EZ Bead Emulsifier that allow mixing the aqueous phase containing the SOLiD EZ Bead, library template and primers with the oil phase (Oil Master Mix). The preparation was then amplified by PCR reaction (amplifier software scale E80). After the run was complete, the samples were purified using the SOLiD EZ Bead Enricher according to the manufacturer’s instructions. The P2-enriched beads were then concentrated and the 3’ends were modified as described in the manufacturer’s protocol. Paired-end stranded RNA-Seq with ribo-depleted total RNA was performed using a 5500xl SOLiD high-throughput sequencer (Life Technologies).

treatment_protocol: For total RNA isolation, cells from each hydrostatic pressure condition were harvested by centrifugation at 6000 xg for 20 min at 4 °C and washed once with 20 mL of 0.1 M Tris-HCl 0.15 M NaCl buffer (pH 7.6). The pellets were rinsed three times with 10 mM Tris-HCl (pH 8.0) RNAse-free buffer and finally resuspended in 200 μL of 10 mM Tris-HCl, 1 mM EDTA (pH 8.0) RNase-free buffer. Total RNA was isolated by using the High Pure RNA Isolation Kit (Roche Diagnostics) according to the manufacturer’s instructions with an extra DNase I digestion step in order to eliminate contaminating DNA. RNAs quality was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNAs were quantified to the spectrophotometer at 260 nm (Nanodrop 2000c ThermoScientific). RNAs were prepared from two independent cultures, for each pressure condition (two RNA pools for each condition)

tag: atmospheric pressure

value: 26 MPa (high hydrostatic pressure)


title: C1TLV30_26MPa_rep2


title: JG_10

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description: cellobiose - stationary - rep 1

data_processing:
The raw sequence data generated was converted into FASTQ files using Illumina CASSAVA 1.8.2, which were then imported into CLC Genomics Workbench 7.5.1. Low quality base pairs were trimmed from the ends and the sequence reads were mapped to the C. japonicus reference genome with RPKM values calculated for genes. Log2 transformation and quantile normalization was performed for the RPKM values and a Student’s T-test conducted to compare gene expression between various groups of samples. Additional analysis and visualization of the data was performed using ArrayStar.
Genome_build: GCA_000019225.1
Supplementary_files_format_and_content: Tab-delimited text file includes comparative analysis (fold change) for glucose vs cellobiose (exponential) samples

organism: Cellvibrio japonicus

source_name: bacterial cell pellet

growth_protocol: MOPS defined medium

extract_protocol:
Standard extraction protocols
Sstandard Illumina protocols

treatment_protocol: 95%EtOH:5%Phenol to stop cellular metabolism

tag: genotype/variation

value: WT

tag: protocol

value: cellobiose - stationary


title: JG_12

description: cellobiose - stationary - rep 3


title: JG_07

description: cellobiose - exponential - rep 1

value: cellobiose - exponential


title: JG_09

description: cellobiose - exponential - rep 3


title: JG_11

description: cellobiose - stationary - rep 2


title: C1TLV30_10MPa_rep2

value: 10 Mpa (high hydrostatic pressure)


title: JG_08

description: cellobiose - exponential - rep 2


title: C1TLV30_10MPa_rep1


title: C1TLV30_0.1MPa_rep2

value: 0.1 Mpa (low hydrostatic pressure)


title: C1TLV30_0.1MPa_rep1


title: siControlN3


title: Control_root

status: Public on Dec 31 2016

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

data_processing:
The SolexaQA software package (Solexa) was used to calculate the quality statistics and create visual representations of the data quality from FASTQ files generated by the Illumina sequencer.
Remove the adaptor;Establish the total and unique read counts
Discard small RNAs that mapped to rRNA,tRNA,snoRNA,snRNA;and the remaining reads were mapped to the assembled date palm genome (PDK_30)
For alignment using Bowtie, one mismatch in the first 16 nt was allowed
Hairpin-like structures were predicted using the UNAFold software with the following default settings:the number of permitted errors in one bulge in stem ≤12, the number of base pairs (bp) in the stem region ≥ 16, free energy (ΔG in kCal/mol) ≤ -15, length of the hairpin 158 (up and down stem + terminal loop) ≥50, length of the terminal loop ≤ 350, number of allowed errors in one bulge in a mature region ≤ 8, number of allowed biased errors in one bulge in mature regions ≤ 4, number of allowed biased bulges in mature regions ≤ 2, number of base pairs (bp) in mature miRNAs or mature* (miRNA*) region ≥ 12, percentage of small RNAs in stem regions (pm) ≥ 80% and number of allowed errors in mature regions ≤ 7.
Small RNAs were filtered using a more stringent strategy with the following specifications:MFE ≤ –40 kcal mol-1;MFEI≥0.85
Bowtie v 0.12.7 was used to identify conserved and novel miRNAs
Genome_build: the assembled date palm genome;the transcripts, accession No. ACYX02000000;the complete chloroplast genome
Supplementary_files_format_and_content: tab-delimited text files include sequence and frequency for each Sample

organism: Phoenix dactylifera

source_name: the root of untreated

growth_protocol:
16/8 h light/dark cycle with 350μE m-2 s-1 125 light intensity and 35/30℃ day/night temperature with 60% humidity
Date palm seeds (Phoenix dactylifera L., cultivar Khalas) were thoroughly cleaned with tap water and then surface sterilized by 75% ethanol for 3 minutes and with 1.0% sodium hypochlorite solution for an additional 3 minutes. After rinsing 4 times with sterile water, the seeds were soaked overnight in water. The next day, the seeds were mixed with sterilized moist vermiculite and incubated at 30℃ for one week in the dark. Subsequently, the germinated seeds were carefully planted in 2-liter pots that contained 66% vermiculite and 34% peat moss and were incubated in a growth chamber programmed for a 16/8 h light/dark cycle with 350μE m-2 s-1 light intensity and 35/30℃ day/night temperature with 60% humidity. The plants were watered to field capacity with distilled water as needed for 5 more weeks.

extract_protocol:
Leaf and root tissues from 6 control and salt-treated seedlings were separately pooled, and small RNAs were isolated using the miRNA Mini Kit (Qiagen), following the manufacturer’s instructions. The quality and quantity of the RNA samples were tested using an Agilent 2100 Bioanalyzer (Agilent).
The small RNAs were ligated with 3’and 5’adaptors, and RT-PCR was performed using the TruSeqTM Small RNA kit (Illumina) according to the manufacturer’s instructions. The expected final PCR product was isolated from the gel and purified and sequenced using Illumina Hiseq2000 sequencing technology (Illumina).

treatment_protocol: At the end of this period, the seedlings were either watered regularly (control treatment) or watered twice with a 300-mM NaCl solution in a 72-h interval (salinity treatment). A week after the beginning of the NaCl treatment, the leaves and roots of the control and treated seedling were separately collected, thoroughly rinsed with tap water, dried in tissue paper and flash frozen in liquid nitrogen

value: root

tag: Stage

value: seedlings


title: NaCl_leaf

source_name: the leaves of NaCl-treated

value: leaf


title: Control_leaf

source_name: the leaves of untreated


title: miRNAs_LDCV_technical replicate_1

description: small RNA library


title: TR - N6W - 2909

city: Zurich

first: Martin

last: Flück

address: Lengghalde 5

department: Balgrist Campus

country: Switzerland

institute: University of Zurich

description: Transcripts were measured after 16 weeks of tendon release (TR) in the N6W group

data_processing:
Raw reads were cleaned by removing adapter sequences and trimming first three and last four bases.
The resulting high-quality reads were aligned to the current genome build (Oar_v3.1.75, Ensembl) using STAR (v2.3.0e). The resulting mapping rate was 90%. Approximately 55% of the reads corresponded to mRNA.
Counting was performed using the countOverlaps-method from the IRanges package in Bioconductor (v2.13 with R 3.0.2).
Raw signals were expressed as ‘normalized signals’, reflecting the frequency of the individual gene transcripts. Subsequently the ‘relative concentration’ of gene transcripts was estimated based on the product of multiplying the ‘normalized value’ for each transcript with the measured ‘RNA concentration’ per volume of muscle tissue.
Genome_build: (Oar_v3.1.75, Ensembl) using STAR (v2.3.0e)
Supplementary_files_format_and_content: signal intensities

organism: Ovis aries

source_name: infraspinatus muscle, pre

growth_protocol: Infraspinatus muscle was subjected to 16 weeks of tendon release and 6 weeks of subsequent repair

extract_protocol:
An approximate of 15 mm3 of cryosections was pooled and processed using the RNeasy kit (Qiagen). The quantity and quality of total RNA were evaluated using Qubit® RNA BR Assay Kit (LifeTechnologies, USA) and Agilent RNA 6000 Nano kit with the Agilent 2100 Bioanalyzer instrument (Agilent Technologies Inc., Santa Clara, USA), respectively. RNA sample was accepted for the study when the RIN was ≥7.0.
The quantity and quality of total RNA were evaluated using Qubit® RNA BR Assay Kit (LifeTechnologies, USA) and Agilent RNA 6000 Nano kit with the Agilent 2100 Bioanalyzer instrument (Agilent Technologies Inc., Santa Clara, USA), respectively. RNA sample was accepted for the study when the RIN was ≥7.0. The Illumina TruSeq® Stranded total RNA protocol with the TruSeq Stranded total RNA Sample Preparation Kit was used to produce library constructs. The library product was generated from 1 µg total RNA subsequent to the removal of ribosomal RNA with human specific probes with the Epicentre Ribo-Zero™ Magnetic Gold Kit and subsequent fragmentation of the enriched RNA. Then first strand cDNA synthesis was carried out using reverse transcriptase and random hexamers, followed by second strand cDNA synthesis with DNA polymerase. During this step the RNA template was removed and double-stranded cDNA was synthetized in the presence of dUTP in place of dTTP. In a next step the 3’ ends of the blunt fragments were adenylated and multiple indexing adapters were ligated to the ends of double strand cDNA. Finally, the cDNA was amplified using PCR in order to both enrich DNA fragments having adapter molecules on both ends and amplify the amount of DNA in the library. Quantification and a quality of generated libraries were determined by qPCR with Illumina adapter specific primers using Roche LightCycler® system (Roche Diagnostics, Basel, Switzerland) and on an Agilent Technologies 2100 Bioanalyzer with DNA-specific chip, respectively. Diluted libraries (10 nM) were pooled and were further used for cluster generation according to the manufacturer’s recommendations using TruSeq SR Cluster Kit v3-cBot-HS reagents and sequenced with TruSeq SBS Kit v3-HS reagents on Illumina HiSeq 2500 in the high output mode. On average 50’000’000 reads were sequenced per library.

treatment_protocol: Biopsies were collected from infraspinatus muscle for all time points (PRE, TR, END and END-CC) of the CONTROL, N22W and N6W group

value: Female

tag: group

tag: weight

tag: breed

value: Swiss Alpine


title: END - N6W - 2909

description: Transcripts were measured after 6 weeks of tendon repair subsequent to 16 weeks of tendon release (END) in the N6W group

tag: Sex


title: END-CC - N6W - 2907

description: Transcripts were measured in the contralateral control after 6 weeks of tendon repair subsequent to 16 weeks of tendon release (END-CC) in the N6W group


title: TR - N6W - 2908


title: TR - N6W - 2907


title: PRE - N6W - 2908

description: Transcripts were measured before (PRE) tendon release in the N6W group


title: PRE - N6W - 2907


title: PRE - N6W - 2909


title: END-CC - N6W - 2909


title: END - N6W - 2908


title: NaCl_root

source_name: the root of NaCl-treated


title: END - N6W - 2907


title: END-CC - N22W - 2915

description: Transcripts were measured in the contralateral control after 6 weeks of tendon repair subsequent to 16 weeks of tendon release (END-CC) in the N22W group


title: END - N22W - 2915

description: Transcripts were measured after 6 weeks of tendon repair subsequent to 16 weeks of tendon release (END) in the N22W group


title: PRE - N22W - 2915

description: Transcripts were measured before (PRE) tendon release in the N22W group


title: TR - N22W - 2915

description: Transcripts were measured after 16 weeks of tendon release (TR) in the N22W group


title: TR - N22W - 2914


title: END-CC - N22W - 2913


title: PRE - N22W - 2914


title: END - N22W - 2914


title: END-CC - N6W - 2908


title: TR - N22W - 2913


title: END - N22W - 2913


title: PRE - N22W - 2913


title: END-CC - CONTROL - 2903

description: Transcripts were measured in the contralateral control after 6 weeks of tendon repair subsequent to 16 weeks of tendon release (END-CC) in the CONTROL group

value: CONTROL


title: PRE - CONTROL - 2903

description: Transcripts were measured before tendon release (PRE) in the CONTROL group


title: TR - CONTROL - 2903

description: Transcripts were measured after 16 weeks of tendon release (TR) in the CONTROL group


title: END - CONTROL - 2903

description: Transcripts were measured after 6 weeks of tendon repair subsequent to 16 weeks of tendon release (END) in the CONTROL group


title: END-CC - CONTROL - 2902


title: END - CONTROL - 2902


title: PRE - CONTROL - 2901


title: END - CONTROL - 2901


title: END-CC - N22W - 2914


title: PRE - CONTROL - 2902


title: Mecp2_ko_p57_Veh_IP

city: Boston

first: Hao

last: Wu

state: Massachusetts

address: 149G Warren Alpert Building, 200 Longwood Avenue

department: Genetics

institute: Harvard Medical School/HHMI

description:
Ribosome-associating mRNA
DESeq2_htseq-counts_Veh.vs.CTEP.txt

data_processing:
Sequencing reads (51bp, single-end) were first mapped to the Mus musculus primary assembly reference genome (Gencode GRCm38/release M6) using STAR-2.4.2a. Uniquely mapped reads that overlapped with exons of known protein coding genes were counted using htseq-count python script. Differential expression was calculated using DESeq2 (Love et al., 2014), and P-values were adjusted for multiple testing using the Benjamini-Hochberg procedure.
Genome_build: GRCm38/release M6
Supplementary_files_format_and_content: tab-delimited text files include DESeq2-normalized count values (dervied from htseq-count script) for each sample.

source_name: Hippocampus

growth_protocol: Mecp2 KO mice (Mecp2 tm1.1bird from The Jackson Laboratory, 003890) and WT littermates were maintained on C57/Bl6 background by breeding Mecp2 -/+ females with WT males from Charles Rivers.The Cck-bacTRAP GM39) line was provided by Dr. Nathaniel Heintz at the Rockefeller University.  In this mouse, EGFP fused to the ribosomal protein L10a was inserted in the bacterial artificial chromosome (BAC) in such a way that expression was driven by the cholecystokinin (Cck) promoter. All experiments were performed on littermate WT and Mecp2 KO mice, with the experimenter blinded to genotype.

extract_protocol:
Translating mRNAs were immunoprecipitated from acutely dissected hippocampal tissue and purified as previously described (Heiman et al., 2008, Heiman et al., 2014). RNA samples were analyzed with Bioanalyzer (Agilent) to confirm RNA integrity (RIN>7). RNA concentrations were determined by Quant-it Ribogreen RNA assay (Life Technologies).
Purified RNA (1~1.5 ng) was converted to cDNAs with Ovation RNA-seq V2 system (NuGEN). 500 ng cDNAs from each sample were fragmented to around 200bp size using a Covaris S2 ultrasonicator. Fragmented cDNA (100 ng) was end-repaired, dA-tailed and ligated to adaptors using the NEBNext Ultra DNA library prep kit (New England Biolabs). Sequencing libraries were prepared using the KAPA HiFi Hotstart Ready Mix PCR Kit (Kapa biosystems) and NEBNext Multiplex Oligos for Illumina (Index Primers Set1 and 2).  Library quality was examined by Qubit dsDNA HS Assay Kit (Life Technologies) and Bioanalyzer using High Sensitivity DNA kit (Agilent).  Final concentrations of sequencing libraries were quantified by qPCR using KAPA Library Quantification Kit (Kapa biosystems). TRAP-seq libraries were sequenced on a HiSeq 2500 or a NextSeq 500 sequencer (Illumina).

treatment_protocol: Chronic CTEP treatment (0.4 mg/kg) was administered via subcutaneous injection (for mice younger than P30) or oral gavage (for mice older than P30) once every 48 hr. This dose was chosen after a pilot study revealed that the dose of 2 mg/kg used in previous studies in fragile X (Michalon et al., 2012) and 16p11.2 microdeletion (Tian et al., 2015) mouse models caused significant weight loss in the Mecp2 mice.

tag: age of animal

value: postnatal day 57

tag: cell-type

value: Hippocampal CA1 neurons (Cck-EGFP-L10a)

tag: drug treatment

value: Vehicle

tag: strain


title: TR - CONTROL - 2902


title: Mecp2_ko_p57.rep1_CTEP_IP

value: CTEP


title: Mecp2_ko_p57.rep2_CTEP_IP


title: KO_1

city: Basel

first: Sean

middle: M

last: O'Toole

state: Basel-Stadt

address: Maulbeerstrasse 66

department: Neuroscience

institute: FMI

data_processing:
trimming 3' adaptor with cutadapt (-a AGATCGGAAGAGC)
mapping on mm10 abundant sequences with bowtie2 to filter reads mapped on abundant sequences
mapping to transcriptome (UCSC mm10) and quantification by rsem-1.2.7
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated TPM values

source_name: parvalbumin positive neurons from lumbar 4 dorsal root ganglion

extract_protocol:
RNA extraction using the PicoPure kit
After extraction, RNA was processed into cDNA and amplified using the Ovation rna-seq system (Nugen). cDNA was sonicated to an average of 200 base pairs using the Covaris S220 system. Subsequently, the fragmented DNA repaired and ligated to adapters using the Ovation Rapid DR Multiplex System (Nugen). Finally, libraries were quantified with the KAPA qPCR system.

value: pvalb driven dicer knockout

tag: age


title: ba_d7_k9ac_re2

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

data_processing:
ChIP-seq reads were aligned to the mm9 genome using bowtie 2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
The mapped reads were further quantified as fragments per kilobase of transcript per million mapped reads (FPKM) based on the RefSeq database using the Cufflinks program
Genome_build: mm9
Supplementary_files_format_and_content: The wig files counted by the number of reads falling into 100bp bin in the genome.

source_name: C3H10T1/2 cells

growth_protocol: Growth medium: DMEM (high glucose), 10% Fetalclone III serum, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3; Differentiation medium (d2-d7): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3. Before differentiation cells were seeded at 70% confluency and growth medium was supplemented with 8.3nM human recombinant BMP7 for 3 days.

extract_protocol:
none provided by submitter
none provided by submitter

tag: tissue

value: mesenchymal stem cell line

tag: chip-antibody

tag: day of differentiation


title: ba_d7_k4m1_re2


title: END-CC - CONTROL - 2901


title: ba_d0_k9ac_re2

value: day 0


title: ba_d0_k27m3_re2


title: ba_d7_k4m3_re2


title: ba_d0_k4m1_re2


title: ba_d0_k4m3_re2


title: RNA-seq, WT replicate5

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
ChIP-seq: To obtain enough read depth, all the biological replicates were pooled together by selecting unique reads for Isl1 and Ldb1 respectively. Peak calling was performed using ‘findPeak’ command in Homer. Peaks within ENCODE blacklist regions were discarded. BigWig files for stack height profiles were generated by 1bp-resolution & RPM scale.
RNA-seq: RNA-seq library sequencing and preprocessing were performed by the Functional Genomics Core at the University of Pennsylvania. Reads were aligned to UCSC mouse genome mm9 and gene expression level were quantified using RUM pipeline. Differential gene expression analysis was done using edgeR and genes with FDR < 0.01 were selected as differentially expressed genes upon KO.
Genome_build: mm9
Supplementary_files_format_and_content: Compressed peak file in BED format with RPM-normalized peak height in 5th column. ChIP-seq stack height profile in bigWig format. Differential gene expression analysis results in excel file.

source_name: FACS-enriched β-cells

extract_protocol:
For RNA-Seq: Islets were enzymatically isolated from the pancreas and separated from residual exocrine debris. Isolated islets were dispersed into single-cell suspensions using trypsin. Lineage-tracing positive cells were enriched using MoFlo Astrios directly into TRIzol. Total RNA was extracted using RNAeasy Micro columns then DNAse-treated with the TURBO DNA-free Kit and purified by RNAeasy Micro column. For ChIP-Seq: Islets were enzymatically isolated from the pancreas and separated from residual exocrine debris. Isolated islets were fixed and nuclear lysates were created. Chromatin was sheared and immunoprecipitated
RNA-Seq Libraries: ScriptSeq Complete Gold – Low Input (Illumina, SCL6G); and ChIP-Seq Libraries: NEBNext Ultra DNA Libray Prep Kit for Illumina (NEB, E7370S)

treatment_protocol: At P28, male mice received 5 oral gavages of tamoxifen (Tm) (Sigma, T5648) prepared at 50mg/ml in 90% sun flower seed oil, 10% EtOH (v/v) and given at 150µg/g bodyweight at 24-hour intervals under inhaled isoflurane anesthesia. Repeated at P35. For Isl1L/L; Rosa26LsLeYFP/ LsLeYFP; MIP-CreERTm mice the dosage was lowered to 100µg/g and not repeated at P35.

tag: genotype

value: Rosa26LsLeYFP/ LsLeYFP; MIP-CreERTm

value: mixed SV/129, C57Bl/6


title: ba_d7_k27ac_re2


title: ba_d7_k27m3_re2


title: RNA-seq, WT replicate3


title: ba_d0_k27ac_re2


title: RNA-seq, Ldb1-KO replicate6

value: Ldb1L/L; Rosa26LsLeYFP/ LsLeYFP; MIP-CreERTm


title: RNA-seq, Ldb1-KO replicate7


title: RNA-seq, Ldb1-KO replicate8


title: RNA-seq, WT replicate4


title: RNA-seq, WT replicate2


title: RNA-seq, Ldb1-KO replicate5


title: TR - CONTROL - 2901


title: RNA-seq, Ldb1-KO replicate4


title: RNA-seq, Ldb1-KO replicate1


title: RNA-seq, Ldb1-KO replicate2


title: RNA-seq, Isl1-KO replicate5

value: Isl1L/L; Rosa26LsLeYFP/ LsLeYFP; MIP-CreERTm


title: RNA-seq, Isl1-KO replicate2


title: RNA-seq, Isl1-KO replicate1


title: RNA-seq, Isl1-KO replicate3


title: ChIP-seq, Islet_Ldb1

source_name: Isolated whole islets

value: WT

tag: antibody

value: CLIM-2 Antibody (N-18)-X (Santa Cruz, sc11198 X)


title: RNA-seq, WT replicate1


title: Naïve_V_R2

city: Heidelberg

first: Stefan

last: Uhlmann

address: INF 400

department: Department of Neurology

country: Germany

institute: University of Heidelberg

description:
WTCHG_100618_240
processed data column: Naïve_V_R2

data_processing:
Sequenced reads were trimmed for adaptor sequences: 3' GATCGTCGGACTGTAGAACTCTGAACCTGTCGCCGACGATC, 5' GATCGTCGGACTGTGAACT, only reads with a length restricted to 15-35 were kept, low quality reads were removed
We combined the paired trimmed fastq files to use them as single files, aligned the sequenced reads to the mouse genome (mouse38) with bowtie version 0.12.9  (bowtie -v 2 -S --best), permitting two mismatches between the sequencing reads
To annotate miRNAs to the sequenced reads, we mapped with bowtie version 0.12.9 (bowtie -f -a –best –strata -v 1 -norc) to known mouse miRNAs extracted from a combination of publicly available databanks including miRBase 20 (http://www.mirbase.org), Ensembl 73 (http://www.ensembl.org), and Rfam 11 (http://rfam.xfam.org).
Reads shorter than 15 nucleotides and longer than 35 nucleotides were filtered given that these were unlikely to map to mature miRNAs
Genome_build: mouse38
Supplementary_files_format_and_content: Excel table, Read counts of circulating miRNAs folllowing acute experimental stroke

extract_protocol:
Blood was incubated for 30 min at room temperature to allow clotting. Blood serum was isolated by spinning at 600 g for 15 min at 15 °C. The serum was additionally spun at 16,000 g for 10 min at 10 °C to remove debris and residual cells. Afterwards the samples were stored at -80 °C until assayed. To exclude hemolysis, samples were assessed using absorbance measurements at λ = 414 nm31. miRNAs were extracted with the miRNeasy Mini Kit or miRNeasy Micro Kit (Qiagen, Germany) according to the manufacturer’s instructions following lysis and homogenization in TRIzol from 200 µL serum. Synthetic Caenorhabditis elegans miRNAs (cel-miR-39) containing 1.6 x 108 copies/μL were supplemented to the serum before starting the RNA isolation procedure. These spiked-in RNAs served as an exogenous control to monitor the efficiency of RNA extraction, cDNA synthesis and qRT-PCR.
Small RNA sequencing libraries were prepared using the NEBNext® Multiplex Small RNA kit according to the manufacturer’s instructions with a fixed volume of input material rather than an equal RNA concentration.
paired-end small RNA deep sequencing (i.e. 2-lane flow cell) performed on the Illumina HiSeq2500 platform.

value: 8-12 week

value: blood serum


title: Naïve_IV_R1

description:
WTCHG_100617_226
processed data column: Naïve_IV_R1


title: Naïve_V_R1

description:
WTCHG_100617_240
processed data column: Naïve_V_R1


title: Naïve_IV_R2

description:
WTCHG_100618_226
processed data column: Naïve_IV_R2


title: RNA-seq, Isl1-KO replicate4


title: Naïve_II_R1

description:
WTCHG_100617_224
processed data column: Naïve_II_R1


title: Naïve_III_R1

description:
WTCHG_100617_225
processed data column: Naïve_III_R1


title: Naïve_I_R2

description:
WTCHG_100618_206
processed data column: Naïve_I_R2


title: Naïve_III_R2

description:
WTCHG_100618_225
processed data column: Naïve_III_R2


title: ICH_Sham_V_R2

description:
WTCHG_100618_218
processed data column: ICH_Sham_V_R2


title: ICH_Sham_IV_R2

description:
WTCHG_100618_217
processed data column: ICH_Sham_IV_R2


title: ICH_Sham_IV_R1

description:
WTCHG_100617_217
processed data column: ICH_Sham_IV_R1


title: Naïve_I_R1

description:
WTCHG_100617_206
processed data column: Naïve_I_R1


title: ICH_Sham_III_R1

description:
WTCHG_100617_216
processed data column: ICH_Sham_III_R1


title: ICH_Sham_III_R2

description:
WTCHG_100618_216
processed data column: ICH_Sham_III_R2


title: ICH_Sham_I_R2

description:
WTCHG_100618_214
processed data column: ICH_Sham_I_R2


title: ICH_Sham_II_R1

description:
WTCHG_100617_215
processed data column: ICH_Sham_II_R1


title: ICH_Sham_II_R2

description:
WTCHG_100618_215
processed data column: ICH_Sham_II_R2


title: Naïve_II_R2

description:
WTCHG_100618_224
processed data column: Naïve_II_R2


title: RNA-seq, Ldb1-KO replicate3


title: ICH_Sham_V_R1

description:
WTCHG_100617_218
processed data column: ICH_Sham_V_R1


title: ICH_Sham_I_R1

description:
WTCHG_100617_214
processed data column: ICH_Sham_I_R1


title: ICH_V_R2

description:
WTCHG_100618_213
processed data column: ICH_V_R2


title: ICH_III_R1

description:
WTCHG_100617_211
processed data column: ICH_III_R1


title: ICH_IV_R2

description:
WTCHG_100618_212
processed data column: ICH_IV_R2


title: MCAO_Sham_VII_R1

description:
WTCHG_100617_204
processed data column: MCAO_Sham_VII_R1


title: ICH_II_R1

description:
WTCHG_100617_210
processed data column: ICH_II_R1


title: ICH_I_R1

description:
WTCHG_100617_209
processed data column: ICH_I_R1


title: ICH_V_R1

description:
WTCHG_100617_213
processed data column: ICH_V_R1


title: MCAO_Sham_VII_R2

description:
WTCHG_100618_204
processed data column: MCAO_Sham_VII_R2


title: ICH_I_R2

description:
WTCHG_100618_209
processed data column: ICH_I_R2


title: MCAO_Sham_V_R1

description:
WTCHG_100617_223
processed data column: MCAO_Sham_V_R1


title: MCAO_Sham_II_R2

description:
WTCHG_100618_222
processed data column: MCAO_Sham_II_R2


title: MCAO_Sham_I_R2

description:
WTCHG_100618_221
processed data column: MCAO_Sham_I_R2


title: MCAO_Sham_IV_R2

description:
WTCHG_100618_205
processed data column: MCAO_Sham_IV_R2


title: MCAO_Sham_IV_R1

description:
WTCHG_100617_205
processed data column: MCAO_Sham_IV_R1


title: ICH_IV_R1

description:
WTCHG_100617_212
processed data column: ICH_IV_R1


title: MCAO_Sham_II_R1

description:
WTCHG_100617_222
processed data column: MCAO_Sham_II_R1


title: ICH_II_R2

description:
WTCHG_100618_210
processed data column: ICH_II_R2


title: MCAO_V_R1

description:
WTCHG_100617_220
processed data column: MCAO_V_R1


title: MCAO_III_R1

description:
WTCHG_100617_202
processed data column: MCAO_III_R1


title: MCAO_III_R2

description:
WTCHG_100618_202
processed data column: MCAO_III_R2


title: MCAO_I_R2

description:
WTCHG_100618_219
processed data column: MCAO_I_R2


title: MCAO_II_R1

description:
WTCHG_100617_201
processed data column: MCAO_II_R1


title: ICH_III_R2

description:
WTCHG_100618_211
processed data column: ICH_III_R2


title: MCAO_IV_R1

description:
WTCHG_100617_203
processed data column: MCAO_IV_R1


title: MCAO_IV_R2

description:
WTCHG_100618_203
processed data column: MCAO_IV_R2


title: MCAO_Sham_V_R2

description:
WTCHG_100618_223
processed data column: MCAO_Sham_V_R2


title: MCAO_V_R2

description:
WTCHG_100618_220
processed data column: MCAO_V_R2


title: MCAO_Sham_I_R1

description:
WTCHG_100617_221
processed data column: MCAO_Sham_I_R1


title: WT_Rep2

city: Buffalo

first: Lee Ann

last: Sinha

state: NY

address: 701 Ellicott St

department: Biochemistry

institute: University at Buffalo

data_processing:
Reads were mapped to mouse transcriptome (mm9 assembly) using Tophat2 version 2.0.13
The aligned reads were assembled and mapped to the mm9 transcriptome.
Cuffdiff was used to calculate differential gene expression and derive FPKM (Fragments per kilobase of transcript per million mapped reads) values
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited files include FPKM values for each sample

source_name: Spleen

extract_protocol:
Quiescent follicular B cells were sorted out from splenocytes and RNA was harvested using Trizol reagent and purified by Direct-zol RNA Miniprep kit
1 μg of total RNA was used to construct the libraries using Illumina TruSeq RNA Sample Prep Kit

tag: cell type

value: Quiescent follicular B cell

value: wild-type


title: WT_Rep1


title: Input_DNA_Rep1

data_processing:
Reads were aligned to mm9 assembly using Bowtie (v1.1.1) with the following parameters :bowtie -S -p 8 -m 1 *.fastq > *.sam
Sam files were converted to Bam format using Samtools (v1.1) and used for peak calling.
Peaks were called using MACS2 (v2.0.10) against paired input samples with the p-value cutoff 0.05 for IDR (Irreproducible Discovery Rate) analysis
Reproducible peaks from each replicate were selected using IDR threshold of 0.01
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

extract_protocol:
Splenic B cells isolated using the Stem Cell Technologies EasySep Mouse B cell isolation kit were rested for 1-2 hours in complete media (RPMI-1640 plus 10% fetal bovine serum, 1X Glutamax, 1X penicillin-streptomycin and 50 micromolar beta-mercaptoethanol) in a tissue culture incubator at 37C. After resting, cells were crosslinked with 0.25% formaldehyde for 8 minutes. Fixed B cells were lysed, chromatin were prepared and immunoprecipitated according to the protocol of ChIP-IT High Sensitivity Kit (Active Motif).
ChIP-seq libraries were prepared using the manufracturer's protocol of Rubicon ThruPlex kit

value: Primary splenic B cells

tag: chip antibody


title: Ets1_ChIPseq_Rep1

value: Ets1 (Santa Cruz, Sc-350X)


title: Ets1_ChIPseq_Rep2


title: Mecp2_wt_p41_IP

description:
Ribosome-associating mRNA
DESeq2_htseq-counts_wt.vs.ko.txt

value: postnatal day 41

value: Hippocampal CA1 neurons (Cck-EGFP-L10a)

value: no


title: Mecp2_wt_p50_IP

value: postnatal day 50


title: Input_DNA_Rep2


title: Mecp2_ko_p41_IP


title: Ets1_KO_Rep1


title: Mecp2_wt_p37_Input

description:
Ribosome-associating mRNA
DESeq2_htseq-counts_IP.vs.input.txt

value: postnatal day 37

value: whole hippocampus


title: MCAO_I_R1

description:
WTCHG_100617_219
processed data column: MCAO_I_R1


title: MCAO_II_R2

description:
WTCHG_100618_201
processed data column: MCAO_II_R2


title: Mecp2_wt_p56_Input

value: postnatal day 56


title: Mecp2_wt_p56_IP

description:
Ribosome-associating mRNA
DESeq2_htseq-counts_IP.vs.input.txt, DESeq2_htseq-counts_wt.vs.ko.txt