title: ADAR2 (E488Q) +GluR2 adRNA

description:
Sample name:
23

value: ADAR2 (E488Q) +GluR2 adRNA


title: ADAR2 + GluR2 adRNA

status: Public on Dec 17 2018

type: SRA

city: La Jolla

first: Dario

last: Meluzzi

state: CA

address: 9500 Gilman Drive #0648

department: School of Medicine

country: USA

institute: UC San Diego

description:
Sample name:
21

library_source: transcriptomic

data_processing:
Basecalls were performed using Illumina RTA 2.7.7.0, and fastq files were then generated using Illumina bcl2fastq v2.18.0.12. Both tasks were carried out by the UCSD IGM Genomics Center.
RNA-seq read pairs with 100 bases per read mate were aligned to the GRCh38 reference genome using STAR aligner version 2.6.0c (Dobin A et al 2013). The genome index was built using primary assembly annotations from GENCODE release 28 (GRCh38.p12). Default parameters were used to run STAR, except for the following relevant settings: readMapNumber=-1, alignSJoverhangMin=5, alignSJDBoverhangMin=1, alignEndsType=EndToEnd, outFilterMismatchNmax=10, outFilterMultimapNmax=1, outSAMunmapped=None, outSAMmultNmax=1
The reads of the resulting uniquely aligned pairs were sorted by genomic coordinate using samtools sort (Li H. et al 2009). Duplicated read pairs were marked using samtools markdup and were removed from subsequent RNA-editing analysis.
The uniquely aligned reads for each sample were down-sampled using samtools view with option -s. Down-sampling fractions were calculated by dividing the smallest number of uniquely aligned reads among all samples by the number of uniquely aligned reads available for the sample being down-sampled. Down-sampling was not performed on the reads of the control sample. The down-sampled reads where then fed to samtools mpileup, whose output was parsed to extract the counts of each base found at each A-site and T-site in the GRCh38 reference genome. Insertions and deletions were ignored. Reference sites with read coverage less than 10 were discarded. From the remaining reference A- and T-sites a final list was selected by choosing sites common to all samples and with at least one G or C at a reference A- or T-site, respectively, in at least one sample.
For each pair of compared control and treatment samples, and for each reference A- or T- site selected as described above, a Fisher exact test was carried out to calculate the p-value for the change in proportion of G or C bases, respectively, at that site. The p-values for all selected reference sites were adjusted for multiple testing using the Benjamini-Hochberg method.
Genome_build: GRCh38
Supplementary_files_format_and_content: pm_adar_rned_003-mcpspc_bfscr_res-bpr-000.tsv.gz: Proportions of G or C bases counted from aligned reads at each selected reference A- or T-site (row), respectively, for each biological sample (column).
Supplementary_files_format_and_content: pm_adar_rned_003-mcpspc_bfscr_res-pad-000.tsv.gz: Adjusted p-values for comparisons of proportions of G or C bases between each treatment sample and control sample, at each selected reference A- or T-site, respectively.

molecule: polyA RNA

organism: Homo sapiens

source_name: HEK 293T

growth_protocol: All HEK 293T cells were grown in Dulbecco’s Modified Eagle Medium supplemented with 10% FBS and 1% Antibiotic-Antimycotic (Thermo Fisher) in an incubator at 37 °C and 5% CO2 atmosphere.

extract_protocol:
Cells were harvested 60 hours post transfection. RNA was extracted using the Qiagen RNeasy mini kit.
RNA-seq libraries were prepared from 300ng of RNA, using the NEBNext Poly(A) mRNA magnetic isolation module and NEBNext Ultra RNA Library Prep Kit for Illumina. Samples were pooled and loaded on an Illumina Hiseq (100bp paired-end run).

treatment_protocol: Cells were transfected with lipofectamine 2000 at 25-30% confluence.

tag: cell line

value: HEK 293T

tag: transfected with

value: ADAR2 + GluR2 adRNA


title: ce_krit1_rep2

status: Public on Dec 18 2018

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.115
Alignment: STAR v2.5.3a
Post alignement QC assessment: RSeQC and Picard tools v2.9.0
Gene transcripts assembly: featureCounts
Differentially expressed genes analysis: DESeq2
Genome_build: UCSC human genome model: hg19; GENCODE mouse genome model: GRCm38 V13 (release_M13); ENSEMBLE worm genome model: c. elegans WBcel235 V87 (release-87)
Supplementary_files_format_and_content: tab-delimited text files include gene features raw counts values summarized by featureCouts for each Sample.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: entire organism

extract_protocol:
For human samples, RNAs was extracted using an RNA isolation kit (RNeasy® Micro Kit, Qiagen, Hilden, Germany). For mouse and C. elegans samples, RNA was extracted using the TRIzol protocol (ThermoFisher, Waltman, MA).
RNA libraries were prepared for sequencing using commercially low-input strand specific RNA-Seq kits (Clontech, California, USA) for human specimens and TruSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) for mouse and C. elegans samples

tag: genotype

value: Kri-1 null (ccm1/kri-1(ok1251) knock out)

tag: age

value: 24 hours past the L4 state

tag: cell type

value: entire organism


title: MCP-ADAR2 DD (E488Q)-NLS - MS2 adRNA

description:
Sample name:
16

value: MCP-ADAR2 DD (E488Q)-NLS - MS2 adRNA


title: 293T+GFP

description:
Sample name:
19


title: MCP-ADAR2 DD (E488Q)-NLS + MS2 adRNA

description:
Sample name:
17

value: MCP-ADAR2 DD (E488Q)-NLS + MS2 adRNA


title: MCP-ADAR2 DD-NLS - MS2 adRNA

description:
Sample name:
14

value: MCP-ADAR2 DD-NLS - MS2 adRNA


title: MCP-ADAR2 DD (E488Q)-NES + MS2 adRNA

description:
Sample name:
13

value: MCP-ADAR2 DD (E488Q)-NES + MS2 adRNA


title: MCP-ADAR2 DD-NLS + MS2 adRNA

description:
Sample name:
15

value: MCP-ADAR2 DD-NLS + MS2 adRNA


title: MCP-ADAR2 DD-NES - MS2 adRNA

description:
Sample name:
10

value: MCP-ADAR2 DD-NES - MS2 adRNA


title: MCP-ADAR1 DD (E1008Q)-NLS +MS2 adRNA

description:
Sample name:
9

value: MCP-ADAR1 DD (E1008Q)-NLS +MS2 adRNA


title: MCP-ADAR1 DD (E1008Q)-NLS - MS2 adRNA

description:
Sample name:
8

value: MCP-ADAR1 DD (E1008Q)-NLS - MS2 adRNA


title: MCP-ADAR1 DD-NLS + MS2 adRNA

description:
Sample name:
5

value: MCP-ADAR1 DD-NLS + MS2 adRNA


title: MCP-ADAR1 DD (E1008Q)-NES - MS2 adRNA

description:
Sample name:
6

value: MCP-ADAR1 DD (E1008Q)-NES - MS2 adRNA


title: MCP-ADAR1 DD (E1008Q)-NES + MS2 adRNA

description:
Sample name:
7

value: MCP-ADAR1 DD (E1008Q)-NES + MS2 adRNA


title: MCP-ADAR1 DD-NES + MS2 adRNA

description:
Sample name:
3

value: MCP-ADAR1 DD-NES + MS2 adRNA


title: MCP-ADAR1 DD-NES - MS2 adRNA

description:
Sample name:
2

value: HEK 293T

value: MCP-ADAR1 DD-NES - MS2 adRNA


title: 293T TR2

description:
Sample name:
1
technical replicate (i.e., separate lanes of the flow cell, or different sequencing runs) of the same RNA-seq library that was used for sample 0.

value: untransfected control


title: 293T

description:
Sample name:
0


title: 293T TR3

description:
Sample name:
18
technical replicate (i.e., separate lanes of the flow cell, or different sequencing runs) of the same RNA-seq library that was used for sample 0.


title: ADAR2 - GluR2 adRNA

description:
Sample name:
20

value: ADAR2 - GluR2 adRNA


title: TEFF-IV

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version 1.22.1, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: TEFF

growth_protocol: T cell purification and genomic editing: TN (TCR+CD62L+CCR7+CD45RA+CD95-), TSCM (TCR+CD62L+CCR7+CD45RA+CD95+) and TEFF (TCR+CD62L-CCR7-CD45RA+CD95+) were sorted by flow cytometry. The CAR cDNA was targeted to the TRAC locus of sorted naïve T cells, followed by in vitro culture and TCR-negative purification.

extract_protocol:
T cells were resuspended in 250ul PBS and placed in 750ul TRIzol LS (Invitrogen). RNA was extracted using the RNeasy Mini Kit (QIAGEN) according to instructions provided by the manufacturer.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50bp/50bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).  An average of 30.6 million paired reads was generated per sample. At the most, ribosomal reads represented 4.69% of the total reads generated. The percent of mRNA bases averaged 69.3%.

treatment_protocol: 7 days after CAR cDNA targeting was performed, CAR T cells were stimulated with 3T3-CD19 for 24 hours, followed by magnetic selection of CD8+ T cells (Miltenyi).

value: CD8 T cells

tag: cell subset

value: CD8 T cell subset TEFF


title: TEFF-III


title: TSCM-V

source_name: TSCM

value: CD8 T cell subset TSCM


title: TEFF-II


title: MCP-ADAR2 DD-NES + MS2 adRNA

description:
Sample name:
11

value: MCP-ADAR2 DD-NES + MS2 adRNA


title: TSCM-III


title: TEFF-I


title: TEFF-V


title: MCP-ADAR2 DD (E488Q)-NES - MS2 adRNA

description:
Sample name:
12

value: MCP-ADAR2 DD (E488Q)-NES - MS2 adRNA


title: TSCM-II


title: TSCM-I


title: TSCM-IV


title: TN-VI

source_name: TN

value: CD8 T cell subset TN


title: TN-V


title: MCP-ADAR1 DD-NLS - MS2 adRNA

description:
Sample name:
4

value: MCP-ADAR1 DD-NLS - MS2 adRNA


title: TN-IV


title: TN-II


title: TEFF-VI


title: TN-I


title: TN-III


title: TRAC-XX3-III

value: CD8 T cells expressing TRAC-XX3


title: THP1_PU1 [NM-L1_S1_L001_R1_001]

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

description:
PU.1 (2 biological replicates)
MACS2_IDR_PU1.txt

library_source: genomic

data_processing:
fastq files for HiSeq 4000 reads were generated using the Illumina pipeline (1.8). NextSeq 500 data (IRF8 and associated Input) fastq files were generated and pre-processed by Illumina BaseSpace
reads not demonstrating a minimal quality level (at least 60% of the read must have PHRED score of at least 20) were filtered prior to mapping using the fastx-toolkit (fastq_quality_filter -q 20 -p 60)
filtered reads were mapped to the reference genome (hg19) using bowtie2 (default parameters, --local)
mapped reads were filtered for high-quality, uniquely mappable reads using samtools (samtools view -b -F 1548 -q 30)
peaks were called on both biological replicates separately using MACS2 with relaxed parameters (-p 1e-3)
transcription factor peaks (PU.1, C/EBPa, IRF8) were then filtered for stringent reproducibility across biological replicates (IDR < 0.01) using IDR and used to design the nextPBM microarray. Peaks shared across the punctate histone mark (H3K4me1 and H3K27ac) replicates were also used
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, narrowPeak (relaxed parameters from MACS2), bed (cross-replicate IDR format)

molecule: genomic DNA

source_name: THP-1 cell line

growth_protocol: THP-1 cells were purchased from ATCC (cat # TIB-202) and cultured in RPMI 1640 media with 10% FBS supplemented by 50 unit/ml Penicillin and 50ug/ml Streptomycin

extract_protocol:
Soluble-chromatin was prepared from 40,000,000 THP-1 cells according to previously described protocols with some modifications (outlined below). Briefly, cells were crosslinked with 1% formaldehyde (final concentration) (Fisher Scientific, cat # F79-500) for 10 minutes at room temperature with gentle shaking. Crosslinking was stopped by adding 125 mM final concentration of glycine solution in PBS . Fixed cells were pelleted at 800xg for 5 minutes at 4˚Ϲ and washed twice with 10 ml of cold PBS in a 15 ml conical tube and pelleted at 800xg for 5 minutes at 4˚Ϲ.  Washed cell pellet was re-suspended in 10 ml of Lysis Buffer 133, nutated for 10 minutes at 4˚Ϲ,  and pelleted at 2000xg for 5 minutes at 4˚Ϲ. The same procedure was repeated with Lysis Buffer 233 at room temperature followed by pelleting at 2000xg for 5 minutes at 4˚Ϲ. To release nuclei from hard-to-disrupt THP-1 membranes, cells were re-suspended in 10 ml of Lysis Buffer 333 and were shaken vigorously (225 rpm) at room temperature for 30 minutes. Cells then were passed through an 18-gauge needle (VWR, cat # BD305195) for 25 times using a 10ml syringe. Nuclei were pelleted at 3000xg for 20 minutes at 4˚Ϲ and re-suspended in 500 μl of Lysis Buffer 3 and then transferred into a 1.5 ml microfuge tube placed in Benchtop 1.5 ml Tube Cooler (Active Motif, cat # 53076).  The nuclei were sonicated using Active Motif Q120AM sonicator with a 3.2 mm Probe (Active motif cat # 53053) at 25% amplitude for 15 minutes with 20 seconds ON and 30 seconds OFF cycles (45 cycles total). Cell-debris was pelleted at 21,000xg for 30 minutes at 4˚Ϲ. 50 μl of the combined soluble-chromatin was saved to be used as the input DNA upon reverse-crosslinking. For immunoprecipitation, 500 μl of the soluble chromatin was mixed with 30 μg of either PU.1, C/EBPα, H3K4me or H3K27ac antibodies (60 μg of IRF8 antibody was mixed with 1 ml of the soluble chromatin), and a tubes were rotated at 25 rpm for one hour at 4˚Ϲ using HulaMixer (ThermoFisher Scientific cat # 15920). 125 μl of the protein A Dynabead slurry (ThermoFisher Scientific cat # 10001D) per each rabbit antibody (PU.1. C/EBPα, H3K4me or H3K27ac), and 250 μl of the protein G Dynabead slurry (ThermoFisher Scientific cat # 10003D) for the goat-IRF8 antibody, were transferred into 1.5 ml microfuges and placed on DynaMag magnet (ThermoFisher Scientific, cat # 12321D) until all beads collected on the side of tubes. The solution was gently aspirated off from each tube and then the rack was removed from the magnet and beads were re-suspended in 1 ml of the Lysis Buffer 3 with several gentle inversions and then the rack was put back on the magnet and the buffer was aspirated off after all beads were collected on the side of the tube. Each bead then re-suspended in 50 μl of Lysis Buffer 3 and were added to the corresponding tube and returned to HulaMixer to rotate at 35 rpm for over-night at 4˚Ϲ. Dynabeads were collected with placing the tubes in the magnet. Beads were washed for 6 times with 1 ml of the Lysis Buffer 3 and two times with 1 ml of the Wash Buffer (RIPA). All ChIP samples along with the 50 μl of the soluble-chromatin were reverse-crosslinked by adding 200 μl of the Elution buffer and 3 μl of 20 mg/ml Proteinase K (ThermoFisher Scientific, cat # AM2546) and incubated at 65˚Ϲ for over-night. Beads were collected by magnets and the solutions were transferred into a new 1.5 microfuges containing 1 μl of 10 mg/ml RNase A (ThermoFisher Scientific, cat # EN0531) and left at room temperature for an hour. The ChIP and input DNA were purified using QIAquick PCR Purification Kit (QIAGEN, cat # 28104) and eluted in 50 μl of 50˚Ϲ Nuclease-Free Water (Thermo Fisher Scientific, AM9932). The concentration and size distribution of the ChIP-DNA samples were defined using Agilent 2100 Bioanalyser
DNA libraries were prepared using NEBNext Ultr II DNA Library Prep kit (NEB, E7645S) following the provider’s instruction manual. Amplified libraries were Bioanalyzed again to check the size selection efficiency and to define the concentrations of libraries before preparing the library pool involving the same molarity of each library

treatment_protocol: untreated

value: untreated monocytes

tag: chip antibody

value: PU.1 (Santa Cruz sc-352x)


title: TRAC-1XX-I

value: CD8 T cells expressing TRAC-1XX


title: TRAC-XX3-II


title: TSCM-VI


title: TRAC-1XX-III


title: TRAC-XX3-I


title: TRAC-1XX-II


title: TRAC-1928z-II

value: CD8 T cells expressing TRAC-1928z


title: TRAC-1928z-III


title: PTM_SP_Hypothalamus_Input

city: San Francisco

first: Walter

last: Eckalbar

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

description: ChIP-peaks.xlsx

data_processing:
Fastq files were generated with Casava 1.8
RNA-seq and ChIP-seq reads were aligned with STAR (version 2.5.2b)
For ChIP-seq, duplicate reads were removed using Picardtools MarkDuplicates
ChIP-seq peak calling: Peaks were called for each sample type by merged repicates and using Macs2 (2.1.1.20160309) using the Inputs and None targeted ChIPs as controls
All differential expression (RNA-seq) tests were carried out using DESeq2 (version 1.16.1).
Genome_build: mm9
Supplementary_files_format_and_content: xlsx, RNA-seq file All_genes.Sim1_RNAseq.xlsx has expression measures (sequencing depth normalized counts and variance stabilized counts for all samples and DE test results for all comparisons). ChIP-peaks.xlsx has the ChIP-seq peaks identified with macs2.

organism: Mus musculus

source_name: Hypothalumus

extract_protocol:
RNA-seq - RNeasy Mini Kit (Qiagen), ChIP-seq - Fresh tissue was homogenized using a hand-held dounce homogenizer, cross-linked in Phosphate buffer saline (PBS) containing 1% formaldehyde for 10 minutes, quenched with 125mM Glycine for 5 minutes and washed three times with PBS. Cross-linked tissue pellet was processed further for chromatin immuoprecipitation using the ‘Low cell Chip Kit’ (Diagenode; catalog number C01010072) following the manufacturer’s protocol. An S. pyogenes Cas9 polyclonal antibody (Diagenode; catalog number C15310258) and an S.aureus Cas9 monoclonal antibody (Diagenode; catalog number C15200230) were used for the pull down.
RNA-seq - Nugen Ovations and Nextera XT, ChIP-seq - Rubicon Genomics ThruPLEX DNA-seq kit

tag: background strain

tag: sgrna

value: Promoter

tag: age (months)

value: adult

tag: Sex

value: female


title: ETM_SP_Hypothalamus_Input

description: ChIP-peaks.xlsx

value: Enhancer

value: pooled male and female


title: PTM_SP_Neuro2A_rep2

description: ChIP-peaks.xlsx

source_name: neuro 2A cells

value: S. pyogenes Cas9 polyclonal antibody (Diagenode; catalog number C15310258)


title: NT_SP_Hypothalamus_Input


title: PTM_SP_Hypothalamus_rep2

description: ChIP-peaks.xlsx


title: PTM_SP_Neuro2A_rep1

description: ChIP-peaks.xlsx


title: TRAC-1928z-I

value: CD8 T cells


title: NT_SP_Hypothalamus_rep1


title: PTM_SA_Hypothalamus_rep2

description: ChIP-peaks.xlsx

value: S.aureus Cas9 monoclonal antibody (Diagenode; catalog number C15200230)


title: PTM_SP_Hypothalamus_rep1

description: ChIP-peaks.xlsx


title: PTM_SA_Hypothalamus_rep1

description: ChIP-peaks.xlsx


title: ETM_SP_Neuro2A_rep2

description: ChIP-peaks.xlsx


title: ETM_SP_Neuro2A_rep1

description: ChIP-peaks.xlsx


title: ETM_SP_Hypothalamus_rep2

description: ChIP-peaks.xlsx


title: ETM_SP_Hypothalamus_rep1

description: ChIP-peaks.xlsx


title: ETM_SA_Hypothalamus_rep2

description: ChIP-peaks.xlsx


title: ETM_SA_Hypothalamus_rep1

description: ChIP-peaks.xlsx


title: WT_M_1

value: WT

value: M


title: WT_F_2

value: F


title: SH_M_1


title: WT_F_4


title: WT_F_3


title: SH_F_4


title: WT_F_1


title: NT_SP_Hypothalamus_rep2


title: SH_F_1


title: SH_F_3


title: PTM_M_3


title: PTM_M_1


title: PTM_F_5


title: PTM_F_1


title: PTM_F_3


title: PTM_F_2


title: ETM_F_1


title: ETM_M_1


title: ETM_F_2


title: hetBT14IX

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

data_processing:
Samples were demultiplexed using deML (Renaud et al., 2015)
Reads were mapped with ngm (Sedlazeck et al., 2013)
HTseq was used to count reads overlapping genes unambigiously (Anders et al., 2015)
Genome_build: mm10
Supplementary_files_format_and_content: Gene/Sample-wise counts

extract_protocol:
Cell type–specific RNA purification by translating ribosome affinity purification (BacTRAP):
Mice (3 months old) were decapitated and fresh brains immediately processed according to Heiman et al. Cortical hemispheres from one animal were dissected from diencephalon and basal ganglia structures, hippocampus and a tip of a rostral cortex, and processed in 2mL of tissue-lysis buffer. 30µl of the supernatant (S20) was collected as an input sample immediately before immunopurification (IP). Affinity matrix was prepared with Dynabeads Protein G (Life Technologies, Novex) (50µl per sample) and anti-GFP rabbit serum (Life Technologies, Molecular Probes) (10µl per sample), and beads were washed in a low-salt buffer.
Library preparation for RNA sequencing was performed using the Smart-seq2 protocol (Picelli et al., 2014)

tag: strain background

tag: genotype/variation

value: heterozygous Foxp2 deletion

value: 3 months

tag: tissue

value: cortex

tag: bactrap sample

value: Input


title: P_496_Postsort_CD8_T

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to hg19 reference build with refGene GTF annotation version 25 using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 and TPM using RSEM v1.2.7
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated text file with raw counts and TPM quantification.

source_name: blood

extract_protocol:
Frozen PBMC were thawed, restored, washed and counted. An aliquot of cells was resuspended in PBS containing 0.1% BSA (PBS/BSA), blocked with mouse IgG, and labeled at room temperature with the mouse anti-human antibodies. The cells were then washed in PBS/BSA, resuspended in 1 ml PBS/BSA, filtered through a 35 micron mesh, and diluted with 1 ml sort buffer. Four-way sorting was performed on a BD FACSAria II sorter, where monocytes, B-cells, CD4T, and CD8T cells were sorted simultaneously. The purification of total and small RNA was prepared using the miRNeasy mini kit (Qiagen).  Quantitative assessment of the purified total RNA was accomplished using a Qubit Broad Range RNA kit (Thermofisher), which was then qualitatively evaluated by a 2100 Bioanalyzer (Agilent technologies).
The sequencing libraries were prepared with the TruSeq Stranded Total RNA kit (Illumina Inc) and sequenced on a HiSeq2500 sequencer using a 100 cycle single-read cluster kit.

tag: subject

value: blood

tag: ptsd

value: Yes


title: P_496_Postsort_CD4_T


title: P_496_Postsort_CD19_B


title: P_462_Postsort_CD4_T


title: P_496_Postsort_CD14_M


title: P_496_UNSEP

value: PBMC


title: P_462_UNSEP


title: P_501_UNSEP


title: E_197_Postsort_CD19_B


title: E_197_Postsort_CD8_T


title: P_462_Postsort_CD19_B


title: E_197_Postsort_CD4_T


title: P_462_Postsort_CD14_M


title: E_197_UNSEP


title: P_501_Postsort_CD19_B


title: wtBT13IP

source_name: wild type_cortex_IP

value: wild type

value: IP


title: P_501_Postsort_CD8_T


title: ETM_M_3

value: Enhancer


title: P_501_Postsort_CD14_M


title: P_343_UNSEP


title: P_501_Postsort_CD4_T


title: E_197_Postsort_CD14_M


title: P_343_Postsort_CD8_T


title: P_343_Postsort_CD4_T


title: I_85_Postsort_CD8_T

value: No


title: P_343_Postsort_CD14_M


title: P_343_Postsort_CD19_B


title: I_85_Postsort_CD4_T


title: I_85_Postsort_CD14_M


title: P_462_Postsort_CD8_T


title: I_75_UNSEP


title: I_75_Postsort_CD8_T


title: I_75_Postsort_CD19_B


title: I_75_Postsort_CD14_M


title: I_52_UNSEP


title: I_52_Postsort_CD8_T


title: I_52_Postsort_CD19_B


title: I_5_UNSEP


title: I_5_Postsort_CD8_T


title: I_5_Postsort_CD14_M


title: I_52_Postsort_CD14_M


title: I_33_Postsort_CD19_B


title: I_33_Postsort_CD14_M


title: I_33_Postsort_CD4_T


title: I_85_UNSEP


title: I_52_Postsort_CD4_T


title: I_5_Postsort_CD4_T


title: I_33_UNSEP


title: I_18_Postsort_CD8_T


title: I_85_Postsort_CD19_B


title: I_18_Postsort_CD4_T


title: I_18_Postsort_CD19_B


title: I_18_UNSEP


title: I_5_Postsort_CD19_B


title: I_12_UNSEP


title: I_75_Postsort_CD4_T


title: I_12_Postsort_CD8_T


title: I_12_Postsort_CD4_T


title: I_12_Postsort_CD14_M


title: E_20_Postsort_CD8_T


title: E_20_Postsort_CD4_T


title: E_20_Postsort_CD19_B


title: E_20_Postsort_CD14_M


title: I_33_Postsort_CD8_T


title: P168_UNSEP


title: P168_Postsort_CD8_T


title: P168_Postsort_CD4_T


title: P168_Postsort_CD19_B


title: I_18_Postsort_CD14_M


title: P168_Postsort_CD14_M


title: P150_UNSEP


title: P135_Postsort_CD8_T


title: P135_UNSEP


title: P150_Postsort_CD4_T


title: P135_Postsort_CD19_B


title: P150_Postsort_CD19_B


title: P135_Postsort_CD4_T


title: P150_Postsort_CD14_M


title: P150_Postsort_CD8_T


title: I_12_Postsort_CD19_B


title: P122_Postsort_CD19_B


title: P135_Postsort_CD14_M


title: P122_Postsort_CD4_T


title: E_20_UNSEP


title: P122_Postsort_CD8_T


title: P122_Postsort_CD14_M


title: I_91_Postsort_CD8_T


title: I_91_UNSEP


title: I_91_Postsort_CD4_T


title: I_91_Postsort_CD19_B


title: I_86_UNSEP


title: I_91_Postsort_CD14_M


title: I_86_Postsort_CD8_T


title: I_86_Postsort_CD19_B


title: I_86_Postsort_CD14_M


title: I_86_Postsort_CD4_T


title: I_8_UNSEP


title: I_8_Postsort_CD8_T


title: P122_UNSEP


title: I_73_Postsort_CD8_T


title: I_8_Postsort_CD19_B


title: I_59_UNSEP


title: I_73_Postsort_CD14_M


title: I_73_UNSEP


title: I_59_Postsort_CD8_T


title: I_8_Postsort_CD14_M


title: I_59_Postsort_CD4_T


title: I_59_Postsort_CD19_B


title: I_59_Postsort_CD14_M


title: I_73_Postsort_CD4_T


title: I_49_UNSEP


title: I_49_Postsort_CD14_M


title: I_49_Postsort_CD19_B


title: I_49_Postsort_CD4_T


title: I_49_Postsort_CD8_T


title: I_38_UNSEP


title: I_38_Postsort_CD19_B


title: I_38_Postsort_CD4_T


title: I_38_Postsort_CD8_T


title: I_8_Postsort_CD4_T


title: I_29_UNSEP


title: I_73_Postsort_CD19_B


title: I_38_Postsort_CD14_M


title: I_29_Postsort_CD19_B


title: I_29_Postsort_CD14_M


title: I_29_Postsort_CD4_T


title: E_80_UNSEP


title: E_80_Postsort_CD8_T


title: E_80_Postsort_CD4_T


title: E_80_Postsort_CD19_B


title: E_80_Postsort_CD14_M


title: E_147_UNSEP


title: E_147_Postsort_CD8_T


title: E_147_Postsort_CD19_B


title: I_29_Postsort_CD8_T


title: E_147_Postsort_CD14_M


title: E_144_UNSEP


title: E_144_Postsort_CD8_T


title: T47D_0.01uM_CC15885_8hr_rep1

type: RNA

city: San Diego

first: Antonia

last: Lopez-Girona

state: California - CA

address: 10300 Campus Point Dr

department: Molecular ＆ Medical Science

institute: Celgene Corporation

hyb_protocol: 15 mg of cRNA was fragmented and hybridized to each human U133A 2.0 gene chipset (Affymetrix, Santa Clara, CA)

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Processed with R statistical software environment (www.r-project.org; v3.2.2) using affy (v1.46.1) package from the Bioconductor suite (www.bioconductor.org; v3.1)

label: biotin

label_protocol: Biotin-labeled cRNA was synthesized using MessageAmp aRNA kit (Ambion, Austin, TX)

growth_protocol: Cells were grown up in 100mm dishes in RPMI1640 + 10%FBS at cell densities that produced 60-80% cell confluency the following day.

extract_protocol: Cells were lysed using TRIzol reagent (Life Technologies Corporation) and total RNA was isolated using miRNeasy (Qiagen). Double-stranded cDNA was synthesized using 200 ng of total RNA.

treatment_protocol: On day 2, cells were treated with indicated compound/concentrations or DMSO.  At the indicated time points, media/treatment was discarded and washed three times with warm PBS.  After the last wash, as much PBS was removed as possible.  600uL of RLT buffer (Qiagen) +BME was added to the sample.  Cells were collected using a cell lifter and transferred to a RNase-free microfuge tube.  Tubes were immediately placed on dry ice and stored at -80oC until ready for genomic testing.

tag: cell line

value: mammary gland; derived from metastatic site:pleural effusion

value: epithelial

value: 54 years adult

tag: gender

value: female

tag: disease

value: ductal carcinoma

tag: compound

tag: dose

tag: treatment time


title: T47D_DMSO_8hr_rep1

tag: cell type

tag: age

value: DMSO


title: T47D_DMSO_4hr_rep1


title: E_144_Postsort_CD19_B


title: E_144_Postsort_CD4_T


title: E_144_Postsort_CD14_M


title: T47D_0.01uM_CC15885_4hr_rep2


title: T47D_DMSO_8hr_rep2


title: E_147_Postsort_CD4_T


title: T47D_DMSO_1hr_rep2


title: SW001 (Atr+/+)

first: Demis

last: Menolfi

address: 1130 St. Nicholas Ave, Herbert Irving Cancer Center, Room 501

department: Institute for Cancer Genetics

institute: Columbia University

data_processing:
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit. Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat [1] (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.  We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings. We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: genes.csv, isoforms.csv, counts

source_name: testes

growth_protocol: testes was recovered from 7 weeks old mice

extract_protocol:
Mouse testes were removed following a sterile procedure and RNA was isolated using TRIzol reagent (Invitrogen). RNA quality was determined using the Bioanalyzer RNA kit (Agilent) and samples with RNA Integrity Number (RIN) higher than 8 were sent for next-generation sequencing (NGS).
TruSeq Stranded mRNA Library Prep Kit from Illumina was used and the library was sequenced with Illumina HiSeq 2000.

tag: strain

tag: organ

value: testes

value: 7 weeks

value: Atr+/+


title: SW002 (Atr+/KD)

value: Atr+/KD


title: RCW040

city: Singapore

first: Jan

last: Gruber

address: 5 Engineering Drive 1

department: Science/ Biochemistry

country: Singapore

institute: Yale-NUS College / NUS

data_processing:
The RNAseq reads from each sample were mapped to the reference C. elegans transcriptome (WBcel235) with kallisto using 100 bootstrap samples and sequence based bias correction.
The estimated counts were imported from kallisto to the R environment (v3.3.2) and summarized to gene-level using the tximport package.
The DESeq2 package followed by the EdgeR package were then used to normalized and replaced outliers culminating on the counts per million (CPM) matrix table.
Genome_build: WBcel235
Supplementary_files_format_and_content: .csv file of the matrix table of CPM of all the genes (wormbase IDs) for every sample.

growth_protocol: Solid Nematode Growth Medium (NGM)

extract_protocol:
Nematodes were collected at day 6 and RNA was harvested using Qiagen RNAeasy micro kit. Illumina HiSeq4000 RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Drug treatment from day 4 to day 6

value: Bristow N2

value: Whole body

value: Day 6

tag: genotype


title: T47D_0.01uM_CC15885_2hr_rep2


title: RCW039

value: wild type


title: T47D_0.01uM_CC15885_1hr_rep2


title: T47D_0.01uM_CC15885_2hr_rep1


title: T47D_DMSO_4hr_rep2


title: I_3_UNSEP

value: blood

value: PBMC


title: T47D_0.01uM_CC15885_1hr_rep1


title: T47D_DMSO_2hr_rep1


title: T47D_0.01uM_CC15885_4hr_rep1


title: T47D_0.01uM_CC15885_8hr_rep2


title: I_3_PostsortCD8T

value: No


title: RCW034


title: T47D_DMSO_2hr_rep2

value: mammary gland; derived from metastatic site:pleural effusion


title: RCW033


title: T47D_DMSO_1hr_rep1

value: epithelial


title: I_3_PostsortCD4T


title: RCW032


title: I_3_PostsortCD19B


title: B6_Unsorted


title: I_3_PostsortCD14M


title: RCW031


title: RCW030


title: RCW029


title: RCW028


title: B6_Cd4T


title: RCW027


title: RCW023


title: RCW025


title: B5_CD8T


title: B5_Cd4T


title: B6_Cd19B


title: B5_CD14Mono


title: B5_Unsorted


title: B5_Cd19B


title: RCW024


title: RCW022


title: B3_Unsorted


title: RCW020


title: RCW021


title: RCW019


title: B3_CD8T


title: B3_Cd4T


title: RCW018


title: B3_Cd19B


title: B3_CD14Mono


title: RCW015


title: B2_Unsorted


title: RCW016


title: RCW014


title: RCW017


title: B2_CD8T


title: B6_CD8T


title: B6_CD14Mono


title: RCW013


title: RCW026


title: B2_Cd4T


title: RCW012


title: RCW010


title: RCW009


title: B1_CD8T


title: B1_Unsorted


title: RCW008


title: B2_CD14Mono


title: RCW007


title: B1_Cd4T


title: B2_Cd19B


title: B1_Cd19B


title: RCW006


title: B1_CD14Mono


title: A5_CD8T

value: Yes


title: RCW005


title: RCW003


title: A5_Cd4T


title: RCW002


title: A5_CD14Mono


title: A5_Cd19B


title: RCW004


title: RCC038


title: RCC037


title: A4_CD8T


title: RCC033


title: A4_Cd4T


title: RCC032


title: RCW011


title: A5_Unsorted


title: A3_Unsorted


title: A4_CD14Mono


title: RCC030


title: RCC028


title: RCC029


title: RCC027


title: A3_Cd19B


title: RCC026


title: RCC025


title: A4_Unsorted


title: RCC024


title: A2_Cd19B


title: RCC021


title: RCC022


title: A2_CD14Mono


title: RCC020


title: RCC031


title: A1_Unsorted


title: A2_CD8T


title: A1_CD8T


title: A3_Cd4T


title: A1_Cd4T


title: A3_CD8T


title: A1_CD14Mono


title: A3_CD14Mono


title: A1_Cd19B


title: Methylaton_97L_WGBS_Rep2

city: Shanghai

first: Jin

state: Shanghai

address: 130 Dong-An Road

department: Institutes of Biomedical Sciences (IBS)

country: China

institute: Fudan University

data_processing:
ChIP-seq: We firstly filtered out low quality reads. The remaining reads were aligned to human reference genome (hg19) with Bowtie (version 1.0.0). The alignment was unique mapping and allowed up to 2 mismatches. Peaks were identified with the MACS (version14) with default parameters and --nomodel
RNA-seq: We firstly filtered out low quality reads. Then mRNA-seq reads were aligned to hg19 with TopHat2 (v2.0.12) with default parameters. The mapped reads were further analyzed by Cufflinks (v2.2.1) with default parameters to call FPKM of genes.
Methylation by GPS: We firstly filtered out low quality reads. Read2 were aligned onto reference genome (hg19) using Bowtie2 (v2.2.3) with default parameters except "-k 20". We used the Smith-Waterman algorithm to map the Read1 to the reference target sequence that is located within 1kb of opposite strand of downstream of the Read2. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Methylation by WGBS: We firstly filtered out low quality reads. Read1 and Read2 were aligned onto reference genome (hg19) using BSMAP with default parameters except -v 3 -g 1. Cytosines which are covered by no less than 5 reads are used for methylation analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylation level/ChIP peak loci/ gene FPKM values for each Sample

source_name: hepatoma cell line

growth_protocol: Cell lines were cultured at 37˚C in 5% CO2 in high-glucose DMEM (Hyclone, USA) supplemented with 10% fetal bovine serum (Hyclone, USA), and collected under standard culture protocols.

extract_protocol:
Methylation: Genomic DNA from tissues and cell lines was extracted using QIAamp DNA Mini Kit (Qiagen, 51306, Valencia, CA). 3μg genomic DNA was fragmented into 300-500bp by sonication. ChIP:Approximate 300 ug fixed chromatin and 5 ug antibody were used for each ChIP pull-down. RNA-seq: We extracted approximate 6 micrograms of total RNA, removed ribosomal RNA (rRNA) according to the manufacturer’s instructions with minor modifications.
Libraries were prepared for sequencing using standard Illumina protocols

value: liver


title: Methylaton_97L_WGBS_Rep1


title: RCC023


title: Methylation_97L_GPS_Rep2


title: Methylation_97L_GPS_Rep1


title: RCC019


title: RCW001


title: A2_Cd4T


title: 3000 ppm phenformin liver at day 14, biological repl 3

city: Wuppertal

first: Heidrun

middle: Christine

last: Ellinger-Ziegelbauer

address: Aprather Weg 18a

institute: Bayer Pharma AG

description: Gene expression of liver tissue from rats treated with 3000 ppm phenformin for 14 days

hyb_protocol: Following fragmentation, 5.2 µg of biotin-labeled single-stranded copyDNA (ss-cDNA) was hybridized for 16 hr at 45C on a GeneChip® Rat Transcriptome Array 1.0. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 using the FS450_001 protocol.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: Intensity values in CEL file data were first adjusted using GCCN correction to normalize the signal distribution based on the specific GC count, and then with the SST-algorithm, to expand the dynamic range of the intensity signals. Both of these algorithms are implemented in the Affymetrix® APT tool, running on an UNIX background. Further processing and quality control of the adjusted CEL files were performed with the Robust Multichip Analysis (RMA) algorithm, all implemented in the software Refiner Array (Genedata Expressionist®, current version 9), including background removal, normalization and then summarization of intensity values, to obtain a single intensity value for a transcript ID.

organism: Rattus norvegicus

label_protocol: Biotin-labeled single-stranded copyDNA (ss-cDNA) was prepared according to the standard Affymetrix protocol from 300 ng high quality total liver RNA (GeneChip® WT Plus Reagent Kit Version1).

growth_protocol: All animal experiments were performed according to the German guidelines for care and use of laboratory animals and are approved by the State Agency for Nature, Environment and Consumer Protection North Rhine-Westphalia in Germany (LANUV). Male RccHan Wistar rats at the age of 7-8 weeks were purchased from Harlan laboratories BV (Horst, Netherlands). Animals were housed under controlled standard conditions in groups with 2 or 3 animals per cage in makrolon cages type IV, with a 12h light-dark cycle at 22 ± 2°C. Standard rodent chow pellets and water were provided ad libitum.

extract_protocol: On days 3 or 14  rats were euthanized and blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from liver (70 mg) using the RNeasy Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

treatment_protocol: Male RccHan Wistar rats (7-8 weeks old) were randomly assigned to the vehicle or treatment group (n=5). 3000 ppm phenformin (Sigma Aldrich, Steinheim, Germany) was administered in the diet for 3 or 14 consecutive days. Control groups received untreated food.

tag: treatment

value: 3000 ppm phenformin liver at day 14

value: Wistar (RccHan:WIST)

value: male


title: 3000 ppm phenformin liver at day 14, biological repl 1

source_name: liver tissue from rats treated with 3000 ppm phenformin


title: 3000 ppm phenformin liver at day 14, biological repl 4


title: 3000 ppm phenformin liver at day 14, biological repl 2


title: 3000 ppm phenformin liver at day 3, biological repl 3

description: Gene expression of liver tissue from rats treated with 3000 ppm phenformin for 3 days

value: 3000 ppm phenformin liver at day 3


title: Control  liver at day 14, biological repl 2

description: Gene expression of liver tissue from control Wistar rats

source_name: liver tissue from control rats

value: Control  liver at day 14


title: 3000 ppm phenformin liver at day 3, biological repl 1


title: 3000 ppm phenformin liver at day 3, biological repl 2


title: 3000 ppm phenformin liver at day 3, biological repl 4


title: A2_Unsorted


title: 3000 ppm phenformin heart at day 14, biological repl2

description: Gene expression of heart tissue from rats treated with 3000 ppm phenformin for 14 days

label_protocol: Biotin-labeled single-stranded copyDNA (ss-cDNA) was prepared according to the standard Affymetrix protocol from 300 ng high quality total heart RNA (GeneChip® WT Plus Reagent Kit Version1).

extract_protocol: On days  3 or 14  rats were euthanized and blood was collected for clinical chemistry and hematology and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from heart (left ventricle apex, 30 mg), using the RNeasy Fibrous Tissue Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

value: 3000 ppm phenformin heart at day 14

value: heart


title: Control  liver at day 14, biological repl 4


title: Control  liver at day 14, biological repl 3


title: 3000 ppm phenformin heart at day 3, biological repl2

description: Gene expression of heart tissue from rats treated with 3000 ppm phenformin for 3 days

value: 3000 ppm phenformin heart at day 3


title: 3000 ppm phenformin heart at day 3, biological repl3

source_name: heart tissue from rats treated with 3000 ppm phenformin


title: 3000 ppm phenformin heart at day 14, biological repl4


title: Control liver at day 14, biological repl 1

value: Control liver at day 14


title: Control liver at day 3, biological repl 1

value: Control liver at day 3


title: Control  liver at day 3, biological repl 2

value: Control  liver at day 3


title: Control heart at day 14, biological repl4

description: Gene expression of heart tissue from control Wistar rats

source_name: heart tissue from control rats

value: Control heart at day 14


title: 3000 ppm phenformin heart at day 14, biological repl3


title: 3000 ppm phenformin heart at day 3, biological repl4


title: Control  liver at day 3, biological repl 4


title: Control  liver at day 3, biological repl 3


title: 3000 ppm phenformin heart at day 14, biological repl1


title: 3000 ppm phenformin heart at day 3, biological repl1


title: Control heart at day 14, biological repl3


title: Control heart at day 14, biological repl2


title: Control heart at day 14, biological repl1


title: TR_dcl5_2_3a_RNAseq

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: Processed tag count text files are from the raw fastq data, containing distinct RNA-seq sequence with their raw abundance after removing the adaptor sequences

data_processing:
FASTX-toolkit to reverse complement sequence if it's stranded RNA-seq data;
Trimmomatic version 0.32 to remove the linker adaptor sequences;
Bowtie to map to B73 version 4 maize genome;
Normalized read counts to 20 million.
Genome_build: AGPv4, B73 RefGen_v4
Supplementary_files_format_and_content: tagcount

organism: Zea mays

source_name: Meiotic anthers

extract_protocol:
Total RNA for sRNA-seq and RNA-seq libraries was isolated using the PureLink Plant RNA Reagent (ThermoFisher) following the manufacturer’s instructions. Total RNA quality was assessed by denaturing agarose gel electrophoresis and quantified by the Qubit RNA BR Assay Kit (ThermoFisher).
For small RNA library preparation, 20 to 30 nt RNAs were excised from a 15% polyacrylamide/urea gel, and ~25 ng of sRNA used for library construction with the TruSeq Small RNA Prep Kit (Illumina) following the manufacturer’s instructions. For RNA-seq, 2 μg of total RNA was treated with DNase I (New England BioLabs) and then cleaned with RNA Clean and Concentrator-5 (Zymo Research). The TruSeq Stranded Total RNA with RiboZero-Plant Kit (Illumina) was used for library construction with 500 ng of treated RNA, following the manufacturer’s instructions.

value: dcl5-1, homozygous

tag: fertility

value: sterile

value: anthers containing spikelets

tag: size

value: 2.0 mm and 3.0 mm

tag: growth temperature

value: Day temperature 28 degreeC, night temperature 22 degreeC


title: TP_dcl5_2_3a_RNAseq

value: fertile

tag: tissue

value: Day temperature 22 degreeC, night temperature 20 degreeC


title: Control heart at day 3, biological repl4

value: Control heart at day 3

value: Wistar (RccHan:WIST)

value: male


title: Control heart at day 3, biological repl3


title: dcl5_4_2mm_2_RNAseq

value: dcl5-4, homozygous

value: anthers


title: 800 mg/kg metformin liver at day 14, biological rep 4

description: Gene expression of liver tissue from rats treated with 800 mg/kg metformin for 14 days

extract_protocol: On days  1, 3 or 14  rats were euthanized and blood was collected for lactate determination and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from liver (70 mg) using the RNeasy Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

treatment_protocol: Male RccHan Wistar rats (7-8 weeks old) were randomly assigned to the vehicle or treatment group (n=5). 800 mg/kg metformin (Sigma Aldrich, Steinheim, Germany) was administered by gavage for 1, 3 or 14 consecutive days. Control groups received the vehicle (Ethanol/Kolliphor HS 15®/Tap Water (10/40/50)).

value: 800 mg/kg metformin liver at day 14

value: liver


title: 800 mg/kg metformin liver at day 3, biological rep 1

description: Gene expression of liver tissue from rats treated with 800 mg/kg metformin for 3 days

value: 800 mg/kg metformin liver at day 3


title: 800 mg/kg metformin liver at day 14, biological rep 1

source_name: liver tissue from rats treated with 800 mg/kg metformin


title: dcl5_4_2mm_1_RNAseq


title: dc5_3_2mm_2_RNAseq

value: dcl5-3, homozygous


title: 800 mg/kg metformin liver at day 1, biological rep 4

description: Gene expression of liver tissue from rats treated with 800 mg/kg metformin for 1 day

value: 800 mg/kg metformin liver at day 1


title: Control heart at day 3, biological repl2

value: heart


title: 800 mg/kg metformin liver at day 3, biological rep 3


title: Control liver at day 14, biological rep 2

value: Control liver at day 14


title: 800 mg/kg metformin liver at day 14, biological rep 3


title: 800 mg/kg metformin liver at day 3, biological rep 4


title: Control liver at day 14, biological rep 1


title: Control liver at day 3, biological rep 4

value: Control liver at day 3


title: Control liver at day 14, biological rep 4


title: dc5_3_2mm_1_RNAseq

value: sterile


title: 800 mg/kg metformin liver at day 1, biological rep 3


title: 800 mg/kg metformin liver at day 14, biological rep 2


title: 800 mg/kg metformin liver at day 3, biological rep 2


title: 800 mg/kg metformin liver at day 1, biological rep 2


title: Control liver at day 3, biological rep 2


title: dc5_2_2mm_2_RNAseq

value: dcl5-2, homozygous

value: partial sterile

value: Day temperature 28 degreeC, night temperature 22 degreeC


title: Control liver at day 14, biological rep 3


title: 800 mg/kg metformin liver at day 1, biological rep 1


title: dc5_2_2mm_1_RNAseq


title: Control liver at day 3, biological rep 1


title: Control heart at day 3, biological repl1

value: Control heart at day 3


title: A4_Cd19B

tag: subject

value: blood

tag: ptsd

value: Yes


title: dc5_1_2mm_1_RNAseq

value: dcl5-1, homozygous


title: dc5F_2mm_2_RNAseq

value: dcl5-1//Dcl5, heterozygous

value: fertile

value: anthers


title: dc5_1_2mm_2_RNAseq


title: Control liver at day 3, biological rep 3

value: Wistar (RccHan:WIST)

tag: gender

value: male

value: liver


title: dc5_1_2mm_3_RNAseq


title: Control liver at day 1, biological rep 2

value: Control liver at day 1


title: sTR_dcl5_1_2a_sRNA

description: Processed tag count text files are from the raw fastq data, containing distinct small RNA sequence with their raw abundance after removing the adaptor sequences

value: anthers containing spikelets

value: 1.0 mm and 2.0 mm


title: Control liver at day 1, biological rep 3


title: Control liver at day 1, biological rep 1


title: 800 mg/kg metformin heart at day 14, biological rep.4

description: Gene expression of heart tissue from rats treated with 800 mg/kg metformin for 14 days

extract_protocol: On days  1, 3 or 14  rats were euthanized and blood was collected for for lactate determination and several organs were removed, weighted, aliquoted, fixed in formalin for histopathological examinations or flash frozen in liquid nitrogen and stored at −80 °C for RNA isolation. Total RNA (mRNA) was isolated from heart (left ventricle apex, 30 mg), using the RNeasy Fibrous Tissue Mini Kit (Qiagen;Hilden,Germany) according to the manufacturer’s instructions. RNA quality was determined with the Bioanalyzer® 2100 and RNA 6000 Nano Kits (Agilent;SantaClara,CA) and quantity was assessed with a Nanodrop® 1000 Spectrophotometer.

value: 800 mg/kg metformin heart at day 14

value: heart


title: 800 mg/kg metformin heart at day 14, biological rep.3

source_name: heart tissue from rats treated with 800 mg/kg metformin


title: 800 mg/kg metformin heart at day 14, biological rep.2


title: 800 mg/kg metformin heart at day 14, biological rep.1


title: sTP_dcl5_1_2a_sRNA

value: Day temperature 22 degreeC, night temperature 20 degreeC


title: dcl5_4_2_0mm_sRNA

value: dcl5-4, homozygous

value: sterile

value: Day temperature 28 degreeC, night temperature 22 degreeC


title: dc5F_2mm_1_RNAseq


title: 800 mg/kg metformin heart at day 3, biological rep.4

description: Gene expression of heart tissue from rats treated with 800 mg/kg metformin for 3 days

value: 800 mg/kg metformin heart at day 3


title: dcl5_3_2_0mm_b_sRNA

value: dcl5-3, homozygous


title: 800 mg/kg metformin heart at day 3, biological rep.1


title: sTR_dcl5_2_3a_sRNA

value: dcl5-1, homozygous

value: 2.0 mm and 3.0 mm


title: dcl5_3_1_5mm_sRNA

value: anthers


title: dcl5_4_1_5mm_sRNA


title: dcl5_3_2_0mm_a_sRNA


title: 800 mg/kg metformin heart at day 3, biological rep.3

value: Wistar (RccHan:WIST)


title: sTP_dcl5_2_3a_sRNA

value: fertile


title: 800 mg/kg metformin heart at day 3, biological rep.2

value: male


title: Control liver at day 1, biological rep 4

value: Control liver at day 1

value: liver


title: dcl5_2_2_0mm_sRNA

value: dcl5-2, homozygous

value: partial sterile


title: dcl5_1_2_0mm_sRNA


title: 800 mg/kg metformin heart at day 1, biological rep.1

description: Gene expression of heart tissue from rats treated with 800 mg/kg metformin for 1 day

value: 800 mg/kg metformin heart at day 1

value: heart


title: dcl5_1_1_5mm_sRNA


title: Control heart at day 14, biological rep.4

value: Control heart at day 14


title: 800 mg/kg metformin heart at day 1, biological rep.3


title: 800 mg/kg metformin heart at day 1, biological rep.4


title: 800 mg/kg metformin heart at day 1, biological rep.2


title: Control heart at day 14, biological rep.3


title: Control heart at day 14, biological rep.1


title: Control heart at day 14, biological rep.2


title: dcl5_1F_2_0mm_sRNA

value: dcl5-1//Dcl5, heterozygous


title: dc5_1_2mm_4_RNAseq

value: Day temperature 28 degreeC, night temperature 22 degreeC


title: dcl5_1F_1_5mm_sRNA


title: B16/BL6

city: Suita city

first: Yumiko

last: Hayashi

address: 3-1 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: melanoma cell

growth_protocol: B16 cells culture in DMEM medium supplemented with 10 % FBS and 1 % penicillin/streptomycin. B16/BL6 cells culture in RPMI medium supplemented with 10 % FBS and 1 % penicillin/streptomycin.

extract_protocol:
Cells were removed and washed with PBS. Total RNA was extracted from cells using RNeasy-plus mini kits (Qiagen, Hilden, Germany).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.


title: D3 DC-Mix

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

hyb_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) and cohybridized to Agilent Chip Whole Human genome, 4x44k slides according to the protocol provided by Agilent.

scan_protocol: The slides were incubated for 17h at 65°C and then the scanned using the Agilent B Scanner.

data_processing: Raw images were obtained by scanning the slides with an Agilent Scan G2505B and Agilent Scan Control software (version 9.5). The images were extracted using the Feature Extraction Software (Agilent Technologies). Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) was used for data visualization, identification of differentially expressed transcripts and hierarchical cluster analysis. We transformed the fluorescence intensity data to log2 ratios of each sample versus the universal human RNA reference (Stratagene, Santa Clara, CA, USA).

source_name: DC culture with mixed serum

extract_protocol: Total RNA from DC samples were isolated and purified by using miRNeasyKit (Qiagen, Germantown, MD, USA). The RNA concentration was determined using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: culture protocol

value: mixed serum

value: Dendritic Cell

source_name: universal human reference RNA

tag: reference

value: pooled whole huam RNA


title: dcl5_2_1_5mm_sRNA


title: Control heart at day 3, biological rep.4

value: Control heart at day 3


title: Control heart at day 3, biological rep.3


title: D3 DC-AB

source_name: DC culture with AB serum

label_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA)

value: AB serum


title: D2 DC-Auto

source_name: DC culture with patient serum

value: patient serum


title: D2 DC-Mix


title: D3 DC-Auto


title: B16


title: Control heart at day 3, biological rep.2

value: Wistar (RccHan:WIST)


title: Control heart at day 3, biological rep.1

value: male


title: Th17_RORg_w_RORg_inhibitor_ko_GFP_KI_N2_14_48h_SL5048

status: Public on Dec 16 2018

city: Cincinnati

first: Emily

middle: R

last: Miraldi

state: Ohio

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

description: RORg (+RORg inhibitor) ko (GFP KI) N2; 48h

data_processing:
Sequences were mapped to the murine genome (mm10) STAR aligner; only a single-end from paired-end samples were used
HTSeq-count was used to map reads to mm10 genes
Genes were normalized to account for 36bp vs. 50bp mappability (see manuscript Methods for details)
DESeq2 was used to normalize gene expression quantification
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2-normalized (VSD) gene quantification.

source_name: Naive CD4+ T cells from spleen

extract_protocol:
Cells were lysed and snap-frozen in trizol, thawed for chloroform extraction and loaded onto a Qiagen RNEasy column
Libraries were constructed using Protocol 1 (poly-A selection, Nextera tagmentation) or Protocol 2 (Ribozero Gold, Illumina TruSeq Stranded Total RNA), as indicated in the characteristic: RNA library protocol

treatment_protocol: CD4+ T cells were purified from the spleen and polarized into Th0, Th2, Treg, and Th17

value: spleen

value: naive CD4+ T cell

tag: polarization

value: Rorc-/-

tag: time point (post tcr stimulation)

tag: rna library protocol


title: Th17_RORg_wt_pp_1_16h_SL599

description: RORg wt (+/+); 16h

tag: cell type

value: Wildtype


title: D1 DC-Mix


title: Control heart at day 1, biological rep.4

value: Control heart at day 1

tag: strain


title: 14 Days Obstructed [PBOO-147]

city: Philadelphia

first: Ettickan

last: Boopathi

state: Pennsylvania

address: 1020 Locust Street

department: Medicine

institute: THOMAS Jefferson University

description: Replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Raw data was generated by the Illumina Bead Array Scanner

data_processing: Illumina Microarray data was anlyzed by Bead Studio 3.0 and GeneSpring 14.4 software and the data were normalized by quantile

label: Biotin

source_name: Bladder

label_protocol: Biotinylated cRNA were prepared for Illumina arrays

growth_protocol: Mice were fed with normal diet

extract_protocol: RNA was extracted using TRIzol reagent and purified by QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Partial bladder outlet obstruction

value: Male


title: Th17_RORa_BM_transfer_w_RORg_inhibitor_wt_pp_N2_15_48h_SL5053

description: RORa (BM transfer) (+RORg inhibitor) wt (+/+) N2; 48h


title: Th17_RORa_RORg_BM_transfer_RORa_ko_RORg_ko_17_48h_SL5880

description: RORa RORg (BM transfer) RORa ko RORg ko; 48h

value: Rora-/-; Rorc-/-


title: Th17_RORg_w_RORg_inhibitor_ko_GFP_KI_DMSO_14_48h_SL5046

description: RORg (+RORg inhibitor) ko (GFP KI) DMSO; 48h


title: Th17_RORg_w_RORg_inhibitor_ko_GFP_KI_C16_14_48h_SL5047

description: RORg (+RORg inhibitor) ko (GFP KI) C16; 48h


title: Th17_RORa_RORg_BM_transfer_RORa_RORg_wt_16_48h_SL5874

description: RORa RORg (BM transfer) RORa RORg wt; 48h


title: Th17_RORg_ko_GFP_KI_1_16h_SL600

description: RORg ko (GFP KI); 16h


title: Th17_RORa_RORg_BM_transfer_RORa_ko_RORg_ko_16_48h_SL5876


title: Th17_RORa_BM_transfer_w_RORg_inhibitor_wt_pp_C16_15_48h_SL5052

description: RORa (BM transfer) (+RORg inhibitor) wt (+/+) C16; 48h


title: Th17_RORa_BM_transfer_w_RORg_inhibitor_ko_mm_C16_15_48h_SL5057

description: RORa (BM transfer) (+RORg inhibitor) ko (-/-) C16; 48h

value: Rora-/-


title: Sham operated [Control-145]

description: Replicate 2


title: Th17_RORa_BM_transfer_w_RORg_inhibitor_ko_mm_DMSO_15_48h_SL5056

description: RORa (BM transfer) (+RORg inhibitor) ko (-/-) DMSO; 48h


title: Th17_RORa_BM_transfer_w_RORg_inhibitor_ko_mm_N2_15_48h_SL5058

description: RORa (BM transfer) (+RORg inhibitor) ko (-/-) N2; 48h


title: D1 DC-Auto


title: D2 DC-AB


title: SFZ cells 10 μM retinoic acid

city: Suita

first: Yoshifumi

last: Takahata

state: Osaka

department: Dentistry

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: femur and tibial joint

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: SFZ cells were cultured with DMEM containing 10% FBS.

extract_protocol: Total RNA was extracted with Nucleospin RNA plus kit

treatment_protocol: SFZ cells were treated with or without 10 μM retinoic acid.

value: stimulated with 10 μM retinoic acid

value: Superficial zone of articular cartilage

tag: age

value: postnatal 4 days

value: ICR


title: Control heart at day 1, biological rep.3

description: Gene expression of heart tissue from control Wistar rats

value: heart


title: Th17_RORa_BM_transfer_w_RORg_inhibitor_wt_pp_DMSO_15_48h_SL5051

description: RORa (BM transfer) (+RORg inhibitor) wt (+/+) DMSO; 48h

tag: genotype


title: Th17_IRF4_ko_flox_s_CD4-Cre_4_48h_SL1863

description: IRF4 ko (flox/CD4-Cre); 48h

value: Irf4-fl/fl; CD4-Cre+/-


title: Th17_IRF4_wt_pCD4-Cre_4_48h_SL1861

description: IRF4 wt (+/CD4-Cre); 48h


title: D1 DC-AB

value: AB serum

value: Dendritic Cell

value: pooled whole huam RNA


title: Th17_RORa_RORg_BM_transfer_RORa_RORg_wt_17_48h_SL5878

value: spleen


title: Th0_RORg_wt_pp_1_16h_SL598

description: RORg wt (+/+); 16h

value: naive CD4+ T cell


title: Control heart at day 1, biological rep.2

tag: treatment

value: Wistar (RccHan:WIST)

value: male


title: 14 Days Obstructed [PBOO-148]

description: Replicate 2


title: SFZ cells control

value: control


title: Th0_RORg_w_RORg_inhibitor_ko_GFP_KI_DMSO_14_48h_SL5044

value: Rorc-/-


title: Th0_RORg_w_RORg_inhibitor_ko_GFP_KI_C16_14_48h_SL5045


title: Th0_RORg_ko_GFP_KI_1_16h_SL601

description: RORg ko (GFP KI); 16h


title: Th0_RORa_RORg_BM_transfer_RORa_RORg_wt_16_48h_SL5873

value: Wildtype


title: Th0_RORa_BM_transfer_w_RORg_inhibitor_ko_mm_C16_15_48h_SL5055

value: Rora-/-


title: Th0_RORa_BM_transfer_w_RORg_inhibitor_wt_pp_C16_15_48h_SL5050


title: Th0_RORa_BM_transfer_w_RORg_inhibitor_wt_pp_DMSO_15_48h_SL5049


title: Th0_RORa_RORg_BM_transfer_RORa_RORg_wt_17_48h_SL5877


title: Th0_RORa_BM_transfer_w_RORg_inhibitor_ko_mm_DMSO_15_48h_SL5054


title: Th0_RORa_RORg_BM_transfer_RORa_ko_RORg_ko_16_48h_SL5875

value: Rora-/-; Rorc-/-


title: miRNA_1023T

city: Berlin

first: Robert

last: Altwasser

address: Robert-Rössle-Str. 10

department: AG Di Virgilio

institute: Max-Delbrück-centrum

description:
M1023T_ATCACG_L002
processed data file: counts_miRNA_mouse.csv

data_processing:
FASTQ files were receiven from Mark Band, USA
repeated runs concatenated
Mapping of read pairs using TopHat (v1.4.1)
Read counting using HTSeq, annotation from BioMart mouse reference
Normalisation using R-package DESeq
Genome_build: Spalax genome: RefSeq/GenBank assembly accession GCF_000622305.1; mouse: GRCm38
Supplementary_files_format_and_content: comma seperated values (csv) with normalized read counts

source_name: mice

extract_protocol:
1ug of total RNA was used to construct the libraries using the TruSeq Small RNA Sample Prep kit (Illumina).   The strand-specific RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane (small RNAs) or two lanes (RNAseq) for 101 cycles on a HiSeq2500 using a TruSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)

tag: diagnosis

value: fibrosarcoma

tag: Sex

value: M

tag: time of operation after treatment

value: 12 weeks

value: muscle tissue

tag: sample side

value: injected side


title: miRNA_512T

description:
M512T_TTAGGC_L002
processed data file: counts_miRNA_mouse.csv

value: 11 weeks

tag: tissue


title: miRNA_512H

description:
M512HM_TGACCA_L002
processed data file: counts_miRNA_mouse.csv

value: uninjected side


title: miRNA_1023H

description:
M1023HM_CGATGT_L002
processed data file: counts_miRNA_mouse.csv


title: Th0_IRF4_ko_flox_s_CD4-Cre_4_48h_SL1862

description: IRF4 ko (flox/CD4-Cre); 48h

value: Irf4-fl/fl; CD4-Cre+/-


title: Th0_IRF4_wt_pCD4-Cre_4_48h_SL1860

description: IRF4 wt (+/CD4-Cre); 48h

value: spleen


title: miRNA_1019T

description:
M1019T_ACAGTG_L002
processed data file: counts_miRNA_mouse.csv

value: 14 weeks


title: miRNA_1019H

description:
M1019HM_GCCAAT_L002
processed data file: counts_miRNA_mouse.csv


title: 1023T

description:
M1023T
M1023T_ATCACG_L00M
processed data file: counts_mouse.csv

extract_protocol:
1ug of total RNA was used to construct the libraries using the TruSeq Small RNA Sample Prep kit (Illumina).   The strand-specific RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'.
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane (small RNAs) or two lanes (RNAseq) for 101 cycles on a Illumina HiSeq 2500 using a TruSeq SBS sequencing kit version 4. Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)

value: muscle


title: 512H

description:
M512H
M512HM_TGACCA_L00M
processed data file: counts_mouse.csv


title: 512T

description:
M512T
M512T_TTAGGC_L00M
processed data file: counts_mouse.csv


title: Th0_RORa_RORg_BM_transfer_RORa_ko_RORg_ko_17_48h_SL5879

description: RORa RORg (BM transfer) RORa ko RORg ko; 48h

value: naive CD4+ T cell


title: 1019T

description:
M1019T
M1019T_ACAGTG_L00M
processed data file: counts_mouse.csv


title: 1019H

description:
M1019H
M1019HM_GCCAAT_L00M
processed data file: counts_mouse.csv


title: M1

description:
M1
M1_S0_GAATTCGT-CAGGACGT_L00M
processed data file: counts_mouse.csv

source_name: mice control

value: healthy


title: M2

description:
M2
M2_S0_GAATTCGT-GTACTGAC_L00M
processed data file: counts_mouse.csv


title: 12251X8

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

department: Pathology

institute: University of Utah, Huntsman Cancer Institute

data_processing:
Transcript expression estimation: The genome index was created with STAR (v2.4.2a)  using the mm10 genome sequence and Ensembl (build 85) gene definitions.  Reads were aligned to the index using the following parameters: outFilterType BySJout, outFilterMultimapNmax 20, outFilterMismatchNmax 999, outFilterMismatchNoverReadLmax 0.04, alignIntronMin 20, alignIntronMax 1000000, alignMatesGapMax 1000000, alignSJoverhangMin 8, alignSJDBoverhangMin 1, sjdbScore 1, outSAMtype BAM SortedByCoordinate, quantMode TranscriptomeSAM.
The RSEM (v1.2.19)  reference was created using the rsem-prepare-reference command. Gene estimates were generated by running rsem-calculate-expression on the STAR alignments.
Clustering: The gene count estimates from RSEM were loaded into a scater (v1.2.0)  (48) SCESet object.  Genes with log2(CPM) > 2 in at least 10 cells were retained in the analysis.  Cells with greater than 20% mitochondrial reads, less than 500 thousand alignments, less than 500 measurable genes or less than 20% mRNA bases were removed from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM estimated gene counts combined into a single txt file

source_name: Sorted murine lung tumor cell

growth_protocol: Mice were infected intratracheally with adenovirus or lentivirus expressing Cre recombinase to initiate tumorigenesis.

extract_protocol:
Sorted tumor cells were mixed with C1 Suspension Reagent (Fluidigm) and loaded on a 5-10 mm C1 Single-cell Auto Prep IFC for mRNA Seq.
Sequencing libraries were prepared using the Nextera XT DNA Library Preparation Kit and dual indexed adapters according to the modified protocol described by Fluidigm.

treatment_protocol: The lungs were inflated with an enzymatic digest solution and filtered to generate a single-cell suspension. Cells were sorted using BD FACSAria for tdTomato-positive and DAPI-negative cells.

value: Mixed B6/129

value: Adult

value: KrasLSL-G12D/+; Nkx2-1F/F; Foxa1F/F; Foxa2F/F

value: sorted lung tumor cell (single cell)


title: 12251X53


title: 12251X52


title: 12251X51


title: 1023H

description:
M1023H
M1023HM_CGATGT_L00M
processed data file: counts_mouse.csv

value: fibrosarcoma


title: 12251X5


title: 12251X48


title: 12251X50


title: 12251X47


title: 12251X45


title: 12251X44


title: 12251X46


title: 12251X43


title: 12251X41


title: M5

description:
M5
M5_S0_CTGAAGCT-TATAGCCT_L00M
processed data file: counts_mouse.csv

value: M


title: 12251X40


title: 12251X4


title: 12251X36


title: 12251X35


title: 12251X33


title: 12251X34


title: Sham operated  [Control-144]

description: Replicate 1

value: Male


title: 12251X49


title: 12251X31


title: Control heart at day 1, biological rep.1

description: Gene expression of heart tissue from control Wistar rats

value: Control heart at day 1

value: Wistar (RccHan:WIST)

value: male

value: heart


title: 12251X3


title: 12251X28


title: IFN-11

city: Chapel Hill

first: Mohanish

last: Deshmukh

state: NC

address: 7109E Neuroscience Research Building, 105 Mason Farm Road

department: Cell Biology and Physiology

institute: University of North Carolina

description: sympathetic neuron + 500 U/ml IFN-γ, 24 hrs; IFN-11

hyb_protocol: Overnight hybridization of two-color whole mouse genome 4x44K microarrays (Agilent Technologies) according to manufacturer recommendations.

scan_protocol: Agilent G2505C microarray scanner according to manufacturer recommendations.

data_processing: Raw data was processed and analyzed by Feature Extraction Software (Agilent Technologies).

source_name: Reference: P5 SCG

label_protocol: 500 ng RNA per sample was labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies)  per manufacturer instructions, 2 color amplification method

extract_protocol: Total RNA extracted by Trizol Reagent (Invitrogen)

value: P5 sympathetic cervical ganglia, untreated

value: sympathetic neuron

tag: protocol

value: 500 U/ml IFN-γ, 24 hrs


title: IFN-13

description: sympathetic neuron + 500 U/ml IFN-γ, 24 hrs; IFN-13


title: IFN-6

description: sympathetic neuron + 500 U/ml IFN-γ, 24 hrs; IFN-6


title: 12251X27


title: IFN-1

description: sympathetic neuron, control, 24 hrs; IFN-1

value: control, 24 hrs


title: IFN-14

description: sympathetic neuron, control, 24 hrs; IFN-14


title: IFN-12

description: sympathetic neuron, control, 24 hrs; IFN-12


title: 12251X26


title: 12251X25


title: 12251X23


title: 12251X16


title: 12251X38


title: 12251X19


title: 12072X50


title: 12072X40


title: 12251X21


title: 12072X54


title: 12072X51


title: 12251X14


title: 12251X13


title: 12072X53


title: 12072X57


title: 12072X6


title: 12251X20


title: 12072X41


title: 12072X55


title: 12072X44


title: 12072X38


title: 12072X49


title: 12072X37


title: 12072X32


title: 12072X3


title: 12072X26


title: 12072X27


title: 12072X21


title: 12072X23


title: 12072X36


title: 12072X19


title: 12072X4


title: 12072X2


title: 12072X17


title: 12072X16


title: 12072X15


title: 12072X18


title: 12072X1


title: 12072X20


title: 12072X14


title: 12072X12


title: 11978X9

value: KrasLSL-G12D/+; Nkx2-1F/F


title: 11978X8


title: 11978X52


title: 11978X6


title: 11978X7


title: 12072X10


title: 11978X5


title: 11978X51


title: 11978X48


title: 12072X25


title: 11978X45


title: 11978X44


title: 11978X4


title: 11978X41


title: 11978X36


title: 11978X38


title: 11978X34


title: 11978X37


title: 11978X35


title: 11978X32


title: 11978X31


title: 11978X26


title: 11978X29


title: 11978X28


title: 11978X49


title: 11978X3


title: 11978X27


title: 11978X46


title: 11978X16


title: 11978X2


title: 11978X17


title: 11978X1


title: 11978X14


title: 11913X7


title: 11913X60


title: 11978X12


title: 11978X11


title: 11913X6


title: 11913X59


title: 11978X25


title: 11913X5


title: 11978X19


title: 11913X57


title: biological replicate 4 - 17:00

city: Raleigh

first: Anna

last: Locke

address: 4112 Williams Hall, 101 Derieux Place

institute: USDA-ARS

description:
sample_16
Random primed libraries
Variety: 93B15

data_processing:
Base calling and demultiplexing performed with Illumina CASAVA version 1.8.2
Adapter sequences were trimmed from reads with Trimmomatic [Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.]
Reads were aligned to the Glycine max cv.Williams 82 genome (assembly version 2, annotation version 1) with Tophat2.  Parameters as follows:  --read-mismatches 2 --mate-inner-dist 359 --mate-std-dev 60 --min-intron-length 50 --max-intron-length 10000 --num-threads 8 \          --max-multihits 1 --no-discordant --no-mixed --library-type fr-unstranded --segment-mismatches 2 --min-segment-intron 50 --max-segment-intron 10000 \          --coverage-search --min-coverage-intron 50 --max-coverage-intron 10000 --b2-sensitive
Aligned reads per gene were counted for each sample with HTSeq-count.  Parameters as follows: -m intersection-strict -s no
Genome_build: Glycine max Williams 82 assembly v. 2 annotation v. 1 (Wm.82.a2.v1)
Supplementary_files_format_and_content: Spreadsheet (read_counts_ALocke_May2018.xls) with HtSeq-count output for every sample.  Gene ID in rows, Sample ID in columns.

organism: Glycine max

source_name: upper canopy whole leaflets

growth_protocol: Soybean (Glycine max) cv. 93B15 (Pioneer Hi-Bred , Johnston, IA) was planted on 27 May 2010 at the SoyFACE research farm near Champaign, Illinois (40.042° N, 88.237° W).

extract_protocol:
Total RNA was isolated from frozen leaf tissue according to Bilgin et al.(2009).  Total RNA was treated with DNA-free kit (Ambion) before being submitted to the Carver Biotechnology Center.
cDNA libraries for each sample were prepared from total RNA using the TruSeq kit (Illumina) at the University of Illinois Roy J. Carver Biotechnology Center

treatment_protocol: Four plots in the field were the four biological replicates. Each replicate was sampled at four time points during the day, and each replicate was sampled on a different day in a 10-day period from 14-24 August 2010, during which all plants were in reproductive development. All three leaflets from an uppermost, fully expanded leaf were detached and immediately flash-frozen in liquid nitrogen at 8:00 (zeitgeber time [ZT] 2:20), 11:00 (ZT5:20), 14:00 (ZT8:20), and 17:00 (ZT11:20), and subsequently stored at -80°C. The three leaflets were combined to create one sample per plot.

value: upper canopy whole leaflets

tag: cultivar

tag: time


title: 11913X43

value: Mixed B6/129


title: 11913X47

value: Adult


title: 11913X46


title: 11913X42


title: 11913X39


title: biological replicate 4 - 14:00

description:
sample_12
Random primed libraries
Variety: 93B15


title: biological replicate 3 - 14:00

description:
sample_11
Random primed libraries
Variety: 93B15


title: biological replicate 2 - 14:00

description:
sample_10
Random primed libraries
Variety: 93B15


title: biological replicate 1 - 17:00

description:
sample_13
Random primed libraries
Variety: 93B15


title: siCHRNA5_day3_rep2

city: Ankara

first: Ozlen

last: Konu

address: Bilkent University

department: Molecular Biology and Genetics

country: Turkey

institute: Bilkent University

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw data was read and RMA normalized using affy package with default Affymetrix cdf (hgu133plus2cdf) in R programming language (R version 3.3.0).

source_name: MCF-7, siCHRNA5

label_protocol: not provided

growth_protocol: 2 x 10^5 MCF7 cells were seeded in each well of the 6-well plates.

extract_protocol: 1 µg RNA was isolated using RNeasy Mini kit (74104, Qiagen, Hamburg, Germany) according to the manufacturer’s protocols.

treatment_protocol: After 24 hours, cells were treated either with 10nM of siRNA against several CHRNA5 spliced variants (FlexiTube, SI03051111, Qiagen) or the respective negative control siRNA at the same concentration  (AllStars Negative Control siRNA, 1027280, Qiagen) using 12 µl of HiPerFect transfection reagent (301704, Qiagen).

tag: cell line

value: breast cancer

tag: group

value: CHRNA5 siRNA treatment


title: siCHRNA5_day3_rep1


title: scrambled_day3_rep2

source_name: MCF-7, Scrambled

value: Control siRNA


title: 11913X32

value: sorted lung tumor cell (single cell)


title: 11913X35


title: 11913X31


title: biological replicate 4 - 11:00

description:
sample_8
Random primed libraries
Variety: 93B15


title: biological replicate 1 - 14:00

description:
sample_9
Random primed libraries
Variety: 93B15


title: biological replicate 2 - 11:00

description:
sample_6
Random primed libraries
Variety: 93B15


title: 11913X30


title: biological replicate 3 - 17:00

description:
sample_15
Random primed libraries
Variety: 93B15


title: biological replicate 2 - 17:00

description:
sample_14
Random primed libraries
Variety: 93B15


title: biological replicate 1 - 11:00

description:
sample_5
Random primed libraries
Variety: 93B15


title: biological replicate 3 - 11:00

description:
sample_7
Random primed libraries
Variety: 93B15


title: 11913X3


title: 11913X28


title: biological replicate 4 - 8:00

description:
sample_4
Random primed libraries
Variety: 93B15


title: 11913X27


title: 11913X29


title: biological replicate 2 - 8:00

description:
sample_2
Random primed libraries
Variety: 93B15


title: 11913X25


title: biological replicate 1 - 8:00

description:
sample_1
Random primed libraries
Variety: 93B15


title: 11913X33


title: biological replicate 3 - 8:00

description:
sample_3
Random primed libraries
Variety: 93B15


title: 11913X24


title: 11913X20


title: scrambled_day3_rep1


title: 11913X2


title: 11913X18


title: 11913X17


title: 11913X13


title: 11913X14


title: 11913X16


title: 11913X15


title: 11913X26


title: 13438X5 NKX2-1-negative replicate 1

description:
counts_13438R.xls
13438X5

data_processing:
Mouse FASTA and GTF files were downloaded from Ensembl release 82 and a reference database was created using RSEM version 1.2.12.
RSEM and the Bowtie 1.0.1 aligner were used to map reads and estimate transcripts and gene counts using rsem-calculate-expression with the forward-prob 0 option for reversely stranded Illumina reads.
The expected gene counts were filtered to remove 12371 features with zero counts and 10100 features with fewer than 10 reads in any sample.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.16.0.
Genome_build: mm10
Supplementary_files_format_and_content: RSEM estimated gene counts combined into a single txt file

source_name: 13438X5 NKX2-1-negative, lung tumor cells

extract_protocol:
RNA was isolated by Trizol-chloroform extraction followed by column-based purification.
Library preparation was performed using the TruSeq Stranded RNA kit with Ribo-Zero Gold (Illumina). Libraries were sequenced on an Illumina HiSeq 2500 (50 cycle single-read sequencing).

value: lung tumor cells


title: 13438X6 NKX2-1-negative replicate 2

description:
counts_13438R.xls
13438X6

source_name: 13438X6 NKX2-1-negative, lung tumor cells


title: 13438X3 NKX2-1-positive replicate 3

description:
counts_13438R.xls
13438X3

source_name: 13438X3 NKX2-1-positive, lung tumor cells


title: A06190

city: Kuopio

first: Mikael

last: Marttinen

address: Yliopistonranta 1E

department: Biomedicine

country: Finland

institute: University of Eastern Finland

hyb_protocol: Cy-3 labeled with Agilent Low Input Quick Amp WT labeling kit, one-color (Prod. Num. 5190-2943)

scan_protocol: Scanned on Agilent Technologies scaner, model G2565CA (Scan profile: AgilentG3_GX_1color)

data_processing:
Data import was done with limma package version 3.16.7. The probe signal intensities were background-corrected using “normexp” method in limma package.
Quantile normalization was used to bring the array signal intensities to comparable levels between each other. Average expression levels between duplicate probes were used as the signal for the probe. For transcript expression analysis, 3′ untranslated region (UTR) probe signal was used as a measure of the respective transcript's global expression level. If multiple such probes targeted the same 3' UTR, average value of the probes was used. The expression level of each individual exon is affected by the global expression level of the transcript, and to adjust for this in the alternative splicing analysis, each exon signal was normalized by the respective transcript's global expression level (measured by 3′UTR probe). Probes that did not map to any known transcript were excluded, and in case of multiple probes mapping to a single transcript outside of the 3'UTR, the probe with the most interquartile-range (IRQ) variation across the samples, was retained in the analysis.  The sample tables include the normalized data filtered for these criteria and were the data used in this analysis. The quantile normalized values of the unfiltered probes are available in the file Data_matrix_full.csv on the series record.

source_name: Inferior termporal cortex

label_protocol: RNA was extracted from frozen brain samples using Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen) and RNA integrity number (RIN) was determined using 2100 Bioanalyzer

extract_protocol:
Post-mortem tissue extraction
grouping protocol: Assessment of the magnitude of AD-relatedneurofibrillary was performed via immunostaining of paraffin sections with AT8 antibody

tag: braak stage

value: brain

tag: brain region

value: Inferior termporal cortex

tag: sex (1= female, 2= male)

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)

tag: gamma secretase activity

tag: alpha secretase activity

tag: beta secretase activity

tag: amyloid-beta 42 levels


title: A01198

tag: age


title: 13438X1 NKX2-1-positive replicate 1

description:
counts_13438R.xls
13438X1

source_name: 13438X1 NKX2-1-positive, lung tumor cells

tag: strain

tag: genotype

tag: cell type


title: 11913X10


title: A03170

tag: tissue


title: 13438X7 NKX2-1-negative replicate 3

description:
counts_13438R.xls
13438X7

source_name: 13438X7 NKX2-1-negative, lung tumor cells


title: A01081


title: A02020


title: A02019


title: A05102


title: A01214


title: A01164


title: A01114


title: A02172


title: A01104


title: A01219


title: A01227


title: A00296


title: A00280


title: Th0_cMAFko_48h_5

description:
accessible DNA
22015_cMafKO_Th0_48h_CCGTTTGT

data_processing:
Sequences were mapped to the murine genome (mm10) with bowtie2 v2.2.3
Sequences were filtered (MAPQ>30) with Samtools
Duplicates were removed using Picard
Peakdeck (parameters -bin 75, -STEP 25, -back 10000, -npBack 100000) was used to call peaks (Praw < 1E-4)
A reference set of peaks was found by taking the union of peaks across samples
HTSeq-count was used to map reads to reference peaks
DESeq2 was used to quantify peak accessibility across samples and test for differential accessibility
Genome_build: mm10
Supplementary_files_format_and_content: Batch-corrected, DESeq2-normalized (RLOG) quantification for ATAC-seq peaks, peak annotations (nearest TSS, transcription factor motifs found within the peak, etc.)

source_name: Naïve CD4+ T cells from spleen

extract_protocol:
Cells harvest was followed by a transposition reaction and purification (Buenrostro  et al. Curr Protoc Mol Biol. 2015)
Prepared as in Buenrostro  et al. Curr Protoc Mol Biol. 2015

treatment_protocol: CD4+ T cells were purified from the spleen and polarized into Th0, Th2, Treg, and Th17 according to (Ciofani et al., Cell. 2012)

value: spleen

value: naive CD4+ T cells

tag: time point (post tcr stimulation)

value: Maf-fl/fl; Il7r-Cre

tag: polarization

tag: batch


title: Th17_cMAFko_48h_5

description:
accessible DNA
22015_cMafKO_Th17_48h_GTGTGGTG


title: A01055

tag: braak stage


title: 13438X2 NKX2-1-positive replicate 2

description:
counts_13438R.xls
13438X2

source_name: 13438X2 NKX2-1-positive, lung tumor cells


title: Th17_STAT3ko_48h_5

description:
accessible DNA
22015_STAT3KO_Th17_48h_AGGTTGGG

value: Stat3-fl/fl; Il7r-Cre


title: Th0_STAT3ko_48h_5

description:
accessible DNA
22015_STAT3KO_Th0_48h_TGGATCTG


title: A00163

tag: brain region


title: A00028

tag: sex (1= female, 2= male)


title: Th17_B6_48h_5

description:
accessible DNA
22015_B6_Th17_48h_TGCTGGGT

value: wild type


title: Th0_B6_48h_5

description:
accessible DNA
22015_B6_Th0_48h_GTCGTGAT


title: A00004

tag: rna quality


title: A00117

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)


title: Th0_IL7rCre_48h_5

description:
accessible DNA
22015_IL7rCre_Th0_48h_ACCACTGT


title: A00001

tag: gamma secretase activity


title: 99250

tag: alpha secretase activity


title: WT_Th17_TGFb_IL6_IL23_IL1B_1

description:
accessible DNA
1_WT_Th17_TGFb_IL6_IL23_IL1B_CAGAGAGG

value: Th17 + IL23 + IL1b


title: WT_Th17_TGFb_IL6_IL23_1

description:
accessible DNA
1_WT_Th17_TGFb_IL6_IL23_TAGGCATG


title: Th17-48h_2

description:
accessible DNA
Th17-48h_TAGGCATG


title: WT_Th17_TGFb_IL6_1

description:
accessible DNA
1_WT_Th17_TGFb_IL6_GGACTCCT


title: Th17-3h_1

description:
accessible DNA
Th17-3h_AGGCAGAA


title: Th17-6h_2

description:
accessible DNA
Th17-6h_TCCTGAGC


title: Th17_IL7rCre_48h_5

description:
accessible DNA
22015_IL7rCre_Th17_48h_GAGGGGTT


title: Th2-48h_2

description:
accessible DNA
Th2-48h_CAGAGAGG


title: WT_Th17_TGFb_IL6_IL23_IL1B_IL21_1

description:
accessible DNA
1_WT_Th17_TGFb_IL6_IL23_IL1B_IL21_GCTACGCT


title: 99206

tag: beta secretase activity


title: Th0-48h_2

description:
accessible DNA
Th0-48h_CTCTCTAC


title: 98251

tag: amyloid-beta 42 levels


title: 99117

tag: age


title: 98273


title: Treg-48h

description:
accessible DNA
Treg-48h_TGGATCTG

tag: strain

value: Treg


title: 98202


title: 98198


title: 98021


title: 98172


title: 97282


title: 97292


title: nCD4

description:
accessible DNA
nCD4_TAAGGCGA

tag: genotype

value: naive CD4+ T cell


title: 97266


title: Treg-2h

description:
accessible DNA
Treg-2h_GGACTCCT

tag: cell type


title: 97260

tag: tissue


title: Treg-16h

description:
accessible DNA
Treg-16h_AAGAGGCA

tag: time point (post tcr stimulation)


title: Th2-48h

description:
accessible DNA
Th2-48h_GTCGTGAT

tag: polarization


title: Th2-2h

description:
accessible DNA
Th2-2h_AGGCAGAA

tag: batch


title: Th2-16h

description:
accessible DNA
Th2-16h_GCTACGCT


title: 97137

tag: braak stage


title: 97098

tag: brain region


title: 97240

tag: sex (1= female, 2= male)


title: 97073

tag: rna quality


title: 97084

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)


title: Th17-2h

description:
accessible DNA
Th17-2h_TCCTGAGC


title: Th17-16h

description:
accessible DNA
Th17-16h_CGAGGCTG


title: Th17-48h

description:
accessible DNA
Th17-48h_ACCACTGT


title: Th0-48h

description:
accessible DNA
Th0-48h_GTAGAGGA


title: 97046

tag: gamma secretase activity


title: Th0-2h

description:
accessible DNA
Th0-2h_CGTACTAG


title: Th0-6h

description:
accessible DNA
Th0-6h_TAGGCATG


title: Th17-6h

description:
accessible DNA
Th17-6h_CTCTCTAC


title: Th0-16h

description:
accessible DNA
Th0-16h_CAGAGAGG


title: RES lamb 2 [H06]

city: León

first: Alba

middle: Santos

last: Baza

state: León

address: Finca Marzanas, Grulleros

department: Nutrición y Producción de Herbívoros

country: Spain

institute: Instituto de Ganadería de Montaña (CSIC)

description:
TPM_H06
H06_S51_L002

data_processing:
Basecalls performed using bcl2fastq 1.8.4
BBDuk version 36.30 (BBMap tools) was applied to raw fastq files for quality trimming (Phred >= 10), filtering short reads (min length = 30) and removing adapter sequences
BBMap version 36.30 was used to map the trimmed reads onto the reference genome; parameters: "maxindel=200k ambig=random intronlen=20"
Bioconductor packages GenomicFeatures (v 1.24.5), GenomicAlignments (v 1.8.4) and the Oar_v4.0 annotation were used to calculate per gene read counts. Bioconductor package mygene was used to obtain the Entrez ID
Differential expression analysis was conducted with the bioconductor package DESeq2 (v 1.12.4).  TPM values were calculated according to Wagner et al. (2012; PMID 22872506) using DESeq2-normalized read counts
Genome_build: GCF_000298735.2_Oar_v4.0
Supplementary_files_format_and_content: The processed data file contains the results of the DESeq2 differential expression analysis, the TPM values for each sample/biological replicate and the Entrez annotation

organism: Ovis aries

source_name: RES lamb_liver

extract_protocol:
Liver samples stabilized in RNAlater were homogenized using RLT (Qiagen), Lysing Matrix D and a FastPrep-24 instrument (MP Biochemicals); RNA purification was performed with the  RNeasy Mini kit and RNase-Free DNase Set kit (Qiagen).
Poly(A)+ mRNA fraction was isolated from total RNA and cDNA libraries were obtained following Illumina´s recommendations. Briefly, poly(A)+ RNA was isolated on poly-T oligo-attached magnetic beads and chemically fragmented prior to reverse transcription and cDNA generation. The cDNA fragments then go through an end repair process, the addition  of a single ‘A’ base to the 3’ end and then ligation of the adapters. Finally, the products are purified and enriched with PCR to create the indexed final double stranded cDNA library. The quality of the libraries was analyzed in Bioanalyzer 2100, High Sensitivity assay; the quantity of the libraries was determined by real-time PCR in LightCycler 480 (Roche). The pool of the libraries was sequenced by paired-end sequencing (100 × 2) in an Illumina HiSeq 2500 instrument.

tag: breed

value: Assaf lambs

tag: diet

value: Restricted 120 mL/kg LBW

tag: slaughter weight

tag: slaughter age (days)

value: Liver


title: RES lamb 4 [H29]

description:
TPM_H29
H29_S53_L002


title: RES lamb 3 [H17]

description:
TPM_H17
H17_S52_L002


title: RES lamb 1 [H05]

description:
TPM_H05
H05_S50_L002


title: th17P_96h_Veh_150812

description: 60h TCR stim; 48h polarization

source_name: Naive CD4+ T cells from spleen

tag: strain

value: Th17, "pathogenic"

value: Wildtype

tag: rna library protocol


title: ADL lamb 4 [H36]

description:
TPM_H36
H36_S49_L002

source_name: ADL lamb_liver

value: milk replacer (200 g dry matter/L) ad libitum (ADL; 192 mL/kg LBW)


title: ADL lamb 3 [H25]

description:
TPM_H25
H25_S48_L002


title: th17P_96h_Veh_150729

description: 60h TCR stim; 48h polarization

tag: cell type

tag: genotype


title: 97029

tag: tissue

tag: age

tag: alpha secretase activity

tag: beta secretase activity

tag: amyloid-beta 42 levels


title: 96242

tag: braak stage

tag: brain region

tag: sex (1= female, 2= male)


title: 96231

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)

tag: gamma secretase activity


title: 96350


title: 97107


title: ADL lamb 2 [H20]

description:
TPM_H20
H20_S47_L002

tag: breed

tag: diet

tag: slaughter weight


title: 96310


title: 96181


title: th17P_48h_Veh_150829

description: 60h TCR stim; 48h polarization

tag: strain

tag: polarization

tag: time point (post tcr stimulation)

tag: rna library protocol


title: U2OS_wt1_S7_L001

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

institute: Institute of Molecular Biology gGmbH

description: genetic background

data_processing:
Cut 10 bp from each edge from each read using cutadapt version 1.14
Merge Read1 and Read2 using pandaseq version 2.11, parameters: -d BFSrk -A pear
Map to hg38 using gmap version 2017-02-15, parameters: --min-intronlength=200 -f samse --nofails -B 4
Use CrispRVariants bioconductor package version 1.6.0 to screen for induced mutations
Genome_build: GRCh38
Supplementary_files_format_and_content: variant_counts

growth_protocol: 37⁰C, 5% CO2, 80% humidity

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen, 51104), target region was PCR-amplified using target specific primers.
DNA libraries were prepared for sequencing using standard Illumina protocols with index primers. Libraries were pooled in equimolar amounts.

treatment_protocol: Selection of transfected cells in 750 ng/mL puromycin

tag: cell line

tag: genotype/variation

value: wildtype

tag: r1 guide sequence

tag: r2 guide sequence

tag: molecule subtype

value: PCR amplicons


title: ADL lamb 1 [H08]

description:
TPM_H08
H08_S46_L002

tag: slaughter age (days)

tag: tissue


title: th17P_48h_Veh_150817

description: 60h TCR stim; 48h polarization

tag: cell type

tag: genotype


title: 96289

tag: braak stage

value: brain

tag: brain region

value: Inferior termporal cortex

tag: age

tag: sex (1= female, 2= male)

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)

tag: gamma secretase activity

tag: alpha secretase activity

tag: beta secretase activity

tag: amyloid-beta 42 levels


title: U2OS_g3_IX_ko4_S14_L001

description: ZBTB10 knockout using crispr-guide

tag: cell line

tag: genotype/variation

value: ZBTB10 knockout clone

tag: r1 guide sequence

value: CACCGAGAGACTTGGGCCGCGCGAG

value: AAACCTCGCGCGGCCCAAGTCTCTC


title: U2OS_g2_12_ko2_S9_L001

description: ZBTB10 knockout using crispr-guide

value: CACCGCGCGAGCGGGAAGTGCTGGA

tag: r2 guide sequence

value: AAACTCCAGCACTTCCCGCTCGCGC

tag: molecule subtype


title: U2OS_g2_1_ko1_S8_L001

description: ZBTB10 knockout using crispr-guide


title: th17P_96h_Dig_150812

description: 108h TCR stim; 96h polarization

tag: strain

tag: tissue

value: spleen

tag: cell type

tag: polarization

tag: time point (post tcr stimulation)

tag: rna library protocol


title: HEK_wt1_S1_L001

description: genetic background


title: HEK_ko5_S6_L001

description: ZBTB10 knockout using crispr-guide


title: th17P_96h_Dig_150729

description: 108h TCR stim; 96h polarization

value: naive CD4+ T cell

tag: genotype


title: HEK_ko4_S5_L001

description: ZBTB10 knockout using crispr-guide


title: 96177

tag: braak stage

tag: brain region

tag: age

tag: sex (1= female, 2= male)

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)


title: 96105

tag: gamma secretase activity

tag: alpha secretase activity

tag: beta secretase activity

tag: amyloid-beta 42 levels


title: 96038


title: 96040


title: HEK_ko3_S4_L001

description: ZBTB10 knockout using crispr-guide

tag: cell line

tag: genotype/variation

tag: r1 guide sequence

tag: r2 guide sequence

tag: molecule subtype


title: 96005

tag: tissue


title: HEK_ko2_S3_L001

description: ZBTB10 knockout using crispr-guide


title: th17P_48h_Dig_150829

description: 60h TCR stim; 48h polarization

tag: strain

tag: cell type

tag: polarization

tag: genotype

tag: time point (post tcr stimulation)

tag: rna library protocol


title: Th17_siFosl2_24h_SL13395

description: 24h siFosl2; 110930; 24h

value: Th17, RPMI


title: HEK_ko1_S2_L001

description: ZBTB10 knockout using crispr-guide


title: Th17_siFosl2_24h_SL13396

description: 24h siFosl2;120309; 24h


title: Th17_siEtv6_24h_SL13391

description: 24h siEtv6; 110930; 24h


title: th17P_96h_Dig_150719

description: 108h TCR stim; 96h polarization


title: Th17_siEtv6_24h_SL13392

description: 24h siEtv6; 111029; 24h


title: Th17_RPMI_siJmjd6_48h_SL11690

description: 48h RPMI siJmjd6; 48h


title: 95218

tag: braak stage

tag: brain region

tag: age

tag: sex (1= female, 2= male)

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)


title: miRNA_2230T

description:
Sp2230T_ATGTCA_L002
processed data file: counts_miRNA_spalax.csv

organism: Nannospalax ehrenbergi

source_name: Spalax fibrosarcoma

tag: diagnosis

value: fibrosarcoma

tag: Sex

value: M

tag: treatment

tag: time of operation after treatment

value: 30 months

value: muscle tissue

tag: sample side

value: injected side


title: 95330

tag: tissue

tag: gamma secretase activity

tag: alpha secretase activity

tag: beta secretase activity

tag: amyloid-beta 42 levels


title: Th17_RPMI_siRorc_48h_SL11704

description: 48h RPMI siRorc; 48h

tag: strain

tag: cell type

tag: polarization

tag: genotype

value: Wildtype

tag: time point (post tcr stimulation)

tag: rna library protocol


title: th17N_96h_Veh_150729

description: 108h TCR stim; 96h polarization


title: th17N_48h_Veh_150829

description: 60h TCR stim; 48h polarization


title: th17N_96h_Veh_150812

description: 108h TCR stim; 96h polarization


title: Th17_RPMI_siJmjd3_48h_SL11694

description: 48h RPMI siJmjd3; 48h


title: miRNA_2230H

description:
Sp2230HM_CCGTCC_L002
processed data file: counts_miRNA_spalax.csv

value: uninjected side


title: th17P_48h_Dig_150817

description: 60h TCR stim; 48h polarization

value: Th17, "pathogenic"


title: Th17_RPMI_siJmjd3_48h_SL11689

description: 48h RPMI siJmjd3; 48h


title: 95326

tag: braak stage

value: brain

tag: brain region

value: Inferior termporal cortex

tag: age

tag: sex (1= female, 2= male)

tag: rna quality

tag: apoe (additive) (0=0 copies of apoee4, 1=1 copy of apoee4, 2=two copies of apoee4)


title: Th17_RPMI_siJmjd6_48h_SL11703

description: 48h RPMI siJmjd6; 48h

tag: tissue


title: th17N_48h_Veh_150817

description: 60h TCR stim; 48h polarization


title: 95096

tag: gamma secretase activity


title: Th17_RPMI_siEtv6_48h_SL11693

description: 48h RPMI siEtv6; 48h