title: Acute cutaneous lupus 3

description:
9440308042_F
c.8


title: Acute cutaneous lupus 2

status: Public on Jul 15 2018

type: RNA

city: Worcester

first: John

middle: E

last: Harris

state: MA

address: 364 Plantation St

department: Dermatology

country: USA

institute: University of Massachusetts Medical School

description:
9249896027_H
c.8

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized with R/Bioconductor and Lumi package using a variance-stabilizing transformation and Robust Spline Normalization

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: skin, acute cutaneous

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using Roche high pure RNA paraffin kit according to the manufacturer’s instructions

tag: disease state

value: ACLE

tag: fas ligand level

tag: tissue

value: skin


title: Control.3 [RISC-IP small RNA]

type: SRA

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description:
RNA-Seq of small RNA from control IP samples.
processed data file: smallrna_riscip_counts.txt

library_source: transcriptomic

data_processing:
Raw reads in FASTQ files were trimmed of adapters and low quality sequences using Trimmomatic.
Trimmed successfully passing the trimming procedure were aligned to human reference genome hg19 using BWA.
Aligned reads were counted on mirBase19 using HTSeq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: smallrna_riscip_counts.txt: Tab-delimited text file containing the output from HTSeq-Counts counting procedure, one miRNA per row and one sample per column.

source_name: Biceps Brachii

extract_protocol:
Two lysis protocols were used: 1) skeletal muscle biopsies were cut into small pieces in RIP lysis buffer (Magna RIP Kit, Merck-Millipore, Burlington, MA) and homogenized by TissueLyser (Qiagen, Hilden, Germany); 2) Cultured cells were lysed with the following buffer: 150mM KCl, 25 mM TrisHCl pH 7.4, 5 mM EDTA, 0.5% NP40, 5 mM DTT, 1 mM PMSF, protease and RNase inhibitors. For both lysates, homogenates were quantified for protein content, snap frozen in liquid nitrogen and stored at -80°C until use. For both muscle tissue and cells, 1 mg of lysate was immunoprecipitated with anti-Ago2 or control mouse IgG antibodies (RIPAb+ Ago2, Merck-Millipore, Burlington, MA), using 5 ug of antibody for 1 mg of lysate. Immunoprecipitation was performed using the Magna RIP Kit (Merck Millipore, Burlington, MA) following the manufacturer’s instructions. IgG-bound RNA (IP RNA) was extracted from magnetic beads using TRIzol reagent (Invitrogen, ThermoFisher Scientific, Waltham, MA).
Extraction and library preparation were performed following manufacturer's instructions for the TruSeq Small RNA Library Preparation Kit.

tag: disease status

value: Myotonic dystrophy-1 (DM1)

value: Biceps brachii

tag: antibody

value: Control mouse IgG


title: Subacute cutaneous lupus 11

description:
9249907024_L
c.8

source_name: skin, subacute cutaneous

value: SCLE


title: Acute cutaneous lupus 4

description:
9249907024_K
c.8


title: Subacute cutaneous lupus 10

description:
9479614023_A
c.8


title: Control.1 [RISC-IP small RNA]


title: SkinControl 9

description:
9440308042_L
c.8

source_name: skin, control

value: SkinControl


title: Acute cutaneous lupus 6

description:
9440308052_G
c.8


title: Acute cutaneous lupus 5

description:
9440308052_F
c.8


title: Subacute cutaneous lupus 12

description:
9479614006_D
c.8


title: DM.6 [RISC-IP long RNA]

description:
RNA-Seq of long RNA from RISC-IP samples.
processed data file: mRNA_counts.txt

data_processing:
Raw reads in FASTQ files were trimmed of adapters and low quality sequences using Trimmomatic.
Trimmed successfully passing the trimming procedure were aligned to human reference genome hg19 using BWA.
Aligned reads were counted on human hg19 reference annotation using HTSeq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: mRNA_counts.txt: Tab-delimited text file containing the output from HTSeq-Counts counting procedure, one gene per row and one sample per column.

extract_protocol:
Two lysis protocols were used: 1) skeletal muscle biopsies were cut into small pieces in RIP lysis buffer (Magna RIP Kit, Merck-Millipore, Burlington, MA) and homogenized by TissueLyser (Qiagen, Hilden, Germany); 2) Cultured cells were lysed with the following buffer: 150mM KCl, 25 mM TrisHCl pH 7.4, 5 mM EDTA, 0.5% NP40, 5 mM DTT, 1 mM PMSF, protease and RNase inhibitors. For both lysates, homogenates were quantified for protein content, snap frozen in liquid nitrogen and stored at -80°C until use. For both muscle tissue and cells, 1 mg of lysate was immunoprecipitated with anti-Ago2 or control mouse IgG antibodies (RIPAb+ Ago2, Merck-Millipore, Burlington, MA), using 5 ug of antibody for 1 mg of lysate. Immunoprecipitation was performed using the Magna RIP Kit (Merck Millipore, Burlington, MA) following the manufacturer’s instructions. IgG-bound RNA (IP RNA) was extracted from magnetic beads using TRIzol reagent (Invitrogen, ThermoFisher Scientific, Waltham, MA).
Extraction, ribodepletion and library preparation were performed following manufacturer's instructions for the Nugen OVATION RNA-Seq System V2 and Nugen OVATION Ultralow Library Systems.


title: Acute cutaneous lupus 1

description:
9249896027_F
c.8


title: Control.5 [RISC-IP long RNA]

description:
RNA-Seq of long RNA from control IP samples.
processed data file: mRNA_counts.txt


title: Control.3 [RISC-IP long RNA]


title: DM.4 [RISC-IP long RNA]


title: DM.2 [RISC-IP long RNA]


title: Subacute cutaneous lupus 9

description:
9440308052_D
c.8


title: Subacute cutaneous lupus 7

description:
9479614006_A
c.8


title: control cauda sperm (test) 4-4b

city: Santa Cruz

first: Upasna

last: Sharma

state: California

address: 1156 High St

department: MCD Biology

institute: UCSC

data_processing:
For each small RNA library, rRNA-mapping reads (which were highly abundant in testis and epididymis samples, but rare in epididymosome and sperm samples) were removed. Remaining reads were mapped to murine tRNAs, to the unique sequences present in the 467 defined pachytene piRNA clusters, to Repeatmasker (tRNA entries from Repeatmasker were deleted to avoid duplicating tRNA-mapping reads), to miRbase, and to Refseq, yielding 27385 data points for each library
Genome_build: mm10
Supplementary_files_format_and_content: counts

organism: Mus musculus

source_name: sperm

growth_protocol: Mice were fed control diet and various tissue samples were collected from mice at age 8-12 weeks old.

extract_protocol:
Total RNA was extracted from the tissues and subjected to gel electrophoresis to isolate small RNA (<40nts).
Small RNA cloning was carried out as in Gu et al, Cell 151, 1488-1500 (2013)

tag: location in epididymis

value: Cauda epididymis

tag: treatment

value: Control


title: Subacute cutaneous lupus 8

description:
9440308052_C
c.8


title: control testis (neg) 4-1b

source_name: testis

value: testis


title: 4-TU cauda sperm (test) 4-4a

value: cauda epididymis


title: 4-TU caput (pos) 4-2a

source_name: caput epididymis

value: caput epididymis


title: 4-TU testis (neg) 4-1a


title: Subacute cutaneous lupus 4

description:
9249907024_H
c.8


title: MBD3_f_-_IPS_H3K4me3_reanalyzed

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
GSM1206838
Processed data available on GSM2739977. Raw data from GSM2739977 and GSM2912473 were combined to produce a single processed data file.

library_source: genomic

data_processing:
We used Illumina bcl2fastq version 2.17.1.14 software to generate fastq files.
Reads were aligned to mouse mm10 reference genome using bowtie2 software, with default parameters.
For transcription factors, peaks were identified with MACS version 1.4.2-157. Whole-cell extract was used as control to define a background model. Duplicate reads aligned to the exact same location are excluded by MACS default configuration. Chromatin modification coverage in the promoters was calculated using in-house script. Shortly, promoters were defined as 1Kb region around the TSS, based on mm10 assembly. Each promoter was divided to 50bp size bins, and the coverage in each bin is estimated.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files (bed format) and *prom_500.matrix.txt files.  In the processed matrix file, for each promoter is the coverage in 20 bins, 50bp each.

molecule: genomic DNA

growth_protocol: ESCs, iPSCs, and 4-8 day DOX induced cells were expaned in N2B27 15% KSR 2i/LIF mouse ESC media; MEF cells in DMEM + 15% FBS

extract_protocol:
Approximately 25*10^6 cells were cross-linked in formaldehyde (1% final concentration, 10 min at room temperature (RT)), and then quenched with glycine (5 min at RT). Fixed cells were lysed in 50mM HEPES KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40 alternative, 0.25% Triton supplemented with protease inhibitor at 4°C (Roche, 04693159001), centrifuged at 950 x g for 10 min and re-suspended in 0.2% SDS, 10mM EDTA, 140mM NaCl and 10mM Tris-HCL. Cells were then fragmented with a Branson Sonifier (model S-450D) at -4°C to a size range between 200 and 800 bp, and precipitated by centrifugation. 10 ug of antibody were pre-bound by incubating with Protein-G Dynabeads (Invitrogen100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 2 hours at room temperature. Washed beads were added to the chromatin lysate, and then incubated overnight. Samples were washed 5 times with RIPA buffer, twice with RIPA buffer supplemented with 500 mM NaCl, twice with LiCl buffer (10 mM TE, 250mM LiCl, 0.5% NP-40, 0.5% DOC), once with TE (10Mm Tris-HCl pH 8.0, 1mM EDTA), and then eluted in 0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris Hcl pH 8.0 at 65°C. Eluate was incubated in 65°C for 4 hours, and then treated sequentially with RNaseA (Roche, 11119915001) for 30 min and Proteinase K (NEB, P8102S) for two hours. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881).
120ul SPRI AMPure XP beads (Agencourt) were added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant were separated from the beads using a magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. The DNA was eluted in 40 ul EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing 25 times. For the remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) a general SPRI cleanup involves addition of buffer containing 20% PEG and 2.5 M NaCl to the DNA reaction products (without moving them from their original well position). After thorough mixing and a 2-minute incubation at room temperature, plates are transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are then washed on the magnet with 150ul 70% ethanol and then air dried for 4 minutes. The DNA is eluted with 40ul of EB buffer by pipette mixing 25 times. Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27 µl of a master mix (17 µl master mix (5 ul T4 buffer, 5ul BSA-1mg/ml, 5ul ATP-10mM -2ul dNTPs 10 mM), 5 ul T4 PNK enzyme, 5 µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12C for 15 min, 25C for 15 min, and finally cooled to 4C. The SPRI bead clean up method was used to purify the product (147 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). The A-base addition was performed by adding 20 µl master mix (17 µl A-base add mix, 3 µl Klenow (3’->5’ exonuclease) to each well and incubated at 37C for 30 min. in a thermal cycler. SPRI bead clean up method was used to purify the product (132 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 19 µl EB). Adaptor ligation was performed by adding 34 µl of a master mix (29 µl 2x DNA ligase buffer, 5 µl DNA ligase) to each well. Finally 5 µl PE Indexed oligo adaptors (0.75 uM ) was added to each well and samples were incubated 25C for 15 min in a thermal cycler. SPRI bead clean up with size selection was used to purify the ligated products (15.5 µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40 µl EB). Finally, enrichment PCR was performed by adding 10 µl of a master mix (2 µl Forward/Reverse Index Primer, 0.5 µl dNTP mix, 5 µl 10x Pfu Ultra Buffer, 1 µl Pfu Ultra-II Fusion, 1.5 µl Nuclease free water) to each well. Plate was transferred to a thermal cycler and ran a Pfu amplification program at 95C for 2 min, 16 cycles of: 95C for 30 sec, 55C for 30 sec, 72C for 60 sec, and finally 72C for 10 min. The final SPRI clean up coupled to size selection was performed (35 µl SPRI beads was added to each sample and eluted in 40 µl). Approximately 5 picomoles of DNA library was then applied to each lane of the flow cell. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq2000 Analyzer following the manufacturer's protocols.

treatment_protocol: DOX induction at day 0 at the relevant plate in final concentration of 2ug/ml

tag: genotype/variation

value: MBD3flox/- mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

tag: stage in reprogramming

value: iPSC

tag: target protein

value: Abcam ab8580


title: MBD3_f_-_8day_DOX_WCE_reanalyzed

value: 8 days after DOX induction


title: Subacute cutaneous lupus 1

description:
9249896027_B
c.8


title: Subacute cutaneous lupus 3

description:
9249907024_F
c.8


title: Subacute cutaneous lupus 6

description:
9479614006_E
c.8


title: Subacute cutaneous lupus 2

description:
9249896027_D
c.8


title: Subacute cutaneous lupus 5

description:
9440308042_E
c.8


title: Chronic cutaneous lupus 3

description:
9249896027_L
c.8

source_name: skin, chronic cutaneous

value: CCLE


title: MBD3_f_-_4day_DOX_WCE_reanalyzed

value: 4 days after DOX induction


title: Chronic cutaneous lupus 4

description:
9249907024_I
c.8

value: skin


title: Chronic cutaneous lupus 6

description:
9440308052_A
c.8


title: Chronic cutaneous lupus 1

description:
9440308042_A
c.8


title: Chronic cutaneous lupus 2

description:
9249896027_J
c.8


title: control caput (pos) 4-2b


title: Chronic cutaneous lupus 5

description:
9440308052_E
c.8


title: WT_MEF_H3K27ac_reanalyzed

value: MBD3+/+ mouse Embryonic Fibroblast Cells (MEF) transgenic for DOX inducible OSKM reprogramming

value: Before DOX induction

value: Abcam ab4729


title: MBD3_f_-_MEF_H3K27ac_reanalyzed


title: MBD3_f_-_MEF_H3K4me3_reanalyzed


title: MBD3_f_-_MEF_WCE_reanalyzed


title: WT_4day_DOX_H3K27ac_reanalyzed


title: WT_8day_DOX_H3K27ac_reanalyzed


title: MBD3_f_-_IPS_Oct4_reanalyzed

value: Santa Cruz sc5279(C-10)


title: CTWT-Batch-3

city: London

first: Helen

middle: M

last: Rowe

address: 90 Gower Street

department: Infection and Immunity

country: United Kingdom

institute: University College London

data_processing:
Run data were demultiplexed and converted to fastq files using Illumina’ s bcl2fastq Conversion Software v2.16. Fastq files were then aligned to the human genome NCBI build 37.2 using Tophat 2.014 then deduplicated using Picard Tools 1.79. Reads per transcript were counted using HTSeq and differential expression was estimated using the BioConductor package DESeq2. P-values were adjusted for multiple testing with the Benjamini-Hochberg false-discovery-rate (FDR) procedure (see Spreadsheet 2).
For analysis of repeats, TrimGalore v0.4.0 was used to remove adaptors and trim read ends using default parameters. Reads were mapped against the RepBase v20.06 human library using Bowtie2v2.2.4. The samtools v.1.19 idxstat utility was used to extract the number of mapped reads per repeat, that were inputted to DESeq2 to identify differentially expressed repeats. P-values were adjusted for multiple testing with the Benjamini-Hochberg false-discovery-rate (FDR) procedure (see Spreadsheet 1).
Genome_build: human genome NCBI build 37.2
Supplementary_files_format_and_content: 4 processed excel files of mRNA-seq data with differentially expressed repeats (Spreadsheet 1) and genes (Spreadsheet 2), as well as gene RPKMs (spreadsheet 3) and repeat raw counts (spreadsheet 4).

growth_protocol: HeLa cells were grown in standard DMEM + 10% FCS and P/S and split 1:4 every 2 days using trypsin.

extract_protocol:
Total RNA was extracted using an RNeasy mini kit (Qiagen) and treated with DNase (Ambion AM1907).
PolyA-tailed mRNA was separated and processed using Illumina’s TruSeq Stranded mRNA LT sample preparation kit (RS-122-2101) according to manufacturer’s instructions with some deviations: Libraries to be multiplexed in the same run were pooled in equimolar quantities, calculated from Qubit and Bioanalyser fragment analysis. Samples were sequenced on a NextSeq 500 instrument (Illumina, San Diego, US) using a 43bp paired end run resulting in >15million reads per sample.
Illumina’s TruSeq Stranded mRNA, 43bp paired end run resulting in >15million reads per sample

treatment_protocol: Guide RNAs (sgRNAs) specific to exons 1 and 9 of KAP1 were designed using the website: http://crispr.mit.edu/ and cloned into the PX459 plasmid (Addgene), which was then transfected into HeLa cells. After 24 hours, the cells were subjected to puromycin selection (added at 2.5ug/ml) for 24 hours or until control cells had completely died. The bulk population was then used for single cell cloning by limiting dilution. Knockout was assessed across a panel of clones by Western Blotting using the KAP1 antibody, MAB3662 (Millipore) and validated functionally using KAP1-KZNF reporter assays.

tag: cell line

value: HeLa

value: wild type

tag: clone id

value: sample 3


title: CT2-5months-Ex1plus-9-8

source_name: HeLa_KAP1 KO

value: KAP1 heLa knockout

value: clone 8


title: CT2-5months-Ex1plus-9-12

value: clone 12


title: CTHeLa-Batch-2-NT

value: sample 2


title: WT_IPS_H3K27ac_reanalyzed

value: iPSC


title: CTHeLa-Batch-1-NT

value: sample 1


title: 13745 - Oox 3

city: Saint Louis

first: Jonathan

last: Lin

state: MO

address: 660 S. Euclid Ave, Campus Box 8096

institute: Washington University School of Medicine

hyb_protocol: We followed manufacturer's instructions.

data_processing:
We processed the array results with Affymetrix Expression Console (v1.3.1.187) at standard settings (RMA background correction, median polish summarization, and quantile normalization) to generate intensity values.
We assigned each probeset of the MoGene 1.0 array a detection call of 'mean + 2×SD' of the negative controls.

source_name: peritoneal macrophages

label_protocol: We performed target labeling with the Encore® biotin kit (NuGEN).

extract_protocol: We extracted RNA with the mirVana kit (Thermo Fisher).

treatment_protocol: Untreated, 25 μg/ml oxLDL for 24 hours, or 25 μg/ml acLDL for 24 hours.

tag: strain/background

value: wild-type

tag: gender

value: female

tag: age

value: 18 months

tag: cell type

value: peritoneal macrophages

value: 25 ug/ml oxLDL for 24 hours


title: 13748 - Oox 4

scan_protocol: We followed manufacturer's instructions.


title: 13746 - Oac 3

value: 25 ug/ml acLDL for 24 hours


title: 13743 - Oac 2


title: 13749 - Oac 4


title: 13737 - Yac 4

value: 3 months


title: 13735 - Yut 4

value: untreated


title: 13747 - Out 4


title: 13742 - Oox 2


title: 13738 - Out 1


title: 13734 - Yac 3


title: 13736 - Yox 4


title: 13741 - Out 2


title: 13744 - Out 3


title: 13729 - Yut 2


title: 13730 - Yox 2


title: 13733 - Yox 3


title: 13732 - Yut 3


title: 13727 - Yox 1


title: 13731 - Yac 2


title: hoxb1b-/- mutant replicate 1 (hoxb1bmut)

first: Charles

middle: G

last: Sagerstrom

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: UMass Medical School

description:
alldetected_genes_WT_vs_hoxb1bmut.tsv
Mut2

data_processing:
reads quality check with FastQC
alignment and read counts with RSEM_v1.2.28
Normalized abundance measurements and identification of differentially expressed genes with DESeq2
Genome_build: GRCz10/DanRer7
Supplementary_files_format_and_content: .tsv containing read count tmp values from each replicate, adjusted p-values, and fold change compared to wildtype samples for all genes detected

molecule: polyA RNA

organism: Danio rerio

source_name: whole embryo

growth_protocol: zebrafish egg water maintained at 28°C

extract_protocol:
Total RNA was extracted from pools of dechrionated, deyolked of hoxb1b homzygous mutants and wildtype embryos at 18hpf using the RNeasy Mini Kit (Qiagen)
Three libraries from wildtype embryos and three libraries from hoxb1b mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). All libraries were analyzed for quality on a bioanalyzer prior to sequencing (Agilent 2100 BioAnalyzer).

tag: developmental stage

value: 18 hours post fertilization

tag: genotype

value: hoxb1b-/- mutant

value: whole embryo


title: wildtype control replicate 1 (hoxb1bmut)

description:
alldetected_genes_WT_vs_hoxb1bmut.tsv
WT1

value: wildtype control


title: wildtype control replicate 2 (hoxb1bmut)

description:
alldetected_genes_WT_vs_hoxb1bmut.tsv
WT2


title: hoxb1b-/- mutant replicate 2 (hoxb1bmut)

description:
alldetected_genes_WT_vs_hoxb1bmut.tsv
Mut3


title: wildtype control replicate 3 (hoxb1bmut)

description:
alldetected_genes_WT_vs_hoxb1bmut.tsv
WT3


title: gas6-/- mutant replicate 3 (gas6mut)

description:
alldetected_genes_wt_vs_gas6.tsv
Mut3

source_name: dissected hindbrain

extract_protocol:
Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit (Qiagen).
Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina). All libraries were analyzed for quality on a bioanalyzer prior to sequencing (Agilent 2100 BioAnalyzer).

value: 48 hours post fertilization

value: gas6-/- mutant

value: hindbrain


title: hoxb1b-/- mutant replicate 3 (hoxb1bmut)

description:
alldetected_genes_WT_vs_hoxb1bmut.tsv
Mut4


title: gas6-/- mutant replicate 2 (gas6mut)

description:
alldetected_genes_wt_vs_gas6.tsv
Mut2


title: gas6-/- mutant replicate 1 (gas6mut)

description:
alldetected_genes_wt_vs_gas6.tsv
Mut1


title: wildtype control replicate 3 (gas6mut)

description:
alldetected_genes_wt_vs_gas6.tsv
WT3


title: wildtype control replicate 2 (gas6mut)

description:
alldetected_genes_wt_vs_gas6.tsv
WT2


title: wildtype control replicate 1 (gas6mut)

description:
alldetected_genes_wt_vs_gas6.tsv
WT1


title: O2_60_3

city: Braunschweig

first: Michael

last: Beckstette

state: Lower Saxony

address: Inhoffenstrase 7

department: Molecular Infection Biology

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
library quality assessment using FastQC
alignment vs. reference genome using Bowtie2 with default parametrization
read count quantification using htseq-count (http://www.huber.embl.de/users/anders/HTSeq) and subsequent RPKM normalization
Detection of differentially expressed genes using DeSEQ2 with raw count data and default parametrization
Genome_build: CP016318 Clostridioides difficile strain 630 delta erm, complete genome
Supplementary_files_format_and_content: *.tab files: CSV format with raw read counts per gene; *.rpkm files: CSV format with RPKM normalized read counts per gene; DESeq2_genes_diffexp*.csv: CSV files with differentially expressed genes

organism: Clostridioides difficile

source_name: exponentially growing cells

growth_protocol: C. difficile was grown anaerobically to an optical density of 0.4

extract_protocol:
Total bacterial RNA was isolated from bacterial cell pellets, from three independent experiments, using acid phenol and glass beads. DNA was digested using TURBO DNase (Ambion) and the DNA-free RNA was purified with phenol:chloroform:isoamylalcohol (25:24:1). Remaining traces of phenol were removed by washing the samples twice with chloroform:isoamylalcohol (24:1). RNA integrity was assessed using the Agilent RNA 6000 Nano Kit on the Agilent 2100 Bioanalyzer. To 2 µg of total RNA 1 µL of 1:10 diluted ERCC ExFold RNA Spike-In Mix 1 or 2 (Ambion) was added. rRNA was depleted using the Ribo-Zero rRNA Removal Kit (Gram-Positive Bacteria) as recommended by the manufacturer (Epicentre).
Strand-specific barcoded cDNA libraries were prepared using the ScriptSeq v2 RNA-Seq Library Preparation Kit as recommended by the manufacturer (Epicentre). Library quality was validated using Agilent 2100 Bioanalyzer (Agilent Technologies) following the manufacturer’s instruction.

treatment_protocol: Control samples were streamed with pure nitrogen for 15 or 60 min; stress samples were streamed with 5% oxygen in nitrogen for 15 or 60 min

value: 60 min O2 streaming

tag: strain


title: N2_60_2

value: 60 min N2 streaming


title: O2_15_3

value: 15 min O2 streaming


title: N2_60_3


title: O2_60_1


title: N2_15_2

value: 15 min N2 streaming


title: N2_15_3


title: N2_15_1


title: A2058-TET2M cell cultured in normal-g

city: Boston

first: Di

last: Wu

address: 221 longwood Ave, EBRC (LMRC) 222A

department: Endocrinology

institute: The Brigham and Women's Hospital

description: Mut-Low

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on HG-U133 Plus 2.0 Array. GeneChips were washed using the Affymetrix fluidics station and stained with streptavidinphycoerythrin.

scan_protocol: Washed arrays will be scanned on a Affymetrix GeneChip Scanner 3000

data_processing: Raw microarray data were analyzed using Affymetrix Expression Console Software and customized R scripts for quality assessment and quality control, background correction, and normalization across arrays.

source_name: A2058-TET2M over-expressing cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in high-g or normal-g for 7 days prior to collection, with splitting every 2-3 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were washed with 4-degree PBS, scraped down, and centrifuged into pellets (1000 rpm, 2 min)

value: melanoma cell line

value: overexpressing TET2M

tag: grown under

value: normal-glc (1g/L) DMEM medium for 7 days


title: A2058-TET2M cell cultured in high-g

description: Mut-High

value: high-glc (4.5g/L) DMEM medium for 7 days


title: Mock cell cultured in normal-g

description: Mock-Low

source_name: A2058-Mock over-expressing cell

value: mock


title: A2058-TET2WT cell cultured in normal-g

description: WT-Low

source_name: A2058-TET2WT over-expressing cell

value: overexpressing TET2WT


title: Mock cell cultured in high-g

description: Mock-High


title: A2058-TET2WT cell cultured in high-g

description: WT-High


title: O2_60_2


title: C2

city: Luoyang

first: Ying

last: Zhang

state: Henan

address: Kaiyuan Road

country: China

institute: Henan University of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to NZ_JRKI00000000.1 whole genome using bowtie 2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
peaks were called using PeaksFind version 2.2
Genome_build: NZ_JRKI00000000.1(Streptomyces natalensis ATCC 27448)
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Streptomyces natalensis

growth_protocol: S. natalensis HW-2 was cultured at 28oC with the shaking of 180r/min for 36h. Then,0.5% L-Valine was added into the fermentation broth of S. natalensis HW-2 and continued to culture for another 84h .

extract_protocol:
Total RNA was extracted using Total RNA Extractor（Trizol） (Cat# B511311, Sangon Biotech)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by Qubit2.0 RNA Kit (Cat Q32855,Life).
Library was prepared according to Illumina's instructions with VAHTS Total RNA-Seq（H/M/R) Library PrepKit (NR603-02, Vazyme）. Briefly, RNA was extracted and rRNA was depleted with Ribo-Zero rRNA Removal Reagents(MRZB12424, Epicentre). mRNA was fragmented with Fragment High Mix. First Strand cDNA was synthesized with First Strand Synthesis Act D Mix and Second Strand cDNA was synthesized with Second Strand Marking Master Mix. Adenylate 3' Ends and Ligate Adapters were treated. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 520 bp were checked with an Agilent 2100 Bioanalyzer. Libraries were sequenced on Illumina Hiseq 2000 System following the manufacturer's protocols.

treatment_protocol: The Valine was added into the fermentation broth of Streptomyces natalensis HW-2 at 36h. The microbe continued to culture. The broth was collected at 48 h,60h and 72 h, respectively. Then, the broth was centrifuged at 10000 r/min for 10 min. A1 was cultured for 48h without the Valine, A2 was cultured for 48h with adding Valine, B1 was cultured for 60h without Valine, B2 was cultured for 60h with adding Valine,C1 was cultured for 72h without Valine, C2 was cultured for 72h with adding Valine

value: adding L-Valine 72h


title: A2

value: adding L-Valine 48h


title: A1

value: without L-Valine 48h


title: B1

value: without L-Valine 60h


title: B2

value: adding L-Valine 60h


title: N2_60_1


title: O2_15_2


title: O2_15_1


title: C1

value: without L-Valine 72h


title: Microglia_WT

status: Public on Jul 14 2018

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
WT Microglia
platform: 10x Genomics

data_processing:
Raw data bcl files were first demultiplexed using Cell Ranger mkfastq
Demultiplexed data was then processed using the Cell Ranger count pipeline
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output CellRanger Count) for each sample

source_name: Brain

extract_protocol:
All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.
10X Genomics protocols.

tag: tissue

value: Brain

tag: number of cells


title: Zeb2KO Splenic Mac

description:
Zeb2KO Splenic Macrophage
platform: 10x Genomics

source_name: Spleen

value: Spleen


title: Colon Mac_WT

description:
WT Colon Macrophage
platform: 10x Genomics

source_name: Colon

value: Colon


title: Splenic Mac_WT

description:
WT Splenic Macrophage
platform: 10x Genomics


title: Zeb2KO Microglia

description:
Zeb2KO Microglia
platform: 10x Genomics


title: cKO 4

city: Philadelphia

first: Preetika

last: Gupta

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Raw RNA-Seq reads were aligned to the mm10.GRCm38.p5  build of the mouse genome using STAR v2.5.3a. STAR was provided with gene models from the Ensembl v90 genome annotation.
The Pipeline of RNA-Seq Transformations (PORT) v0.8.2a-beta was used to perform gene-level quantification of the aligned data. PORT is an implementation of the re-sampling approach for normalization proposed by Li and Tibshirani. Briefly, PORT accounts for potential confounding factors like reads mapping to rRNA and mitochondrial DNA. Next, PORT determines the input samples with the fewest number of gene-mapping reads and re-samples all datasets to the same number of reads. Lastly, PORT quantifies the normalized gene-level reads counts for each sample.
Genome_build: mm10.GRCm38.p5
Supplementary_files_format_and_content: txt files contain PORT-normalized and quantified read counts for each gene in each sample

source_name: hippocampus

extract_protocol:
Qiagen RNA mini kit
TruSeq RNA sample prep kit

value: male

value: cKO


title: cKO 3


title: Zeb2KO Colon Mac

description:
Zeb2KO Colon Macrophage
platform: 10x Genomics


title: KO_scRNA_batch2

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw reads were separated by cell barcodes, trimmed, aligned to the mm9 mouse transcriptome and de-duplicated by UMIs information.
The transcript copy numbers of each gene were counted and used for the subsequent analysis. Single cells with less than 30% mapping efficiency, 2,000 detected genes and 20,000 transcripts were excluded.
Genes with averaged counts above 0.2 among all the retained 586 single cells were used, and the transcripts were normalized.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include expression values (log2(nomalized count +1)). Cells and genes have been filtered.

source_name: Bone Marrow

extract_protocol:
Bone marrow HSCs from WT or Med23-dificient adult mice were isolated by cell sorting (LSKsCD150+CD34-CD48-).
Single mouse hematopoietic stem cells which were isolated by cell sorting, were manually picked, lysed and subjected to first-strand cDNA synthesis by using barcoded oligo-dT primers. Then, second-strand cDNA were synthesized, amplified and fragmented by sonication (Covaris). Final RNA-seq library was prepared by using the KAPA Hyper Prep Kit (KAPA Biosystems).

value: Hematopoietic Stem Cells

value: Bone Marrow


title: KO_scRNA_batch3


title: KO_scRNA_batch4


title: Ctrl 1

value: control


title: Ctrl 3


title: cKO 2


title: Ctrl 2


title: KO_scRNA_batch1


title: cKO 1


title: WT_scRNA_batch3

value: wild type


title: WT_scRNA_batch1


title: WT_scRNA_batch2


title: Ctrl 4


title: WT_scRNA_batch4


title: MM_BMSC20_miR10

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

country: Japan

institute: Tokyo Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® human Gene 2.0 ST Array, and washed according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

scan_protocol: GeneChips were and stained, and scanned by Scanner 3000 7G system according to the protocol described in WT PLUS Reagent Kit User Manual (P/N 703174 Rev. 2).

data_processing: The data were analyzed with Command Console Software ver. 3.2 and Expression Console Software ver. 1.3.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: BMSCs derived from MM patient

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

growth_protocol: BMSCs were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2, and the adherent cells were collected after two or three passages for subsequent cytogenetic analysis and exosome isolation.

extract_protocol: QIAzol extraction of total RNA was performed according to the manufacturer's instructions.

tag: disease state

value: multiple myeloma patient

value: bone marrow stromal cells

value: transfected with miR-10a mimic


title: MM_BMSC12_miR10

tag: treatment


title: MM_BMSC5_NC

value: transfected with scramble-miR control


title: participant.50704.post.training

city: Baton Rouge

first: Claude

last: Bouchard

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

description: gene expression profile of study participant at the end of the endurance training study

hyb_protocol: Labelled and amplfied mRNA was hybridised to Affymetrix HG-U133+2 arrays according to the manufacturer's instructions

scan_protocol: Affymetrix Scanner 3000 7G

data_processing: Data has been normalised using the RMA method contained within the R library affy

source_name: vastus lateralis

label_protocol: mRNA amplified and labelled with Biotin with Ambion MessageAmp Premier following manufacturer’s instructions

extract_protocol: Muscle biopsies of vastus lateralis muscle were performed at baseline and at the conclusion of the exercise program using the percutaneous needle biopsy technique in 41 HERITAGE White subjects from the Québec Clinical Center. Total RNA was isolated from frozen muscle biopsies preserved in Tissue-Tek using Trizol.

treatment_protocol: Gene expression assessed after completion of exercise program

tag: status

value: post-training


title: participant.51465.post.training


title: participant.51684.post.training


title: MM_BMSC20_NC


title: participant.51761.post.training


title: participant.51765.post.training


title: participant.51686.post.training


title: MGUS_BMSC2_miR10

source_name: BMSCs derived from MGUS patient

value: monoclonal gammopathy of undetermined significance (MGUS) patient


title: participant.51721.post.training


title: participant.51571.post.training


title: participant.51463.post.training


title: MM_BMSC5_miR10


title: CT2-5months-Ex1plus-9-15

value: HeLa

tag: genotype/variation

value: KAP1 heLa knockout

value: clone 15


title: participant.51762.post.training


title: MGUS_BMSC1_NC


title: MGUS_BMSC2_NC


title: MM_BMSC12_NC


title: participant.51681.post.training


title: participant.50701.post.training


title: participant.51685.post.training


title: MM_BMSC2_NC


title: participant.51242.post.training


title: MM_BMSC2_miR10


title: Normal_BMSC_miR10

source_name: BMSCs derived from healthy donor

value: healthy donor


title: MGUS_BMSC1_miR10


title: Normal_BMSC_NC


title: participant.51464.post.training


title: LXRaKO Kupffer Cell

description:
LXRaKO Kupffer Cell
platform: 10x Genomics

source_name: Liver

value: Liver


title: Kupffer Cell_WT_Nr1h3fl/fl

description:
WT Kupffer Cell
platform: 10x Genomics


title: Zeb2KO Alveolar Mac

description:
Zeb2KO Alveolar Macrophage
platform: 10x Genomics

source_name: Lung

value: Lung


title: Alveolar Mac _WT

description:
WT Alveolar Macrophage
platform: 10x Genomics


title: participant.51223.post.training


title: Kupffer Cell_WT

description:
WT Kupffer Cell
platform: 10x Genomics


title: KC_Cre+T4+_6

description: Zeb2KO Kupffer Cell (Tim4+)

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

source_name: Zeb2KO Kupffer Cell (Tim4+)

extract_protocol: All Methods listed in Scott et al.  Transcription Factor Zeb2 is required to maintain tissue-sepcific identities of macrophages. Immunity. 2018.

value: Kupffer Cell


title: Zeb2KO Kupffer Cell

description:
Zeb2KO Kupffer Cell
platform: 10x Genomics


title: participant.51461.post.training


title: KC_Cre+T4-_6

description: Zeb2KO Kupffer Cell (Tim4-)

source_name: Zeb2KO Kupffer Cell (Tim4-)


title: KC_Cre+T4+_5

description: Zeb2KO Kupffer Cell (Tim4+)


title: Mock irradiated Human HaCaT cells, biological rep3

city: Suzhou

first: huimin

last: Jia

address: No.199 Ren'ai Road, Wuzhong District

institute: Soochow University

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) following the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing:
Raw data were normalized by RMA algorithm, GeneSpring Software 13.1 (Agilent Technologies, Santa Clara, CA, US).
probe group file: HTA-2_0.r2.pgf
meta-probeset file: HTA-2_0.r2.Psrs.mps

source_name: Human keratinocyte HaCaT cells

label_protocol: Total RNA were amplified, labeled and purified by using Ambion WT Express kit following the manufacturer’s instructions to obtain biotin-labeled cRNA.

growth_protocol: Human keratinocyte HaCaT cells were routinely cultured with DMEM high glucose complete medium (include 10% FBS and 5% Penicillin and streptomycin antibody), in 37℃ 5% CO2 environment.

extract_protocol: Total RNA was isolated using an RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol.

treatment_protocol: HaCaT cells were treated with 0 or 20Gy X-ray irradiation using an X-ray linear accelerator (RADSOURCE, GA, USA) at a fixed dose rate of 1.15 Gy/min.

value: HaCaT

value: keratinocyte cell line

value: mock irradiation


title: participant.50673.post.training


title: KC_Cre+T4-_5

description: Zeb2KO Kupffer Cell (Tim4-)


title: 20 Gy X-ray irradiated Human HaCaT cells, biological rep2

value: 20 Gy X-ray irradiation


title: participant.51221.post.training


title: participant.50953.post.training


title: participant.51241.post.training


title: participant.51201.post.training


title: participant.51222.post.training


title: Mock irradiated Human HaCaT cells, biological rep2


title: participant.50963.post.training


title: KC_Cre+T4+_4

description: Zeb2KO Kupffer Cell (Tim4+)


title: participant.51725.post.training


title: participant.50921.post.training


title: participant.50672.post.training


title: Mock irradiated Human HaCaT cells, biological rep1


title: 20 Gy X-ray irradiated Human HaCaT cells, biological rep3


title: participant.50924.post.training


title: participant.50903.post.training


title: KC_Cre+T4+_3

description: Zeb2KO Kupffer Cell (Tim4+)


title: KC_Cre+T4-_3

description: Zeb2KO Kupffer Cell (Tim4-)


title: KC_Cre+T4-_4

description: Zeb2KO Kupffer Cell (Tim4-)


title: 20 Gy X-ray irradiated Human HaCaT cells, biological rep1


title: participant.50955.post.training


title: participant.50926.post.training


title: participant.51745.post.training


title: participant.50904.post.training


title: participant.50961.post.training


title: participant.51576.post.training


title: participant.51746.post.training


title: participant.50905.post.training


title: participant.50954.post.training


title: participant.50902.post.training


title: participant.51573.pre.training

description: gene expression profile of study participant at the start of the endurance training study

value: pre-training


title: participant.51573.post.training


title: participant.51574.post.training


title: KC_Cre-_6

description: Kupffer Cell_WT

source_name: Kupffer Cell_WT


title: KC_Cre+T4+_1

description: Zeb2KO Kupffer Cell (Tim4+)


title: KC_Cre-_4

description: Kupffer Cell_WT


title: KC_Cre+T4+_2

description: Zeb2KO Kupffer Cell (Tim4+)


title: KC_Cre-_5

description: Kupffer Cell_WT


title: KC_Cre+T4-_2

description: Zeb2KO Kupffer Cell (Tim4-)


title: KC_Cre-_3

description: Kupffer Cell_WT


title: KC_Cre+T4-_1

description: Zeb2KO Kupffer Cell (Tim4-)


title: KC_Cre-_1

description: Kupffer Cell_WT


title: AMF_Cre-_5

description: Alveolar Mac _WT

source_name: Alveolar Mac _WT

value: alveolar macrophages


title: AMF_Cre-_4

description: Alveolar Mac _WT


title: participant.51721.pre.training


title: participant.51761.pre.training


title: participant.51686.pre.training


title: KC_Cre-_2

description: Kupffer Cell_WT


title: AMF_Cre-_3

description: Alveolar Mac _WT


title: participant.51765.pre.training


title: AMF_Cre-_2

description: Alveolar Mac _WT


title: participant.51684.pre.training


title: participant.51685.pre.training


title: participant.51571.pre.training


title: participant.51681.pre.training


title: participant.51762.pre.training


title: participant.50704.pre.training


title: AMF_Cre+11b+_5

description: Zeb2KO Alveolar Mac (CD11b+)

source_name: Zeb2KO Alveolar Mac (CD11b+)


title: AMF_Cre-_1

description: Alveolar Mac _WT


title: AMF_Cre+11b+_4

description: Zeb2KO Alveolar Mac (CD11b+)


title: AMF_Cre+11b-_5

description: Zeb2KO Alveolar Mac (CD11b-)

source_name: Zeb2KO Alveolar Mac (CD11b-)


title: AMF_Cre+11b+_3

description: Zeb2KO Alveolar Mac (CD11b+)


title: participant.51463.pre.training


title: participant.51242.pre.training


title: participant.50701.pre.training


title: participant.51461.pre.training


title: participant.51464.pre.training


title: AMF_Cre+11b-_3

description: Zeb2KO Alveolar Mac (CD11b-)


title: AMF_Cre+11b-_4

description: Zeb2KO Alveolar Mac (CD11b-)


title: AMF_Cre+11b+_2

description: Zeb2KO Alveolar Mac (CD11b+)


title: participant.51241.pre.training


title: participant.51465.pre.training


title: AMF_Cre+11b-_2

description: Zeb2KO Alveolar Mac (CD11b-)


title: AMF_Cre+11b-_1

description: Zeb2KO Alveolar Mac (CD11b-)


title: participant.51222.pre.training


title: participant.51223.pre.training


title: AMF_Cre+11b+_1

description: Zeb2KO Alveolar Mac (CD11b+)


title: participant.51201.pre.training


title: participant.50673.pre.training


title: participant.50953.pre.training


title: MDA-MB-231-shCEP55#2

type: genomic

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: Illumina Protocol

scan_protocol: Arrays were scanned using an iScan (Illumina).

data_processing: SNP arrays data was processed using the Genotyping module (v1.9.4) in GenomeStudio v2011.1 (Illumina, San Diego CA) to calculate B-allele frequencies (BAF) and logR ratios.

source_name: cell line

label_protocol: SNP array analysis (Omni2.5M BeadChips, Illumina) was performed according to the manufacturer’s protocol using 200 ng of DNA.

growth_protocol: The breast cancer cell lines used in this study were purchased from the American Type Culture Collection (ATCC), otherwise stated in acknowledgment, cultured and maintained as per ATCC recommendations and as described previously (Anderson et al, 2017).

extract_protocol: Qiagen Allprep Kit

treatment_protocol: Doxycycline-inducible shCEP55 MDA-MB-231-luc cells were established using the lenti viral Invitrogen BLOCK-iTTM Pol II miR RNAi Expression vector kit (Life Technologies). Two different CEP55 shRNAs with its respective scrambled shRNA sequences were used as shown below. Knockdown cells were selected using 50 μg/mL Zeocin and 5 μg/mL Blastocydin.

value: CEP55 knockdown


title: MDA-MB-231-shCEP55#8


title: MDA-MB-231-shCEP55#8_B2


title: MDA-MB-231-ShSCR_B2

value: control (scramble control)


title: MDA-MB-231-ShSCR


title: MDA-MB-231-HM5_shCEP55


title: participant.50954.pre.training


title: MDA-MB-231-HM5_shSCR


title: participant.50961.pre.training


title: MDA-MB-231-shCEP55#2_B2


title: participant.50926.pre.training


title: participant.50955.pre.training


title: participant.50903.pre.training


title: participant.50963.pre.training


title: participant.50924.pre.training


title: participant.51221.pre.training


title: DLBCL Sample 17

city: Naestved

first: Steffen

last: Jørgensen

address: Parkvej 190

country: Denmark

institute: absalon university college

description: Test

data_processing: File non-normalized_data.txt represents raw cq values.   Values were normalized to miR-23a using the deltadelta ct method.  The ΔΔCt was transformed to fold change using the equation 2-ΔΔCt

label: SYBR Green

source_name: Plasma

label_protocol: Four μl of purified total RNA was reverse transcribed in 20-μL-reactions using the Universal cDNA Synthesis Kit II and the UniSP6 spike-in (Exiqon). Conditions for reverse transcription reaction were incubation at 42°C for 60 minutes followed by five minutes at 95°C. The resulting cDNA was subsequently diluted 60 times in the ExiLENT SYBR® Green master mix (Exiqon) and assayed in 10 μL reactions according to the manufacturer's instruction. As inter-plate calibrator we used UniSP3 oligonucleotide. Relative quantitative real-time PCR was performed using the LightCycler 480 and the LightCycler 480 software, version 1.5 (Roche Applied Biosciences). RT-PCR conditions were incubation at 95°C for 10 minutes followed by 45 cycles of 95°C for 10 seconds and 60°C for one minute.

extract_protocol: plasma total RNA purified using the  miRNeasy Serum/Plasma Kit (Qiagen, cat. No. 217184)

value: Plasma

value: DLBCL


title: DLBCL Sample 16

description: Test


title: participant.50904.pre.training


title: DLBCL Sample 15

description: Test


title: MCF10A_EV

value: control (empty vector)


title: MCF10A_FlagCEP55#C17

value: CEP55 overexpression


title: DLBCL Sample 14

description: Test


title: DLBCL Sample 13

description: Test


title: participant.50921.pre.training


title: participant.51725.pre.training


title: participant.51746.pre.training


title: DLBCL Sample 12

description: Test


title: DLBCL Sample 11

description: Test


title: DLBCL Sample 7

description: Test


title: participant.50905.pre.training


title: DLBCL Sample 6

description: Test


title: DLBCL Sample 10

description: Test


title: DLBCL Sample 8

description: Test


title: DLBCL Sample 9

description: Test


title: Col-H3K4me3

city: Madison

first: Christine

last: Wooddell

state: WI

address: 502 S Rosa Rd

institute: Arrowhead Pharmaceuticals

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.bedtools was used to generate bedGraph file; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: ChIP-seq (BigWig file)

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown in soil at 22 degree under long day (16 hrs light) or short day (8 hrs light) conditions .

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850. H3 and H3K4me3 antibody is from Millipore (04-745).
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330).

tag: ecotype

value: Wild type

value: Aerial tissue

tag: molecule subtype

value: Genomic DNA isolated from immunoprecipitated chromatin using H3K4me3 antibody

tag: chip antibody

value: H3K4me3 (Millipore, catalog# 04-745, Lot# 2739249)


title: DLBCL Sample 5

description: Test


title: DLBCL Sample 4

description: Test


title: DLBCL Sample 2

description: Test


title: Col-H3

value: Genomic DNA isolated from immunoprecipitated chromatin using H3 antibody

value: H3 (Abcam, catalog# ab1791, lot# GR3188868-1)


title: DLBCL Sample 3

description: Test


title: DLBCL Sample 1

description: Test


title: participant.51574.pre.training


title: ZDB475 As+P rep3

city: Hangzhou

first: Gerald

last: Zvobgo

state: Zhejiang

address: Yuhang

department: Crop Science

institute: Zhejiang University

description: wild type barley

data_processing:
Sequencing read filtering was done using SOAPnuke software
Genome mapping was done using HISAT to align RNA-seq reads to the barley genome
Novel transcript, SNP and indel detection was done using StringTie and Cuffcompare
Gene ontology and pathway analysis of differentially expressed genes were done using Blast2GO
Transcription factor prediction was done by aligning the open reading frame to the transcription factor domain using hmmsearch.
Genome_build: http://webblast.ipk-gatersleben.de/barley_ibsc/downloads/
Supplementary_files_format_and_content: text files contain fpkm for genes per each sample

organism: Hordeum vulgare

source_name: Barley

growth_protocol: Ten-days-old seedlings were transplanted into 1L plastic pots for hydroponic culture, with the basic nutrient solution. The BNS was renewed every 5 d. Initially the plants were supplied with half strength BNS for 7d thereafter full strength was supplied. At three-leaf stage As and P treatments were performed by adding Na2HasO4 and Na2HPO4 into the BNS, respectively to form 100 µM As and50 µM P.

extract_protocol:
For total RNA extraction, roots of 10 seedlings were collected and mixed together after 24 h of treatments. RNA extraction was done for 18 samples [2 genotypes × 3 treatments × 3 replicates] with TRIzol reagent following manufacturer instructions
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: At three-leaf stage As and P treatments were performed by adding Na2HasO4 and Na2HPO4 into the basic nutrient solution, respectively to form 100 µM As and 50 µM P.

tag: cultivar

value: root

tag: phenotype

value: Arsenic sensitive


title: Control 14

description: Control

value: Control


title: ZDB475 As+P rep2

description: wild type barley

tag: age


title: participant.51576.pre.training

value: pre-training


title: ZDB475 As+P rep1

description: wild type barley


title: ZDB475 As rep3

description: wild type barley


title: EBSΔC-H3K4me3-Rep1

description: pEBS::EBSΔC-FLAG transformed into ebs mutant background

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850. FLAG antibody is from Sigma company (A8592). H3K4me3 antibody is from Millipore (04-745).
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330).

value: ebs mutant

tag: transformed with

value: Genomic DNA isolated from immunoprecipitated chromatin using FLAG antibody (Sigma)


title: EBSΔC-H3K4me3-Rep2


title: Control 13

description: Control


title: participant.51745.pre.training


title: ZDB475 As rep2

description: wild type barley


title: participant.50672.pre.training


title: participant.50902.pre.training


title: MSC derived from 201B7 via mesoderm (PSP-MSC)

city: kumamoto

first: Shinya

last: Eto

address: honjo 2-2-1

institute: Kumamoto univercity

description: MSC derived from 201B7 via mesoderm

hyb_protocol: Biotin labelling samples were hybridized to a GeneChip® Human Genome U133 Plus 2.0 (Affymetrix).

scan_protocol: the arrays were scanned by a GeneChip® Scanner 3000 (Affymetrix)

data_processing: the array data were analyzed with GeneSpring GX 12.5 software (Agilent technologies)

source_name: mesenchymal stem cell derived from human iPS

label_protocol: We isolated 200 ng of total RNA from the N1-12 iPSCs, BM-MSCs (PRC-010; Bay bioscience), PSP-MSC, and RA-Pα-MSC derived from N1-12 and 201B7 for biotin labeling and fragmentation according to the manufacturer’s protocol.

growth_protocol: Human iPSCs were cultured with mitomycin C-treated mouse embryonic fibroblast feeder cells in human iPSC medium containing Dulbecco's modified Eagle’s.  BM-MSC and MSC derived from human iPSC were cultured with alpha modification of Eagle's medium (αMEM) (Gibco) supplemented with 10% FBS and 0.1 mM 2-ME in type IV collagen-coated dishes (Corning)medium: nutrient mixture F-12 (DMEM/F12) (SIGMA) supplemented with 20% KnockOut serum replacement (KSR, Invitrogen), 0.1 mM 2-mercaptoethanol (2-ME) (SIGMA), 2 mM L-glutamine (Life Technologies), 0.1 mM nonessential amino acids (NEAA, SIGMA), 0.5% penicillin and streptomycin (Nacalai Tesque, Japan), and 5 ng/ml basic fibroblast growth factor (bFGF, WAKO, Japan)

extract_protocol: Total RNAs was purified by Sepasol® Super G reagent (Nacalai Tesque, Japan).

treatment_protocol: human iPSCs Cells were harvested by treatment with CTK [1 mg/ml collagenase type IV (Invitrogen), 0.25% trypsin (Difco) and KSR]. BM-MSC and MSC derived from human iPS were harvested by TrypLE express (Gibco)

tag: cell

value: MSC derived from human iPSC


title: MSC derived from N1-12 via neuroepithelia (RA-Pa-MSC)


title: BM-MSC

description: BM-MSC

source_name: mesenchymal stem cell derived from human bone marrow

value: human BM-MSC


title: Control 12

description: Control

value: Plasma


title: MSC derived from 201B7 via neuroepithelia (RA-Pa-MSC)


title: N1-12 iPS

description: N1-12 iPSC

source_name: iPS derived from fibroblast (N1-12)

value: human iPSC


title: Control 11

description: Control


title: Control ZDB475 rep3

description: wild type barley


title: ZDB475 As rep1

description: wild type barley


title: EBS-H3K4me3-Rep1

description: pEBS::EBS-FLAG transformed into ebs mutant background


title: Control ZDB475 rep2

description: wild type barley


title: Control ZDB475 rep1

description: wild type barley


title: EBSΔC-FLAG-Rep2

source_name: EBSΔC-FLAG


title: P2

city: Chengdu

first: Jie

last: Luo

state: Sichuan

address: Huimin road

department: College of Animal Science and Technology

institute: Sichuan Agricultural University

data_processing:
Initial sequence was subjected to a series of stringent filters (such as removing low quality-reads, repeated sequences and adaptor sequences) and the output was called clean data. Filtered sequences then were mapped to carp reference genome with stringent criteria.
For each sample, counts were first normalized by the total count of mappable reads which is denoted as reads per million (RPM).
Genome_build: Genome database:Cyprinus carpio:common carp genome (assembly GCF_000951615.1); miRbase release 21
Supplementary_files_format_and_content: Identified miRNAs in each library with count reads and normalized data

organism: Cyprinus carpio

source_name: miRNA from liver tissue of common carp fed with duckweed(P)

growth_protocol: Fish are all from the same batch (body weight 517.8 ±50g) and were randomly divided into three groups (n = 90 for each group), set two repetitions in each group.The three groups were group A (animal bait: earthworm), group M (mixed diets: earthworm : duckweed by weight ratio of 1:1), group P (plant diet: duckweed). The trial was operated in a circulating aquarium system with a 21 ± 1 °C of natural photoperiod for 2 weeks training. Fish were fed thrice a day at 9:00, 13:00 and 17:00. The daily feeding rate is 4% of its body weight. In order to ensure the group M were fed with adequate amount of earthworm + duckweed (1:1), we fed the 1/2 total amount of earthworm at first, we fed 1/2 duckweed after 10 minutes, we fed 4 times at each time point, the group A and group P also followed same feeding schedule.After two weeks temporary rearing, all fish were fasted for 24h and the formal trial was starting and lasted for 56 days.

extract_protocol:
RNA was harvested using Trizol reagent.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sampled after fasting for 24h, the fish were anesthetized with MS-222. Their livers were collected from three groups  and immediately snap-frozen in liquid nitrogen, stored at -80℃ until use.

tag: developmental stage

value: adult

tag: diet group

value: group P (plant diet:duckweed)

value: liver

value: microRNA


title: ZDB160 As+P rep3

description: cultivated barley

value: Arsenic tolerant


title: P1


title: EBS-H3K4me3-Rep2

value: Aerial tissue


title: EBSΔC-FLAG-Rep1


title: Control 10

description: Control


title: Control 9

description: Control


title: Control 8

description: Control


title: M2

source_name: miRNA from liver tissue of common carp fed with earthworm + duckweed(M)

value: group M (mixed diets:earthworm :duckweed by weight ratio of 1:1)


title: EBS-FLAG

source_name: EBS-FLAG


title: M1


title: ZDB160 As+P rep1

description: cultivated barley

value: root


title: ZDB160 As rep3

description: cultivated barley


title: HB9_c

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

data_processing:
Fastq files were imported into Partek Flow.
Quality analysis and quality control (QA/QC) were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
Trimmed reads were processed using the STAR v2.4.1d aligner and the hg38 genome to generate aligned and unaligned. STAR v2.4.1d unaligned reads were further analyzed using Bowtie 2 v2.2.5 and aligned reads were combined before quantifying to the ENSEMBL (release 82 v2) database by the Partek Expectation-Maximization (E/M) algorithm.
Data was exported as a txt matrix.
Genome_build: Hg38
Supplementary_files_format_and_content: .txt file reports normalized counts

source_name: HB9-transduced CD34+ cells

extract_protocol:
AllPrep DNA/RNA  kit
TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San 171 Diego, CA, USA) was used to prepare the barcoded libraries from 100ng total RNA.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on Bioanalyzer (Agilent, Böblingen, Germany); 7.5pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional 7 cycles for index reading.

treatment_protocol: transduction

tag: vector

tag: cell type

value: Cord blood-derived CD34+ cells


title: A2

source_name: miRNA from liver tissue of common carp fed with earthworm(A)

value: group A (animal bait:earthworm)

tag: tissue


title: Control 7

description: Control

tag: disease state

value: Control


title: Control 6

description: Control


title: A1


title: MSC derived from N1-12 via mesoderm (PSP-MSC)

description: MSC derived from N1-12 via mesoderm


title: HB9_b


title: ZDB160 As rep2

description: cultivated barley


title: HB9_a


title: ZDB160 As rep1

description: cultivated barley


title: Control 5

description: Control


title: ZDB160 As+P rep2

description: cultivated barley


title: Control ZDB160 rep3

description: cultivated barley


title: Control ZDB160 rep2

description: cultivated barley


title: Control ZDB160 rep1

description: cultivated barley


title: Control 2

description: Control


title: Control 4

description: Control


title: GFP_a

source_name: GFP-transduced CD34+ cells


title: Control 1

description: Control


title: Control 3

description: Control


title: GFP_b


title: GFP_c


title: cbMg TRAP 6mo Eed-ko rep 2

status: Public on Jul 13 2018

city: New York

first: Pinar

last: Ayata

state: New York

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mt Sinai

description:
processed data file: TRAP_rpkms.txt; X74.CB_S4
74-CB_S4

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Sequences were mapped using the TopHat2 package (v2.1.0)71.
Reads were counted using HTSeq-count (v0.6.0) against the Ensembl v67 annotation.
The read alignment, read counting, and quality assessment were done using SPEctRA.
The raw counts were processed through VST procedure using the DESeq2 package.
Genome_build: mm9
Supplementary_files_format_and_content: peaks, RPKM

source_name: cbMg TRAP 6mo Eed-ko

extract_protocol:
Microglial RNA was isolated from cerebellum using TRAP.
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

treatment_protocol: Mice were treated with Tamoxifen at 4-6 weeks of age.

tag: strain background

value: Cerebellar microglia


title: cbMg TRAP 6mo Eed-ko rep 1

description:
processed data file: TRAP_rpkms.txt; X70.CB_S3
70-CB_S3


title: cbMg TRAP 9mo Eed-ko rep 2

description:
processed data file: TRAP_rpkms.txt; X48.CB_S2
48-CB_S2

source_name: cbMg TRAP 9mo Eed-ko


title: cbMg TRAP 9mo control rep 2

description:
processed data file: TRAP_rpkms.txt; X52.CB_S2
52-CB_S2

source_name: cbMg TRAP 9mo control


title: cbMg TRAP 9mo control rep 1

description:
processed data file: TRAP_rpkms.txt; X50.CB_S1
50-CB_S1


title: stMg TRAP 9mo control rep 1

description:
processed data file: TRAP_rpkms.txt; X50.ST_S1
50-ST_S1

source_name: stMg TRAP 9mo control

extract_protocol:
Microglial RNA was isolated from striatum using TRAP.
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

value: Striatal microglia


title: cbMg TRAP 9mo Eed-ko rep 1

description:
processed data file: TRAP_rpkms.txt; X38.CB_S1
38-CB_S1


title: cbMg TRAP 6mo control rep 1

description:
processed data file: TRAP_rpkms.txt; X77.CB_S3
77-CB_S3

source_name: cbMg TRAP 6mo control


title: cbMg TRAP 6mo control rep 2

description:
processed data file: TRAP_rpkms.txt; X78.CB_S4
78-CB_S4


title: stMg TRAP 9mo control rep 2

description:
processed data file: TRAP_rpkms.txt; X52.ST_S2
52-ST_S2


title: stMg TRAP 6mo control rep 1

description:
processed data file: TRAP_rpkms.txt; X77.ST_S3
77-ST_S3

source_name: stMg TRAP 6mo control


title: pool sample of ileum collected on three high weight gain piglets (MLD025a-1)

city: Sherbrooke

first: Martin

last: Lessard

state: Qc

address: 2000 College

department: Sherbrooke Research Centre

country: Canada

institute: Agriculture and AgriFood Canada

hyb_protocol: genome Quebec platform protocol

scan_protocol: genome Quebec platform protocol

data_processing: using Flexarray software version 1.6.1

organism: Sus scrofa

source_name: ileum, three high weight gain piglets

label_protocol: genome Quebec platform protocol

growth_protocol: piglets were born from Yorkshire × Landrace sows inseminated with certified semen from Duroc boars provided by the Centre d’insémination porcine du Québec (St-Lambert de Lauzon, Quebec, Canada)

extract_protocol: ileum slices that were conserved in -80˚C were homogenized in buffer RLT supplemented with β-mercaptoethanol (Qiagen, Toronto, Canada) using a KINEMATICA Polytron homogenizer (Thermo Fisher Scientific, Mississauga, ON). Total RNA was extracted with RNeasy Plus mini kit (Qiagen) following the manufacturer’s recommendations and was eluted in 50 μl of water. Contaminating DNA from RNA preparations was removed with DNA-free™ DNase Treatment and Removal Reagents kit according to manufacturer instructions (Thermo Fisher Scientific, Life technologies, Mississauga, ON).

treatment_protocol: piglets were fed from lactating sows

value: ileum slice

value: 16 days

tag: weight

value: high weight gain


title: stMg TRAP 6mo control rep 2

description:
processed data file: TRAP_rpkms.txt; X78.ST_S4
78-ST_S4

tag: genotype/variation


title: pool sample of ileum collected on 2 low weight gain piglets (MLD026a-1)

source_name: ileum, 2 low weight gain piglets

value: low weight gain


title: Control 2 [Mars-seq]

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

data_processing:
Bcl files were converted into fastq by bcl2fastq v2.17.1.14. Demultiplexing is done using the sample barcode found on R2, the UMI found on R2 is inserted in the read name (in R1 fastq).
Adapters and low quality bases were removed from the raw reads using cutadapt version 1.8.3 (parameters -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a "A{100}" -a "T{100}" --times 2 -q 20  -m 30 )
The remaining reads (raw data submitted)  were mapped to mm10 (igenomes) using STAR.
Read counts per gene were calculated using HTSeq-count and a Refseq gtf file (downloaded from igenomes), which was modified to contain a window surrounding the 3' UTR.
Genes were filtered out if thier sum counts   <=5 .  Normalization and differential expression analysis was performed using the DESeq2 R-package (Bioconductor, https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: contains normalized DESeq2 counts (not UMI counts)

source_name: Mouse embryonic fibroblasts

growth_protocol: MEFs were grown in standard growth condition in 10 cm plates

extract_protocol:
Cell lysates were thawed and messanger RNA was captured with 15ul of NEB oligo(dT) beads, and washed according to manufacture guidelines.
Purified messanger RNA was eluted at 70C with 60ul of 10mM Tris-Cl pH 7.5 and stored at -80C.For library preparation RNA was used for the bulk MARS-seq  protocol (Jaitin et al. 2014 Science.343:776-9). MARS-seq libraries were sequenced using Illumina NextSeq 500 High Output v2 Kit (75 cycles).

treatment_protocol: Si-RNA [Si-Negative control or Si-eIF1A (X+18)] tranfection was performed using Lipofectamine RNAimax

value: fibroblasts

tag: passage

value: passages 5-8

tag: treatment

value: Si-Negative control transfection


title: eIF1A KD1 [Mars-seq]

value: Si-eIF1A (X+18) transfection


title: Control 1 [Mars-seq]


title: eIF1A KD2 [Mars-seq]


title: pool sample of ileum collected on 2 low weight gain piglets (MLD026b-1)


title: stMg TRAP 6mo Eed-ko rep 2

description:
processed data file: TRAP_rpkms.txt; X74.ST_S4
74-ST_S4

source_name: stMg TRAP 6mo Eed-ko


title: pool sample of ileum collected on three high weight gain piglets (MLD025b-1)


title: stMg TRAP 6mo Eed-ko rep 1

description:
processed data file: TRAP_rpkms.txt; X70.ST_S3
70-ST_S3


title: stMg TRAP 9mo Eed-ko rep 2

description:
processed data file: TRAP_rpkms.txt; X48.ST_S2
48-ST_S2

source_name: stMg TRAP 9mo Eed-ko


title: stMg TRAP 9mo Eed-ko rep 1

description:
processed data file: TRAP_rpkms.txt; X38.ST_S1
38-ST_S1


title: eIF1A KD2 [Ribo-Seq]

description: Ribosome protected RNA

data_processing:
Library strategy: Ribo-seq
Removing first base and adapter and keeping only sequences of length 20 to 50 (initial length 61) that had adapter, no trimming by quality.   cutadapt -a CTGTAGGCACCATCAATAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --discard-untrimmed --times 1 -u 1 -m 20 -M 50
rRNA removal was done by bowtie to make fastq file with non-RNA sequences (bowtie run with parameter norc)
Filtering for  reads of length 28-33  using cutadapt (-m 28 -M 33)
Mapping the reads to mm10 mouse using TopHat2  with parameters : --no-novel-juncs --library-type fr-firststrand
UTR and CDS gtf files were created from refseq gtf file, avoiding regions found in both files. HTSeq was used for the quantification (parameters -s yes -t exon -m intersection-nonempty). The option intersection-nonempty allows to assign junction reads to either the CDS or UTR, depending where most of read is placed.
Counts presented were normalized with DESeq2 (normalization was computed for the sum 5' UTR and CDS)
Genome_build: mm10
Supplementary_files_format_and_content: Ribo-Seq norm counts

extract_protocol:
cell lysate was treated with Rnase I followed by ultracentrifugation according to Ingolia et al. 2012
purified RNA was processed to make ribosome profiling liberaries (Ingolia et al. 2012). Ribo-seq libraries were sequenced on HiSeq2500 High-Output instrument (Illumina) to yield 60 bp single-end reads


title: P50_WT_Tail_Dermis_RNAseq

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
For analysis, raw transcriptome sequence data were mapped to the mouse genome (GRCm38/mm9) using TopHat (v2.0.13) with default settings to produce a reference-guided transcript assembly.
Cufflinks (v2.2.1) was used to normalize expression levels for each sample to fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: GRCm38/mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: skin

extract_protocol:
Total RNA was isolated from FACS-purified cells lysed with Trizol (Life Techologies) followed by extraction using a direct-Zol RNA mini prep kit (Zymo research). For cDNA synthesis, equal amounts of RNA were added to re¬verse-transcriptase reaction mix (Vazyme, R222-01).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Wt/Wt

value: post natal day 50

value: skin


title: Control 2 [Ribo-Seq]

description: Ribosome protected RNA


title: eIF1A KD1 [Ribo-Seq]

description: Ribosome protected RNA


title: Control 1 [Ribo-Seq]

description: Ribosome protected RNA


title: Dropseq P30

city: Cincinnati

first: Mike

last: Adam

state: Ohio

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

data_processing:
Read2 was aligned with bowtie2-2.2.7 using the -k 1 option
The aligned reads were tagged with their corresponding UMI and barcode from read1
Each aligned read was tagged with its gene name
An expression matrix was generated by counting the number of unique UMIs per gene per cell
Reads were normalized by dividing the read count of each gene by the total number of reads per cell and multiplying by 10000
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited gene counts per cell

source_name: Heart Valve

extract_protocol:
Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol

value: Heart Valve


title: Dropseq P7


title: DY11T3

city: Stanford

first: Dian

last: Yang

address: B261 Beckman Center, 1291 Welch Rd.

institute: Stanford University

data_processing:
We used Kallisto (Bray et al. 2016) to quantify expression. We kept only transcripts with max TPM value greater than 1 in at least one sample and with standard deviation greater than 1.
We performed the asinh() transformation to variance stabilize the data.
We used SVA (Leek & Storey 2007) to remove batch effects from the data.
fit a linear model (lmFit in R) modeling metastatic effect
rank genes in order of evidence for differential expression using an empirical Bayes method. We only compared genes with non-zero variance.
Genome_build: mm10
Supplementary_files_format_and_content: CMV_samples_TPM_pre_Merge.txt (Batch1_CMV TKO tumor samples TPM)
CGRP _samples_TPM_pre_Merge.txt (Batch2_CGRP TKO tumor samples TPM)
comp1_CMV_primary_v_CMV_met_data_corrected_no_sva_top_hits.txt (CMV_primary_tumor_vs_CMV_metastasis)
comp2_CMV_primary_v_CGRP_primary_data_corrected_no_sva_top_hits.txt (CMV_primary_tumor_vs_CGRP_primary_tumor)
comp3_CMV_primary_v_CGRP_all_data_corrected_no_sva_top_hits.txt (CMV_primary_tumor_vs_CGRP_all_tumors(primary+met))
comp4_CGRP_primary_tumor_vs_coo_metastasis_data_corrected_no_sva_top_hits.txt (CGRP_primary_v_CGRP_met)

source_name: primary tumor from the CMV TKO model

growth_protocol: All murine SCLC samples are prepared fresh from tumor bearing mice

extract_protocol:
Qiagen Allprep DNA/RNA kit
[Reverse transcription and amplification protocol] Nugen Ovation v2 kit
Illumina TruSeq v2 kit

value: lung tumor

tag: genotype

tag: expression vector

value: Ad-CMV-Cre


title: DY4T1


title: DY4T2


title: DY9T1


title: DY53N1

source_name: lymph node metastasis from the CMV TKO model

value: lymph node metastasis


title: DY53Lm

value: liver metastasis


title: DY2T1_R2

description: technical replicate, merge with DY2T1 during analysis


title: DY53L1

source_name: liver metastasis from the CMV TKO model


title: DY5L2


title: DY11N1


title: Control.1 [RISC-IP long RNA]

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

institute: IRCCS-Policlinico San Donato

description:
RNA-Seq of long RNA from control IP samples.
processed data file: mRNA_counts.txt

data_processing:
Raw reads in FASTQ files were trimmed of adapters and low quality sequences using Trimmomatic.
Trimmed successfully passing the trimming procedure were aligned to human reference genome hg19 using BWA.
Aligned reads were counted on human hg19 reference annotation using HTSeq-count.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: mRNA_counts.txt: Tab-delimited text file containing the output from HTSeq-Counts counting procedure, one gene per row and one sample per column.

source_name: Biceps Brachii

extract_protocol:
Two lysis protocols were used: 1) skeletal muscle biopsies were cut into small pieces in RIP lysis buffer (Magna RIP Kit, Merck-Millipore, Burlington, MA) and homogenized by TissueLyser (Qiagen, Hilden, Germany); 2) Cultured cells were lysed with the following buffer: 150mM KCl, 25 mM TrisHCl pH 7.4, 5 mM EDTA, 0.5% NP40, 5 mM DTT, 1 mM PMSF, protease and RNase inhibitors. For both lysates, homogenates were quantified for protein content, snap frozen in liquid nitrogen and stored at -80°C until use. For both muscle tissue and cells, 1 mg of lysate was immunoprecipitated with anti-Ago2 or control mouse IgG antibodies (RIPAb+ Ago2, Merck-Millipore, Burlington, MA), using 5 ug of antibody for 1 mg of lysate. Immunoprecipitation was performed using the Magna RIP Kit (Merck Millipore, Burlington, MA) following the manufacturer’s instructions. IgG-bound RNA (IP RNA) was extracted from magnetic beads using TRIzol reagent (Invitrogen, ThermoFisher Scientific, Waltham, MA).
Extraction, ribodepletion and library preparation were performed following manufacturer's instructions for the Nugen OVATION RNA-Seq System V2 and Nugen OVATION Ultralow Library Systems.

tag: disease status

value: Myotonic dystrophy-1 (DM1)

value: Biceps brachii

tag: antibody

value: Control mouse IgG


title: DY5L1


title: DY2L2_R2

description: technical replicate, merge with DY2L2 during analysis


title: DY9N1


title: DY53T1


title: DY11T2


title: DY4T4


title: DY53T3


title: DY9Lm


title: DY5T4


title: DY9T2


title: DY5N1


title: DY5T2


title: DY5T1


title: DY2L2


title: DY2L1


title: DY2N1


title: DY2T3


title: DY53T2


title: DY2T2


title: DY2T1


title: cerebellum single nuclei RNA rep 27

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb88
Cb_M88_TAGGCATGTATCCTCT_L002

data_processing:
Raw sequencing data was processed using Illumina bcl2fastq2 Conversion Software v2.17.
Single end cDNA .fastq files were aligned using STAR (2.4.0a).
Aligned reads were mapped using featureCounts from the subread package (1.4.4)
Negative binomial model was implemented in edgeR (3.10.0) for single cell differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: peaks, RPKM

source_name: cerebellum single nuclei RNA

extract_protocol:
Microglial nuclei were isolated using FACS. RNA was obtained from single nuclei using Fluidigm C1™ System
cDNA was prepared suing using SMARTer® Ultra™ Low RNA Kit for the Fluidigm C1™ System. Libraries were constructed using Nextera XT DNA Sample Preparation Kit.

tag: age

value: Cerebellar microglia


title: cerebellum single nuclei RNA rep 24

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb82
Cb_M82_TAGGCATGCTCTCTAT_L002


title: POL-Seq, CTRL cells, rep 2

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

institute: University of Trento

description: processed data file: HuD_TOTPOL_counts.txt

data_processing:
CRAC: adapter removal and collapse of duplicate reads (also with identical random barcode, marking PCR duplicates) were performed with hyb (https://github.com/gkudla/hyb). Reads were aligned to the mouse genome (GRCm38.p4) with Tophat (version 2.0.14), using the Gencode M6 transcript annotation as transcriptome guide. In order to detect CRAC binding sites, we developed and implemented a dedicated computational methodology (MAPAS, standing for Mutation And PWM Assisted Search) that takes advantage of cross-linking induced mutations, consisting primarily in deletions in our experiment, in order to localize candidate binding sites (similar in this step to CIMS, (Zhang and Darnell, 2011). After the integration of replicates, to increase specificity, we penalized locations with aligned reads and deletions in control experiments (noise subtraction and removal). For each of the remaining locations, we calculated a combined p-value based on a) the number of deletions, b) the number of aligned reads (coverage). P-values were empirically calculated from the genome-wide experimental distributions of coverage and number of deletions. Coverage and deletion p-values were combined with the Fisher method.  A pool of 753 sequences surrounding unique genomic locations with a combined p-value < 0.05 were selected to build a PWM (Positional Weight Matrix), hence used as a “seed” matrix to score to all the other candidate binding sites. To create the seed PWM, we defined a region spanning seven nucleotides around the deletion site. PWM analysis was performed with functions implemented in the Biostrings R package. The seed PWM was used to score all deletion sites and select high-confidence HuD bound sites. A PWM score threshold was chosen, based on the 95 percentile of scores obtained from random heptamers. HuD “high confidence” binding sites were selected among those with i) PWM score > PWM score threshold, ii) number of HuD deletions >= 3 (at least one for replicate), iii) number of aligned reads >= 6 (at least two for replicate).    POL-Seq and RNA-Seq: after quality control (FastQC) reads generated from each sample were aligned to the mouse genome (GRCm38.p4) with STAR (version 2.5.3a, --quantMode TranscriptomeSAM GeneCounts), using the Gencode M6 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of genes with altered TE upon HuD overexpression were performed with the edgeR package.    3'end mRNA sequencing: after quality control (FastQC), reads generated from each sample were aligned to the mouse genome (GRCm38.p4) with STAR (version 2.5.3a, --quantMode TranscriptomeSAM GeneCounts), using the Gencode M6 transcript annotation as transcriptome guide. Polyadenylation site usage (pAu) values were determined counting the number of reads starting within 10 nucleotides from known polyadenylation sites. Normalization and differential polyadenylation analysis were performed with the edgeR package.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: HuD_APA_counts.txt: tab-delimited text file including transcript annotations (columns 1-10) and sample-specific counts of aligned reads starting within 10 nucleotides from the polyadenylation site.   HuD_RNA_interactome.txt: tab-delimited text file of HuD bound exonic RNA regions. The file contains the genomic coordinates (columns 1-4), binding analysis and annotation of the regions.  HuD_TOTPOL_counts.txt: tab-delimited text file including gene annotations (columns 1-7) and sample-specific counts of aligned reads.

growth_protocol: NSC-34 cells were grown in DMEM medium with 10% FBS, 100 U/ml penicillin streptomycin and 0.01 mM L-glutamine

extract_protocol:
CRAC: growing cells were UV crosslinked on ice with λ = 254 nm in Stratalinker 1800 (Stratagene). The cells were lysed and treated with DNase (Promega M610A). Cell lysates were incubated with HA agarose beads (26181 Pierce). Ribonucleoprotein complexes on HA beads were trimmed with 0.5 unit RNaseA+T1 mix (RNace-IT, Stratagene 400720-81) and HuD-RNA complexes were eluted. The eluate was incubated with Ni-NTA Agarose (Ni-NTA Superflow 50% suspension IBA 2-3206-010). RNAs bound to HuD were radiolabelled with 32P-γ-ATP and 3′ miRCat-33 linker ligation was performed. Then RNA ligase 1 and barcoded 5′ linker were added and the reaction mixture HuD-RNA complexes were eluted by incubation with NuPage-Eluition buffer. Protein-RNA complexes were resolved on a 4%–12% Bis-TrisNuPAGE gel (Life Technologies, NP0335) in NuPAGE SDS MOPS running buffer (Life Technologies, NP0001) and transferred to nitrocellulose membrane (GE Healthcare, AmershamHybond ECL). Air-dried membrane was exposed on film o.n. and the radioactive bands corresponding to the HuD complexes were cut out.    POL-Seq and RNA-Seq: cells were treated with cycloheximide and then lysed in 300μl of cold lysis buffer. The lysate was centrifuged at 4 °C for 5min at 20.000 g to pellet cell debris. The cytoplasmic lysates loaded on a linear 15–50% [w/v] sucrose gradient and centrifuged in a SW41Ti rotor (Beckman) for 1 h 40 min at 180.000 g at 4 °C in a Beckman Optima™ Optima XPN-100 Ultracentrifuge. Fractions of 1 ml of volume, were then collected monitoring the absorbance at 254 nm with the UA-6 UV/VIS detector (Teledyne Isco). Sucrose fractions corresponding to polysomes and total RNA were pooled together and the RNA was extracted with phenol/chloroform.    3'end mRNA sequencing: RNAs were isolated using Trizol reagent (Life Technologies) following the manufacturer’s instructions.
CRAC: RNA was extracted and reverse transcribed. cDNA was amplified and PCR products were precipitated, resuspended and separated on a 2.5% MetaPhoragarose (Lonza). After purification with Gel Extraction Kit with MinElute columns (QIAGEN) the samples were sequenced on Illumina HiSeq 2000 platform.     POL-Seq and RNA-Seq:  libraries were prepared with the Illumina TruSeq mRNA stranded Kit. Samples were sequenced on Illumina HiSeq 2500 platform.    3'end mRNA sequencing: libraries were prepared with the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit REV. Samples were sequenced on Illumina HiSeq 2500 platform.

treatment_protocol: CRAC: Trex-HuD NSC-34 and control Trex NSC-34 cells were induced for human HuD production with 10 μg/ml Tetracycline for 24 h.   POL-Seq, RNA-Seq and 3'end sequencing: Trex-HuD NSC-34 were induced for human HuD production with 2 μg/ml Tetracycline for 48 h.

tag: cell line

tag: sequencing method

value: POL-Seq

tag: condition

value: control


title: RNA-Seq, HuD induced cells, rep 2

value: RNA-Seq

value: HuD induced


title: POL-Seq, CTRL cells, rep 1


title: POL-Seq, HuD induced cells, rep 1


title: 3'end mRNA-Seq, CTRL cells, rep 3

description: processed data file: HuD_APA_counts.txt

value: 3'end mRNA-Seq


title: 3'end mRNA-Seq, HuD induced cells, rep 1

description: processed data file: HuD_APA_counts.txt


title: 3'end mRNA-Seq, CTRL cells, rep 2

description: processed data file: HuD_APA_counts.txt


title: cerebellum single nuclei RNA rep 26

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb87
Cb_M87_GGACTCCTTATCCTCT_L002


title: cerebellum single nuclei RNA rep 23

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb81
Cb_M81_GGACTCCTCTCTCTAT_L002


title: cerebellum single nuclei RNA rep 25

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb86
Cb_M86_TCCTGAGCTATCCTCT_L002


title: RNA-Seq, HuD induced cells, rep 1


title: 3'end mRNA-Seq, CTRL cells, rep 1

description: processed data file: HuD_APA_counts.txt


title: cerebellum single nuclei RNA rep 22

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb77
Cb_M77_TAAGGCGACTCTCTAT_L002


title: 3'end mRNA-Seq, HuD induced cells, rep 3

description: processed data file: HuD_APA_counts.txt


title: 3'end mRNA-Seq, HuD induced cells, rep 2

description: processed data file: HuD_APA_counts.txt


title: cerebellum single nuclei RNA rep 19

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb74
Cb_M74_TCCTGAGCTAGATCGC_L002


title: cerebellum single nuclei RNA rep 20

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb75
Cb_M75_GGACTCCTTAGATCGC_L002


title: cerebellum single nuclei RNA rep 21

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb76
Cb_M76_TAGGCATGTAGATCGC_L002


title: cerebellum single nuclei RNA rep 17

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb71
Cb_M71_TAAGGCGATAGATCGC_L002


title: cerebellum single nuclei RNA rep 29

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb92
Cb_M92_TCCTGAGCAGAGTAGA_L002


title: cerebellum single nuclei RNA rep 28

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb89
Cb_M89_TAAGGCGAAGAGTAGA_L002


title: RNA-Seq, CTRL cells, rep 1


title: RNA-Seq, CTRL cells, rep 2


title: POL-Seq, HuD induced cells, rep 2


title: cerebellum single nuclei RNA rep 16

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb70
Cb_M70_GGACTCCTAGAGTAGA_L001


title: cerebellum single nuclei RNA rep 15

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb68
Cb_M68_AGGCAGAAAGAGTAGA_L001


title: cerebellum single nuclei RNA rep 14

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb65
Cb_M65_TAGGCATGTATCCTCT_L001


title: cerebellum single nuclei RNA rep 13

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb63
Cb_M63_TCCTGAGCTATCCTCT_L001


title: cerebellum single nuclei RNA rep 11

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb61
Cb_M61_CGTACTAGTATCCTCT_L001


title: cerebellum single nuclei RNA rep 18

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb73
Cb_M73_AGGCAGAATAGATCGC_L002


title: cerebellum single nuclei RNA rep 10

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb60
Cb_M60_TAAGGCGATATCCTCT_L001


title: cerebellum single nuclei RNA rep 6

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb55
Cb_M55_CGTACTAGCTCTCTAT_L001


title: cerebellum single nuclei RNA rep 3

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb50
Cb_M50_AGGCAGAATAGATCGC_L001


title: cerebellum single nuclei RNA rep 8

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb58
Cb_M58_GGACTCCTCTCTCTAT_L001


title: striatum single nuclei RNA rep 34

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St94
St_M94_TAGGCATGAGAGTAGA_L001

source_name: striatum single nuclei RNA

value: Striatal microglia


title: cerebellum single nuclei RNA rep 1

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb48
Cb_M48_TAAGGCGATAGATCGC_L001


title: cerebellum single nuclei RNA rep 2

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb49
Cb_M49_CGTACTAGTAGATCGC_L001


title: cerebellum single nuclei RNA rep 12

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb62
Cb_M62_AGGCAGAATATCCTCT_L001


title: striatum single nuclei RNA rep 33

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St93
St_M93_GGACTCCTAGAGTAGA_L001


title: cerebellum single nuclei RNA rep 5

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb53
Cb_M53_TAGGCATGTAGATCGC_L001


title: cerebellum single nuclei RNA rep 7

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb57
Cb_M57_TCCTGAGCCTCTCTAT_L001


title: striatum single nuclei RNA rep 28

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St85
St_M85_AGGCAGAATATCCTCT_L001


title: cerebellum single nuclei RNA rep 4

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb51
Cb_M51_TCCTGAGCTAGATCGC_L001


title: striatum single nuclei RNA rep 29

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St86
St_M86_TCCTGAGCTATCCTCT_L001


title: striatum single nuclei RNA rep 31

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St90
St_M90_CGTACTAGAGAGTAGA_L001


title: striatum single nuclei RNA rep 27

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St84
St_M84_CGTACTAGTATCCTCT_L001


title: striatum single nuclei RNA rep 23

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St79
St_M79_AGGCAGAACTCTCTAT_L001


title: striatum single nuclei RNA rep 26

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St83
St_M83_TAAGGCGATATCCTCT_L001


title: striatum single nuclei RNA rep 24

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St81
St_M81_GGACTCCTCTCTCTAT_L001


title: striatum single nuclei RNA rep 21

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St75
St_M75_GGACTCCTTAGATCGC_L001


title: striatum single nuclei RNA rep 30

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St88
St_M88_TAGGCATGTATCCTCT_L001


title: striatum single nuclei RNA rep 22

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St77
St_M77_TAAGGCGACTCTCTAT_L001


title: striatum single nuclei RNA rep 25

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St82
St_M82_TAGGCATGCTCTCTAT_L001


title: cerebellum single nuclei RNA rep 9

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; Cb59
Cb_M59_TAGGCATGCTCTCTAT_L001


title: striatum single nuclei RNA rep 32

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St92
St_M92_TCCTGAGCAGAGTAGA_L001


title: striatum single nuclei RNA rep 18

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St72
St_M72_CGTACTAGTAGATCGC_L001


title: striatum single nuclei RNA rep 13

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St66
St_M66_TAAGGCGAAGAGTAGA_L001


title: striatum single nuclei RNA rep 20

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St74
St_M74_TCCTGAGCTAGATCGC_L001


title: striatum single nuclei RNA rep 15

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St68
St_M68_AGGCAGAAAGAGTAGA_L001


title: striatum single nuclei RNA rep 16

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St69
St_M69_TCCTGAGCAGAGTAGA_L001


title: striatum single nuclei RNA rep 10

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St62
St_M62_AGGCAGAATATCCTCT_L001


title: striatum single nuclei RNA rep 12

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St65
St_M65_TAGGCATGTATCCTCT_L001


title: striatum single nuclei RNA rep 6

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St57
St_M57_TCCTGAGCCTCTCTAT_L001


title: striatum single nuclei RNA rep 14

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St67
St_M67_CGTACTAGAGAGTAGA_L001


title: striatum single nuclei RNA rep 8

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St60
St_M60_TAAGGCGATATCCTCT_L001


title: striatum single nuclei RNA rep 5

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St56
St_M56_AGGCAGAACTCTCTAT_L001


title: striatum single nuclei RNA rep 17

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St70
St_M70_GGACTCCTAGAGTAGA_L001


title: striatum single nuclei RNA rep 4

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St55
St_M55_CGTACTAGCTCTCTAT_L001


title: striatum single nuclei RNA rep 7

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St59
St_M59_TAGGCATGCTCTCTAT_L001


title: striatum single nuclei RNA rep 9

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St61
St_M61_CGTACTAGTATCCTCT_L001


title: cerebellum tissue RNA rep 2

description:
processed data file: TRAP_rpkms.txt; ctrl_UB_CB
ctrl_UB_CB_CAGATC_L008

source_name: cerebellum tissue RNA

extract_protocol:
Microglial RNA was isolated from the unbound fraction of TRAP in the cerebellum
cDNA was generated using Nugen Ovation V2 kit. Libraries were produced using TruSeq DNA Sample kit. Multiplexed libraries were directly loaded on NextSeq 500 (Ilumina) with High Output single read sequencing for 75 cycles.

value: Cerebellum tissue


title: striatum single nuclei RNA rep 11

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St63
St_M63_TCCTGAGCTATCCTCT_L001


title: cerebellum tissue RNA rep 1

description:
processed data file: TRAP_rpkms.txt; CB_IN
CB_IN_GTCCGC_L003


title: striatum single nuclei RNA rep 1

description:
processed data file:
supplementary table 6 - single nuclei gene expression.xlsx; St49
St_M49_CGTACTAGTAGATCGC_L001