title: At_6mA-seq_Input

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

data_processing:
Library strategy: 6mA-seq
Raw fastq files were trimmed by trim-galore to remove adapters and low-quality bases.
Genome_build: TAIR10

source_name: 9-day-old seedling

growth_protocol: The Columbia-0 (Col-0) ecotype of Arabidopsis thaliana were vertically grown at 1/2 Murashige and Skoog medium (MS) salts (Phytotech) in the chambers under long days conditions (16-hour photoperiods) under 22 ℃.

extract_protocol:
Genomic DNA was extracted from 9-day-old seedlings and sonicated to ~300 bp. Fragmented DNA was incubated with antibody against N6-methyladenosine modifications of RNA and DNA (Synaptic Systems) in in immunoprecipitation (IP) buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% IPEGAL) for 2 hours at 4 ℃. Subsequently, the mixture was incubated with protein A beads (Thermo Fisher Scientific) that was pre-bound with acetylated bovine serum albumin (Sigma-Aldrich) at 4 ℃ for another 2 hours. After washing 4 times, 6mA antibody-bound DNA was eluted from beads in elution buffer (90 µL 5X IP Buffer, 30 µL of 100 mM antibody against 6mA, 330 µL H20) at 50 ℃ for 45 minutes. The eluted DNA was purified with 2:1 ratio of AMPure SPRI beads (Beckman Coulter) and quantified with Qubit High Sensitivity Kit (Thermo Fisher).
Library synthesis was performed using the SMARTer ThruPLEX DNA-Seq Kit (Takara), library size was determined using the Bioanalyzer High Sensitivity Kit (Agilent) and the quantification done with KAPA Library Quantification Kit (Roche).
Sequencing was performed on an Illumina NovaSeq 6000 sequencer using an SP 300 cycles flowcell in paired-end mode

tag: ecotype

value: Columbia-0 (Col-0)

value: seedling


title: 3139

status: Public on Apr 22 2020

type: SRA

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

country: USA

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Library strategy: Targeted enhancer resequencing
The adaptor and low quality bases (quality < 20) were trimmed using trim_galore version 0.4.0 with parameter --stringency 1 -e 0.1 --length 20.
Bowtie version 2.1.078 was used to align the read pairs for each sample.
PCR duplications were marked using customized pipeline.
RealignerTargetCreator/IndelRealigner from The Genome Analysis Toolkit (GATK version 3.3)18 were used to realign the reads around insertions and deletions. BaseRecalibrator/PrintReads from GATK were used to perform base quality score recalibration.
Mutations were called by the following algorithms: GATK, MuTect, Strelka, Scalpel and VarScan2.
Genome_build: hg19
Supplementary_files_format_and_content: TXT format

molecule: genomic DNA

organism: Homo sapiens

source_name: Leukemia cell

extract_protocol: Targeted resequencing of enhancer elements was performed using Ovation® Target Enrichment System (NuGEN) following the manufacture’s protocols. Target enriched library were purified, quantified, and sequenced on an Illumina NextSeq500 system using the 150bp high output sequencing kit

tag: tissue

value: Blood cells

tag: cell type

value: Leukemia cell


title: Primary2_D1

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

library_source: transcriptomic

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v2.1.1 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina)
Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v2.1.1 count pipeline (10x Genomics)
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv, mtx files generated by CellRanger v2.1.1

molecule: polyA RNA

source_name: Sorted PBMC

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics) according to the manufacture's protocol (User guide RevC)
Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). In short, sequencing libraries were generated by  1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Cryopreserved PBMCs were thawed and washed with RPMI media supplemented with 10% fetal calf serum prior to analysis. Populations of interest (CD3+CD19- T cells and CD3-CD19+ B cells) were isolated from the unfractionated PBMCs by flow cytometric sorting using a BD FACSAria Fusion instrument. Post-sort population purity was assessed prior to downstream analysis, and sorted T and B cells pooled together in for subsequent processing. Sorted cells were washed in PBS supplemented with 2% fetal calf serum prior to scRNAseq library generation

tag: patient diagnosis

value: natural primary DENV infection

value: Pooled CD3+CD19- T cells and CD3-CD19+ B cells

tag: subject

value: Primary #2

tag: fever day

value: Fever day 1


title: At_6mA-seq_rep1

organism: Arabidopsis thaliana


title: 3106


title: 3101


title: BALF, C142 (TCR-seq)

city: Shenzhen

first: Zheng

last: Zhang

state: Guangdong

address: No. 29, Bulan Road

country: China

institute: Shenzhen 3rd People's Hospital

description: TCRseq data

data_processing:
Library strategy: TCR-seq
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 5’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, gene-barcode matrix of all 6 donors and 8 previously reported healthy control was integrated with Seurat v3 to remove batch effect across different donors. Following criteria were then applied to each cell, i.e., gene number between 200 and 6000, UMI count above 1000 and mitochondrial gene percentage below 0.1.
The filtered gene-barcode matrix was normalized with LogNormalize methods in Seurat and analyzed by principal component analysis (PCA) using the top 2, 000 most variable genes. Then Uniform Manifold Approximation and Projection (UMAP) was performed on the top 50 principal components for visualizing the cells. Meanwhile, graph-based clustering was performed on the PCA-reduced data for clustering analysis with Seurat v3.
MAST in Seurat v3 was used to perform differential analysis. For each cluster, differentially-expressed genes (DEGs) were generated relative to all of the other cells.
The TCR sequences for each single T cell were assembled by Cell Ranger vdj pipeline (v3.1.0), leading to the identification of CDR3 sequence and the rearranged TCR gene. Cells with both TCR alpha and beta chains were kept and cells with only one TCR chain were discarded.
Genome_build: GRCh38 + COVID(MN908947)
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count; csv, tcr contig annotations generated by Cell Ranger vdj

source_name: BALF

extract_protocol: Total 11 µl of single cell suspension and 40 µl barcoded Gel Beads were loaded to Chromium Chip A to generate single-cell gel bead-in-emulsion (GEM). The poly-adenylated transcripts were reverse-transcribed later. The single-cell capturing and downstream library constructions were performed using the Chromium Single Cell 5’ library preparation kit according to the manufacturer’s protocol (10x Genomics). Full-length cDNA along with cell-barcode identifiers were PCR-amplified and sequencing libraries were prepared and normalized to 3 nM.

tag: disease state

value: Coronavirus infected disease-19 (COVID-19)

tag: patient group

value: mild

tag: organ

value: lung

tag: sample type

value: BALF

tag: cell subsets

value: Total cell


title: BALF, C141 (TCR-seq)

description: TCRseq data


title: Primary1_D-1

value: Primary #1

value: Fever day -1


title: NC3

city: Qingdao

first: Da

last: HUO

address: No. 7 Nanhai Road, Qingdao, China

institute: Institute of Oceanology,Chinese Academy of Science

description: processed data file: union_fpkm.txt

data_processing:
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows: 1) Remove the adaptor-polluted reads. Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low-quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads whose number of N bases accounting for more than 5%. As for paired-end sequencing data, both reads would be filtered out if any read of the paired-end reads are adaptor-polluted. The obtained Clean Data after filtering will be carried out on statistics analyses on its quantity and quality, including Q30, data quantity and base content statistics, etc.
The reference genomes and the annotation file of A. japonicus were used (Zhang, 2017). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12. TopHat, specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again. Moreover, TopHat calls Bowtie2 for mapping, which makes it more accurate and faster. Cufflinks was used to predict the new transcripts and those with length over 200bp, exon over 2 and cover degree ≥ 3 were selected. Coding Potential Calculator (CPC), Coding-Non-Coding-Index (CNCI), Coding Potential Assessment Tool (CPAT) and Pfam were used to identify lncRNAs, and those who were only identified in one sample, were removed.
FPKM (Fragments Per Kilobase per Million Mapped Fragments) was then calculated to estimate the expression level of genes in each sample (Trapnell, C et al., 2010).
DESeq (v1.16) was used for differential gene expression analysis between two samples with biological replicates using a model based on the negative binomial distribution. Genes with p  ≤ 0.05 and |log2 ratio| ≥ 1 are identified as differentially expressed genes (DEGs). The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Genome_build: Apostichopus japonicus genome (PMID 29023486, NCBI BioProject PRJNA354676).
Supplementary_files_format_and_content: union_fpkm.txt: Tab-delimited text file includes FPKM values.

molecule: total RNA

organism: Apostichopus japonicus

source_name: respiratory tree

extract_protocol:
Total RNA from tissues was extracted using phenol/chloroform following manufacturer’s recommendations. RNA degradation and contamination were detected by 1% agarose gels; RNA purity was checked using the kaiaoK5500® Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All samples had an RNA integrity number (RIN) ≥ 8.0.
A total amount of 3 µg RNA per sample was used as initial material for the RNA sample preparations. Ribosomal RNA was removed using Epicentre Ribo-Zero™ Gold Kits (Human/Mouse/Rat) (Epicentre, USA). Subsequently, the sequencing libraries were generated following manufacturer recommendations with varied index label by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (NEB, Ispawich, USA). The details of library construction showed as follow: Firstly, ribosomal RNA was removed by kits, RNA fragmentation and short RNA strands were carried out by NEBNext First Strand Synthesis Reaction Buffer under elevated temperature. Subsequently, first cDNA strand was synthesized using random hexamer primers and RNA fragments as template. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair, add poly(A)and adapter were implemented. In order to select cDNA fragments of preferentially 300bp in length, the library fragments were purified with agarose gel electrophoresis and the UNG enzyme was used to digest second strand of cDNA. PCR was performed, aimed products were retrieve by agarose gel electrophoresis, and the library was completed.

treatment_protocol: Thermal stress (26℃), hypoxic stress (2mg/L), thermal and hypoxic stress (26℃+2mg/L).

value: Respiratory tree

tag: treatment

value: Normal control


title: NC2

description: processed data file: union_fpkm.txt


title: Female WT microglia, 6

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

institute: Massachusetts General Hospital

data_processing:
Total RNA was isolated and sequencing libraries were made using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). Sequencing was done using an Illumina MiniSeq and bioinformatic analysis was performed using DESeq2 in R
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and removed.
The uniquely aligned reads were then counted against Gencode’s GRCm38.p3 GTF annotations using htseq-count in the intersection-strict mode
Data analysis of mapped counts was performed in R 3.2.3 using the DESeq2 package
Samples with less than 6000 genes with at least 5 mapped reads were excluded from analysis
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text file with read counts per sample

organism: Mus musculus

source_name: Mouse brain

extract_protocol:
Microglia are isolated from mouse brain following protocol described in Hickman et al. 2013. Total RNA was isolated using RNeasy Plus Micro kit (Qiagen) using the total RNA isolation protocol.
Total RNA was isolated and sequencing libraries were made using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) . Sequencing was done using an Illumina MiniSeq

tag: genotype/variation

value: wildtype

tag: strain

tag: age

value: 12 -18 weeks

value: microglia

tag: Sex

value: Female


title: Female WT microglia, 7


title: 3004

value: Blood cells

value: Leukemia cell


title: NC1

description: processed data file: union_fpkm.txt


title: BALF, C146 (scRNA-seq)

description: Single-cell RNAseq data

data_processing:
The Cell Ranger Software Suite (Version 3.1.0) was used to perform sample de-multiplexing, barcode processing and single-cell 5’ UMI counting with human GRCh38 as the reference genome. Specifically, splicing-aware aligner STAR was used in FASTQs alignment. Cell barcodes were then determined based on distribution of UMI count automatically. Finally, gene-barcode matrix of all 6 donors and 8 previously reported healthy control was integrated with Seurat v3 to remove batch effect across different donors. Following criteria were then applied to each cell, i.e., gene number between 200 and 6000, UMI count above 1000 and mitochondrial gene percentage below 0.1.
The filtered gene-barcode matrix was normalized with LogNormalize methods in Seurat and analyzed by principal component analysis (PCA) using the top 2, 000 most variable genes. Then Uniform Manifold Approximation and Projection (UMAP) was performed on the top 50 principal components for visualizing the cells. Meanwhile, graph-based clustering was performed on the PCA-reduced data for clustering analysis with Seurat v3.
MAST in Seurat v3 was used to perform differential analysis. For each cluster, differentially-expressed genes (DEGs) were generated relative to all of the other cells.
The TCR sequences for each single T cell were assembled by Cell Ranger vdj pipeline (v3.1.0), leading to the identification of CDR3 sequence and the rearranged TCR gene. Cells with both TCR alpha and beta chains were kept and cells with only one TCR chain were discarded.
Genome_build: GRCh38 + COVID(MN908947)
Supplementary_files_format_and_content: h5, raw count matrix generated by Cell Ranger count; csv, tcr contig annotations generated by Cell Ranger vdj

value: severe


title: Primary3_D-1

value: natural primary DENV infection

value: Pooled CD3+CD19- T cells and CD3-CD19+ B cells

value: Primary #3


title: 2990T


title: Female WT microglia, 5


title: BALF, C145 (scRNA-seq)

description: Single-cell RNAseq data

value: Coronavirus infected disease-19 (COVID-19)

value: lung


title: BALF, C144 (TCR-seq)

description: TCRseq data

value: mild

value: BALF

value: Total cell


title: At_6mA-seq_rep2

value: Columbia-0 (Col-0)

value: seedling


title: Primary1_D3

value: Primary #1

value: Fever day 3


title: HL3

description: processed data file: union_fpkm.txt

value: Respiratory tree

value: Thermal and hypoxic stress


title: Female WT microglia, 4

value: wildtype

value: 12 -18 weeks

value: microglia

value: Female


title: BALF, C144 (scRNA-seq)

description: Single-cell RNAseq data


title: HL2

description: processed data file: union_fpkm.txt


title: 2966

value: Blood cells

value: Leukemia cell


title: BALF, C143 (scRNA-seq)

description: Single-cell RNAseq data

value: Coronavirus infected disease-19 (COVID-19)

value: severe


title: HL1

description: processed data file: union_fpkm.txt


title: 2949


title: BALF, C142 (scRNA-seq)

description: Single-cell RNAseq data

value: mild

value: lung


title: Female WT microglia, 2


title: Female WT microglia, 3


title: LO3

description: processed data file: union_fpkm.txt

value: Hypoxic stress


title: 3095


title: 0101


title: 0100


title: Female WT microglia, 1


title: LO2

description: processed data file: union_fpkm.txt


title: Female Trem2 KO microglia, 4

value: Trem2-/- (knock-out mouse project KOMP, UCDavis)


title: RS4;11_Bortezomib

first: Maolin

last: Ge

department: MGH Cancer Center

institute: Harvard Medical School

data_processing:
Basecalls performed using BGISEQ-500.
SOAPnuke was used to get the "clean reads".
Mapping clean reads to hg19 whole genome using HISAT2.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample.

source_name: pro-B MLL leukemia cell line RS4;11

growth_protocol: Cells were cultured in Gibco RPMI 1640 containing 10% FBS at 37°C with 5% CO2 and were maintained between a density of 5 × 10^5 cells/ml and 2 × 10^6 cells/ml.

extract_protocol:
Tissue blocks were lysed in TRIzol reagent (Sigma-Aldrich). The lysate was well mixed with chloroform and spun for 15 min at 13000 g at 4 °C. RNA in top aqueous phase was collected and mixed with propan-2-ol to precipitate total RNA.
RNA libraries were prepared for sequencing using MGIEasymRNA Library Prep Kit V2.

treatment_protocol: Induced drug-tolerant cells were generated by treating parental MLL leukemia cell line RS4;11 with gradually increasing concentration of bortezomib for at least 4 weeks. Bortezomib treatment was started with a concentration of 1 nM and the concentration of bortezomib was increased by 1 nM every 3 days. The remaining cells after the treatment were considered as bortezomib-tolerant cells and were collected for analysis. RS4;11-tolerant cells were treated with PBS, RS4;11-Nexo (5 ug/ml), or RS4;11-Rexo (5 ug/ml) for 4 days.

value: pro-B mix linage leukemia (MLL) cell line

tag: cell line

tag: drug treatment


title: RS4;11_DMSO

tag: tissue


title: LO1

description: processed data file: union_fpkm.txt


title: input siCtrl rep1

city: philadelphia

first: Fange

last: Liu

address: 415 curie blvd, Clinical Research Building Rm 350

institute: UPENN

data_processing:
Library strategy: m6A-seq
exomePeak was used to call m6A different peaks between siTRMT10A and siCtrl.
CTK was used to call TRMT10A CLIP peaks.
PARalyzer was used to call FTO CLIP peaks.
Gene expression levels were normalized using DEseq2
Genome_build: hg38
Supplementary_files_format_and_content: m6A_diff_peak file contains different m6A peaks between siTRMT10A and siCtrl, *xlsx files include CLIP peaks

growth_protocol: HEK293T cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% FBS and 1% Pen/Strep in 37 °C, 5% CO2 incubator.

extract_protocol:
For m6A-IP,total RNA was purified by TRIzol reagent (Invitrogen), following the manufacture’s instruction. mRNA was extracted from the total RNA by using Dynabeads mRNA Purification Kit (Ambion) following the instruction. The rRNA was further removed by RiboMinus Eukaryote Kit (Invitrogen). mRNA was fragmented by sonication. The m6A-immunoprecipitation was performed using NEB EpiMark N6-Methyladenosine Enrichment Kit (E1610S). For CLIP, FTO or TRMT10A overexpression cells were UV crosslinked three times in a Stratagene Stratalinker 2400 UV Crosslinker. After irradiation, cells were harvested by cell lifter and pelleted by centrifugation at 500g for 4 min at 4 ℃. The pellet was then resuspended in lysis buffer (1 x PBS supplemented with 0.1% SDS, 1% Nonidet P-40, 0.5% Sodium Deoxycholate, Protease Inhibitor Cocktail) and kept on ice for 15 min. T1 digestion was carried out under 2 U/μl for 15 min at 22 °C. 200 μl anti-Flag beads (Millipore, M8823) were subsequently added to the supernatant and kept at 4 °C for overnight with rotation. The beads were then washed for 3 times with 1 ml of high salt buffer (5 x PBS supplemented with 0.1% SDS, 1% Nonidet P-40 and 0.5% Sodium Deoxycholate) and another 3 times with 1 ml of wash buffer (20 mM Tris-HCl, pH 7.4, 10 mM MgCl2 and 0.2% Tween-20). The RNAs were then isolated by 200 μl of elution buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, and 1% SDS) containing 2 mg/ml proteinase K under incubation at 37 °C for 40 min. The beads were removed and RNAs were recovered by RNA Clean & Concentrator (Zymo Research).
m6A profiling libraries were constructed by TruSeq stranded mRNA samples preparation kit from Illumina. CLIP-seq libraries were constructed by NEBNext® Small RNA Library Prep Set for Illumina (NEB7330).

treatment_protocol: Cells were treated with TRMT10A siRNA or control siRNA.

tag: genotype

value: siCtrl


title: RS4;11_Rexo_2

value: proteasome inhibitor-resistant cell-derived exosomes


title: input siCtrl rep2


title: HT3

description: processed data file: union_fpkm.txt

value: Respiratory tree

value: Thermal stress


title: m6A-seq siCtrl rep2


title: Female Trem2 KO microglia, 2

tag: cell type


title: Female Trem2 KO microglia, 3


title: HT2

description: processed data file: union_fpkm.txt


title: RS4;11_Rexo_1


title: m6A-seq siCtrl rep1


title: HT1

description: processed data file: union_fpkm.txt


title: RS4;11_Nexo_2

value: naive RS4;11-derived exosomes


title: input siTRMT10A rep2


title: Female ApoE KO microglia, 4

value: 12 -18 weeks


title: BALF, C141 (scRNA-seq)

description: Single-cell RNAseq data

value: BALF

value: Total cell


title: rice.2.m6A.merip.input

city: Los Angeles

first: Ye

last: Wang

state: California

address: 611 Charles E Young Dr E

department: Bioinformatics

institute: UCLA

data_processing:
Single-end and paired-end sequencing data were trimmed by single-end and paired-end model of cutadapt (v1.18) software respectively. Reads longer than 20 bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 (v2.1.0) software using the default parameter for single or pair-end model
Peakcalling were performed by macs2(v3.8), the enrichment fold threshold is 1, FDR threshold is 0.05.
Comparison of m6A sites from MeRIP-m6A-seq and m6A-SEAL are performed by intersectBed in BEDtools.
Peaks from input and IP samples in both MeRIP-m6A-seq and m6A-SEAL are converted to bigwig files by bamCoverage script in deepTools for visualization and analysis.
Genome_build: Human genome hg38.  Rice genome built on MSU Rice Genome Annotation (Osa1) Release 7.
Supplementary_files_format_and_content: bigwig

organism: Oryza sativa

source_name: rice (Nipponbare)

growth_protocol: HEK293T cell were cultured by DMEM medium(10% FBS) and 1% Penicillin Streptomycin in 15cm dish under 37℃, 5%CO2.   Rice were cultivated in a half-strength Kiruma B solution (pH 5.6, changed every two days.) at 28℃ and 80% relative humidity for 15 days.

extract_protocol:
Total RNA was first extracted from HEK293T cells or rice tissue by Trizol reagent, The polyA RNA was then purified with oligo d(T)25 magnetic beads
PolyA RNA was fragmented by NEBNext Magnesium RNA Fragmentation Module. A portion of fragmented RNA was reserved as m6A input sample.For MeRIP-m6A-seq,  the left RNA was incubated with anti-m6A antibody and then eluted to get the m6A IP sample. For m6A-SEAL, the left RNA was enzymatically oxidized by FTO and then conjugated with biotin by dithiothreitol under acidic aqueous solution. The biotinylated RNA are enriched by streptavidin beads and then eluted by dithiothreitol to get m6A IP sample. Both input and m6A IP samples were prepared for next-generation sequencing library by standard protocol of NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.
m6A-SEAL and MeRIP-m6A-seq. Library was sequenced in PE150 model on Illumina X-Ten platform or in SR75 model on Illumina NextSeq 500 platform.

tag: cultivar

value: Nipponbare

tag: method

tag: merip antibody

value: leaf


title: Female ApoE KO microglia, 3

value: microglia

value: Female


title: rice.2.m6A.merip.ip

value: anti-m6A (Synaptic System,Polyclonal, rabbit,Cat. No. 202 003)


title: Female ApoE KO microglia, 2


title: m6A-seq siTRMT10A rep2


title: rice.1.m6A.merip.input


title: m6A-seq siTRMT10A rep1


title: OmniATAC-seq_Pig_PigMel_BL

city: Leuven

first: Stein

last: Aerts

address: O&N4 Herestraat 49 PO Box 602

country: Belgium

institute: KU Leuven

data_processing:
Data processing of human melanoma baseline OmniATAC-seq samples: Paired-end reads were mapped to the human genome (hg19-Gencode v18) using bowtie2 (v2.2.6). Mapped reads were sorted using SAMtools (v1.8) and duplicates were removed using Picard MarkDuplicates (v1.134). Reads were filtered by removing chromosomal reads and filtering for Q>30 using SAMtools. Bam files of technical replicates of the same cell line were merged at this point using samtools merge. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and --extsize 150 per sample. Chromosomal peaks, blacklisted regions (ENCODE) and peaks overlapping with alternative chromosomes were removed. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing human chromosome sizes. Peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score by keeping the peak with the highest score. For visualisation in IGV, normalised bigWigs were made by bamCoverage (Deeptools, v3.3.1), using as parameters --normalizeUsing None, -bl EncodeBlackListedRegions --effectiveGenomeSize 2913022398 and as scaling parameter (-scaleFactor) 1/(RIP/1E6), where the RIP stands for the number of reads in peaks.
Data processing of non-human (Omni)ATAC-seq samples, and of human SOX10 and TFAP2A knock-down OmniATAC-seq data: Adapter sequences were trimmed from the fastq files using fastq-mcf (as part of eautils; v1.05) and the read quality was checked using FastQC (v0.11.8). Reads were mapped using STAR (v2.5.1b) (for the zebrafish samples paired-end reads were mapped) to the genome which were downloaded from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/) (for human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10) and by applying the parameters --alignIntronMax 1 and --aslignIntronMin 2. Mapped reads were filtered for quality using SAMtools (v1.2) view with parameter –q4, sorted with SAMtools sort and indexed using SAMtools index. Peaks were called using MACS2 (v2.1.2) callpeak using the parameters -q 0.05, --nomodel, --call-summits, --shift -75 --keep-dup all and with the genome size for the correct species in --g, and this for each sample per species separately. Summits were extended by 250bp up- and downstream using slopBed (bedtools; v2.28.0), providing the chromosome sizes for the specific species. Per sample, peaks were normalised for the library size using a custom script and overlapping peaks were filtered using the peak score (keeping the highest scoring peak). Normalised bedGraphs were produced by genomeCoverageBed (as part of bedtools; v2.28.0) using as scaling parameter (-scale) 1E6/(number of non-chromosomal mapping reads). BedGraphs were converted to bigWigs by the bedtools suit functions bedSort to sort the bedGraphs, followed by bedGraphToBigWig to create the bigWigs, which were used in IGV for visualisation.
Genome_build: For human: hg19-Gencode v18; for dog: canFam3; for horse: equCab2; for pig: susScr11; for mouse: mm10; for zebrafish: danRer10.
Supplementary_files_format_and_content: bigWig files represent the coverage of the ATAC-seq signal.

organism: Sus scrofa domesticus

source_name: Normal melanocyte cell line

growth_protocol:
Cell were cultured at 37°C with 10% CO2  in MEM medium supplemented with 1X MEM non essential amino acids  (Thermo Fisher Scientific), 10mM Na pyruvate, 2mM glutamine, 100U/ml penicilin/streptomycin  (Thermo Fisher Scientific), 10% FCS and 3,7g/ml Na bicarbonate.
Mentioned per sample in the SAMPLE section.

extract_protocol:
Cells were washed, trypsinised, spun down at 1000 RPM for 5 min, medium was removed and the cells were resuspended in 1 mL medium. Cells were counted and experiments were only continued when a viability of above 90% was observed. 50,000 cells were used per sample. OmniATAC-seq was performed as described previously in Corces et al., 2017; and ATAC-seq as described in Buenrostro et al., 2015.
Library prep was performed as described before in Corces et al., 2017 for OmniATAC-seq samplas; and as in Buenrostro et al., 2013 for ATAC-seq samples.

treatment_protocol: For the knock-down data: SOX10, TFAP2A and the control knockdown was performed in MM001 using respectively a SMARTpool of four siRNAs against, respectively, SOX10 (SMARTpool: ON-TARGETplus SOX10 siRNA, number L017192-00-0005, Dharmacon), TFAP2A (SMARTpool: ON-TARGETplus TFAP2A siRNA, number L-006348-02-0005, Dharmacon) and a negative control pool (ON-TARGETplus non-targeting pool, number D-001810-10-05, Dharmacon) at a concentration of 20 nM for SOX10-KD, and 40 nM for TFAP2A-KD and the control using as medium Opti-MEM (Thermo Fisher Scientific) and omitting antibiotics. The cells were incubated for 72 h before processing.

value: PigMel

tag: tissue type

value: Pigmented melanocytes from the epidermis of Meishan pig

tag: condition

value: Baseline


title: Female ApoE KO microglia, 1


title: rice.1.m6A.merip.ip


title: OmniATAC-seq_Pig_MeLiM_BL

source_name: Melanoma cell line

growth_protocol:
Cells were cultured in DMEM high glucose  (Thermo Fisher Scientific), 10% FCS, Pen/Strep, 5% CO2.
Mentioned per sample in the SAMPLE section.

value: MeLiM

value: Melanoma derived from MeLiM minipig model


title: OCT6Flag_d2_input_rep2

status: Public on Apr 21 2020

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

institute: tongji university

description: Input replicates were summarized and processed data were included in a single file. Processed data for this sample is available on GSM4487608.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to hg19 reference genome using bowtie2 (v 2.2.9) with default parameters.
ChIP peaks were called using macs14(v 1.4.2) with parameter: macs14 –t Sample.bam –c input.bam –g hs –p 1e-7 –n name.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig and macs2 with parameter --SPRM.

source_name: reprogramming cells

extract_protocol:
DNA was extracted by reverse crosslinking at 65 °C overnight with proteinase K (20 μg/μl) and RNaseA (20 ug/ul) and purified using phenol/chloroform extraction.
Sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit (NEB).

treatment_protocol: The cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 min at at room temperature. The cross-linked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH [pH 7.5], 140 mM NaCl, 1 mM 0.5 M EDTA, 10% glycerol, 0.5% IGEPAL CA630, 0.25% Triton X-100, and 1 ´ Complete Protease inhibitor) for 30 min at 4 °C and washed in lysis buffer 2 (10 mM Tris-HCl [pH 8.0], 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 1 ´ Complete Protease inhibitor) for 10 min at 4 °C. The cells were then resuspended in sonication buffer and sonicated using the Diagenode Bioruptor (high power, 30 cycles of 30 s on and 30 s off). 100 μg of sonicated chromatin was then incubated with Dynabeads protein G (Invitrogen) coupled to 15 μg of FLAG antibody (Sigma) in 4 ´ volume of ChIP dilution buffer at 4 °C overnight. Beads were washed once with low-salt buffer, twice with high-salt buffer, twice with RIPA buffer, and once with TE containing 50 mM NaCl. Elution was done with elution buffer for 15 min at 65 °C.

value: TRA1-60+ reprogramming cells

tag: reprogramming factor

tag: reprogramming day

tag: antibody


title: OCT6Flag_d2_input_rep1

description: Processed data file on this records represents both Replicate 1 and 2.


title: OCT6Flag_d2_ChIP_rep2

description: ChIP-seq replicates were summarized and processed data were included in a single file. Processed data for this sample is available on GSM4487606

value: Flag


title: Female Trem2 KO microglia, 1

tag: genotype/variation

value: Trem2-/- (knock-out mouse project KOMP, UCDavis)


title: OCT6Flag_d2_ChIP_rep1


title: input siTRMT10A rep1


title: RS4;11

value: pro-B mix linage leukemia (MLL) cell line

tag: treatment

value: untreated


title: RS4;11_Nexo_1

value: naive RS4;11-derived exosomes


title: Microglia-GMcsf-R1

city: Montreal

first: Jo

middle: Anne

last: Stratton

state: Quebec

address: 3801 University street

department: Neurology and Neurosurgery

country: Canada

institute: McGill University

data_processing:
standard illumina base caller (bustrad) was used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR software v2.5.2b
Transcript Per Milion (TPM) were calculated using edgeR package
Genome_build: Homo_sapiens_assembly19/v1
Supplementary_files_format_and_content: two excel files include TPM values for each  sample of microglia and macrophage separately.

source_name: brain

growth_protocol: Monocte-derived-macrophages were grown in RPMI media supplemented with 5% fetal calf serum, penicillin/streptomycin, and glutamine. Microglia were grown in DMEM media supplemented with 5% fetal calf serum, penicillin/streptomycin, and glutamine.

extract_protocol:
Cells were lysed in TRIzol (Invitrogen). Total RNA extraction was performed using standard protocols followed by DNAse treatment according to the manufacturer’s instructions (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary human microglia and primary human monocyte-derived-macrophages were differentiated into their CNS homeostatic phenotype (M-CSF[25ng/mL]+TGFβ[50ng/mL]) and proinflammatory phenotype (GM-CSF[25ng/mL]) over 6 days in the presence of 100nM calcitriol. Control populations were differentiated in the absence of calcitriol. 500000 cells were seeded in each condition. Experiment samples consist of three (3) biological replicates.

value: brain

tag: phenotype

value: GM-CSF

tag: age

value: adult

value: wild type


title: Microglia-M0 + Calcitriol-R2

value: M-CSF+TGFbeta

value: 100nM calcitriol


title: Microglia-GMcsf + Calcitriol-R3


title: Microglia-M0-R3


title: Microglia-M0 + Calcitriol-R3


title: Macrophage-M0 + Calcitriol-R3

source_name: blood

value: blood


title: Microglia-GMcsf-R3


title: Microglia-M0-R1


title: Microglia-GMcsf + Calcitriol-R2


title: Microglia-GMcsf + Calcitriol-R1


title: Microglia-M0-R2


title: Macrophage-M0 + Calcitriol-R1


title: Macrophage-M0 + Calcitriol-R2


title: Macrophage-M0-R3


title: Macrophage-M0-R1


title: Macrophage-M0-R2


title: Macrophage-GMcsf + Calcitriol-R3


title: Macrophage-GMcsf + Calcitriol-R1


title: Macrophage-GMcsf + Calcitriol-R2


title: GOX60

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: GOX T60

data_processing:
mapping of reads was done using: bowtie2  --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Staphylococcus aureus 04-02981|VERSION Date:   2010/11/05 | ASM2514v1 | GenBank assembly accession: GCA_000025145.2
Supplementary_files_format_and_content: counts (text tab delimited table)

organism: Staphylococcus aureus

source_name: human

growth_protocol: Bacterial cells were grown in Tryptic Soy Broth at 37°C, 150 rpm shaking

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq

treatment_protocol: The bacterial culture was exposed to either uncoated cellulose fibers or GOX fibers (coated on cellulose) or AGXX® fibers (coated on cellulose) or GOX+AGXX® fibers, the culture without addition of any antimicrobial fibers served as the control

tag: strain

value: GOX

tag: time

value: 60 min


title: Microglia-M0 + Calcitriol-R1

tag: tissue


title: Macrophage-GMcsf-R2

tag: genotype


title: Macrophage-GMcsf-R3


title: Macrophage-GMcsf-R1


title: LIG3_siCTR_rep2

city: Mainz

first: Helle

last: Ulrich

state: Germany

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
Library strategy: GLOE-Seq
Reads were mapped to the human genome (GRCh37/hg19) using bowtie2 (version 2.3.4) and only reads with mapping quality scores greater than 30 were retained using samtools (version 1.5; parameter: -q 30).
BAM files were converted into BED files using BEDTools bamToBed (version 2.25.0) and the location of putative breaks was inferred from the mapped position of sequencing reads, by extracting the nucleotide immediately upstream of the 5’-end of a sequencing read, on the opposite strand.
BED files containing the positions of breaks were converted into BigWig files and were split into plus (FWD) and minus (REV) strands using BEDTools sortBED, genomeCoverageBed (version 2.25.0) and bedGraphToBigWig (version 365).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files based on replication fork directionality (RFD) ratio (RFD = (REV – FWD)/(REV + FWD)) were generated using deepTools (version 3.1.0) bigwigCompare program (parameter: -bs 1000 or 10000).

source_name: colon cancer cell line

growth_protocol: HCT116 cells were from Cancer Research UK – London Research Institute’s Cell Production Services. HCT116 LIG3-/-:mL3 cells were from Eric Hendrickson (doi: 10.1016/j.dnarep.2014.04.015). All cells were grown as monolayers in a humidified incubator at 37° C and 5% (v/v) CO2 in DMEM supplemented with 10% foetal bovine serum, penicillin (100 U/ml), streptomycin (100 µg/ml) and glutamine (300 µg/ml).

extract_protocol:
Nuclei were prepared from cells, harvested by trypsinization and washed in PBS + 5 mM EDTA, by incubation in nuclear isolation buffer (10 mM Tris-HCl pH 8.0, 50 mM NaCl, 50 mM EDTA pH 8.0, 0.34 M sucrose, 10% (w/v) glycerol, 0.1% (w/v) Triton X-100) on ice for 10 min. These nuclei were washed once in nuclear isolation buffer and then treated with RNase A at a final concentration of 100 µg/µl in nuclear isolation buffer at 37° C for 15 min. RNase-treated nuclei were resuspended in PBS + 25 mM EDTA prewarmed to 50° C to yield about 700,000 nuclei per 22.5 µl, mixed with an equal volume of molten 1.2% low-melting point agarose in PBS + 25 mM EDTA, and immediately pipetted into a plug mould. After the agarose had solidified, the plugs were incubated twice in Proteinase K solution (1 mg/ml Proteinase K, 1% (w/v) sarkosyl, 125 mM EDTA pH 9.0) overnight at 42° C. The plugs were then washed three times in plug wash buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA) + 1 mM PMSF for 10 min, once in plug wash buffer + 1 mM PMSF for 1 h and once in plug wash buffer for 1 h. Next, individual plugs were transferred to 1.5 ml tubes, rinsed twice with 1 ml 10 mM Tris-HCl pH 8.0 + 0.1 mM EDTA, washed once with 1 ml 10 mM Tris-HCl pH 8.0 + 0.1 mM EDTA for 30 min, twice with 1 ml 0.1 mM EDTA for 15 min, and finally rinsed once with water.
After removing as much residual water from the plugs as possible, the DNA was denatured by heating to 95° C for 4 min followed by quenching on slushy ice for 5 min. The plugs were then melted and equilibrated to 37° C, before being supplemented with a ligation mix (6.5 µl 10× T4 ligase buffer, 3.5 µl proximal adaptor (40 µM in 60 mM NaCl), 7 µl water and 3 µl high concentration T4 DNA ligase, NEB) and incubated overnight at 16° C. These reactions were inactivated by addition of EDTA pH 8.0 (10 mM final, in a total volume of 97 µl) and heating to 65° C for 10 min, prior to digestion of the agarose with 3 µl β-agarase at 42° C for 3-4 h. Next, the DNA was fragmented by sonication in a Bioruptor Pico (16 cycles, 30 s on - 30 s off), cleaned up with AMPure beads and eluted in 100 water. This eluate was transferred to a microfuge tube containing 20 µl Streptavidin MyOne C1 Dynabeads (ThermoFisher Scientific, prewashed once with 1 ml 10 mM Tris-HCl pH 8.5, 2 M NaCl) and incubated for 15 min at room temperature with rotation. The beads were washed on a rotating wheel at room temperature: twice with 50 µl 1× SSC buffer each for 5 min at room temperature, once with 25 µl 20 mM NaOH for 10 min and briefly with 100 µl water. The DNA was eluted in 16 µl of water by incubation at 95° C for 5 to 10 min. For second-strand synthesis, the eluted DNA (14.85 µl) was combined with 15 µl Phusion FLASH mix (ThermoFisher Scientific) and 0.15 µl 100 µM oligonucleotide 3790, and incubated at 95° C for 2 min, 60° C for 3 min and 72° C for 2 min. The resulting double-stranded DNA was purified with AMPure beads and eluted in 19 µl water. This elution (17 µl) was A-tailed with 2.3 µl End Prep Reaction Buffer and 1 µl End Prep Enzyme Mix (NEBNext® Ultra™ II DNA Library Prep kit, NEB) for 20° C for 30 min, followed by inactivation at 65° C for 30 min. Distal adaptor (2.25 µl, 40 µM in 60 mM NaCl) was ligated to the A-tailed DNA in the presence of 13.5 µl Ligation Master Mix, 0.45 µl Ligation Enhancer (NEBNext® Ultra™ II DNA Library Prep kit, NEB) and 8.8 µl water at 20° C for 20 min. The ligated DNA was cleaned up twice with AMPure beads, before being eluted in 20 µl water. This DNA (7.25 µl) was mixed with 5 µl 5× Q5 reaction buffer, 2.5 µl 1 µM Illumina P5 primer, 2.5 µl 1 µM Illumina P7 primer, 0.5 µl 10 mM dNTPs, 0.25 µl Q5 DNA polymerase (NEB) and 7 µl water and amplified by PCR, using the following programme: 95° C for 2 min, 8× (95° C for 15 s, 60° C for 30 s, 72° C for 20 s). The amplified DNA was cleaned up twice with AMPure beads, before being eluted in 25 µl water and sequenced following the guidelines supplied by Illumina.  Oligonucleotides:  proximal adaptor: 3898/3899;   distal adaptor: 3791/3792;   3898: CTACACGACGCTCTTCCGATCTNNNNN*N-NH2 (*: phosphorothioate bond, IDT code *; NH2: 3’-amino modification, IDT code /3AmMO/);   3899: PO4-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGTTTT-Bio (PO4: 5’-phosphorylation, IDT code /5Phos/; T-Bio: 3’-biotin-dT, IDT code /3BiodT/);   3790: CGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   3791: GACTGGAGTTCAGACGTGTGCTCTTCCGATCT;   3792: GATCGGAAGAGCACACGTCTGAACTCCAGTC;   P5: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT;   P7: CAAGCAGAAGACGGCATACGAGAT(X)6GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT.

treatment_protocol: Treatment with siRNA was carried out 24 h after seeding 200,000 wildtype cells in 6-cm plates (21.3 cm2) with 5.5 ml medium and 1.23 million LIG3-/-:mL3 cells in 10-cm plates (59 cm2) with 15.5 ml medium, to account for the slower growth rate of the latter and the consequent lower cell yield at the end of the procedure. For the 10-cm plates, 185 pmol of control (control num. 1 Silencer™ Select, Thermo Fisher) or Ligase 1 (s8174 Silencer™ Select, Thermo Fisher) siRNAs were mixed with 31 µl Lipofectamine RNAiMAX (Thermo Fisher) in a final volume of 3.1 ml OptiMEM (Thermo Fisher) and added to the cells. For the 6-cm plates, these amounts were scaled down according to surface area. Two days post siRNA transfection, cells were passaged into 10-cm plates and grown for two more days before being harvested and immediately processed for GLOE-Seq.

tag: cell line

tag: modification

value: LIG3-/-:mL3 + siRNA control


title: KD hypoxia rep2

city: Frankfurt am Main

first: Kathi

last: Zarnack

address: Max-von-Laue-Str. 15

institute: BMLS - Buchmann Institute for Molecular Life Sciences

data_processing:
Quality check of reads was performed before and after trimming using FastQC (version 0.11.5, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Flexbar (version 2.5) was used to filter sequencing reads based on sequencing quality (Phred score > 20) and read length (> 20 nt).
Cleaned reads were mapped to the human genome (hg38/GRCh38) and its annotation (GENCODE release 24) (Harrow et al., 2012) using STAR (version 2.4.5a, Dobin et al., 2013) allowing up to 2 mismatches.
The htseq-count script from the python package HTSeq (version 0.6.1, Anders et al., 2015) was used to summarize uniquely mapped reads from STAR per gene.
Alternative splicing events were detected using rMATS (version 3.2.5, Shen et al. 2014) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includind raw counts per gene as obtained with htseq-count

source_name: KD hypoxia

growth_protocol: MCF-7 cells (DSMZ no. ACC-115) were cultured in T75 flasks in RPMI-1640 medium (Sigma-Aldrich), supplemented with 10% FBS (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific) and Penicillin Streptomycin (Pen Strep, Thermo Fisher Scientific).

extract_protocol:
Total RNA was isolated using the miRNeasy Mini kit (Qiagen), including the optional on-column DNA digestion with the RNase-Free DNase Set (Qiagen).
After isolation, total RNA was used to generate polyA-enriched strand-specific cDNA libraries (TruSeq stranded mRNA library preparation kit, Illumina). Libraries were sequenced on a Illumina NextSeq 500 sequencer with HighOutput

treatment_protocol: 200,000 MCF-7 cells were seeded in 12-well plates and incubated under normoxic conditions (37°C, 5% CO2, 21% O2). 24 h after seeding, cells were exposed to hypoxia (0.5% O2, 37°C, 5% CO2) for 48 h. For reverse transfection of siRNA, 200,000 MCF-7 were transfected after the manufacturer's protocol using Lipofectamine RNAiMAX. For subsequent RNA isolation, cells were transfected in a 12-well format with 200 pmol of an siRNA targeting MBNL2 (siMBNL2: 5'-CACCGUAACCGUUUGUAUG[dT][dT]-3', Paul, 2006, EMBO) or a nonsilencing control siRNA (siCTRL: 5'-UUCUCCGAACGUGUCACGU[dT][dT]-3', Qiagen)

value: MCF-7 (DSMZ no. ACC-115)

value: MBNL2 siRNA

value: hypoxia


title: Microglia-GMcsf-R2


title: WT_siLIG1_rep2

value: siRNA LIG1


title: LIG3_siCTR_rep1


title: WT_siLIG1_rep1


title: KD hypoxia rep1


title: LS06_pres_ALL

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
fastq conversion (bcl2fastq 1.8.4)
alignment and transcript abundance estimation: Salmon (0.8.2)
gene-level abundance estimation: Tximport (1.4.0)
batch effect minimisation: RUVSeq on upper-quartile normalized counts
differential gene expression analysis: DESeq2 (1.16.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file contains per-gene normalised read count values resulted from RUVr normalization

source_name: PBMC

growth_protocol: All patient samples were collected at the point of diagnosis, remission following treatment or relapse and stored with written informed consent for research in one of four centres (Newcastle Haematology Biobank, Newcastle, UK; University Hospital Schleswig-Holstein, Kiel, Germany; Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Haematological Malignancy Diagnostic Service, Leeds, UK). Mononuclear cells were isolated from bone marrow or peripheral blood by density centrifugation followed by immediate extraction of DNA or RNA, or cryopreservation in the presence of 10% v/v DMSO.

extract_protocol:
Total RNA was extracted with AllPrep DNA/RNA Mini Kit (Qiagen), innuPREP DNA/RNA Mini Kit (Analytik Jena), or TRIzol (Thermo Fisher Scientific) followed by RNeasy Mini Kit (Qiagen) from either bone marrow or peripheral blood, according to manufacturers’ instructions. Messenger RNA was captured using the NEBNext poly(A) mRNA Magnetic Isolation Module.
Libraries were prepared using the NEBNext Ultra Directional RNA Kit according to manufacturer's instruction, and submitted for paired-end 100, 150 or 75 bp sequencing on Illumina HiSeq 2000, 4000 and NextSeq 500 instruments, respectively.

value: PBMC

tag: disease state

value: presentation ALL patient


title: LS05_pres_ALL


title: IL-1b_CTL_3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description:
ETOH-il1b_3
processed data file: counts.matrix.norm_anno.txt

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg19 (GRCh37.p5) using STAR 2.4.0a with the parameter “-- outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62. Adjusted p-values were determined by Benjamini-Hochberg correction with a p-value of 0.05 considered significant.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: counts.matrix.norm_anno.txt: Tab-delimited text file includes library size normalized counts.

source_name: human aortic smooth muscle cells

growth_protocol: Cells grow on collagen Type I coated dishes (50µg/mL collagen in 0.02 M acetic acid).

extract_protocol:
RNA Mini Kit Bio&SELL.
500ng-1μg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech) following standard instructions.

treatment_protocol: 1% FCS media over night, 100nM AEA/ EtOH 4h and 10ng/mL IL-1β last 1.5h in presence of 10µM diclofenac.

tag: cell type

value: Aortic smooth muscle cells

value: ETOH

tag: treatment 2


title: IL-1b_AEA_3

description:
AEA-il1b_3
processed data file: counts.matrix.norm_anno.txt

value: AEA


title: LS05_relapse_AML

value: relapse AML patient


title: ctrl hypoxia rep1

source_name: ctrl hypoxia

value: control siRNA

tag: condition


title: CTL_3

description:
ETOH_3
processed data file: counts.matrix.norm_anno.txt


title: LIG3_siLIG1_rep2

value: LIG3-/-:mL3 + siRNA LIG1


title: IL-1b_CTL_2

description:
ETOH-il1b_2
processed data file: counts.matrix.norm_anno.txt


title: CTL_2

description:
ETOH_2
processed data file: counts.matrix.norm_anno.txt


title: ctrl hypoxia rep2


title: LIG3_siLIG1_rep1


title: WT_siCTR_rep2

value: siRNA control


title: IL-1b_AEA_1

description:
AEA-il1b_1
processed data file: counts.matrix.norm_anno.txt


title: AEA_2

description:
AEA_2
processed data file: counts.matrix.norm_anno.txt


title: IL-1b_CTL_1

description:
ETOH-il1b_1
processed data file: counts.matrix.norm_anno.txt


title: CTL_1

description:
ETOH_1
processed data file: counts.matrix.norm_anno.txt


title: WT_siCTR_rep1


title: MCF-7 hypoxia rep2

data_processing:
Stranded RNA sequencing (RNA-seq) libraries were sequenced on Illumina NextSeq sequencer (75-nt single-end), yielding ca. 100 million reads per sample.
Reads were filtered based on sequencing quality (Phred score > 20) and read length (> 20 nt) using Flexbar (version 2.5).
Sequencing qualities were checked before and after trimming using FastQC (version 0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the human genome (hg38/GRCh38) and its annotation (GENCODE release 24) (Harrow et al., 2012) using the splice-aware aliger STAR (version 2.4.5a) (Dobin et al., 2013) allowing up to 2 mismatches and with parameters --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15 for chimeric reads detection. For circRNA detection using find_circ, the same reads were also mapped using Bowtie2 as described in (Memczak et al., 2013).
Uniquely mapped reads from STAR were summarized per gene using htseq-count  from the python package HTSeq (version 0.6.1) (Anders et al., 2015). Chimeric reads from STAR were used to quantify circRNA expression.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw back-splicing read counts for each sample.

source_name: MCF-7 hypoxia

growth_protocol: A549 and MCF-7 cells were cultured in T75 flasks in DMEM (Sigma-Aldrich) or RPMI-1640 medium (Sigma-Aldrich), respectively, supplemented with 10% FBS, 1 mM sodium pyruvate and Pen Strep (all Thermo Fisher Scientific).

extract_protocol:
Total RNA was isolated using the miRNeasy Mini kit (Qiagen), including the optional on-column DNA digestion with the RNase-Free DNase Set (Qiagen).
After isolation, 500 ng RNA were quality checked on a 1% agarose gel. rRNA was depleted using the RiboZero kit (Zymo). Libraries were prepared and sequenced on a Illumina NextSeq sequencer with HighOutput

treatment_protocol: For hypoxia treatment, 100,000 A549 or 200,000 MCF-7 cells were seeded in 12-well plates. 24 h after seeding, cells were exposed to hypoxia (0.5% O2, 37°C, 5% CO2) for 48 h.

tag: oxygen condition


title: AEA_1

description:
AEA_1
processed data file: counts.matrix.norm_anno.txt


title: MCF-7 hypoxia rep1


title: MCF-7 normoxia rep2

source_name: MCF-7 normoxia

value: normoxia


title: MCF-7 normoxia rep1


title: A549 hypoxia rep1

source_name: A549 hypoxia

value: A549 (DSMZ no. ACC-107)


title: LS06_relapse_AML


title: A549 hypoxia rep2


title: A549 normoxia rep2

source_name: A549 normoxia


title: AEA_3

description:
AEA_3
processed data file: counts.matrix.norm_anno.txt


title: IL-1b_AEA_2

description:
AEA-il1b_2
processed data file: counts.matrix.norm_anno.txt


title: A549 normoxia rep1


title: control2dpi-2

city: Zurich

first: Tomas

last: Valenta

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

data_processing:
Adapters trimming with cutadapt, alignment on GRCh38 using Bowtie2 with default mapping parameters (Landmead and Salzberg, 2012), as well as duplicate filtering with Picard and peak calling with MACS2 (p<0.01) were performed on the ENCODE pipeline (Davis et al, 2018) supported by the SUSHI application AtacENCODEApp, for every biological replicate separately.
Differential peaks between sample groups were identified using the exact test function in edgeR. Only peaks with a log fold change > 1 and an p value < 0.01 were considered as differentially accessible for further analysis.
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: narrowPeak files

source_name: small intestinal crypts

growth_protocol: All animals were kept on a C57BL/6 background. Mice were 8-12 weeks old at the time of treatments and cell isolations. Mice of both sexes were used in all experiments and littermates were used as controls.

extract_protocol:
Control (n=3) and D164A (n=3) mice were sacrificed 2d pi and processed independently for ATACSeq library preparation, following the protocol by Buenrostro et al, 2015. Briefly, single cell suspension of duodenal crypts was performed as described (Sato and Clevers, 2013). 50’000 cells were lysed in 50ml cold Lysis buffer (10 mM Tris-HCl,pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After centrifugation at 500 g for 10 min at 4°C, cells were resuspended in 50 mL 1X Illumina transposition mix (25ml Tagment DNA Buffer, 2.5ml Tagment DNA Enzyme, 22.5ml nuclease-free H2O) and incubated for 30 min at 37°C on a shaker. Immediately following the transposition reaction, DNA was purified using the QIAgen MinElute PCR Purification Kit according to the manufacturer’s instructions.
Library was amplified with Nextera Sequencing primers in NEBNext Hot Start High-Fidelity 2X PCR master mix for 5 cycles. The appropriate number of additional PCR cycles was determined by qPCR. Amplified libraries were purified using the QIAgen MinElute PCR Purification Kit. DNA was eluted in 20ml EB buffer and quantified and visualized for quality control with a 2200 TapeStation System (Agilent). Libraries were sequenced on an Illumina HiSeq2500 with paired end 70 bp read configuration.

treatment_protocol: To induce Cre-ERT2-mediated recombination, tamoxifen (Sigma, 80 mg/kg) was injected intraperitoneally on two consecutive days. Mice were sacrificed 48 hours after the first tamoxifen injection.

value: small intestinal crypts

tag: strain/genotype

value: Tg(Vil1-cre/ERT2); Ctnnb1-wt/flox

tag: days post cre induction

tag: background strain


title: control2dpi-1


title: D164A2dpi-1

value: Tg(Vil1-cre/ERT2); Ctnnb1-D164A/flox


title: Tph1_cKO_nILC2_9

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

description: IL7R-cre, Tph1-flox nILC2 sample 4

data_processing:
Base calling and demultiplexing with Illumina Casava 2.1.7
Adapter trimming using FLEXBAR (v2.4)
Raw sequence reads were mapped to the mouse genome mm10/GRCm38 using the STAR aligner
Mapped reads were counted at the gene level using the Rsubread R package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez gene ID) in each sample

source_name: nILC2s from mesenteric lymph node

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

value: mesenteric lymph node

value: IL7R-cre, Tph1-flox


title: Tph1_cKO_1

description: IL7R-cre, Tph1-flox sample 1

source_name: ILC2s sorted from small intestine lamina propria

value: small intestine lamina propria


title: IL7R_9_1

description: IL7R-cre sample 3


title: IL7R_4

description: IL7R-cre sample 2


title: Tph1_cKO_3

description: IL7R-cre, Tph1-flox sample 3


title: ILTR_7_1

description: IL7R-cre sample 4


title: Tph1_cKO_2

description: IL7R-cre, Tph1-flox sample 2


title: IL7R_10

description: IL7R-cre sample 1


title: Tph1_cKO_nILC2_11

description: IL7R-cre, Tph1-flox nILC2 sample 3


title: Tph1_cKO_iILC2_9

description: IL7R-cre, Tph1-flox iILC2 sample 4

source_name: iILC2s from mesenteric lymph node


title: Tph1_cKO_nILC2_10

description: IL7R-cre, Tph1-flox nILC2 sample 2


title: Tph1_cKO_iILC2_11

description: IL7R-cre, Tph1-flox iILC2 sample 3


title: Tph1_cKO_iILC2_10

description: IL7R-cre, Tph1-flox iILC2 sample 2


title: IL7R_nILC2_4

description: IL7R-cre nILC2 sample 4


title: IL7R_nILC2_3

description: IL7R-cre nILC2 sample 3


title: IL7R_nILC2_2

description: IL7R-cre nILC2 sample 2


title: IL7R_iILC2_4

description: IL7R-cre iILC2 sample 4


title: IL7R_iILC2_3

description: IL7R-cre iILC2 sample 3


title: D164A2dpi-2


title: control2dpi-3


title: D164A2dpi-3


title: IL7R_iILC2_2

description: IL7R-cre iILC2 sample 2


title: Tph1_cKO_iILC2_13

description: IL7R-cre, Tph1-flox iILC2 sample 1


title: IL7R_nILC2_1

description: IL7R-cre nILC2 sample 1


title: Gplus3 miRNA-seq

city: Modena

first: Martina

last: Dori

address: Via G. Campi 287

department: Department of Life Sciences

country: Italy

institute: Center for Genome Research

data_processing:
Base calling was performed with bcl2fastq 1.8.2
Sequenced reads were trimmed for adapter sequence, reads shorter than 30 bp were aligned to miRBase v.20 using gsnap (2014-10-09)
All reads were also used to predict putative novel miRNAs using miRDeep2 (default parameters) and mm10 plus miRBase v20 as references
To build a unique reference for novel miRNA, we ordered them based on precursors genomic location, then a custom name was assigned following miRBase structure and consisting of miR-n- plus a progressive number to uniquely identify each hairpin, mature and star sequence
Differential expression analysis was performed using DESeq2 using default parameters
Genome_build: miRBase v20 and mm10

source_name: Newborn neurons

extract_protocol:
Brain of E14.5 embryos were dissected to remove meningies, ganglionic eminences and olofactory bulb. The isolated lateral cortex was then dissociated using the Neural Tissue Dissociation Kit with papain (Miltenyi Biotech, cat. no. 130-092-628) according to the manufacturer’s protocol and cell suspension was then sorted with a BD FACS Aria III using the reporter endogenous fluoresence. Sorted cells were kept on ice and total RNA was then extracted using the Quick RNA Mini Prep (Zymo Research, cat. no. R1054)
Libraries were prepared using the NEBNext Small RNA Library Prep Kit for Illumina (NEB, cat. no. E7330L)

value: brain lateral cortex

value: Embryonic day (E) 14.5


title: Tph1_cKO_nILC2_13

description: IL7R-cre, Tph1-flox nILC2 sample 1


title: Gplus2 miRNA-seq


title: RplusGminus2 miRNA-seq

source_name: Neural differentiative progenitor cells


title: IL7R_iILC2_1

description: IL7R-cre iILC2 sample 1


title: RminusGminus2 miRNA-seq

source_name: Neural proliferative progenitor cells


title: dm2

data_processing:
FastQC, alignment and counting on RSEMApp supported by SUSHI.
Pairwise comparisons were performed with the SUSHI application EdgeRApp
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: normalized counts and FPKM values from EdgeR

source_name: Intestinal epithelium

extract_protocol:
Control (n=3), KO (n=2), dm (n=3), ∆C (n=2) and D164A (n=3) mice were sacrificed 2d pi and the duodenal epithelial RNA isolation was performed as described (Gracz et al., 2012). Briefly, dissected duodenum was flushed thoroughly in ice-cold PBS, then opened longitudinally and incubated for 20 min on ice in dissociation buffer 1 (30 mM EDTA, 1.5 mM DTT in PBS), followed by 10 min incubation in dissociation buffer 2 (30 mM EDTA in PBS) at 37 °C under gentle agitation. The epithelium was released by vortexing, pelleted by centrifugation at 4 °C for 5 min at 1000g, and resuspended in 500 mL TRI Reagent (Sigma). RNA was extracted by phenol-chloroform precipitation. DNAse treatment was carried out with DNA-free DNA Removal Kit (Invitrogen) according to the manufacturer’s instructions.
Library preparation was performed with the Illumina TruSeq RNA Kit. RNA sequencing was performed on the Illumina NextSeq500 by the Functional Genomics Centre Zurich (FGCZ).

value: Intestinal epithelium

value: Tg(Vil1-cre/ERT2); Ctnnb1-dm/flox


title: RplusGminus1 miRNA-seq


title: RminusGminus3 miRNA-seq


title: DeltaC2

value: Tg(Vil1-cre/ERT2); Ctnnb1-DeltaC/flox


title: RminusGminus1 miRNA-seq


title: dm1


title: KO1

value: Tg(Vil1-cre/ERT2); Ctnnb1-flox/flox


title: DeltaC1


title: D164A3


title: D164A1


title: control4


title: control2


title: control1


title: control3


title: 2_0392_00EBOsaka_ocum2-treated

city: Osaka

first: Shugo

last: Suzuki

state: Osaka

address: 1-4-3 Asahi-machi, Abeno-ku

department: Molecular Pathology

country: Japan

institute: Osaka Metropolitan University Graduate School of Medicine

description: DMA

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering were applied.
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BW = Signal map in bigWIG format (UCSC).
Supplementary_files_format_and_content: BED = Standard BED file containing MACS peaks.

growth_protocol: Male and female 10-week-old CD-1 mice were mated.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: Mice were given 0 (control) or 200 ppm DMA for 10 days in the drinking water at the 8 days after mating. After parturition, the offspring were sacrificed on postnatal day 0.

tag: strain/background

value: Neonatal

tag: gender

value: Male

value: Lung

tag: treatment

value: Transplacental dimethylarsinic acid (DMA)

tag: antibody


title: 3_0397_00EBOsaka_Pooled_Input

description: Input DNA

tag: age

value: Pool of control and DMA treated


title: 1_0391_00EBOsaka_ocum1-control

description: Control

tag: tissue

value: Control


title: Gplus1 miRNA-seq

tag: strain


title: RplusGminus3 miRNA-seq


title: golli-τ-eGFP+ Foxp2 cKO 2 scRNA-seq

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
GTE-CKO2
GTE_UMI_count_table.txt
GTE_meta_data.txt

data_processing:
BCL files were demultiplexed with the i7 index using Illumina’s bcl2fastq v2.17.1.14 and mkfastq from 10x Genomics CellRanger v2.1.1
Extracted paired-end fastq files  include a 26 bp cell barcode (first 16 nt) and unique molecular identifier (UMI; next 10 nt)) (R1), and a 124 bp transcript sequence (R2), were checked for read quality using FASTQC v0.11.5 (Andrews 2010).
R1 reads were used to estimate and identify real cells using whitelist from UMI-tools v0.5.4 (Smith et al. 2017)
A whitelist of cell barcodes and R2 fastq files were used to extract reads corresponding to cells using extract from UMI-tools v0.5.4. This step also appended the cell barcode and UMI sequence information from R1 to read names in the R2 fastq file.
Extracted R2 reads were then aligned to the mouse reference genome (MM10/GRCm38p6) from the UCSC genome browser (Kent et al. 2002) and reference annotation (Gencode vM17) using STAR v2.5.2b (Dobin et al. 2013) allowing up to 5 mismatches
Uniquely mapped reads were then assigned to exons using featureCounts from the Subread package (v1.6.2) (Liao et al. 2014)
Assigned reads were sorted and indexed using Samtools v1.6 (Liao et al. 2014) and then used to generate raw expression UMI count tables using count from UMI-tools v0.5.4.
UMI counts from the same cell and gene from separate sequencing runs of the same libraries were summed. Only cells identifed in all sequencing runs from the same library were included.
Genome_build: MM10/GRCm38p6
Supplementary_files_format_and_content: raw UMI count tables (cells x genes); meta data by cell

source_name: golli-τ-eGFP+ cells from frontal isocortex

growth_protocol: All procedures were approved by the Institutional Animal Care and Use Committee of UT Southwestern. Emx1-Cre (Gorski et al. 2002) (#005628, Jackson Laboratory), Foxp2flox/flox (French et al. 2007) (#026259, Jackson Laboratory), Drd1a-tdTomato line 6 (Ade et al. 2011) (#016204, Jackson Laboratory), and golli-τ-eGFP (Jacobs et al. 2007) mice were backcrossed with C57BL/6J mice for at least 10 generations. Experimental mice (Foxp2 cKO) and control littermates were generated by crossing male Emx1-Cre; Foxp2flox/flox mice with female Foxp2flox/flox mice. The Drd1a-tdTomato BAC or golli-τ-eGFP transgene was present in mice of either sex for breeding. Mice were group-housed under a 12 h light/dark cycle and given ad libitum access to food and water.

extract_protocol:
Tissue was dissociated for scRNA-seq based on (Tasic et al. 2016). P7 mice were sacrificed by rapid decapitation and brains were quickly removed and placed in ice-cold artificial cerebrospinal fluid (ACSF) (126 mM NaCl, 20 mM NaHCO3, 20 mM D-Glucose, 3 mM KCl, 1.25 mM NaH2PO4, 2 mM CaCl2, 2 mM MgCl2) bubbled with 95% O2 and 5% CO2. 400-µm coronal sections were made in ACSF using a VF-200 Compresstome and transferred to a room temperature recovery chamber with ACSF containing channel blockers DL-AP5 sodium salt (50 µM), DNQX (20 µM), and tetrodotoxin (100 nM) (ACSF+). Frontal isocortex was separated from olfactory areas, cut into smaller pieces and incubated in 1 mg/ml pronase (#P6911, Sigma-Aldrich) in ACSF+ for 5 min. Pronase solution was replaced with 1% BSA in ACSF and tissue pieces were gently triturated into single-cell suspension using polished glass Pasteur pipettes with 600 µm, 300 µm, and 150 µm openings. Cells were filtered twice through Flowmi 40 µm Cell Strainers (#H13680-0040, Bel-Art) and live, single tdTomato+ cells were sorted using a BD FACSAria (BD Biosciences) at the UT Southwestern Flow Cytometry Facility. Tissue and library preparation were performed in the following batches on two separate days: Batch 1 – CTL1 (F), CKO1 (F); Batch 2 – CTL2 (F), CKO2 (M). For each batch, libraries were pooled and sequenced using an Illumina NextSeq 500 at the McDermott Sequencing Core at UT Southwestern.
After sorting, cells were centrifuged and resuspended in 0.04% BSA in ACSF to target 1000 cells/sample using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (#120237, 10x Genomics) (Zheng et al. 2017)

tag: genotype

value: golli-T-eGFP; Foxp2 flox/flox; Emx1-Cre; Foxp2 flox/flox

tag: Sex

value: Female

value: frontal isocortex

value: golli-T-eGFP+ cells


title: golli-τ-eGFP+ Control 2 scRNA-seq

description:
GTE-CTL2
GTE_UMI_count_table.txt
GTE_meta_data.txt

value: golli-T-eGFP; Foxp2 flox/flox


title: golli-τ-eGFP+ Foxp2 cKO 1 scRNA-seq

description:
GTE-CKO1
GTE_UMI_count_table.txt
GTE_meta_data.txt


title: KO2


title: Drd1a-tdTomato+ Foxp2 cKO 2 scRNA-seq

description:
D1Tom-CKO2
D1Tom_UMI_count_table.txt
D1Tom_meta_data.txt

source_name: Drd1a-tdTomato+ cells from frontal isocortex

value: Drd1a-tdTomato; Emx1-Cre; Foxp2 flox/flox

value: Drd1a-tdTomato+ cells


title: golli-τ-eGFP+ Control 1 scRNA-seq

description:
GTE-CTL1
GTE_UMI_count_table.txt
GTE_meta_data.txt


title: Drd1a-tdTomato+ Control 1 scRNA-seq

description:
D1Tom-CTL1
D1Tom_UMI_count_table.txt
D1Tom_meta_data.txt

value: Drd1a-tdTomato; Foxp2 flox/flox


title: bcCML Control shRNA Replicate 1

city: La Jolla

first: Michael

last: Hamilton

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UCSD

data_processing:
Kallisto – transcript quantification
Sleuth – gene differential expression analysis/gene normalized abundance measurements
Genome_build: hg38
Supplementary_files_format_and_content: .xls, TPM values and sleuth output

source_name: K562 cells

extract_protocol:
Rneasy Micro Plus kit
Illumina's Stranded Truseq

value: K562 cells

value: Control shRNA


title: D164A2

value: Intestinal epithelium

value: Tg(Vil1-cre/ERT2); Ctnnb1-D164A/flox


title: LS01_pres_ALL

source_name: PBMC

value: PBMC

tag: disease state

value: presentation ALL patient


title: bcCML Control shRNA Replicate 2


title: bcCML Stau2 shRNA Replicate 1

value: STAU2 shRNA


title: bcCML Control shRNA Replicate 3


title: LS01_relapse_AML

value: relapse AML patient


title: bcCML Stau2 shRNA Replicate 2


title: bcCML Stau2 shRNA Replicate 3


title: A-103_V16_MP216A-103_L5.LB8

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

data_processing:
Alignment STAR version STAR_2.3.1d
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using star STAR_2.3.1d
Gene counts were calculated by using HTSeq count
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited normalized gene counts table

source_name: Blood

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: patient id

tag: ethnicity

value: African heritage / african american

tag: protection

value: NOT PROTECTED


title: Reference_Pool_32_L7.LB15

value: Reference


title: A-33_V13_MP213A-33_L5.LB6

value: Female

value: Other

value: PROTECTED


title: R-136_V4_MP204R-136_L3.LB9

value: Male

value: White - caucasian / european heritage

value: RTSS+RTSS+RTSS


title: A-145_V2_MP000079_L3.LB8


title: A-145_V13_MP213A-145_L5.LB18


title: A-87_V7_MP207A-87_L4.LB18


title: R-23_V20_MP220R-23_L2.LB3


title: A-39_V19_MP219A-39_L6.LB3


title: US-1473439_L8.LB20


title: A-35_V9_MP209A-35_L5.LB5


title: R-155_V2_MP000081_L2.LB13


title: R-155_V7_MP207R-155_L3.LB22


title: A-103_V4_MP2R-7561_L3.LB19


title: R-72_V4_MP2R-7538_L5.LB16


title: Drd1a-tdTomato+ Foxp2 cKO 1 scRNA-seq

description:
D1Tom-CKO1
D1Tom_UMI_count_table.txt
D1Tom_meta_data.txt

value: Drd1a-tdTomato; Emx1-Cre; Foxp2 flox/flox

value: frontal isocortex

tag: cell type

value: Drd1a-tdTomato+ cells


title: Drd1a-tdTomato+ Control 2 scRNA-seq

description:
D1Tom-CTL2
D1Tom_UMI_count_table.txt
D1Tom_meta_data.txt

value: Drd1a-tdTomato; Foxp2 flox/flox


title: A-104_V10_MP210A-104_L6.LB25

value: Asian - central/south asian heritage


title: A-168_V2_MP0R-2301_L2.LB6


title: A-153_V5_MP205A-153_L3.LB11


title: R-28_V21_MP22R-1555_L2.LB4


title: R-75_V2_MP000A-149_L4.LB16


title: A-41_V22_MP222A-41_L3.LB11


title: R-36_V4_MP2R-7511_L2.LB14


title: R-159_V9_MP209R-159_L6.LB1


title: R-72_V21_MP22R-1598_L2.LB3


title: US-1472735_L6.LB12


title: R-64_V9_MP209R-64_L5.LB6


title: A-67_V19_MP219A-67_L2.LB3


title: A-135_V21_MP221A-135_L3.LB8


title: R-151_V13_MP213R-151_L1.LB21


title: US-1472785_L7.LB13


title: US-1472739_L6.LB20


title: R-28_V20_MP220R-28_L1.LB1


title: A-172_V20_MP22R-363_L2.LB1


title: A-139_V21_MP221A-139_L2.LB2


title: A-131_V8_MP208A-131_L3.LB27


title: A-35_V19_MP219A-35_L1.LB2


title: US-1472773_L6.LB12


title: A-47_V13_MP213A-47_L5.LB27


title: A-39_V8_MP208A-39_L4.LB19


title: R-136_V22_MP222R-136_L2.LB4


title: R-136_V21_MP221R-136_L1.LB25


title: A-172_V21_MP221A-172_L3.LB5


title: R-112_V9_MP209R-112_L6.LB6

value: American indian or alaskan native


title: R-72_V13_MP213R-72_L7.LB7


title: US-1473447_L1.LB19


title: A-131_V20_MP220A-131_L6.LB5


title: A-67_V5_MP205A-67_L7.LB21


title: A-168_V5_MP205A-168_L2.LB10


title: R-165_V19_MP219R-165_L1.LB2


title: R-40_V15_MP215R-40_L6.LB5


title: R-37_V8_MP208R-37_L6.LB4


title: R-159_V13_MP213R-159_L7.LB5


title: R-48_V4_MP2R-7520_L3.LB12


title: A-33_V20_MP220A-33_L1.LB6


title: R-112_V16_MP216R-112_L8.LB18


title: R-40_V5_MP205R-40_L4.LB15


title: A-157_V10_MP21A-352_L5.LB27


title: R-36_V9_MP209R-36_L4.LB1


title: A-41_V2_MP000R-136_L4.LB15


title: US-1469802_L6.LB10


title: R-165_V10_MP21A-358_L5.LB6


title: R-159_V4_MP204R-159_L4.LB15


title: A-107_V7_MP207A-107_L4.LB20


title: A-139_V8_MP208A-139_L4.LB18


title: US-1473463_L8.LB8


title: R-37_V4_MP204R-37_L4.LB19


title: US-1473470_L7.LB15


title: A-41_V9_MP209A-41_L6.LB5


title: A-87_V22_MP222A-87_L2.LB6


title: A-67_V16_MP216A-67_L3.LB19


title: A-67_V15_MP215A-67_L7.LB15


title: A-149_V22_MP222A-149_L2.LB10


title: Reference_Pool_07_L1.LB1


title: R-37_V13_MP213R-37_L7.LB11


title: R-155_V4_MP204R-155_L3.LB16


title: R-140_V2_MP000R-81_L1.LB16


title: Reference_Pool_19_L1.LB22


title: R-136_V5_MP205R-136_L3.LB11


title: R-48_V10_MP2R-15520_L5.LB2


title: A-149_V8_MP208A-149_L4.LB25


title: A-47_V22_MP222A-47_L2.LB7


title: A-180_V21_MP221A-180_L2.LB9


title: A-180_V22_MP222A-180_L2.LB11


title: R-140_V9_MP209R-140_L1.LB3


title: A-153_V9_MP209A-153_L4.LB18


title: A-117_V15_MP215A-117_L7.LB6


title: US-1472733_L7.LB14


title: R-64_V5_MP205R-64_L3.LB22


title: A-83_V4_MP204A-83_L4.LB21


title: US-1470R-48_L7.LB18


title: R-176_V19_MP219R-176_L1.LB23


title: A-145_V10_MP2R-15593_L2.LB20


title: Reference_Pool_14_L2.LB2


title: R-111_V7_MP207R-111_L4.LB25


title: R-155_V15_MP215R-155_L5.LB7


title: A-35_V13_MP213A-35_L6.LB11


title: Reference_Pool_04_L8.LB21


title: A-131_V19_MP219A-131_L3.LB3


title: R-28_V4_MP204R-28_L3.LB14


title: Reference_Pool_20_L7.LB14


title: R-64_V16_MP216R-64_L6.LB18


title: US-1472749_L6.LB12


title: R-151_V7_MP207R-151_L2.LB13


title: A-172_V2_MP202A-172_L4.LB13


title: R-75_V20_MP220R-75_L3.LB8


title: A-61_V2_MP000A-87_L2.LB8


title: R-40_V8_MP208R-40_L5.LB23


title: R-140_V5_MP205R-140_L1.LB19


title: R-176_V7_MP207R-176_L4.LB18


title: R-28_V22_MP222R-28_L2.LB7


title: US-1473479_L4.LB25


title: A-61_V21_MP221A-61_L1.LB1


title: A-83_V7_MP207A-83_L5.LB1


title: A-61_V9_MP209A-61_L5.LB25


title: R-128_V8_MP2R-12880_L6.LB3


title: R-128_V20_MP220R-128_L2.LB5


title: A-35_V10_MP21R-230_L6.LB9


title: R-155_V9_MP209R-155_L4.LB4


title: A-131_V15_MP215A-131_L2.LB12


title: R-81_V4_MP204R-81_L2.LB14


title: A-139_V5_MP205A-139_L3.LB13


title: R-68_V9_MP209R-68_L5.LB23


title: US-1472751_L8.LB13


title: A-172_V10_MP21R-363_L6.LB2


title: R-155_V8_MP208R-155_L4.LB27


title: A-71_V2_MP00R-282_L1.LB13


title: US-1469896_L7.LB8


title: A-83_V9_MP209A-83_L6.LB7


title: A-149_V2_MP00A-331_L2.LB13


title: A-39_V4_MP204A-39_L3.LB8


title: R-68_V10_MP2R-15535_L5.LB25


title: A-41_V16_MP216A-41_L7.LB14


title: US-1473387_L6.LB10


title: A-39_V15_MP215A-39_L5.LB1


title: R-72_V15_MP215R-72_L8.LB10


title: A-139_V7_MP207A-139_L4.LB16


title: A-33_V7_MP207A-33_L4.LB23


title: A-41_V7_MP207A-41_L5.LB25


title: A-47_V21_MP221A-47_L2.LB3


title: R-111_V15_MP215R-111_L6.LB11


title: A-35_V21_MP221A-35_L1.LB8


title: A-61_V19_MP219A-61_L6.LB12


title: A-39_V5_MP205A-39_L3.LB12


title: R-155_V21_MP221R-155_L1.LB5


title: A-103_V13_MP213A-103_L5.LB4


title: US-1473455_L6.LB13


title: A-83_V8_MP208A-83_L5.LB2


title: A-67_V22_MP222A-67_L1.LB13


title: A-139_V2_MP000R-111_L2.LB6


title: US-1472729_L7.LB20


title: R-28_V8_MP208R-28_L4.LB22


title: A-117_V16_MP216A-117_L7.LB8


title: R-128_V16_MP216R-128_L1.LB16


title: A-107_V15_MP215A-107_L6.LB7


title: A-25_V19_MP219A-25_L1.LB22


title: R-151_V16_MP216R-151_L4.LB25


title: R-37_V10_MP210R-37_L6.LB6


title: A-47_V7_MP207A-47_L4.LB16


title: A-47_V16_MP216A-47_L6.LB5


title: US-1472732_L7.LB10


title: R-75_V22_MP222R-75_L3.LB13


title: A-83_V22_MP222A-83_L3.LB11


title: US-1473388_L8.LB19


title: R-136_V19_MP219R-136_L1.LB21


title: A-35_V8_MP208A-35_L3.LB2


title: R-68_V8_MP208R-68_L5.LB21


title: A-139_V22_MP222A-139_L2.LB5


title: A-25_V7_MP207A-25_L4.LB19


title: R-75_V13_MP213R-75_L7.LB12


title: A-153_V4_MP2R-7599_L3.LB9


title: A-131_V4_MP2R-7582_L1.LB20


title: R-159_V15_MP215R-159_L7.LB9


title: A-157_V13_MP213A-157_L5.LB3


title: US-1472737_L6.LB14


title: A-103_V5_MP205A-103_L3.LB20


title: R-112_V13_MP213R-112_L7.LB10


title: A-35_V7_MP207A-35_L4.LB27


title: A-117_V10_MP210A-117_L5.LB27


title: A-25_V22_MP222A-25_L2.LB6


title: A-157_V20_MP22A-352_L2.LB1


title: R-75_V15_MP215R-75_L8.LB15


title: R-72_V8_MP208R-72_L6.LB23


title: A-145_V7_MP207A-145_L2.LB14


title: R-68_V19_MP219R-68_L1.LB23


title: A-149_V5_MP205A-149_L3.LB18


title: Reference_Pool_25_L2.LB22


title: A-157_V5_MP205A-157_L8.LB16


title: Reference_Pool_10_L6.LB16


title: A-157_V21_MP221A-157_L3.LB5


title: US-1472756_L7.LB10


title: A-67_V8_MP2R-12834_L5.LB3


title: R-128_V10_MP2R-15580_L6.LB5


title: A-131_V16_MP216A-131_L7.LB14


title: Reference_Pool_22_L8.LB21


title: Reference_Pool_09_L1.LB22


title: R-40_V22_MP222R-40_L3.LB9


title: R-37_V15_MP215R-37_L7.LB13


title: R-72_V22_MP222R-72_L3.LB7


title: R-176_V13_MP213R-176_L5.LB4


title: R-165_V9_MP209R-165_L5.LB3


title: R-68_V2_MP000A-153_L3.LB8


title: A-172_V5_MP205A-172_L4.LB14


title: A-168_V20_MP22R-360_L1.LB1


title: R-23_V21_MP221R-23_L3.LB4


title: A-61_V4_MP2R-7530_L3.LB11


title: R-36_V2_MP00R-286_L2.LB11


title: US-1473426_L7.LB15


title: A-33_V16_MP216A-33_L5.LB11


title: R-68_V21_MP221R-68_L1.LB1


title: R-36_V8_MP208R-36_L4.LB25


title: A-139_V13_MP213A-139_L5.LB22


title: A-180_V8_MP208A-180_L4.LB27


title: A-107_V19_MP219A-107_L7.LB10


title: R-140_V21_MP221R-140_L4.LB6


title: R-37_V9_MP209R-37_L7.LB9


title: R-128_V7_MP207R-128_L5.LB25


title: R-176_V2_MP0R-2303_L2.LB10


title: A-104_V7_MP207A-104_L4.LB15


title: A-47_V20_MP22R-239_L1.LB25


title: R-140_V8_MP208R-140_L3.LB1


title: US-1472787_L6.LB11


title: R-151_V4_MP204R-151_L1.LB9


title: R-36_V13_MP213R-36_L5.LB5


title: R-75_V16_MP216R-75_L8.LB19


title: R-128_V15_MP215R-128_L1.LB14


title: US-1472767_L7.LB16


title: R-72_V10_MP2R-15538_L6.LB3


title: A-39_V20_MP22R-233_L1.LB23


title: R-72_V16_MP216R-72_L8.LB12


title: US-1472758_L6.LB11


title: R-165_V16_MP216R-165_L6.LB10


title: Reference_Pool_18_L7.LB20


title: R-140_V16_MP216R-140_L7.LB15


title: R-48_V5_MP205R-48_L3.LB13


title: R-37_V5_MP205R-37_L4.LB20


title: A-153_V21_MP221A-153_L5.LB2


title: US-1472741_L8.LB14


title: Reference_Pool_15_L1.LB1


title: R-28_V13_MP213R-28_L5.LB2


title: R-36_V22_MP222R-36_L2.LB9


title: A-172_V22_MP222A-172_L3.LB8


title: A-39_V7_MP207A-39_L4.LB14


title: A-33_V19_MP219A-33_L1.LB2


title: R-81_V20_MP220R-81_L1.LB4


title: US-1473462_L6.LB13


title: A-39_V10_MP21R-233_L5.LB23


title: R-159_V21_MP221R-159_L3.LB6


title: A-103_V21_MP221A-103_L2.LB8


title: A-135_V5_MP205A-135_L4.LB16


title: R-165_V20_MP22A-358_L1.LB6


title: Reference_Pool_21_L2.LB1


title: A-157_V16_MP216A-157_L4.LB6


title: R-112_V20_MP220R-112_L2.LB6


title: A-131_V2_MP000048_L5.LB14


title: US-1472768_L6.LB14


title: R-165_V22_MP222R-165_L2.LB12


title: R-81_V5_MP205R-81_L3.LB16


title: R-64_V10_MP2R-15532_L4.LB7


title: R-159_V7_MP207R-159_L5.LB21


title: R-112_V10_MP2R-15568_L6.LB8


title: R-37_V7_MP207R-37_L5.LB27


title: R-48_V19_MP219R-48_L6.LB11


title: Reference_Pool_06_L8.LB15


title: A-87_V4_MP2R-7549_L3.LB11


title: A-153_V20_MP220A-153_L4.LB27


title: R-48_V15_MP215R-48_L7.LB6


title: R-151_V21_MP221R-151_L3.LB4


title: A-33_V4_MP2R-7509_L3.LB15


title: US-1473504_L6.LB12


title: A-41_V21_MP221A-41_L2.LB7


title: US-1473449_L6.LB13


title: R-28_V5_MP205R-28_L3.LB15


title: A-67_V20_MP22A-254_L1.LB5


title: R-48_V20_MP220R-48_L1.LB27


title: A-157_V22_MP222A-157_L3.LB6


title: R-165_V2_MP000077_L2.LB13


title: R-128_V4_MP2R-7580_L4.LB18


title: A-180_V20_MP220A-180_L1.LB5


title: R-36_V16_MP216R-36_L5.LB9


title: R-159_V19_MP219R-159_L2.LB27


title: R-155_V22_MP222R-155_L2.LB10


title: R-23_V22_MP222R-23_L3.LB7


title: A-61_V10_MP2R-15530_L5.LB1


title: A-172_V8_MP208A-172_L5.LB22


title: A-104_V19_MP219A-104_L2.LB23


title: A-172_V7_MP207A-172_L5.LB19


title: A-107_V5_MP205A-107_L4.LB18


title: A-117_V20_MP220A-117_L1.LB27


title: A-107_V16_MP216A-107_L7.LB9


title: A-104_V2_MP000A-83_L3.LB9


title: A-131_V10_MP2R-15582_L3.LB6


title: R-72_V2_MP000A-139_L4.LB11


title: A-39_V13_MP213A-39_L5.LB25


title: A-117_V8_MP208A-117_L4.LB23


title: A-131_V22_MP222A-131_L3.LB11


title: A-71_V16_MP216A-71_L7.LB13


title: R-165_V4_MP204R-165_L3.LB19


title: A-180_V13_MP213A-180_L5.LB5


title: A-71_V8_MP208A-71_L5.LB25


title: US-1472744_L7.LB11


title: A-149_V7_MP207A-149_L4.LB22


title: A-172_V13_MP213A-172_L7.LB6


title: US-1473460_L7.LB12


title: A-104_V5_MP205A-104_L6.LB13


title: US-1469774_L4.LB1


title: R-111_V8_MP208R-111_L4.LB2


title: A-145_V9_MP209A-145_L5.LB19


title: Reference_Pool_17_L1.LB1


title: R-151_V2_MP000A-107_L2.LB7


title: R-112_V22_MP222R-112_L3.LB12


title: R-64_V4_MP2R-7532_L7.LB23


title: A-131_V21_MP221A-131_L4.LB7


title: A-33_V15_MP215A-33_L5.LB10


title: A-25_V20_MP220A-25_L2.LB2


title: A-180_V4_MP204A-180_L3.LB16


title: R-40_V13_MP213R-40_L6.LB4


title: A-135_V19_MP219A-135_L2.LB2


title: A-35_V20_MP22R-230_L2.LB6


title: R-28_V7_MP207R-28_L4.LB20


title: Reference_Pool_01_L1.LB1


title: A-33_V21_MP22R-1559_L1.LB7


title: R-75_V5_MP205R-75_L5.LB22


title: Reference_Pool_28_L1.LB5


title: R-40_V10_MP21R-234_L5.LB2


title: R-176_V5_MP205R-176_L3.LB16


title: US-1469858_L5.LB14


title: Reference_Pool_16_L4.LB21


title: A-71_V21_MP221A-71_L5.LB9


title: R-37_V19_MP219R-37_L2.LB3


title: A-61_V13_MP213A-61_L6.LB5


title: US-1472770_L6.LB15


title: A-39_V9_MP209A-39_L5.LB21


title: A-61_V5_MP205A-61_L3.LB14


title: R-140_V20_MP220R-140_L4.LB4


title: R-48_V8_MP208R-48_L4.LB20


title: R-23_V5_MP205R-23_L8.LB12


title: R-72_V5_MP205R-72_L5.LB18


title: R-151_V19_MP219R-151_L4.LB27


title: A-67_V13_MP213A-67_L7.LB12


title: A-103_V10_MP2R-15561_L4.LB2


title: A-71_V22_MP222A-71_L4.LB12


title: A-172_V19_MP219A-172_L2.LB25


title: R-64_V8_MP208R-64_L4.LB4


title: A-107_V20_MP220A-107_L2.LB3


title: R-111_V5_MP205R-111_L3.LB21


title: US-1472734_L4.LB2


title: A-33_V2_MP000078_L2.LB12


title: A-35_V16_MP216A-35_L5.LB16


title: US-1473488_L8.LB15


title: A-87_V15_MP215A-87_L5.LB4


title: A-41_V8_MP208A-41_L6.LB4


title: A-107_V13_MP213A-107_L5.LB1


title: A-61_V16_MP216A-61_L6.LB10


title: A-71_V9_MP209A-71_L2.LB2


title: A-107_V4_MP2R-7564_L3.LB13


title: A-41_V19_MP219A-41_L2.LB2


title: A-61_V20_MP220A-61_L1.LB25


title: R-128_V19_MP219R-128_L2.LB4


title: A-33_V9_MP209A-33_L4.LB2


title: A-139_V4_MP204A-139_L3.LB10


title: US-1472730_L7.LB14


title: R-64_V13_MP213R-64_L3.LB10


title: R-72_V20_MP22A-258_L2.LB2


title: A-145_V15_MP215A-145_L4.LB23


title: A-145_V19_MP219A-145_L4.LB1


title: R-37_V22_MP222R-37_L3.LB12


title: US-1471975_L6.LB5


title: A-117_V13_MP213A-117_L5.LB3


title: R-155_V20_MP22A-350_L1.LB3


title: A-25_V5_MP205A-25_L3.LB13


title: A-168_V13_MP213A-168_L3.LB21


title: A-139_V20_MP220A-139_L1.LB1


title: A-71_V5_MP205A-71_L1.LB18


title: R-155_V5_MP205R-155_L3.LB20


title: A-168_V8_MP208A-168_L4.LB14


title: A-61_V7_MP207A-61_L4.LB19


title: R-111_V21_MP221R-111_L1.LB7


title: A-157_V9_MP209A-157_L4.LB23


title: R-68_V15_MP215R-68_L6.LB4


title: A-135_V8_MP208A-135_L5.LB25


title: A-87_V13_MP213A-87_L5.LB1


title: A-168_V22_MP222A-168_L2.LB5


title: US-1473365_L7.LB21


title: A-25_V4_MP2R-7503_L3.LB11


title: A-41_V15_MP215A-41_L7.LB13


title: R-151_V20_MP220R-151_L5.LB2


title: A-180_V2_MP202A-180_L3.LB15


title: R-75_V7_MP207R-75_L5.LB1


title: A-103_V20_MP220A-103_L1.LB5


title: A-180_V16_MP216A-180_L6.LB12


title: R-176_V8_MP208R-176_L4.LB22


title: R-176_V21_MP221R-176_L2.LB4


title: A-67_V4_MP2R-7534_L6.LB19


title: Reference_Pool_29_L4.LB1


title: A-168_V21_MP221A-168_L1.LB3


title: A-180_V9_MP209A-180_L5.LB4


title: R-64_V15_MP215R-64_L5.LB14


title: US-1472745_L6.LB13


title: R-75_V9_MP209R-75_L6.LB7


title: R-28_V9_MP209R-28_L5.LB25


title: A-168_V15_MP215A-168_L5.LB22


title: R-36_V5_MP205R-36_L3.LB19


title: US-1472721_L8.LB20


title: R-140_V7_MP207R-140_L2.LB22


title: R-140_V13_MP213R-140_L2.LB8


title: A-83_V19_MP219A-83_L2.LB2


title: R-112_V19_MP219R-112_L2.LB3


title: US-1472760_L4.LB14


title: A-47_V19_MP219A-47_L7.LB9


title: Reference_Pool_24_L7.LB12


title: A-39_V22_MP222A-39_L2.LB3


title: R-68_V22_MP222R-68_L2.LB5


title: R-128_V9_MP209R-128_L6.LB8


title: R-176_V15_MP215R-176_L7.LB8


title: R-159_V2_MP000A-145_L4.LB12


title: R-165_V7_MP207R-165_L4.LB23


title: US-1472776_L7.LB13


title: A-83_V2_MP000076_L4.LB15


title: A-103_V15_MP215A-103_L5.LB7


title: R-64_V20_MP22A-252_L2.LB7


title: R-23_V13_MP213R-23_L6.LB2


title: A-153_V10_MP2R-15599_L2.LB20


title: A-157_V2_MP00R-288_L3.LB8


title: R-68_V7_MP207R-68_L4.LB18


title: US-1472725_L8.LB18


title: A-157_V15_MP215A-157_L7.LB5


title: A-135_V22_MP222A-135_L3.LB11


title: Reference_Pool_02_L6.LB18


title: A-103_V19_MP219A-103_L1.LB2


title: A-33_V5_MP205A-33_L3.LB18


title: A-131_V9_MP209A-131_L2.LB4


title: R-112_V5_MP205R-112_L5.LB23


title: A-103_V22_MP222A-103_L2.LB11


title: A-87_V16_MP216A-87_L6.LB5


title: R-111_V2_MP00A-332_L2.LB14


title: R-36_V15_MP215R-36_L5.LB8


title: R-81_V21_MP221R-81_L1.LB6


title: A-47_V5_MP205A-47_L3.LB12


title: A-104_V13_MP213A-104_L6.LB1


title: A-149_V20_MP220A-149_L1.LB3


title: A-103_V9_MP209A-103_L4.LB1


title: US-1469773_L7.LB18


title: R-48_V7_MP207R-48_L3.LB15


title: R-159_V16_MP216R-159_L8.LB11


title: R-48_V22_MP222R-48_L2.LB6


title: R-72_V19_MP219R-72_L2.LB23


title: R-37_V16_MP216R-37_L1.LB18


title: R-159_V20_MP22A-353_L3.LB4


title: A-145_V22_MP222A-145_L2.LB6


title: R-64_V21_MP22R-1592_L2.LB10


title: R-128_V13_MP213R-128_L7.LB12


title: A-145_V4_MP2R-7593_L1.LB11


title: R-112_V7_MP207R-112_L5.LB27


title: A-153_V15_MP215A-153_L3.LB23


title: Reference_Pool_03_L2.LB1


title: R-140_V22_MP222R-140_L5.LB10


title: R-136_V13_MP213R-136_L5.LB27


title: R-176_V22_MP222R-176_L2.LB7


title: A-104_V4_MP204A-104_L4.LB11


title: R-136_V7_MP207R-136_L4.LB15


title: A-41_V20_MP220A-41_L2.LB5


title: A-157_V19_MP219A-157_L2.LB25


title: US-1472747_L7.LB15


title: R-40_V21_MP221R-40_L2.LB6


title: US-1473428_L6.LB16


title: R-140_V19_MP219R-140_L6.LB2


title: A-103_V2_MP000073_L2.LB12


title: A-117_V2_MP00R-285_L2.LB8


title: R-151_V5_MP205R-151_L5.LB10


title: A-117_V21_MP221A-117_L1.LB3


title: A-135_V10_MP210A-135_L6.LB3


title: R-68_V16_MP216R-68_L6.LB7


title: R-23_V2_MP000R-128_L3.LB10


title: A-35_V15_MP215A-35_L4.LB13


title: R-68_V4_MP2R-7535_L4.LB14


title: A-117_V22_MP222A-117_L2.LB5


title: A-71_V15_MP215A-71_L3.LB10


title: A-153_V22_MP222A-153_L5.LB4


title: Reference_Pool_08_L7.LB21


title: A-149_V13_MP213A-149_L5.LB3


title: A-67_V7_MP207A-67_L4.LB25


title: A-41_V4_MP204A-41_L4.LB19


title: R-128_V5_MP205R-128_L5.LB23


title: R-36_V21_MP221R-36_L2.LB8


title: R-112_V8_MP208R-112_L5.LB2


title: A-25_V8_MP208A-25_L4.LB20


title: R-48_V13_MP213R-48_L5.LB3


title: R-75_V8_MP208R-75_L6.LB3


title: R-165_V8_MP208R-165_L4.LB1


title: A-47_V4_MP204A-47_L3.LB10


title: R-48_V9_MP209R-48_L4.LB23


title: R-68_V13_MP213R-68_L6.LB2


title: R-112_V4_MP204R-112_L4.LB21


title: A-25_V15_MP215A-25_L6.LB6


title: US-1472775_L7.LB18


title: R-111_V4_MP2R-7567_L3.LB20


title: A-107_V8_MP208A-107_L5.LB22


title: A-25_V13_MP213A-25_L5.LB1


title: A-149_V16_MP216A-149_L5.LB6


title: A-67_V21_MP22R-1594_L1.LB9


title: A-145_V21_MP221A-145_L3.LB5


title: A-35_V5_MP205A-35_L3.LB20


title: R-159_V22_MP222R-159_L3.LB9


title: A-104_V21_MP221A-104_L2.LB2


title: A-168_V19_MP219A-168_L5.LB23


title: A-168_V4_MP204A-168_L1.LB8


title: US-1472759_L1.LB20


title: R-111_V19_MP219R-111_L1.LB3


title: A-117_V19_MP219A-117_L1.LB23


title: A-67_V2_MP2R-4834_L3.LB15


title: A-41_V13_MP213A-41_L7.LB11


title: US-1473453_L1.LB27


title: A-117_V7_MP207A-117_L4.LB19


title: A-131_V5_MP205A-131_L6.LB21


title: R-165_V13_MP213R-165_L5.LB7


title: A-135_V15_MP215A-135_L6.LB6


title: R-72_V9_MP209R-72_L6.LB27


title: A-135_V7_MP207A-135_L4.LB19


title: US-1473389_L7.LB19


title: R-136_V20_MP220R-136_L1.LB22


title: A-180_V15_MP215A-180_L6.LB9


title: A-104_V20_MP220A-104_L2.LB27


title: US-1471990_L6.LB10


title: R-159_V10_MP21A-353_L7.LB4


title: R-136_V8_MP208R-136_L4.LB20


title: R-36_V7_MP207R-36_L3.LB21


title: A-67_V10_MP2R-15534_L6.LB8


title: US-1472726_L6.LB9


title: R-128_V21_MP22R-1650_L3.LB9


title: R-151_V8_MP208R-151_L3.LB16


title: A-107_V2_MP000060_L3.LB12


title: US-1473458_L7.LB11


title: R-48_V16_MP216R-48_L7.LB9


title: A-71_V13_MP213A-71_L6.LB7


title: US-1472740_L8.LB16


title: A-172_V4_MP204A-172_L4.LB10


title: R-128_V22_MP222R-128_L3.LB13


title: R-128_V2_MP00A-335_L4.LB16


title: US-1473452_L7.LB14


title: R-81_V2_MP00A-330_L3.LB15


title: A-103_V7_MP207A-103_L4.LB23


title: A-145_V5_MP205A-145_L3.LB12


title: A-61_V8_MP208A-61_L4.LB21


title: R-176_V20_MP22R-366_L1.LB2


title: Reference_Pool_13_L1.LB22


title: R-176_V9_MP209R-176_L5.LB27


title: US-1472750_L7.LB13


title: R-165_V15_MP215R-165_L5.LB8


title: Reference_Pool_23_L1.LB20


title: A-135_V16_MP216A-135_L6.LB8


title: US-1472769_L7.LB15


title: A-83_V21_MP221A-83_L3.LB8


title: A-83_V20_MP220A-83_L2.LB6


title: A-131_V13_MP213A-131_L4.LB9


title: A-39_V21_MP221A-39_L1.LB27


title: A-135_V13_MP213A-135_L5.LB27


title: A-157_V4_MP204A-157_L7.LB14


title: US-1473337_L7.LB13


title: Reference_Pool_27_L1.LB1


title: Reference_Pool_26_L5.LB16


title: A-180_V7_MP207A-180_L4.LB22


title: A-87_V5_MP205A-87_L3.LB12


title: A-145_V20_MP220A-145_L1.LB3


title: R-112_V21_MP221R-112_L3.LB9


title: A-107_V21_MP221A-107_L2.LB7


title: A-87_V2_MP000044_L2.LB9


title: A-172_V15_MP215A-172_L7.LB8


title: US-1473427_L6.LB19


title: A-117_V5_MP205A-117_L3.LB16


title: A-135_V4_MP204A-135_L3.LB14


title: R-23_V7_MP207R-23_L4.LB18


title: A-83_V10_MP210A-83_L7.LB10


title: R-40_V20_MP22R-234_L2.LB5


title: A-25_V9_MP209A-25_L5.LB22


title: A-145_V8_MP208A-145_L3.LB15


title: A-39_V2_MP000R-75_L2.LB7


title: R-112_V2_MP000042_L3.LB14


title: A-61_V22_MP222A-61_L2.LB5


title: A-47_V15_MP215A-47_L6.LB3


title: R-28_V2_MP00A-334_L2.LB10


title: US-1472720_L6.LB7


title: A-25_V16_MP216A-25_L6.LB8


title: R-64_V22_MP222R-64_L2.LB12


title: R-140_V15_MP215R-140_L6.LB11


title: A-35_V4_MP204A-35_L5.LB18


title: A-168_V10_MP21R-360_L5.LB19


title: US-1472722_L7.LB9


title: A-168_V7_MP207A-168_L3.LB12


title: A-153_V13_MP213A-153_L1.LB16


title: R-28_V16_MP216R-28_L7.LB9


title: R-48_V2_MP000047_L2.LB9


title: R-75_V10_MP2R-15540_L7.LB9


title: A-153_V8_MP208A-153_L4.LB15


title: R-37_V2_MP00R-287_L3.LB14


title: R-64_V7_MP207R-64_L7.LB1


title: A-103_V8_MP208A-103_L4.LB27


title: R-165_V21_MP22A-1688_L2.LB8


title: A-35_V22_MP222A-35_L2.LB11


title: R-75_V4_MP2R-7540_L4.LB18


title: R-111_V22_MP222R-111_L2.LB10


title: R-36_V10_MP21R-231_L4.LB3


title: A-149_V15_MP215A-149_L5.LB5


title: US-1472757_L7.LB15


title: A-25_V21_MP22R-1553_L2.LB4


title: A-153_V19_MP219A-153_L3.LB25


title: US-1473518_L7.LB19


title: R-64_V2_MP000075_L1.LB14


title: R-72_V7_MP207R-72_L5.LB20


title: R-75_V21_MP221R-75_L3.LB10


title: R-64_V19_MP219R-64_L2.LB4


title: Reference_Pool_05_L2.LB22


title: A-153_V2_MP000084_L5.LB7


title: A-87_V21_MP221A-87_L1.LB2


title: A-157_V8_MP208A-157_L8.LB22


title: US-1472728_L6.LB6


title: A-71_V20_MP220A-71_L6.LB8


title: A-131_V7_MP207A-131_L5.LB23


title: A-25_V2_MP000087_L3.LB9


title: A-71_V19_MP219A-71_L7.LB16


title: R-48_V21_MP221R-48_L1.LB3


title: A-153_V7_MP207A-153_L2.LB13


title: A-117_V4_MP204A-117_L3.LB13


title: US-1472727_L5.LB9


title: A-157_V7_MP207A-157_L8.LB19


title: R-81_V22_MP222R-81_L2.LB9


title: A-61_V15_MP215A-61_L7.LB7


title: R-36_V20_MP22R-231_L1.LB4


title: R-37_V20_MP220R-37_L2.LB7


title: A-107_V22_MP222A-107_L3.LB10


title: R-140_V10_MP210R-140_L5.LB5


title: A-87_V8_MP208A-87_L4.LB21


title: R-111_V20_MP220R-111_L1.LB4


title: R-68_V20_MP220R-68_L1.LB27


title: Reference_Pool_11_L2.LB1


title: R-40_V7_MP207R-40_L4.LB21


title: R-68_V5_MP205R-68_L4.LB15


title: US-1473478_L8.LB11


title: R-28_V15_MP215R-28_L7.LB7


title: US-1472762_L7.LB19


title: R-159_V8_MP208R-159_L6.LB25


title: A-149_V21_MP221A-149_L1.LB7


title: US-1473454_L7.LB16


title: US-1472772_L6.LB14


title: US-1472742_L6.LB16


title: Reference_Pool_12_L1.LB21


title: US-1469861_L6.LB4


title: A-83_V5_MP205A-83_L5.LB22


title: R-28_V19_MP219R-28_L1.LB25


title: US-1472771_L2.LB3


title: R-151_V15_MP215R-151_L5.LB22


title: A-39_V16_MP216A-39_L6.LB2


title: US-1473445_L7.LB11


title: Reference_Pool_31_L1.LB21


title: Reference_Pool_30_L7.LB20


title: R-140_V4_MP204R-140_L2.LB15


title: A-104_V15_MP215A-104_L7.LB4


title: US-1472723_L7.LB12


title: A-104_V8_MP208A-104_L5.LB21


title: R-112_V15_MP215R-112_L8.LB16


title: R-75_V19_MP219R-75_L2.LB4


title: R-23_V8_MP208R-23_L5.LB20


title: R-81_V7_MP207R-81_L3.LB21


title: US-1472748_L6.LB13


title: A-135_V20_MP220A-135_L2.LB4