title: ssCAGE, Heart, (Sample 57)

value: F

value: right ventricle


title: AS4

status: Public on Oct 20 2022

type: SRA

city: Wuhan

first: Qiang

last: Li

state: Saskatchewan

address: #1 Shizishan Street

country: China

institute: Huazhong Agricultural University

library_source: transcriptomic

data_processing:
Trimming using Trimmomatics
Read mapping using STAR
Alignment using Cufflinks
featureCounts was then employed to count the reads spread across the exonic regions of each gene model.
Differentially expression analysis using DESeq2
Genome_build: IWGSC RefSeq 1.1
Supplementary_files_format_and_content: featureCounts was then employed to count the reads of each gene model.

molecule: total RNA

organism: Triticum aestivum

growth_protocol: Wheat plants were grown in growth chambers under long-day conditions of 16 h of light, 22°C and 8 h of dark, 20°C, with light intensity of 100 to 120 μmol m−2 s−1 (Philips high-output F54T5/835-841 bulbs) for the whole life cycle.

extract_protocol:
Total RNA from crowns were extracted using a Plant RNA Isolation Mini Kit (Agilent Technologies, Mississauga, ON).
144 cDNA libraries were constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) with two replicates for each sample at each stage.

treatment_protocol: Spikelets were emasculated and pollinated at the heading stage to ensure sufficient and developmentally coordinated F1 seed production for embryo and endosperm isolation.

tag: tissue

value: embryo

tag: developmental stage

value: leaf early

tag: maternal ploidy

value: hexploid

tag: paternal ploidy

value: tetraploid

tag: line

value: A×S


title: AS3

value: transition


title: AS2

value: octant


title: EGJ_014N

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: high methylation gastric cancer case

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from cell lines or clinical samples using QIAquick DNA mini kit according to standard instructions

tag: sample type

value: clinical sample

tag: disease state

value: non-neoplastic gastric mucosa


title: EGJ459T

value: gastric cancer


title: AS1

value: 2 cell


title: ssCAGE, Heart, (Sample 54)

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

institute: Juntendo University

data_processing:
Illumina Casava1.8 software used for basecalling.
CAGE sequences were trimmed with fastx_trimmer ( -Q33 -l 50), adapters were removed with trimmomatic, rRNAdust program was used to remove ribosomal sequences matched to ribosomal DNA repeating unit U13369.1
Reads were mapped with BWA, unmapped reads remapped by HISAT2.
CAGE transcription start sites (CTSS) files produced by CAGEr Bioconductor package with the following parameters: sequencingQualityThreshold = 10, mappingQualityThreshold = 20, removeFirstG = TRUE, correctSystematicG = TRUE
Signal clustering done through DPI (https://github.com/hkawaji/dpi1/) and bidir_enhancers (https://github.com/anderssonrobin/enhancers) algoritms
Genome_build: hg38 UCSC
Supplementary_files_format_and_content: CTSS files were created from BAM files using python script and shell commands; BED files for robust (TPM>1), permissive (>3 tags) DPI clusters, and bidirectional enhancers were produced with DPI and bidir_enhancers algorithms.

source_name: Heart

extract_protocol:
Explanted hearts were arrested with the cardioplegic solution and cooled down to +4 °C for transportation. 0.5 cm3 pieces were collected from the left and right atrial free wall, right and left ventricular base, and inferior and superior sinoatrial node. The tissue was flash frozen or stored in RNAlater (Invitrogen) overnight at +4 °C and stored at -80 °C. Total mRNA was extracted from 40 mg of tissue with RNeasy Fibrous Tissue Mini Kit (Qiagen). RNA purity and yield were quality checked with Agilent Bioanalyzer to satisfy RIN >7 and total RNA amount 3-5 μg.
Total RNA was submitted for no-amplification non-tagging CAGE (nAnT-iCAGE) library preparation for the first 13 samples; the rest of the samples were processed through recent single strand (ss) CAGE protocol (Morioka et al., Methods in Molecular Biology, 2020).

tag: gender

tag: chamber

value: left atrium

tag: age

tag: state

value: healthy


title: ssCAGE, Heart, (Sample 56)

value: right atrium


title: ssCAGE, Heart, (Sample 55)

value: left ventricle


title: ssCAGE, Heart, (Sample 67)

value: M


title: EGJ431T


title: AC19

value: endorsperm

value: late endosperm

value: A×C


title: ssCAGE, Heart, (Sample 52)

value: F


title: ssCAGE, Heart, (Sample 53)

value: right ventricle


title: ssCAGE, Heart, (Sample 51)


title: AC18

value: early endosperm

value: hexploid

value: tetraploid


title: AC17

value: embryo

value: mature


title: EGJ_534T_1

value: clinical sample

value: gastric cancer


title: AC16

value: leaf late


title: ssCAGE, Heart, (Sample 50)

value: left atrium

value: healthy


title: ssCAGE, Heart, (Sample 49)

value: iSAN


title: AC14

value: leaf early


title: EGJ082T


title: ssCAGE, Heart, (Sample 48)

value: sSAN


title: GC191T_HME

source_name: immortalised normal gastric epithelial cell


title: ssCAGE, Heart, (Sample 47)


title: EGJ050T


title: AC13

value: transition


title: EGJ198N

value: non-neoplastic gastric mucosa


title: AC12

value: octant

value: A×C


title: AC15

value: leaf middle


title: EGJ013N


title: ssCAGE, Heart, (Sample 45)

value: F

value: left ventricle


title: GC177T_OUT_EGJ-II


title: EGJ179T


title: AC9

value: endorsperm

value: late endosperm

value: hexploid

value: tetraploid


title: EGJ258N

value: clinical sample


title: EGJ385N


title: AC7

value: embryo

value: mature


title: AC11

value: 2 cell


title: ssCAGE, Heart, (Sample 41)

value: right ventricle

value: healthy


title: ssCAGE, Heart, (Sample 46)

value: right atrium


title: ssCAGE, Heart, (Sample 42)

value: sSAN


title: ssCAGE, Heart, (Sample 43)

value: iSAN


title: AC6

value: leaf late

value: A×C


title: EGJ176T_II

value: gastric cancer


title: GC177N_IM+

value: non-neoplastic gastric mucosa


title: AC5

value: leaf middle


title: EGJ105T_II


title: GC226T_OUT_EGJ-II


title: AC3

value: transition


title: GC215T_HME-U_EGJ-II


title: ssCAGE, Heart, (Sample 38)

value: F

value: left atrium


title: EGJ269T_II

value: clinical sample


title: ssCAGE, Heart, (Sample 40)

value: left ventricle


title: EGJ013T_II


title: H04-05353 T


title: AC4

value: embryo

value: leaf early

value: hexploid

value: tetraploid


title: AC8

value: endorsperm

value: early endosperm


title: ssCAGE, Heart, (Sample 36)

value: healthy


title: mKRC.1_MRTX_3day

city: Aurora

first: Lynn

last: Heasley

state: CO

department: Craniofacial Biology

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
Fastq files were quality checked with FastQC
illumina adapters trimmed with bbduk, and mapped to the mouse mm10 genome with STAR aligner
Counts were generated by STAR’s internal counter and reads were normalized to counts per million (CPM) using the edgeR R package
Assembly: Mus musculus mm10
Supplementary files format and content: excel files include CPM values for each sample.
Supplementary files format and content: matrix table excel file (.xlsx) includes CPM values for all samples

organism: Mus musculus

growth_protocol: LLC, CMT, and mKRC.1 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillen/streptomycin in a humidified incubator with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using Rneasy mini plus kit (Qiagen), including the genomic DNA elimination step.
Libraries were constructed using an Illumina TruSEQ stranded mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA was combined with RNA purification beads to bind PolyA RNA to oligodT magnetic beads. mRNA was eluted and converted to double stranded DNA. A-tailing, adapter ligation, and PCR amplification using 15 cycles was performed to complete the library construction.

treatment_protocol: Cells were treated with 100nM MRTX-1257 or DMSO control

tag: cell line

tag: genotype

value: parental

tag: treatment


title: AC2

value: octant

value: A×C


title: mKRC.1_MRTX_2day


title: AC1

value: 2 cell


title: ssCAGE, Heart, (Sample 37)

value: right ventricle


title: SC19

organism: Triticum turgidum

value: late endosperm

value: S×C


title: mKRC.1_MRTX_6hr


title: ssCAGE, Heart, (Sample 35)

value: F

value: right atrium


title: ssCAGE, Heart, (Sample 44)

value: left atrium


title: ssCAGE, Heart, (Sample 33)


title: H14-06219 T

value: clinical sample

value: gastric cancer


title: mKRC.1_DMSO_2day

value: DMSO


title: ssCAGE, Heart, (Sample 31)


title: SC15

value: embryo

value: leaf middle

value: tetraploid


title: H05-00557 T


title: ssCAGE, Heart, (Sample 34)

value: healthy


title: SC18

value: endorsperm

value: early endosperm


title: H14-06190 T


title: H08-10327 T


title: mKRC.1_DMSO_3day

value: parental


title: mKRC.1_DMSO_6hr


title: H13-08975 T


title: mKRC.1_DMSO_1day


title: SC16

value: leaf late


title: H14-06190 N

value: non-neoplastic gastric mucosa


title: CMT55_MRTX_D5

value: edited


title: ssCAGE, Heart, (Sample 32)

value: left ventricle


title: ssCAGE, Heart, (Sample 29)

value: F

value: right ventricle


title: SC13

value: transition

value: S×C


title: ssCAGE, Heart, (Sample 39)

value: right atrium


title: ssCAGE, Heart, (Sample 28)


title: H08-10116 T

value: clinical sample

value: gastric cancer


title: H12-12936 T


title: H07-08275 T


title: ssCAGE, Heart, (Sample 27)


title: SC14

value: embryo

value: leaf early


title: CMT55_MRTX_D3


title: SC11

value: 2 cell

value: tetraploid


title: CMT55_MRTX_D2


title: ssCAGE, Heart, (Sample 30)

value: left atrium

value: healthy


title: SC12

value: octant


title: H07-06422 T


title: ssCAGE, Heart, (Sample 25)

value: M


title: SC9

value: endorsperm

value: late endosperm


title: ssCAGE, Heart, (Sample 26)

value: F


title: CMT55_DMSO_D3

value: edited

value: DMSO


title: SC8

value: early endosperm

value: S×C


title: ssCAGE, Heart, (Sample 23)

value: right atrium


title: CMT55_DMSO_D2


title: SC7

value: mature


title: SC6

value: embryo

value: leaf late


title: SC5

value: leaf middle


title: CMT55_DMSO_D5


title: CMT55_MRTX_D1


title: ssCAGE, Heart, (Sample 22)


title: CMT54.10_MRTX_D3


title: ssCAGE, Heart, (Sample 21)

value: right ventricle


title: ssCAGE, Heart, (Sample 24)

value: left ventricle


title: ssCAGE, Heart, (Sample 20)

value: healthy


title: CMT54.10_MRTX_D5


title: CMT54.10_MRTX_D2


title: SC3

value: transition

value: tetraploid


title: SC2

value: octant


title: CMT54.10_MRTX_D1


title: SC1

value: 2 cell


title: CMT54.10_DMSO_D5


title: ssCAGE, Heart, (Sample 18)

value: M

value: left atrium


title: ssCAGE, Heart, (Sample 17)


title: CMT54.10_DMSO_D3

value: edited

value: DMSO


title: CS18

value: endorsperm

value: early endosperm

value: C×S


title: ssCAGE, Heart, (Sample 16)


title: CS19

value: late endosperm


title: ssCAGE, Heart, (Sample 15)

value: right atrium


title: CMT54.10_DMSO_D2


title: SC4

value: embryo

value: leaf early

value: S×C


title: CS16

value: leaf late


title: ssCAGE, Heart, (Sample 14)

value: healthy


title: CS17

value: mature

value: tetraploid


title: CS15

value: leaf middle


title: CMT_Parental_3

source_name: CMT

value: CMT

value: parental


title: ssCAGE, Heart, (Sample 19)

value: M


title: nAnTi-CAGE, Heart, (Sample 13)

value: F

value: left ventricle


title: nAnTi-CAGE, Heart, (Sample 12)

value: left atrium


title: CMT_Parental_2


title: CS13

value: transition

value: C×S


title: nAnTi-CAGE, Heart, (Sample 11)


title: LLC 46 D5 MRTX-1257

source_name: LLC 46

value: LLC 46

value: edited


title: CMT_Parental_1


title: nAnTi-CAGE, Heart, (Sample 10)


title: LLC 46 D3 MRTX-1257


title: LLC 46 D2 MRTX-1257


title: CS9

value: endorsperm

value: late endosperm


title: CMT54.10_DMSO_D1

value: DMSO


title: CS11

value: embryo

value: 2 cell


title: LLC 46 D1 MRTX-1257


title: nAnTi-CAGE, Heart, (Sample 8)

value: healthy


title: CS8

value: early endosperm

value: tetraploid


title: CS7

value: mature


title: LLC 46 D3 DMSO


title: LLC 46 D2 DMSO


title: nAnTi-CAGE, Heart, (Sample 7)

value: M


title: CS6

value: leaf late


title: nAnTi-CAGE, Heart, (Sample 9)

value: F

value: left ventricle


title: CS12

value: octant


title: LLC 46 D5 DMSO


title: nAnTi-CAGE, Heart, (Sample 6)

value: left atrium


title: nAnTi-CAGE, Heart, (Sample 2)


title: CS5

value: leaf middle

value: C×S


title: LLC 46 D1 DMSO

value: LLC 46

value: edited


title: LLC 23 D5 MRTX-1257

source_name: LLC 23

value: LLC 23


title: nAnTi-CAGE, Heart, (Sample 4)


title: LLC 23 D3 MRTX-1257


title: nAnTi-CAGE, Heart, (Sample 3)


title: nAnTi-CAGE, Heart, (Sample 1)


title: CS3

value: embryo

value: transition


title: CS4

value: leaf early


title: CS2


title: LLC 23 D2 MRTX-1257


title: CS1

value: 2 cell


title: nAnTi-CAGE, Heart, (Sample 5)

value: healthy


title: Luscinia megarhynchos LM14, DNA depleted mRNA from testis

city: Prague

first: Jakub

last: Ridl

address: Vídeňská 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the Czech Academy of Sciences

data_processing:
Trimmomatic v0.39 was used to trim the mRNA-seq reads.
The Trimmomatic command used was as follows: trimmomatic SE <raw_fastq_file> trim/<trimmed_fastq_file> ILLUMINACLIP:<illumina_adapters.fasta>:2:30:10 SLIDINGWINDOW:4:20 TRAILING:10 MINLEN:60
The trimmed reads were aligned to the reference somatic genome combined with the GRC assembly of the corresponding species (L. megarhynchos, L. luscinia) using STAR v2.7.9a
Only reads that mapped uniquely to the GRC exons were considered for FPKM calculations
Assembly: Combination (not published) of reference genome assembly combined with GRC assembly of L. megarhynchos and L. luscinia
Supplementary files format and content: Tab-delimited file with FPKM values for individual genes per species per tissue

organism: Luscinia megarhynchos

source_name: testis

extract_protocol:
Total RNA using TRIzol reagent (ThermoFisher Scientific). 9 μl of the total RNA was treated with TURBO DNase (Ambion) to remove genomic DNA followed by a column clean up using RNA Clean & Concentrator kit (Zymo Research)
mRNA-seq libraries were constructed with NEB Ultra II stranded mRNA kit (New England Biolabs) including Oligo dT magnetic beads for mRNA enrichment. The libraries were prepared on Biomek i7 Automated Workstation (Beckman Coulter) and sequenced using HiSeq 2500 (Illumina) in 150 bp single-end mode.

value: testis

tag: Sex

value: male


title: LLC 23 D5 DMSO

value: DMSO


title: periostracum groove between outer and middle folds

city: Beijing

first: Maoguo

last: Luo

address: Haidian District, Beijing Zhongguancun South Street, 5th

institute: Beijing Institute of Technology

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp)with default parameters.
Then clean data from the samples were used to do de-novo assembly with Trinity (http://trinityrnaseq.sourceforge.net/).
Then the assembled transcripts were assessed and optimized with BUSCO (Benchmarking Universal Single-Copy Orthologs, http://busco.ezlab.org), TransRate (http://hibberdlab.com/transrate/) and CD-HIT (http://weizhongli-lab.org/cd-hit/).
All the assembled transcripts were searched against the NCBI protein non-redundant (NR, ftp://ftp.ncbi.nlm.nih.gov/blast/db/), Swiss-Prot (http://web.expasy.org/docs/swiss-prot_guideline.html), Pfam (http://pfam.xfam.org/), Clusters of Orthologous Groups of proteins (COG, http://www.ncbi.nlm.nih.gov/COG/), GO ( http://www.geneontology.org) and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.genome.jp/kegg/) databases using BLASTX to identify the proteins that had the highest sequence similarity with the given transcripts to retrieve their function annotations and a typical cut-off E-values less than 1.0×10−5 was set.
Assembly: Then clean data from the samples were used to do de-novo assembly with Trinity (http://trinityrnaseq.sourceforge.net/). Then the assembled transcripts were assessed and optimized with BUSCO (Benchmarking Universal Single-Copy Orthologs, http://busco.ezlab.org), TransRate (http://hibberdlab.com/transrate/) and CD-HIT (http://weizhongli-lab.org/cd-hit/). And the assembled sequences was named as"Trinity.filter" with the FASTA format.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Perna viridis

source_name: mantle

extract_protocol:
Tissues (50-100 mg) were frozen in liquid nitrogen and ground them into fine power with a pestle and mortar and the total RNAs were extracted using Total RNA Extraction Reagent (TAKARA Japan) according to the user instruction. Genome contamination was removed by DNase I.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.
The RNA library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA

value: mantle

tag: cell type

value: all types

value: unknown

value: untreated


title: submarginal zone between the folds and pallial line


title: LLC 23 D3 DMSO


title: Luscinia megarhynchos LM30, DNA depleted mRNA from ovaries

source_name: ovaries

value: ovaries

value: female


title: LLC 23 D2 DMSO


title: LLC 23 D1 DMSO


title: 3LL 86 D5 MRTX-1257


title: 3LL 86 D3 MRTX-1257


title: SC17

value: mature

value: tetraploid

value: S×C


title: macrophages, Vehicle, LPS1h

city: Utrecht

first: Kathryn

middle: A.

last: Wierenga

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Universitiet Utrecht

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting  were done using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Mus

source_name: liver

growth_protocol: Cells were grown in 10% fetal bovine serum with 1% penicillin-streptomycin and 30 ng/mL murine GM-CSF

extract_protocol:
Cells were lifted using Accutase and then washed twice with ice cold PBS. Single cells were isolated using the 10x Chromium SingleCell 3'RNAseq kit
Library was prepared according to the 10x Chromium SingleCell 3'RNAseq kit (v3 Chemistry)

treatment_protocol: Cells were treated in 0.25% fetal bovine serum with 1% penicillin-streptomycin and 30 ng/mL muring GM-CSF. Control cells were collected prior to any treatment. Cells were treated for 24 hr with 25 µM DHA/8.3 uM BSA, or 8.3 µM BSA as vehicle. Cells not stimultaed with LPS were collected after the 24 hr incubation with DHA/BSA. For cells treated with LPS, DHA/BSA media was removed and replaced with 20 ng/mL LPS in the treatment media. Cells were collected at the indicated timepoints (1 or 4 hrs) following LPS stimulation.

value: liver

value: fetal liver-derived macrophage

value: macrophage

value: wt

value: BSA, LPS 1 hr


title: 3LL 86 D2 MRTX-1257

value: edited


title: macrophages, Vehicle, LPS4h

description: 10x genomics

value: BSA, LPS 4 hr


title: macrophages, DHA

description: 10x genomics

value: DHA-BSA complex


title: macrophages, DHA, LPS1h

description: 10x genomics

value: DHA-BSA complex, LPS 1 hr


title: Luscinia luscinia LL32, DNA depleted mRNA from ovaries

organism: Luscinia luscinia


title: 3LL 86 D1 MRTX-1257


title: LLC 23 D1 MRTX-1257

value: LLC 23


title: macrophages, DHA, LPS4h

description: 10x genomics

value: DHA-BSA complex, LPS 4 hr


title: 3LL 86 D5 DMSO

value: DMSO


title: macrophages, Vehicle

description: 10x genomics

value: BSA


title: 3LL 86 D3 DMSO


title: macrophages, Control

description: 10x genomics

value: untreated


title: 3LL 86 D2 DMSO


title: 3LL 86 D1 DMSO


title: BKO [snRNA-seq]

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Raw read sequences produced by the Illumina pipeline in FASTQ format were  pre-processed through Trimmomatic software which can be summarized as below:  (1)Remove low-quality reads: scan the read with a 4-base wide sliding window,  cutting when the average quality per base drops below 10 (SLIDINGWINDOW: 4:10)(2)Remove trailing low quality or N bases (below quality 3) (TRAILING:3)  (3)Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence, the number of matching bases were greater than  7 and mismatch=2; b.when read1 and read2 overlapping base scoring greater than 30,  removed non-overlapping portions (ILLUMINACLIP: adapter.fa: 2: 30: 7)  (4)Drop reads below the 26 bases long(5)Discard those reads that can not form  pairedThe remaining reads that passed all the filtering steps was counted as clean  reads and all subsequent analyses were based on this. At last, we use FastQC to  perform basic statisticson the quality of the cleanreads
Raw reads were demultiplexed and mapped to the reference genome by 10X  Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/  software/pipelines/latest/what-is-cell-ranger) using default parameters. All  downstream single-cell analyses were performed using Cell Ranger and Seurat. In brief, for  each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers  were counted to construct digital expression matrices. Secondary filtration by Seurat :  A gene with expression in more than 3 cells was considered as expressed, and each  cell was required to have at least 200 expressed genes. And filter out some of the  foreign cells.
Simultaneous data normalization/scaling and variable feature detection wasperformed using“LogNormalize”. Cells were integrated bycanonical correlation analysis (CCA). Cells were clustered via Seurat’s shared nearest neighbor clustering algorithm(“FindNeighbors” and “FindClusters”) using the the top 20PCs and a resolution of 0.5. The top 8 most variable PCs were used for subsequent clustering.The clusteringwas visualized using t-Distributed Stochastic Neighbor Embedding(tSNE).Cluster markers were obtained withthe Seurat function ‘‘FindAllMarkers’’ using default settings.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: mtx, tsv

source_name: brown adipose tissue

extract_protocol:
Nuclei were isolated from frozen iBAT samples for 10x snRNA-seq. Each sample was pooled from 4 mice for each group.
The nuclei suspension was loaded into Chromium microfluidic chips with 30 v3.1 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 30 v3.1 reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with IlluminaNovaseq 6000 according to the manufacturer’s instructions (Illumina).
10x Genomics Single Nucleus RNA-seq

treatment_protocol: Wtapflox/flox and BKO mice were fed with normal chow diet for 8 weeks old

tag: strain

value: BKO (Wtap flox/flox UCP1-iCre)

value: brown adipose tissue


title: Luscinia luscinia LL22, DNA depleted mRNA from testis

tag: tissue

value: testis

value: male


title: FF [snRNA-seq]

value: Wtapflox/flox


title: RNA-Seq from Mod(mdg4)-N mutant ovary rep3

city: Shinjuku-ku

first: Chikara

last: Takeuchi

state: Tokyo

address: 35 Shinanomachi

department: Molecular biology

institute: Keio University

description: Sample 44

data_processing:
RNA-Seq: Reads of mRNA were mapped to dm6 by RSEM and STAR using following parameter (rsem-calculate-expression --paired-end -p 8 --star --star-path ~/anaconda3/bin --gzipped-read-file). DEG were detected by limma. For analysis of transposable elements, reads were mapped to dm6 using following parameter (--runMode genomeGenerate --genomeDir ${path_to_index} --genomeSAindexNbases 12 --genomeFastaFiles ${path_to_fasta}).
ChIP-Seq: Adaptors added by NEBNext Ultra II were cut by cutadapt using following parameters (cutadapt -j 12 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 20 -o trim/${name2}_R1_trim.fastq.gz -p trim/${name2}_R2_trim.fastq.gz raw_file/${name2}_R1.fastq.gz raw_file/${name2}_R2.fastq.gz). For mapping to the genome, subsequent reads were mapped to the dm6 by bowtie2 using following parameters (bowtie2 -p 16 -x ${reference}/dm6 -N 1 -1 trim/${name2}_R1_trim.fastq.gz -2 trim/${name2}_R2_trim.fastq.gz -S sam_file/${name2}.sam). Peak call is performed by MACS using following parameter: for Mod(mdg4) isoforms(macs2 callpeak -t merge_file/Ty-AF_merge.sort.bam -c bam_file/Input-AF.sort.bam -n Ty-AF -f BAM -q 1e-15 -g dm --outdir peakcall_strict) and for PolII(macs2 callpeak -t ${item} -c ../bam_file/Input_All.sort.bam -n ${item%%.bam} -f BAM -g dm --outdir ../peakcall).
Micro-C XL: Distiller (https://github.com/open2c/distiller-nf) pipeline is used to process Micro-C datasets. First, sequencing reads were mapped to dm6 using bwa mem with flags-SP. Second, mapped reads were parsed and classified using the pairtools package (https://github.com/open2c/pairtools) to get cool file. PCR and/optical duplicates removed by matching the positions of aligned reads with 2bp flexibility. Next, pairs were filtered using mapping quality scores (MAPQ > 30) on each side of aligned chimeric read, binned into multiple resolutions and low coverage bins are removed. Finally multiresolution cooler files were created using the cooler package (https://github.com/open2c/cooler.git)(Abdennur and Mirny, 2019). We normalized contact matrices using the iterative correction procedure(Imakaev et al., 2012).
Genome_build: dm6
Supplementary_files_format_and_content: RNA-Seq: TPM and FPKM of each genes (flybase ID)
Supplementary_files_format_and_content: ChIP-Seq: bigwig file
Supplementary_files_format_and_content: Micro-C XL: multi-resolution cooler file

organism: Drosophila melanogaster

source_name: Ovary

growth_protocol: Flies were kept at strandard conditions at 25º C.

extract_protocol: Total RNAs were isolated with the Isogen II reagent (NipponGene). Poly(A)+ RNAs were obtained using Oligo-dT beads. Libraries are prepared with illumine TruSeq stranded mRNA kit according to manufacturer’s protocol.

value: whole ovary

value: Ovary


title: mKRC.1_MRTX_1day

value: parental


title: LLC D5 MRTX-1257

source_name: LLC

value: LLC


title: RNA-Seq from Mod(mdg4)-N mutant ovary rep1

description: Sample 42


title: RNA-Seq from Mod(mdg4)-N mutant ovary rep2

description: Sample 43


title: LLC D2 MRTX-1257


title: RNA-Seq from WT ovary rep3

description: Sample 41


title: LLC D1 MRTX-1257


title: TNBC tumor, patient85

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

country: Spain

institute: CIMA

data_processing:
Alignments were performed using the STAR method to human genome build hg38.
Reads were then split and trimmed using GATK SplitNTrim tool.
In/Del realignment and base recalibration were performed using GATK toolbox.
Duplicates were marked and Sorted using Picard’s MarkDuplicates tool.
Gene counts were calculated using featureCount
Assembly: hg38
Supplementary files format and content: Subread files in txt format

source_name: Triple negative breast cancer tumor

extract_protocol:
complementary DNA libraries were constructed from High quality RNA (1 μg) using TruSeq stranded Total RNA Sample Prep Kit. Library was subjected to paired-end sequencing using the NovaSeq platform (10 Gb 100PE 100Mreads/sample)
Truseq mRNA (Illumina)
full length strand specific mRNA sequencing

tag: individual

value: Patient 85

tag: race

value: caucasian

value: Triple negative breast cancer

tag: Stage

value: II-III stage TNBC

value: Breast


title: RNA-Seq from WT ovary rep2

description: Sample 40


title: LLC D5 DMSO

value: DMSO


title: TNBC tumor, patient73

value: Patient 73


title: TNBC tumor, patient75

value: Patient 75


title: RNA-Seq from WT ovary rep1

description: Sample 39


title: TNBC tumor, patient88

value: Patient 88


title: RNA-Seq from Mod(mdg4)-All-KD rep1

description: Sample 37

source_name: Mod(mdg4)-All-KD OSC

growth_protocol: Cells were grown at 26 degrees on OSC medium (Fly Extract added M3 medium).

value: Ovarian Somatic Cells (OSC)

value: RNAi Mod(mdg4)-All


title: LLC D3 DMSO


title: LLC D2 DMSO


title: RNA-Seq from Mod(mdg4)-All-KD rep2

description: Sample 38


title: TNBC tumor, patient69

value: Patient 69


title: LLC D1 DMSO


title: RNA-Seq from Mod(mdg4)-N-KD rep1

description: Sample 35

source_name: Mod(mdg4)-N-KD OSC

value: RNAi Mod(mdg4)-N


title: LLC D3 MRTX-1257


title: CS14

value: embryo

tag: developmental stage

value: leaf early

tag: maternal ploidy

value: tetraploid

tag: paternal ploidy

tag: line

value: C×S


title: RNA-Seq from Mod(mdg4)-N-KD rep2

description: Sample 36


title: Tumor tissue, Medulloblastoma, Patient2

first: LiXin

last: Ma

address: Haidian District

department: Neurosurgery

institute: Sanbo Brain Hospital

description: T-tissue-wjw

library_source: other

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.1), the high quality clean reads were aligned to the reference genome with bwa software v(v0.7.12).
Then, circle-map software (v1.1.4) was used to detect eccDNA within all samples, and samtools (v0.2) software was used to get raw soft-clipped read counts of the break point.
Then edgeR (v0.6.9) software was used to perform normalization and differentially expressed eccDNA filter by p-value and fold change. bedtools (v2.27.1) software was used to annotate the eccDNAs.
Assembly: hg19
Supplementary files format and content: excel format
Library strategy: circle seq

molecule: other

source_name: Medulloblastoma

extract_protocol:
For samples of cerebrospinal fluid, cerebrospinal fluid DNA extractions were performed using QIAamp Circulating Nucleic Acid Kit (Qiagen). DNA was digested with exonuclease V (New England Biolabs) at 37℃ for 5 min to remove linear DNA.. The circular structure of eccDNA is opened by transposable enzymesand the ends of the DNA fragments are attached to the joints. To fill these gaps and ends, the Klenow enzyme was used for gap/end repair. Then the products were amplified and purified by PCR.
For samples of tissue, samples were suspended in L1 solution (Plasmid Mini AX; A&A Biotechnology) and supplemented with Proteinase K (ThermoFisher) before incubation overnight at 50 °C with agitation. After Lysis, samples were alkaline treated,followed by precipitation of proteins and separation of chromosomal DNA from circular DNA through an ion exchange membrane column (Plasmid Mini AX; A&A Biotechnology). Column-purified DNA was treated with FastDigest MssI (Thermo Scientifific) to remove mitochondrial circular DNA and incubated at 37 °C for 16 h. Remaining linear DNA was removed by exonuclease (Plasmid-Safe ATP-dependent DNase, Epicentre) at 37 °C in a heating block and enzyme reaction was carried out continuously for 1 week, adding additional ATP and DNase every 24 h (30 units per day) according to the manufacturer’s protocol (Plasmid-Safe ATP-dependent DNase, Epicentre). eccDNA-enriched samples was used as template for phi29 polymerase amplification reactions (REPLI-g Midi Kit) amplifying eccDNA at 30 °C for 2 days (46–48 h).
Illumina sequencing libraries were generated with NEBNext® Ultra™ DNA Library Prep Kit (New England Biolabs) by following the manufacturer’s manual. The library quality was determined by using Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., USA).Sequencing was carried out on Illumina NovaSeq 6000 with 150bp paired end mode according to the manufacturer’s instructions.

value: male

value: Medulloblastoma


title: Tumor tissue, Medulloblastoma, Patient3

description: T-tissue-dyn

value: female


title: ApoE4_Stim_rep6

city: Lexington

first: Joshua

middle: M

last: Morganti

state: KY

address: 789 S. Limestone St

department: Sanders-Brown Center on Aging

institute: University of Kentucky

data_processing:
Illumina base call (BCL) files from the sequencing instrument were converted to FASTQ format.  Sequencing reads were aligned to the mm10 reference genome using STAR (v2.5.1b) aligner.
Assembly: mm10
Supplementary files format and content: Count CSV files

source_name: Brain

extract_protocol:
Cells were lysed with RLTplus buffer and RNA harvested per manufacturer's suggested protocol (Qiagen # 74034).
Sample libraries were constructed and the final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).

value: Brain

value: Brain cells

value: LPS


title: RNA-Seq from EGFP-KD rep2

description: Sample 34

source_name: EGFP-KD OSC

value: RNAi EGFP


title: ApoE4_Stim_rep5


title: RNA-Seq from EGFP-KD rep1

description: Sample 33


title: TNBC tumor, patient83

value: Patient 83

value: caucasian

tag: disease state

value: Triple negative breast cancer

value: II-III stage TNBC

value: Breast


title: ApoE4_Stim_rep4


title: ApoE4_Stim_rep3


title: Micro-C XL from Mod(mdg4)-N-KD rep3

description:
Sample 31
siN_library.dm6.mapq_30.200.mcool

library_source: genomic

data_processing:
Library strategy: Micro-C XL
RNA-Seq: Reads of mRNA were mapped to dm6 by RSEM and STAR using following parameter (rsem-calculate-expression --paired-end -p 8 --star --star-path ~/anaconda3/bin --gzipped-read-file). DEG were detected by limma. For analysis of transposable elements, reads were mapped to dm6 using following parameter (--runMode genomeGenerate --genomeDir ${path_to_index} --genomeSAindexNbases 12 --genomeFastaFiles ${path_to_fasta}).
ChIP-Seq: Adaptors added by NEBNext Ultra II were cut by cutadapt using following parameters (cutadapt -j 12 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -m 20 -o trim/${name2}_R1_trim.fastq.gz -p trim/${name2}_R2_trim.fastq.gz raw_file/${name2}_R1.fastq.gz raw_file/${name2}_R2.fastq.gz). For mapping to the genome, subsequent reads were mapped to the dm6 by bowtie2 using following parameters (bowtie2 -p 16 -x ${reference}/dm6 -N 1 -1 trim/${name2}_R1_trim.fastq.gz -2 trim/${name2}_R2_trim.fastq.gz -S sam_file/${name2}.sam). Peak call is performed by MACS using following parameter: for Mod(mdg4) isoforms(macs2 callpeak -t merge_file/Ty-AF_merge.sort.bam -c bam_file/Input-AF.sort.bam -n Ty-AF -f BAM -q 1e-15 -g dm --outdir peakcall_strict) and for PolII(macs2 callpeak -t ${item} -c ../bam_file/Input_All.sort.bam -n ${item%%.bam} -f BAM -g dm --outdir ../peakcall).
Micro-C XL: Distiller (https://github.com/open2c/distiller-nf) pipeline is used to process Micro-C datasets. First, sequencing reads were mapped to dm6 using bwa mem with flags-SP. Second, mapped reads were parsed and classified using the pairtools package (https://github.com/open2c/pairtools) to get cool file. PCR and/optical duplicates removed by matching the positions of aligned reads with 2bp flexibility. Next, pairs were filtered using mapping quality scores (MAPQ > 30) on each side of aligned chimeric read, binned into multiple resolutions and low coverage bins are removed. Finally multiresolution cooler files were created using the cooler package (https://github.com/open2c/cooler.git)(Abdennur and Mirny, 2019). We normalized contact matrices using the iterative correction procedure(Imakaev et al., 2012).
Genome_build: dm6
Supplementary_files_format_and_content: RNA-Seq: TPM and FPKM of each genes (flybase ID)
Supplementary_files_format_and_content: ChIP-Seq: bigwig file
Supplementary_files_format_and_content: Micro-C XL: multi-resolution cooler file

extract_protocol:
Micro-C XL: Micro-C XL is performed as previously described (Hsieh et al., 2020). 1.5x107 OSC were fixed with 1% Formaldehyde for 10min and quenched with final 0.75M Tris-HCl (pH 7.5) for 5min. After twice wash, OSC were fixed again with final 3mM DSG for 45min at room temperature and quenched with final 0.75M Tris-HCl(pH 7.5) for 5min. Nuclei were isolated with 100µl MBuffer#1 (50mM NaCl, 10mM Tris-HCl pH 7.5, 5mM MgCl2, 1mM CaCl2, 0.2% NP-40 and 1x Protease inhibitor(EDTA free)) and were incubated on ice for 20min. After washed with MBufer#1, nuclei were resuspended in MBuffer#1 again and 4,000gel units of MNase is added to solution, followed by incubation at 37°C for 10min with rotation. Reaction was stopped by adding 1µl of 0.5M EGTA (pH 8.0) and nuclei were washed twice with MBuffer#2(50mM NaCl, 10mM Tris-HCl pH 7.5, 10mM MgCl2). DNA ends are phosphorylated by 45µl end-chewing mix(5µl 10xNEBuffer 2.1, 10µl ATP(10mM), 2.5µl DTT(100mM), 2.5µl T4PNK(10U/µl), 25µl Milli-Q) and incubated at 37°C for 15min. After incubation, 5µl of Klenow fragment(5U/µl) was added and incubated at 37 °C for 15min again. DNA overhangs were filled with biotin by adding 25µl end-labeling mix(5µl biotin-14-dATP(1mM), 5µl biotin-14-dCTP(1mM),0.5µl d[G+T]TP(10mM), 2.5µl 10x T4 DNA Ligase Buffer, 0.25µl BSA(10mg/ml), 11.75µl Milli-Q), and incubated at 25°C for 45min. End labeling is stopped by adding 5µl 0.5M EDTA and inactivated by incubation at 65 °C for 20min. Collecting by centrifugation(12000g 5min), samples were washed with 1ml MBuffer#3(50mM Tris-HCl pH7.5, 10mM MgCl2). Chromatin pellet was resuspended in 250µl End-ligation mix(25µl 10xT4 DNA Ligase Buffer, 2.5µl BSA(10mg/ml), 12.5µl T4 DNA ligase(400U/µl), 210µl Milli-Q) and had rotated slowly at room temperature for 4hr. Collecting by centrifugation (16000g 5min), pellet was resuspended in Exonuclease solution (10µl 10xNEBuffer #1, 5µl Exonuclease III (100U/µl), 85µl Milli-Q) and sample was incubated at 37 °C for 15minto remove biotin from unligated ends. For deproteination and reverse crosslinking, 25 μl Proteinase K (20mg/ml) and 15µl RNase (0.5mg/ml) and 15µl 10% SDS were added and the sample was incubated at 65°C o/n. Ligated DNA was purified with isopropanol precipitation using Pellet Paint NF Co-precipitant (Merck) and resuspend in 150µl Milli-Q.
5μl Dynabeads MyOne Streptavidin C1 were washed twice with 300μl Tween wash buffer (5 mM Tris-HCl, pH 7.5, 0.5 mM EDTA, 1 M NaCl) and suspended in 150μl 2x Biotin binding buffer (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl). 150μl washed Streptavidin beads in 2x TBW were added to the sample and incubated rotation at RT for 20 min. Beads were washed twice with 300μl Tween wash buffer. These were used for library preparation with the GenTrack library preparation kit following the manufacturer’s protocol. To remove monomer or tetramer sized fragment, size-selection was performed with SPRI select after amplification of library.

value: Ovarian Somatic Cells (OSC)

value: RNAi Mod(mdg4)-N


title: Cerebrospinal fluid, Medulloblastoma, Patient2

description: T-CSF-wjw

source_name: Cerebrospinal fluid

value: Cerebrospinal fluid


title: Tumor tissue, Medulloblastoma, Patient4

description: T-tissue-chf


title: Cerebrospinal fluid, Medulloblastoma, Patient1

description: T-CSF-fjb


title: Cerebrospinal fluid, Medulloblastoma, Patient3

description: T-CSF-dyn


title: ApoE4_Stim_rep1


title: Micro-C XL from Mod(mdg4)-N-KD rep1

description:
Sample 29
siN_library.dm6.mapq_30.200.mcool


title: Micro-C XL from Mod(mdg4)-N-KD rep2

description:
Sample 30
siN_library.dm6.mapq_30.200.mcool


title: Cerebellar tissue, Normal

description: N-tissue

source_name: Cerebellar

value: Cerebellar


title: ApoE4_Ctrl_rep6

value: NaCl


title: Micro-C XL from EGFP-KD rep4

description:
Sample 28
siE_library.dm6.mapq_30.200.mcool


title: Tumor tissue, Medulloblastoma, Patient1

description: T-tissue-fjb

value: male


title: ApoE4_Ctrl_rep5


title: Cerebrospinal fluid, Normal

description: N-CSF


title: ApoE4_Ctrl_rep4


title: CMT55_DMSO_D1

value: edited

value: DMSO


title: DIPG4_MMF treated [MMF_3]

city: Grand Rapids

first: Bin

state: Michigan

address: 15 Michigan ST NE

department: Department of Pediatrics and Human Development

institute: Michigan State University

description: Total RNA was isolated form DIPG4 cells

data_processing:
RNA-Seq reads were mapped on Hg38 transcriptome using the ENSEMBL GRCh38.p3 annotation with the STAR aligner
Normalized count was obtained from the STAR aligner
Genome_build: UCSC human reference genome (hg38)
Supplementary_files_format_and_content: CSV file includes human ensembl_gene_id and normalized counts (TPM) for each gene in individual samples

source_name: DIPG4_MMF treated

growth_protocol: SU-DIPG4 cell lines was kindly provided by Dr. Michelle Monje (Stanford University, Stanford, CA) and maintained in tumor stem medium (TSM) which consisted of 50% of neurobasal-A medium, 50% of DMEM/F12 medium, 10 mM of HEPES buffer, 1 mM of MEM sodium pyruvate, 100 uM of MEM non-essential amino acids, 1x GlutaMAX-I and 1x antibiotic-antimycotics, supplemented with B27 minus vitamin A supplement, 20 ng/ml of hEGF and 20 ng/ml of hFGF.

extract_protocol:
RNA was extracted using the RNeasy plus mini kit (Qiagen).
Libraries were prepared using the Illumina TruSeq Stranded mRNA Library Preparation Kit; prepared libraries were quality controlled and quantified using a Qubit and Labchip Bioanalyzer. Libraries were pooled and run on a Illumina NovaSeq 6000 instrument
Sequencing was performed by 2 × 150 bp paired-end read format.

treatment_protocol:
Cells were grown for 24h with 1uM of Mycophenolate mofetil
DIPG4 cells were treated with appropriate drugs at their IC50 concentration (2 nM of triptolide, 1 uM of MMF and 30 uM of triamterene )  for 24 hours.

value: MMF

tag: time

tag: replicates


title: ApoE4_Ctrl_rep3

value: Brain

value: Brain cells


title: Micro-C XL from EGFP-KD rep2

description:
Sample 26
siE_library.dm6.mapq_30.200.mcool

value: RNAi EGFP


title: Micro-C XL from EGFP-KD rep3

description:
Sample 27
siE_library.dm6.mapq_30.200.mcool


title: Micro-C XL from Mod(mdg4)-N-KD rep4

description:
Sample 32
siN_library.dm6.mapq_30.200.mcool


title: ApoE4_Ctrl_rep1


title: ChIP-Seq Input from Mod(mdg4)-All-KD

description:
Sample 24
pol_All1.sort.bw

extract_protocol:
ChIP experiments of Ty1-tagged Mod(mdg4) isoforms are performed by truChIP Chromatin Shearing Kit according to manufactures instruction with minor modifications. 2x107 OSC were fixed with 1% formaldehyde 10min and quenched and lysed with buffers of truChIP Chromatin Shearing Kit. Fixed chromatin is sheered with Bioruptor II (BMbio BR2012A) for 20 cycles of 30s ON/30s OFF, high settings. Sheered chromatin is immunoprecipitated by antibody-conjugated Dynabeads protein G for 2hr. Immunoprecipitated chromatin was incubated with Proteinase K and RNase, and de-crosslinked at 65°C overnight.
For ChIP experiments of RNA polymerase II, 2x107 OSC were fixed with 1% formaldehyde 10min and quenched with final 0.1M Glycine for 5min. After twice wash with PBS, nuclei were isolated with 1ml of swelling buffer (25mM HEPES-KOH(pH 7.5), 1.5mM MgCl2, 10mM KCl, 0.1% NP-40, 1mM DTT and 1x Protease Inhibitor). Isolated nuclei were lysed in 400µl of sonication buffer(50mM HEPES-KOH(pH 7.4), 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS and 1xProtease Inhibitor) and were sheered with Bioruptor II (BMbio BR2012A) for 20 cycles of 30s ON/30s OFF, high settings. 3µg of antibody were incubated with chromatin for overnight. Next day, 20µl of Dynabeads M-280 Sheep anti-Mouse IgG is added to sample and incubated for 1hr. Beads were washed and treated with Proteinase K and RNase as described (Haring et al., 2007). DNA was purified with isopropanol precipitation using Pellet Paint NF Co-precipitant (Merck: 70748).
Fragments from the ChIP experiment were sheared to ∼200 bases using Covaris S220. These were used for library preparation with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following the manufacturer’s protocol.

value: RNAi Mod(mdg4)-All


title: Micro-C XL from EGFP-KD rep1

description:
Sample 25
siE_library.dm6.mapq_30.200.mcool


title: DIPG4_MMF treated [MMF_1]

description: Total RNA was isolated form DIPG4 cells

tag: cell line


title: ApoE4_Stim_rep2

tag: genotype

value: LPS


title: DIPG4_MMF treated [MMF_2]

description: Total RNA was isolated form DIPG4 cells

tag: treatment


title: DIPG4_TPL treated [TPL_3]

description: Total RNA was isolated form DIPG4 cells

source_name: DIPG4_TPL treated

treatment_protocol:
Cells were grown for 24h with 2nM of triptolide
DIPG4 cells were treated with appropriate drugs at their IC50 concentration (2 nM of triptolide, 1 uM of MMF and 30 uM of triamterene )  for 24 hours.

value: TPL


title: DIPG4_TPL treated [TPL_2]

description: Total RNA was isolated form DIPG4 cells


title: cKO MED1 rep4

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
sample name:
s3184

data_processing:
Alignment : STAR (v2.4.0a) versus mm10 following ENCODE RNA-seq options
Counts : featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options using Ensembl GRCm38.83 release
Normalization : R (v3.4) DESeq2 (v3.6) Generate a DESeqDataSetFromMatrix object using the featureCounts table, then send the object to DESeq() function to calculate the sizeFactors and use the function counts() with option normalized=TRUE on DESeqDataSetFromMatrix object to get normalized counts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including normalized counts for each sample using DESeq2 sizeFactors

source_name: LPS +IL4 in vitro activated B cells

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen) from purified splenic B cells stimulated in vitro 4 days in RMPI 1640 medium (Lonza) supplemented with 10% fetal calf serum (Lonza) and with 1µg/mL LPS (invivogen) and IL4 (20ng/ml, peprotech),
1 µg of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (14 cycles) with the reagents from the truseq stranded total RNA kit (illumina). Libraries were quantified with the Bioanalyzer DNA 1000 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations.  Paired-end 150-bp reads were sequenced on an Illumina Nextseq 500 sequencer.

value: spleen

value: B cells

tag: activation

value: LPS and IL4

value: cKO MED1


title: cKO MED1 rep3

description:
sample name:
s3182

tag: cell type


title: ApoE3_Stim_rep6


title: ChIP-Seq Input from EGFP-KD

description:
Sample 22
pol_E1.sort.bw

value: Ovarian Somatic Cells (OSC)


title: cKO MED1 rep2

description:
sample name:
s3146


title: DIPG4_TRIAM treated [TRIAM_3]

description: Total RNA was isolated form DIPG4 cells

source_name: DIPG4_TRIAM treated

treatment_protocol:
Cells were grown for 24h with 30uM of triamterene
DIPG4 cells were treated with appropriate drugs at their IC50 concentration (2 nM of triptolide, 1 uM of MMF and 30 uM of triamterene )  for 24 hours.

value: TRIAM


title: DIPG4_TPL treated [TPL_1]

description: Total RNA was isolated form DIPG4 cells


title: cKO MED1 rep1

description:
sample name:
s3145


title: Pol II ChIP from Mod(mdg4)-All-KD rep2

description:
Sample 21
pol_All2.sort.bw


title: ApoE3_Stim_rep3


title: ApoE3_Stim_rep4


title: Pol II ChIP from Mod(mdg4)-All-KD rep1

description:
Sample 20
pol_All1.sort.bw


title: Pol II ChIP from Mod(mdg4)-N-KD rep2

description:
Sample 19
pol_N2.sort.bw

value: RNAi Mod(mdg4)-N


title: DIPG4_TRIAM treated [TRIAM_1]

description: Total RNA was isolated form DIPG4 cells


title: ApoE3_Stim_rep2


title: ApoE4_Ctrl_rep2

value: NaCl


title: DIPG4_TRIAM treated [TRIAM_2]

description: Total RNA was isolated form DIPG4 cells


title: WT rep3

description:
sample name:
WT9

value: wildtype


title: WT rep2

description:
sample name:
WT8


title: Pol II ChIP from Mod(mdg4)-N-KD rep1

description:
Sample 18
pol_N1.sort.bw


title: WT rep1

description:
sample name:
WT7


title: Pol II ChIP from EGFP-KD rep2

description:
Sample 17
pol_E2.sort.bw


title: DIPG4_DMSO treated [DMSO_3]

description: Total RNA was isolated form DIPG4 cells

source_name: DIPG4_DMSO treated

treatment_protocol:
Cells were grown for 24h with DMSO
DIPG4 cells were treated with appropriate drugs at their IC50 concentration (2 nM of triptolide, 1 uM of MMF and 30 uM of triamterene )  for 24 hours.

value: DMSO


title: ApoE3_Stim_rep1


title: ChIP-Seq Input from Mod(mdg4)-N-KD

description:
Sample 23
pol_N1.sort.bw


title: ApoE3_Ctrl_rep6


title: Oocyte, 4E (Danio)

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Low quality reads and adaptor sequences were removed using Trimmomatic PE. Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Reads were aligned against reference genome using STAR (v 2.5.3a).
Annotated reads were counted using htseq-count with the reference model Danio_rerio.GRCz11.95
Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT-qPCR method called NormQ (Naraine et al, 2020).
Genome_build: GRCz11.dna.primary_assembly
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized number of reads for each sample and normalized number of reads with name of the sample in first row of each column.

organism: Danio rerio

source_name: Oocyte, 4E

extract_protocol:
Oocyte was mounted to OCT medium and sliced using cryostat. RNA was isolated using Qiagen MicroKit. 5.5 ng of total RNA was used for rRNA depletion (Lexogen RiboCop rRNA Depletion Kit).
Lexogen SENSE TOtal RNA-Seq Library Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.

tag: segment

value: E (last vegetal)

value: Oocyte

tag: oocyte id


title: ApoE3_Stim_rep5

tag: tissue

value: Brain

value: Brain cells


title: ApoE3_Ctrl_rep4


title: DIPG4_DMSO treated [DMSO_1]

description: Total RNA was isolated form DIPG4 cells


title: ChIP-Seq Input from WT

description:
Sample 15
Ty-WT_merge.bw

source_name: WT OSC


title: Oocyte, 4B (Danio)

source_name: Oocyte, 4B

value: B


title: hPGCLC aggregates from participant MZT06-C

city: Los Angeles

first: Fei-Man

last: Hsu

state: California

address: 610 Charles E Young Dr S

department: MCDB

institute: UCLA

data_processing:
Valid cells and UMIs were determined by UMI-tools to generate whitelist.
Reads corresponding to valid barcodes were aligned to GRCh38 with STAR 2.7, and only uniquely mapped reads were kept for further analyses.
Count matrices were generated by featureCounts v2.0.1 from the Subread R package, with UMIs info further appended to the alignment .bam file.  Finally, the count matrix of all valid cells was generated with umi_tools count function.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene per cell in each biological sample

molecule: polyA RNA

source_name: hPGCLC aggregates

growth_protocol: Media was changed daily and colonies were passaged with collagenase (ThermoFisher, 17104019) every 7 days.

extract_protocol:
hPGCLC aggregates were trypsinized d made two aliquots. After confirming the quality and population with FACS on one aliquot, the other one was submitted to library prep immediately.
The libraries were made according to 10X Genomics protocols
10X Genomics

treatment_protocol: hPGCLC induction followed previously published protocols with minor modifications(Chen et al., 2017; Sasaki et al., 2015)

tag: participant

tag: participant origin

value: Infertile participant

value: hiPSC derived hPGCLC aggregates


title: ApoE3_Ctrl_rep3


title: ApoE3_Ctrl_rep2


title: Oocyte, 4A (Danio)

source_name: Oocyte, 4A

value: A (first animal)


title: ChIP-Seq Input from Ty1-Mod(mdg4)-V

description:
Sample 13
Ty-V_merge.bw

source_name: 2×Ty1-Mod(mdg4)-V stable OSC

value: 2XTy1-Mod(mdg4)-V stable expression


title: ApoE3_Ctrl_rep1


title: hPGCLC aggregates from participant MZT06-B


title: Oocyte, 3E (Danio)

source_name: Oocyte, 3E


title: DIPG4_DMSO treated [DMSO_2]

description: Total RNA was isolated form DIPG4 cells


title: hPGCLC aggregates from participant MZT05-L

value: Fertile participant


title: ChIP-Seq Input from Ty1-Mod(mdg4)-N

description:
Sample 12
Ty-N_merge.bw

source_name: 2×Ty1-Mod(mdg4)-N stable OSC

value: 2XTy1-Mod(mdg4)-N stable expression


title: Oocyte, 3D (Danio)

source_name: Oocyte, 3D

value: D


title: ChIP-Seq Input from Ty1-Mod(mdg4)-AF

description:
Sample 11
Ty-AF_merge.bw

source_name: 2×Ty1-Mod(mdg4)-AF stable OSC

value: Ovarian Somatic Cells (OSC)

value: 2XTy1-Mod(mdg4)-AF stable expression


title: hPGCLC aggregates from participant MZT05-F


title: Pol II ChIP from EGFP-KD rep1

description:
Sample 16
pol_E1.sort.bw

source_name: EGFP-KD OSC

value: RNAi EGFP


title: Oocyte, 3C (Danio)

source_name: Oocyte, 3C

value: C


title: hPGCLC aggregates from participant MZT05-D


title: Oocyte, 3A (Danio)

source_name: Oocyte, 3A


title: Ty1-ChIP-Seq from WT OSC rep2

description:
Sample 10
Ty-WT_merge.bw


title: ApoE3_Ctrl_rep5

source_name: Brain

value: NaCl


title: E4_NaCl_spatial

description: 10x Genomics

data_processing:
Raw FASTQ data and H&E images were processed by the Space Ranger v1.3.0 (10X Genomics) pipeline. Illumina base call (BCL) files from the sequencing instrument were converted to FASTQ format for each sample using the mkfastq. Visium spatial expression libraries were analyzed with the count command. Image alignment to predefined spots was performed by the fiducial alignment grid of the tissue image to determine the orientation and position of the input image. Sequencing reads were aligned to the mm10 reference genome using STAR (v2.5.1b) aligner. Gene expression profiling in each spot was performed with UMI and 10X barcode information.
Assembly: mm10
Supplementary files format and content: HDF5 feature-barcode matrix; tab-separated values; count matrix files

extract_protocol:
Right hemisphere from brains were immediately placed in OCT compound (Fisher HealthCare Tissue Plus O.C.T. Compound Clear 4585) and gently lowered into isopentane (Sigma Aldrich 2-Methylbutane M32631) in a beaker surrounded by dry ice (isopentane chilled to approximately -70°C). Brains were submerged for 60 seconds, placed on dry ice, wrapped in aluminum foil, and stored at -80°C until sectioning. Prepared brain hemispheres were cryosectioned to 10 μm thick coronal sections at approximately Bregma -2.00 mm. Serial 10 μm sections immediately rostral and caudal to the section mounted on the Visium Spatial Gene Expression slide (10X Genomics) were collected for immunohistochemistry. Optimal tissue permeabilization time was determined using the manufacturer’s optimization protocols (10X Genomics, Visium Spatial Tissue Optimization), and accordingly, experimental tissues were permeabilized for 18 min for Visium Spatial Gene Expression analysis. Prior to library preparation, tissue sections were methanol-fixed, stained with hematoxylin and eosin (H&E), and imaged on a Nikon NiU microscope with Fi3 color camera. Sections were then permeabilized and processed to obtain cDNA libraries, which were subsequently prepared according to the manufacturer’s protocol (https://support.10xgenomics.com/spatial-gene-expression/libraryprep).
Sample libraries were constructed using Next GEM automated 3’ reagents (10X Genomics, v3.1) following manufacturer’s suggested protocol (#CG000286 Rev B). Final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).
Visium spatial transcriptomics

value: non-neuronal brain cells


title: E4_LPS_spatial

description: 10x Genomics

value: LPS


title: Oocyte, 4C (Danio)

source_name: Oocyte, 4C

value: Oocyte


title: Ty1-ChIP-Seq from WT OSC rep1

description:
Sample 9
Ty-WT_merge.bw


title: ChIP-Seq Input from Ty1-Mod(mdg4)-T

description:
Sample 14
Ty-T_merge.bw

source_name: 2×Ty1-Mod(mdg4)-T stable OSC

value: 2XTy1-Mod(mdg4)-T stable expression


title: E3_LPS_spatial

description: 10x Genomics

value: Brain

value: Brain cells


title: hPGCLC aggregates from participant MZT04-D

value: hiPSC derived hPGCLC aggregates


title: hPGCLC aggregates from participant MZT06-A

value: Infertile participant


title: Ty1-Mod(mdg4)-T ChIP-Seq rep2

description:
Sample 8
Ty-T_merge.bw


title: Ty1-Mod(mdg4)-T ChIP-Seq rep1

description:
Sample 7
Ty-T_merge.bw


title: Oocyte, 2B (Danio)

source_name: Oocyte, 2B

value: B


title: hPGCLC aggregates from participant MZT04-C

value: Fertile participant


title: Ty1-Mod(mdg4)-V ChIP-Seq rep2

description:
Sample 6
Ty-V_merge.bw

value: 2XTy1-Mod(mdg4)-V stable expression


title: hPGCLC aggregates from participant MZT04-J


title: Oocyte, 2C (Danio)

source_name: Oocyte, 2C


title: Oocyte, 2A (Danio)

source_name: Oocyte, 2A

value: A (first animal)


title: ApoE4_NaCl_scRNA_seq

data_processing:
Illumina base call (BCL) files from the sequencing instrument were converted to FASTQ format for each sample using the mkfastq. The barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.0 (10xgenomics)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and count matrix files

extract_protocol:
Brain tissues from 3 replicate mice per group were processed for ‘glia-enriched’ single cell suspensions (see Early et al., 2020).
Sample libraries were constructed using Next GEM automated 3’ reagents (10X Genomics, v3.1) following manufacturer’s suggested protocol (#CG000286 Rev B). Final library quantification and quality check was performed using BioAnalyzer (Agilent), and sequencing performed on a NovaSeq 6000 S4 flow cell, 150 bp Paired-End sequencing (Novogene).


title: ApoE3_LPS_scRNA_seq


title: hPGCLC aggregates from participant MZT02-G


title: Ty1-Mod(mdg4)-V ChIP-Seq rep1

description:
Sample 5
Ty-V_merge.bw

value: Ovarian Somatic Cells (OSC)


title: ApoE4_LPS_scRNA_seq


title: Oocyte, 1E (Danio)

source_name: Oocyte, 1E

value: E (last vegetal)


title: hPGCLC aggregates from participant MZT02-D

source_name: hPGCLC aggregates


title: Ty1-Mod(mdg4)-N ChIP-Seq rep2

description:
Sample 4
Ty-N_merge.bw

value: 2XTy1-Mod(mdg4)-N stable expression


title: Oocyte, 2D (Danio)

source_name: Oocyte, 2D

value: D


title: hPGCLC aggregates from participant MZT01-N


title: Oocyte, 1D (Danio)

source_name: Oocyte, 1D


title: ApoE3_NaCl_scRNA_seq

value: NaCl


title: hPGCLC aggregates from participant MZT01-F


title: E3_NaCl_spatial

description: 10x Genomics

value: non-neuronal brain cells


title: Oocyte, 1C (Danio)

source_name: Oocyte, 1C

value: C


title: Oocyte, 1B (Danio)

source_name: Oocyte, 1B

value: Oocyte


title: Ty1-Mod(mdg4)-AF ChIP-Seq rep2

description:
Sample 2
Ty-AF_merge.bw

value: 2XTy1-Mod(mdg4)-AF stable expression


title: Immune-enriched cells from 8 mouse tumors, generated by shSCR or shcircCsnk1g3 sarcoma cells [pooled; HTO-lib]

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

data_processing:
Cell Ranger software (10X Genomics, v6.0.1) was used to demultiplex, align, filter, and count reads.
Seurat package (v4) for R was used to demultiplex sample identity based on oligo hashtags, and to filter for doublets and dead cells.
Assembly: mm10
Supplementary files format and content: tarball: feature count data as sparse matrix (output from Cell Ranger software)
Supplementary files format and content: csv: original sample ID of each single-cell barcode corresponding to a high-quality cell.

source_name: Immune-enriched cells from 8 mouse subcutaneous tumors, generated by sarcoma cells either expressing or silenced for circCsnk1g3 [pooled]

growth_protocol: Soft-tissue sarcoma cells were generated as transformed mesenchymal stem cells (bearing p53 KO and Ccne1 overexpression, allowed to form subcutaneous tumors in primary recipient mice).

extract_protocol:
Mouse tumors were digested into single-cell suspensions using the Mouse Tumor Dissociation Kit and gentleMACS dissociator (Miltenyi). CD45+ cells were enriched from each sample with magnetic beads. Enriched samples were individually hashtagged with a unique oligonucleotide barcode (TotalSeq-A, Biolegend) and then pooled together in equal proportions at a concentration of 1000 cells/uL. Single cells were partitioned for RNA capture using 10X Chromium protocols.
10X libraries were prepared from two reactions of the 10X Single Cell 3' Gene Expression kit v3, and sequenced on the NovaSeq 6000 as 800M paired-end reads.

treatment_protocol: Sarcoma cells were transduced with either shSCR or shcircCsnk1g3. Transduced cells were implanted with inert polyurethane scaffolds subcutaneously in mice.

tag: strain

value: Immune-enriched cells


title: Soft-tissue sarcoma cells - shcircCsnk1g3

description:
met_shcircCsnk1g3_v_shCTR__tmm_norm_cts.txt
JG-8194_shcircCsnk1g3_v_shCTR_RAW_COUNTS.csv

data_processing:
Quality control and alignment was performed by the Cedars-Sinai Applied Genomics, Computation and Translational Core, using the MultiQC modules FastQC, RSeQC, and STAR.
Lowly expressed genes were filtered.
Normalization for RNA composition and read depth were performed in edgeR using the TMM method (trimmed mean of M-values)
Supplementary_files_format_and_content: Raw counts (csv)
Supplementary_files_format_and_content: Normalized counts calculated with TMM method in edgeR package (txt)

growth_protocol: Soft-tissue sarcoma cells were generated as mesenchymal stem cells bearing p53 KO and Ccne1 overexpression, allowed to form subcutaneous tumors in primary recipient mice, collected and seeded in lungs of secondary recipients, and reisolated from sarcoma foci in the lungs.

extract_protocol:
Trizol extraction followed by column purification.
Libraries were prepared according to Illumina protocols for the TruSeq Stranded mRNA Library Prep kit, and sequenced on the NovaSeq platform, SP flowcell.

treatment_protocol: Sarcoma cells collected from lung foci were transduced with either shCTR or shcircCsnk1g3.

value: STS tumor cells (p53-/-Ccne1+) seeded in lungs

tag: transduction


title: Immune-enriched cells from 8 mouse tumors, generated by shSCR or shcircCsnk1g3 sarcoma cells [pooled; mRNA-lib]


title: Ty1-Mod(mdg4)-AF ChIP-Seq rep1

description:
Sample 1
Ty-AF_merge.bw

source_name: 2×Ty1-Mod(mdg4)-AF stable OSC


title: hPGCLC aggregates from participant MZT01-E

value: hiPSC derived hPGCLC aggregates


title: hPGCLC aggregates from participant MZT02-H


title: Oocyte, 1A (Danio)

source_name: Oocyte, 1A


title: Soft-tissue sarcoma cells - shCTR

source_name: Soft-tissue sarcoma cells - shCTR

value: shCTR


title: SZ95 sebocytes, PM2.5, 1 day, 2

status: Public on Oct 19 2022

city: Yongin-si

first: Hye-Won

state: Gyeonggi-do

address: 20, Yonggu-daero 1916beon-gil, Giheung-gu

country: South Korea

institute: Research and Innovation Center, AMOREPACIFIC

data_processing:
All samples were sequenced with 101 bp paired-end reads using Illumina HiSeq 2500 according to HiSeq 2500 System User Guide Document # 15035786 v01 HCS 2.2.70.
To remove adapter contamination, reads were trimmed using Trimmomatic 0.32.
The libraries were quantified using qPCR according to the Illumina qPCR Quantification Protocol Guide and Roche's Rapid library standard Quantification solution and calculator.
The trimmed reads were mapped to the human genome (UCSC hg19) using HISAT2 (version 2.0.5) and assembled using StringTie (version1.3.3b)
The abundance and gene levels were determined based on the fragments per kilobase of transcript per million fragments mapped (FPKM) value. Analysis of differentially expressed genes (DEGs) was performed using DESeq2.
Assembly: UCSC hg19
Supplementary files format and content: Matrix table with read count

source_name: SZ95 sebocyte

growth_protocol: SZ95 sebocyte was cultured in DMEM/F-12 containing 10% heat-inactivated FBS, 1% P/S, 5 ng/mL EGF, and 1 mM CaCl2. Cells were maintained in a humidified atmosphere of 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was isolated using Trizol (QIAzol Lysis Reagent; Qiagen) and qualified using a 2100 Bioanalyzer.
cDNA libraries were generated with the TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E.

treatment_protocol: SZ95 sebocytes were treated with 20% ethanol (control) or PM2.5 (100 μg/mL) in phenol-red free DMEM/F-12 containing 1% P/S for 24 h for RNA-seq

value: SZ95 sebocyte

value: epithelial cells

value: WT

value: Day 1


title: Ty1-Mod(mdg4)-N ChIP-Seq rep1

description:
Sample 3
Ty-N_merge.bw

source_name: 2×Ty1-Mod(mdg4)-N stable OSC

value: Ovarian Somatic Cells (OSC)


title: SZ95 sebocytes, control, 1 day, 3

value: vehicle


title: SZ95 sebocytes, PM2.5, 1 day, 3


title: SZ95 sebocytes, control, 1 day, 2


title: SZ95 sebocytes, control, 1 day, 1


title: RA, NP, replicate 3

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

country: Australia

institute: University of Sydney

data_processing:
Raw sequencing reads were assessed for quality using FastQC (version 0.11.3) (Babraham Bioinformatics). Per base quality scores were over Phred 30 and no adapters were detected, therefore no trimming was performed.
STAR (version 2.5.2a) was used to align the reads to Release 19 of the human reference genome (GRCh37/hg19), with the GENCODE (Release 28) annotation (http://www.gencodegenes.org/) provided, using default parameters.
Raw gene-level read counts were obtained using HTSeq (version 0.9.1) in “union” mode to exclude multi-mapping or ambiguously aligned reads.
Assembly: hg19
Supplementary files format and content: Tab-demited text files containing raw counts per feature

source_name: synovial tissue

growth_protocol: Human fibroblast like synoviocytes, rheumatoid arthritis cells were cultured and maintained in synoviocyte growth medium (Cell Applications Inc, San Diego, CA) at 37°C and 5% CO2.

extract_protocol: Stranded RNA libraries were prepared from 350 ng RNA using the Illumina® TruSeq Stranded mRNA sample prep kit, following the manufacturer's protocol

value: synovial tissue

value: rheumatoid arthritis

value: fibroblast like synoviocytes

value: endocannabinoid-NP treated


title: NSD2_1

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Barcode correction, alignment are performed using umitools and STAR aligner
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Cells were annotated using known cell type markers
Assembly: Human: GRCh38, Mouse: GRCm38
Supplementary files format and content: processed expression matrix: RDS files that contain seurat objects with or without CellBender step
Supplementary files format and content: Intronic read ratios per cell type: Text file, one row per cell barcode
Supplementary files format and content: processed expression matrix of only OPC: RDS files that contain seurat objects (with CellBender) that contain OPC clustering information

source_name: Post-mortem brain, Brodmann Area 23

extract_protocol: RNA-seq

tag: Sex

value: F

tag: age


title: RA, NP, replicate 1

tag: disease state


title: RA, TNF, NP, replicate 1

value: TNF-α stimulated, endocannabinoid-NP treated


title: RA, TNF, NP, replicate 2


title: RA, TNF, replicate 3

value: TNF-α stimulated


title: RA, UT, replicate 3

value: untreated


title: RA, TNF, NP, replicate 3


title: RA, TNF, replicate 2


title: RA, TNF, replicate 1


title: RA, UT, replicate 2


title: RA, UT, replicate 1


title: SZ95 sebocytes, PM2.5, 1 day, 1

tag: time


title: Day 21 wild type AEP organoid ATACseq

city: CINCINNATI

first: William

last: Zacharias

state: OH

address: 3333 BURNET AVE

institute: Cincinnati Children's Hospital Medical Center

library_source: genomic single cell

data_processing:
Cellranger pipeline from 10x genomics used for alignment
RNA alignment to spliced/nonspliced genome via Velocyto
RNA analysis in Seurat for clustering and differential gene expression
ATAC analysis in ArchR for clustering and analysis

source_name: Lung

growth_protocol: Lung alveolar organoids in 3D matrix

extract_protocol: Lung alveolar epithelial progenitor derived organoids were digested into a single cell suspension and analyzed by scRNAseq. Nuclei were prepared from this single cell suspension for separate analysis by scATACseq

value: Lung

value: Day 21

value: AEP organoid

value: wild type


title: Day 14 wild type AEP organoid ATACseq

value: Day 14


title: Day 28 AAVControl organoid RNAseq

value: Day 28

value: control


title: Day 28 wild type AEP organoid ATACseq


title: Day 28 AAV NKX2-1 KO organoid RNAseq

value: NKX2-1 KO


title: Day 28 wild type AEP organoid RNAseq


title: Day 21 wild type AEP organoid RNAseq


title: RA, NP, replicate 2


title: Day 14 wild type AEP organoid RNAseq


title: E17.5 Nex-Cre; Foxg1fl/fl  mice telencephalon medial pallium

city: Nanjing

first: Ru

last: Ba

state: Jiangsu

address: Southeast University

institute: Southeast University

description: 10x Genomics

data_processing:
All these analyses were performed in the Seurat package v4.0.6 (https://satijalab.org/seurat/).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: telencephalon medial pallium

extract_protocol:
medial pallium were cut into pieces and dissociated into a single-cell suspension using a Papain Cell Dissociation Kit by following the manufactures instruction.
The Chromium droplet-based sequencing platform (10X Genomics) was employed to generate scRNA-Seq libraries, following the manufactures instructions (manual document part number: CG00052 Rev C). The cDNA libraries were purified, quantified using an Agilent 2100 Bioanalyzer, and sequenced on an Illumina Hiseq4000.

value: telencephalon medial pallium

value: Nex-Cre; Foxg1fl/fl


title: LRA, replicate 2, scRNAseq

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).  Ambient RNA contamination was removed by SoupX package. Doublets were evaluated by scrublet and removed.
Downstream single cell RNA-seq analysis was performed using Seurat Package version 4.0 following the standard workflow posted on Satija lab website (https://satijalab.org/seurat/). Cells with unique feature counts less than 200 or over 7500 were removed. Cells with RNA counts less than 400 or over 40000 were removed. Cells having larger than 10% mitochondrial counts were removed.
The data was normalized by “LogNormalize” method and variable features were selected by “vst” method. Reciprocal principal component analysis (RPCA) was used for the data integration.
Cell types were identified using both manual annotations based on positive markers from FindAllMarkers function in the Seurat pipeline and a supervised annotation tool, SingleR.
Assembly: mm10
Supplementary files format and content: HDF5 of processed data

extract_protocol:
Allograft was removed and digested with 3 mL dispase (Corning) with DNase I (Sigma), and gently teased using forceps into small (1-2 mm) fragments followed by incubation at room temperature with gentle agitation for 30 minutes. The resulting suspension (in DMEM + 5% FBS) was passed through 70 μm cell strainer, erythrocytes were lysed and filtered through 40 μm cell strainers. Cells were counted using AO/PI and Cellometer K2 (Nexcelom), and cell viability exceeded 90%.
Single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell V2 Reagent Kit and Controller (10x Genomics). Libraries were assessed for quality (TapeStation 4200, Agilent) and then sequenced on  HiSeq 4000 instruments (Illumina).

value: All lung cells

value: 12 weeks old


title: E17.5 Foxg1fl/fl  mice telencephalon medial pallium

description: 10x Genomics


title: WT Cortex male mRNA rep52

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
Zswim6_9_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

data_processing:
Libraries for RNA-seq were sequenced using an Illumina HiSeq 4000 PE-75.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.3a with default parameter settings.
Raw counts were obtained with HTSeq 0.10.0 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Genome_build: Genome version Mouse GRCm38 (mm10)
Supplementary_files_format_and_content: FPKM_ensembl.txt: Tab-delimited text file includes FPKM values for each Sample (reference: RefSeq).
Supplementary_files_format_and_content: FPKM_ensembl.txt: Tab-delimited text file includes FPKM values for each Sample (reference: Ensembl).
Supplementary_files_format_and_content: metaReadCount_refSeq.txt: Tab-delimited text file includes Count values for each Sample (reference: RefSeq).
Supplementary_files_format_and_content: metaReadCount_ensembl.txt: Tab-delimited text file includes Count values for each Sample (reference: Ensembl).

source_name: Cortex

extract_protocol:
Brain cortical tissues were dissected from all mice at 6 months of age. RNA was extracted using Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded libraries preparation protocol (Illumina Inc).

value: Cerebral Cortex

value: Wild type

tag: strain/background

value: 6 months

value: male

tag: batch

value: Zswim6 group

tag: corresponding striatum sample name

value: WT Striatum male mRNA rep206

tag: plate id

value: Plate 01

tag: well address


title: WT Cortex male mRNA rep51

description:
Zswim6_7_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

tag: genotype

value: WT Striatum male mRNA rep205


title: WT Cortex male mRNA rep49

description:
Zswim6_2_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep203


title: WT Cortex male mRNA rep50

description:
Zswim6_4_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep204


title: Isotype, replicate 1, scRNAseq

description: 10x Genomics

tag: cell type

value: Lung


title: Isotype, replicate 2, scRNAseq

description: 10x Genomics


title: LRA, replicate 1, scRNAseq

description: 10x Genomics


title: WT Cortex female mRNA rep50

description:
Zswim6_1_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female


title: WT Cortex female mRNA rep52

description:
Zswim6_6_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep208


title: WT Cortex male mRNA rep47

description:
Tbc1d8_5_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Tbc1d8 group

value: WT Striatum male mRNA rep183

value: Plate 02


title: WT Cortex male mRNA rep45

description:
Tbc1d8_4a_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep184


title: WT Cortex female mRNA rep51

description:
Zswim6_3_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: WT Striatum female mRNA rep207


title: WT Cortex male mRNA rep48

description:
Tbc1d8_7_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: 6 months

value: WT Striatum male mRNA rep182


title: WT Cortex male mRNA rep46

description:
Tbc1d8_4a_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: male

value: WT Striatum male mRNA rep181


title: WT Cortex female mRNA rep48

description:
Tbc1d8_8_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep191

value: Plate 01


title: WT Cortex female mRNA rep47

description:
Tbc1d8_6_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep189


title: WT Cortex female mRNA rep46

description:
Tbc1d8_4_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep190


title: WT Cortex male mRNA rep42

description:
Rgs9_12_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Rgs9 group

value: WT Striatum male mRNA rep163


title: WT Cortex female mRNA rep45

description:
Tbc1d8_2_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female

value: Tbc1d8 group


title: WT Cortex male mRNA rep44

description:
Rgs9_5_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep161


title: WT Cortex male mRNA rep41

description:
Rgs9_12_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep162


title: WT Cortex female mRNA rep43

description:
Rgs9_6_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: WT Striatum female mRNA rep171


title: WT Cortex male mRNA rep43

description:
Rgs9_17_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: WT Striatum male mRNA rep164


title: WT Cortex female mRNA rep44

description:
Rgs9_6_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: 6 months

value: WT Striatum female mRNA rep172

value: Plate 02


title: WT Cortex female mRNA rep42

description:
Rgs9_4_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep170


title: WT Cortex female mRNA rep49

description:
Zswim6_10_5
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Zswim6 group

value: WT Striatum female mRNA rep209

value: Plate 01


title: WT Cortex male mRNA rep39

description:
Rasgef1a_5_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: male

value: Rasgef1a group

value: WT Striatum male mRNA rep155


title: WT Cortex female mRNA rep40

description:
Rasgef1a_9_5
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female

value: WT Striatum female mRNA rep163


title: WT Cortex male mRNA rep37

description:
Rasgef1a_1_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep153


title: WT Cortex female mRNA rep41

description:
Rgs9_4_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: Rgs9 group

value: WT Striatum female mRNA rep169


title: WT Cortex male mRNA rep40

description:
Rasgef1a_6_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: WT Striatum male mRNA rep156


title: WT Cortex female mRNA rep38

description:
Rasgef1a_4_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: 6 months

value: WT Striatum female mRNA rep161


title: WT Cortex female mRNA rep39

description:
Rasgef1a_9_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep162


title: WT Cortex male mRNA rep38

description:
Rasgef1a_5_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep154


title: WT Cortex male mRNA rep35

description:
Ppp1ca_14_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Ppp1ca group

value: WT Striatum male mRNA rep133


title: WT Cortex male mRNA rep36

description:
Ppp1ca_6_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: male

value: WT Striatum male mRNA rep135

value: Plate 01


title: WT Cortex male mRNA rep33

description:
Ppp1ca_11_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt


title: WT Cortex female mRNA rep36

description:
Ppp1ca_4_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female

value: WT Striatum female mRNA rep141


title: WT Cortex female mRNA rep37

description:
Rasgef1a_11_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Rasgef1a group

value: WT Striatum female mRNA rep164


title: WT Cortex female mRNA rep35

description:
Ppp1ca_2_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: WT Striatum female mRNA rep144


title: WT Cortex female mRNA rep33

description:
Ppp1ca_13_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: WT Striatum female mRNA rep143


title: WT Cortex female mRNA rep34

description:
Ppp1ca_15_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: 6 months

value: WT Striatum female mRNA rep142


title: WT Cortex male mRNA rep32

description:
Pcdh20_6_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Pcdh20 group

value: WT Striatum male mRNA rep123


title: WT Cortex male mRNA rep31

description:
Pcdh20_4_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt


title: WT Cortex male mRNA rep30

description:
Pcdh20_1_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep122


title: WT Cortex male mRNA rep29

description:
Pcdh20_1_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep121


title: WT Cortex female mRNA rep32

description:
Pcdh20_7_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep132


title: WT Cortex female mRNA rep31

description:
Pcdh20_3_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep131


title: WT Cortex female mRNA rep30

description:
Pcdh20_2_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep129

value: Plate 01


title: WT Cortex female mRNA rep29

description:
Pcdh20_2_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female


title: WT Cortex male mRNA rep34

description:
Ppp1ca_1_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: male

value: Ppp1ca group

value: WT Striatum male mRNA rep134


title: WT Cortex male mRNA rep27

description:
Morf4l1_14_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: Morf4l1 group

value: WT Striatum male mRNA rep108


title: WT Cortex male mRNA rep28

description:
Morf4l1_4_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: 6 months

value: WT Striatum male mRNA rep110


title: WT Cortex male mRNA rep25

description:
Morf4l1_11_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep111


title: WT Cortex female mRNA rep26

description:
Morf4l1_12_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep118


title: WT Cortex female mRNA rep28

description:
Morf4l1_5_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep120


title: WT Cortex male mRNA rep24

description:
Kdm3b_2_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Kdm3b group

value: WT Striatum male mRNA rep99


title: WT Cortex male mRNA rep22

description:
Kdm3b_11_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep100


title: WT Cortex female mRNA rep25

description:
Morf4l1_10_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep119

value: Plate 02


title: WT Cortex female mRNA rep27

description:
Morf4l1_12_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female

value: Plate 01


title: WT Cortex male mRNA rep23

description:
Kdm3b_17_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: male


title: WT Cortex male mRNA rep21

description:
Kdm3b_11_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: WT Striatum male mRNA rep98


title: WT Cortex female mRNA rep24

description:
Kdm3b_5_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt


title: WT Cortex female mRNA rep21

description:
Kdm3b_1_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep108


title: WT Cortex male mRNA rep17

description:
Hrk_10_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: Hrk group

value: WT Striatum male mRNA rep79


title: WT Cortex female mRNA rep23

description:
Kdm3b_5_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: 6 months


title: WT Cortex male mRNA rep18

description:
Hrk_2_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep81


title: WT Cortex male mRNA rep19

description:
Hrk_4_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep80


title: WT Cortex female mRNA rep20

description:
Hrk_6_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep76


title: WT Cortex female mRNA rep19

description:
Hrk_3_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep77


title: WT Cortex female mRNA rep18

description:
Hrk_14_4
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep78


title: WT Cortex female mRNA rep17

description:
Hrk_12_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep79


title: WT Cortex male mRNA rep26

description:
Morf4l1_14_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Morf4l1 group

value: WT Striatum male mRNA rep112


title: WT Cortex male mRNA rep16

description:
Gsg1l_9_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Gsg1l group

value: Plate 01


title: WT Cortex male mRNA rep15

description:
Gsg1l_7_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: male

value: WT Striatum male mRNA rep73


title: WT Cortex male mRNA rep14

description:
Gsg1l_5_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: WT Striatum male mRNA rep72


title: WT Cortex female mRNA rep16

description:
Gsg1l_8_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female

value: WT Striatum female mRNA rep68

value: Plate 02


title: WT Cortex female mRNA rep14

description:
Gsg1l_11_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: 6 months

value: WT Striatum female mRNA rep70


title: WT Cortex male mRNA rep13

description:
Gsg1l_3_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum male mRNA rep70


title: WT Cortex female mRNA rep15

description:
Gsg1l_13_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: WT Striatum female mRNA rep71


title: WT Cortex male mRNA rep20

description:
Hrk_9_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Hrk group

value: WT Striatum male mRNA rep78


title: WT Cortex male mRNA rep12

description:
Ece2_8_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Ece2 group

value: WT Striatum male mRNA rep51


title: WT Cortex female mRNA rep22

description:
Kdm3b_3_1
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Kdm3b group

value: WT Striatum female mRNA rep105

value: Plate 01


title: WT Cortex male mRNA rep10

description:
Ece2_10c_3
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Cerebral Cortex

value: male

value: WT Striatum male mRNA rep48


title: WT Cortex male mRNA rep9

description:
Ece2_10c_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: Wild type

value: WT Striatum male mRNA rep52


title: WT Cortex female mRNA rep11

description:
Ece2_4_2
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: female

value: WT Striatum female mRNA rep51


title: WT Cortex male mRNA rep11

description:
Ece2_12_5
mRNA
processed data file: FPKM_ensembl.txt
processed data file: FPKM_refSeq.txt
processed data file: metaReadCount_ensembl.txt
processed data file: metaReadCount_refSeq.txt

value: 6 months

value: WT Striatum male mRNA rep49