title: 10BTreg73

tag: Sex

tag: donor group


title: 10BTreg71

status: Public on Nov 17 2020

type: SRA

city: Berkeley

first: Allon

last: Wagner

state: CA

address: 378 Stanley Hall

country: USA

institute: UC Berkeley

library_source: transcriptomic

data_processing:
Reads were pseuoaligned with Kallisto v0.46.0 to the Ensembl v96 human transcripome
Transcript TPMs were aggregated and summed for gene-level analysis, and then log2-transformed; non-protein-coding transcripts were excluded
Genome_build: GRCh38.96
Supplementary_files_format_and_content: linear-scale count matrix in csv format

molecule: total RNA

organism: Homo sapiens

source_name: iTreg

extract_protocol:
PBMCs were isolated from peripheral blood and Treg cells were single sorted into 96-well plates by FACS using CD4+CD25hiCD127lo/neg antibodies. For adipose tissue, we first performed collagenase digestion. Next, the lymphocytes were isolated from the sample by Ficoll gradient and centrifugation (as done with PBMC isolation) in a ratio of 9 mL of sample to 4 mL of Ficoll. The lymphocyte layer was removed and washed. The Treg cells were then single sorted by FACS using CD4+CD25hiCD127lo/neg antibodies.
Illumina TruSeq Stranded mRNA kit was used for library prep, and sequenced with a 2 × 100 bp paired-end protocol on the HiSeq 2000 Sequencing System (Illumina).

tag: donor id

tag: tissue

value: Blood

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi

value: M


title: G477-K27R_RNA-seq rep2

city: Santiago de Compostela

first: Carmen

last: Rivas

address: Avda Barcelona

department: CIMUS

country: Spain

institute: Universidad de Santiago de Compostela

data_processing:
Raw RNA sequencing reads were aligned using STAR version 2.5.3a with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: brain tumor derived cell line

growth_protocol: Tumor-derived cell lines were maintained in NeuroCult NS-A proliferation media (StemCell Technologies) supplemented with bFGF (10ng/mL) (StemCell Technologies), rhEGF (20 ng/mL) (StemCell Technologies) and heparin (0.0002%) (StemCell Technologies) on plates coated in poly-L-ornithine (0.01%) (Sigma) and laminin (0.01 mg/mL) (Sigma).  Drosophila S2 cells were cultured in Schneider's Drosophila Medium (Invitrogen) containing 10% heat-inactivated FBS.

extract_protocol:
Total RNA was extracted from cell pellets and mouse tumors using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to instructions from the manufacturer.
Library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts.

tag: cell line

tag: genotype

value: H3.3 (H3F3A) K27R overexpression


title: G477-K27R_RNA-seq rep3


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A12_AD001

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 INTACT reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10 INTACT
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

value: brain

tag: source

value: VIS

tag: target

value: STR

tag: gender

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A11_AD004

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A5_AD001


title: 10BTreg72

tag: Sex


title: 10BTreg75

tag: donor group


title: singleCell_spheroid_plate1_K10_S114

city: Stanford

first: Rachel

last: Agoglia

address: 371 Jane Stanford Way

institute: Stanford University

data_processing:
Remove sequencing adapters with SeqPrep version 1.2
Map reads to GRCh38 and PanTro5 with STAR version 2.5.1b
Remove duplicate reads withSamtools version 0.1.19 with randomized discarding of duplicates
Remove reads which exhibit mapping bias with WASP (Hornet)
Count allele specific and total reads
Genome_build: Human: GRCh38; Chimpanzee: PanTro5
Supplementary_files_format_and_content: Counts matrix with total and allele-specific raw read counts (rows are genes, there are 3 columns per sample: total, human and chimpanzee read counts); matrix text files are provided for samples mapped on both the human and chimpanzee genomes; text files with sample meta data are also included for each data set

molecule: polyA RNA

organism:
Pan troglodytes
Homo sapiens

source_name: iPSC-derived cortical spheroid

extract_protocol:
Qiagen Rneasy Mini Kit with on-column DNAse digestion (Qiagen)
Illumina TruSeq Stranded mRNA library prep kit (Illumina)

tag: cell type

value: iPSC-derived cortical spheroid

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_J8_S88


title: 10BTreg76

tag: donor id

tag: tissue

tag: age at procedure

tag: date of procedure


title: singleCell_spheroid_plate1_K11_S115


title: singleCell_spheroid_plate1_J7_S87


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A11_AD002


title: singleCell_spheroid_plate1_J9_S89


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A11_AD006


title: HSJ019-K27M1_H3K27me3

description: According to manufacturer's protocol

data_processing:
Raw ChIP sequencing reads were aligned using BWA version 0.7.17 with default parameters. After alignment, we sorted the bam files using samtools, then igvtools was used to generate wig files (igvtools count -w 25 -e 200). Finally, bigWig files were obtained using wigToBigWig.
Genome_build: hg19 and dm6 for human and drosophila data, respectively
Supplementary_files_format_and_content: bigWig

source_name: brain tumor derived cell line & S2 cells (spike in)

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing. ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. 25ul Protein A beads (Invitrogen) or 70ul of sheep anti-mouse IgG beads (Invitrogen) were washed and then incubated with antibodies (protein A beads with: anti-H3K27me3 (1:40, CST 9733), anti-H3K27me2 (1:50, CST 9728), anti-H3K36me2 (1:50, CST 2901), anti-H3K9me3 (1:66, Abcam ab8898); anti-mouse IgG beads with: anti-H3K27me1 (1:50, Active Motif 61015), anti-H3K36me3 (1:100, Active Motif 61021)), and 2 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. ChIP reaction for SUZ12 was performed as follows: antibodies (anti-SUZ12 (1:150, CST 3737)) were conjugated by incubating with 40ul protein A beads at 4°C for 6 hours, then chromatin from ~4 million cells was added in RIPA buffer, incubated at 4°C o/n, washed using buffers from Ideal ChIP-seq Kit (1 wash with each buffer, corresponding to RIPA, RIPA+500mM NaCl, LiCl, TE), eluted from beads by incubating with Elution buffer for 30 minutes at room temperature. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol.
Library preparation was carried out using Kapa HTP or HyperPrep Illumina library preparation reagents, according to manufacturer's instructions.

tag: chip antibody

value: H3K27me3 (Cell Signaling Technology, #9733)


title: 10BTreg69

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi


title: G477-K27M_RNA-seq rep1

tag: cell line

tag: genotype

value: H3.3 (H3F3A) K27M overexpression


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A10_AD006

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_J6_S86

tag: cell type

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_J5_S85


title: G477-K27M_RNA-seq rep2


title: 10BTreg68

tag: donor id

tag: tissue

tag: age at procedure

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A10_AD004


title: HSJ019-K27M1_H3K36me2

description: According to manufacturer's protocol

tag: chip antibody

value: H3K36me2 (Cell Signaling Technology, #2901)


title: 10BTreg67

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 10BTreg66


title: 10BTreg70


title: HSJ019-K27M1_H3K27me2

description: According to manufacturer's protocol

tag: cell line

value: H3K27me2 (Cell Signaling Technology, #9728)

tag: genotype


title: G477-K27R2_Input

description: According to manufacturer's protocol


title: 10BTreg65


title: singleCell_spheroid_plate1_J4_S84


title: singleCell_spheroid_plate1_J3_S83


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A10_AD001

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P7_180313_P8_A11_AD001

tag: tissue


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H9_AD004

value: PTLp


title: 10BTreg64

tag: donor id

tag: age at procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H9_AD006


title: G477-K27R2_H3K36me2

description: According to manufacturer's protocol


title: G477-K27R1_H3K27me2

description: According to manufacturer's protocol


title: singleCell_spheroid_plate1_J2_S82

tag: cell type

tag: differentiation id

tag: age (days)


title: G477-K27R2_H3K27me1

description: According to manufacturer's protocol

tag: chip antibody

value: H3K27me1 (Active Motif, #61015)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H9_AD002


title: singleCell_spheroid_plate1_J24_S104


title: singleCell_spheroid_plate1_J23_S103


title: G477-K27R1_H3K27me3

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H7_AD006


title: 10BTreg62

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: Sex

tag: donor group


title: 10BTreg61

tag: weight (kg)

tag: bmi


title: 10BTreg60


title: singleCell_spheroid_plate1_J22_S102

tag: cell line


title: G477-K27M2_Input

description: According to manufacturer's protocol

tag: genotype


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H7_AD004

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_J21_S101

tag: cell type

tag: differentiation id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H7_AD002

tag: tissue


title: singleCell_spheroid_plate1_J20_S100

tag: age (days)


title: 10BTreg59

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed


title: G477-K27M2_H3K27me1

description: According to manufacturer's protocol

tag: chip antibody


title: G477-K27M2_H3K36me2

description: According to manufacturer's protocol


title: 10BTreg58

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H7_AD001

tag: strain

tag: age

tag: source


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H9_AD001

tag: target

tag: gender


title: singleCell_spheroid_plate1_J1_S81

tag: cell type

tag: cell line

tag: differentiation id


title: 10BTreg57

tag: donor id

tag: tissue

tag: age at procedure


title: G477-K27M1_H3K27me3

description: According to manufacturer's protocol

tag: chip antibody

tag: genotype


title: singleCell_spheroid_plate1_J19_S99

tag: age (days)


title: singleCell_spheroid_plate1_J18_S98


title: 10BTreg63

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: bmi


title: 10BTreg55

tag: Sex

tag: donor group


title: singleCell_spheroid_plate1_J17_S97


title: G477-K27M1_H3K27me2

description: According to manufacturer's protocol


title: DIPGXIII-KO2_H3K27me3

description: According to manufacturer's protocol

value: SU-DIPGXIII

value: H3.3 (H3F3A) K27M-KO by introducing frameshift indel to the H3F3A allele carrying K27M mutation and leaving wild-type allele


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H6_AD004

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H6_AD006

tag: tissue


title: DIPGXIII-KO2_Input

description: According to manufacturer's protocol

tag: cell line


title: 10BTreg56

tag: donor id

value: Blood

tag: age at procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H6_AD002


title: 10BTreg54

value: M


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H6_AD001


title: singleCell_spheroid_plate1_J16_S96

tag: cell type

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_J15_S95


title: 10BTreg53

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: DIPGXIII-KO2_H3K27me2

description: According to manufacturer's protocol

tag: chip antibody

tag: genotype


title: DIPGXIII-KO2_H3K36me2

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H5_AD006

tag: strain


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H5_AD004

tag: age


title: singleCell_spheroid_plate1_J14_S94


title: 10BTreg52

tag: weight (kg)

tag: bmi

tag: Sex

tag: donor group


title: 10BTreg51

tag: tissue


title: DIPGXIII-KO1_SUZ12

description: According to manufacturer's protocol

tag: cell line

value: SUZ12 (Cell Signaling Technology, #3737)


title: singleCell_spheroid_plate1_J13_S93


title: DIPGXIII-KO1_H3K27me3

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H5_AD002

value: brain

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_J12_S92

tag: cell type

tag: differentiation id

tag: age (days)


title: DIPGXIII-KO1_Input

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H5_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H4_AD006


title: DIPGXIII-KO1_H3K9me3

description: According to manufacturer's protocol

value: H3K9me3 (Abcam, #ab8898)


title: 10BTreg49

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: 10BTreg50

tag: weight (kg)


title: singleCell_spheroid_plate1_J10_S90


title: 10BTreg48

tag: bmi


title: DIPGXIII-KO1_H3K36me2

description: According to manufacturer's protocol

tag: chip antibody

tag: genotype


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H4_AD004

tag: strain

tag: age

tag: tissue

value: STR


title: 10BTreg47

tag: Sex

tag: donor group


title: singleCell_spheroid_plate1_I9_S65

tag: cell type

tag: cell line


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H4_AD002

tag: source

tag: target

tag: gender


title: DIPGXIII-KO1_H3K27me2

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H4_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H3_AD006

value: male


title: singleCell_spheroid_plate1_I8_S64

tag: differentiation id

tag: age (days)


title: DIPGXIII-KO1_H3K27me1

description: According to manufacturer's protocol


title: 10BTreg45

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: singleCell_spheroid_plate1_I7_S63


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H3_AD004

tag: strain


title: DIPGXIII-K27M5_Input

description: According to manufacturer's protocol

tag: chip antibody

tag: genotype


title: 10BTreg44

tag: tissue

tag: weight (kg)

tag: bmi

tag: Sex


title: singleCell_spheroid_plate1_I6_S62

tag: cell type

tag: cell line


title: 10BTreg43

tag: donor group


title: singleCell_spheroid_plate1_J11_S91

tag: differentiation id


title: singleCell_spheroid_plate1_I5_S61

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H3_AD002

tag: age

tag: source

tag: target

tag: gender

value: female


title: DIPGXIII-K27M5_H3K27me1

description: According to manufacturer's protocol


title: DIPGXIII-K27M5_H3K27me2

description: According to manufacturer's protocol


title: singleCell_spheroid_plate1_I4_S60

value: iPSC-derived cortical spheroid


title: 10BTreg42

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H3_AD001

tag: strain

tag: tissue


title: singleCell_spheroid_plate1_I3_S59


title: 10BTreg40

tag: weight (kg)

tag: bmi

tag: Sex


title: 10BTreg41

tag: donor group


title: DIPGXIII-K27M4-DMSO_Input

description: According to manufacturer's protocol

tag: cell line

tag: chip antibody

tag: genotype


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H2_AD006

tag: age

tag: source


title: 10BTreg46


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H2_AD004

tag: target

tag: gender


title: DIPGXIII-K27M4-DMSO_H3K9me3

description: According to manufacturer's protocol


title: DIPGXIII-K27M4-DMSO_H3K27me3

description: According to manufacturer's protocol

value: H3K27me3 (Cell Signaling Technology, #9733)


title: singleCell_spheroid_plate1_I2_S58

tag: cell type

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_I24_S80


title: singleCell_spheroid_plate1_I23_S79


title: BT245-NSD-dKO_Input

description: According to manufacturer's protocol


title: 10BTreg39

tag: donor id

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H12_AD006

tag: strain

tag: tissue


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H2_AD001


title: 10BTreg38

tag: weight (kg)

tag: bmi

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H12_AD004

tag: age

tag: source


title: BT245-NSD-dKO_H3K27me3

description: According to manufacturer's protocol

tag: cell line

tag: chip antibody

tag: genotype


title: 10BTreg36


title: BT245-NSD-dKO_H3K27me2

description: According to manufacturer's protocol


title: singleCell_spheroid_plate1_I21_S77

tag: cell type

tag: differentiation id

tag: age (days)


title: 10BTreg37

tag: donor id

tag: age at procedure

tag: date of procedure


title: singleCell_spheroid_plate1_I22_S78


title: BT245-NSD-dKO_H3K36me2

description: According to manufacturer's protocol


title: 10BTreg35

tag: year diagnosed

tag: height (cm)


title: singleCell_spheroid_plate1_I20_S76


title: 10BTreg34

tag: tissue

tag: weight (kg)


title: BT245-KO2-r2_SUZ12

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H2_AD002

tag: strain

tag: target

tag: gender


title: BT245-KO2-r2_Input

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H12_AD002

tag: age

tag: source


title: BT245-KO2-r2_H3K27me2

description: According to manufacturer's protocol

tag: cell line

tag: chip antibody


title: singleCell_spheroid_plate1_I18_S74

tag: cell type


title: 10BTreg32

tag: bmi

tag: Sex

tag: donor group


title: 10BTreg33

tag: donor id

tag: age at procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H11_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H12_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H11_AD004


title: singleCell_spheroid_plate1_I19_S75

tag: differentiation id

tag: age (days)


title: BT245-KO2-r2_H3K27me1

description: According to manufacturer's protocol

tag: genotype


title: BT245-KO2_H3K27me3

description: According to manufacturer's protocol


title: 10BTreg31

tag: tissue

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)


title: 10BTreg30


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H11_AD002

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H11_AD001


title: singleCell_spheroid_plate1_I15_S71

tag: cell type

tag: cell line


title: singleCell_spheroid_plate1_I16_S72


title: singleCell_spheroid_plate1_I17_S73


title: BT245-KO2_H3K9me3

description: According to manufacturer's protocol

tag: chip antibody


title: 10BTreg28

tag: donor id

tag: age at procedure

tag: bmi

tag: Sex

tag: donor group


title: singleCell_spheroid_plate1_I14_S70

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H10_AD006

tag: tissue


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H10_AD004


title: 10BTreg27

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)


title: BT245-KO2_H3K36me2

description: According to manufacturer's protocol

tag: genotype


title: BT245-KO1-r2_Input

description: According to manufacturer's protocol


title: 10BTreg26


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H10_AD002

tag: strain

tag: age

tag: source

tag: target

tag: gender


title: singleCell_spheroid_plate1_I12_S68

tag: cell type

tag: cell line


title: singleCell_spheroid_plate1_I1_S57


title: 10BTreg25

tag: donor id

tag: age at procedure

tag: bmi

tag: Sex


title: singleCell_spheroid_plate1_I11_S67

tag: differentiation id

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G9_AD006

tag: tissue


title: BT245-KO1-r2_H3K36me2

description: According to manufacturer's protocol

tag: chip antibody


title: 10BTreg29

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G9_AD004

tag: strain

tag: age

tag: source

tag: target


title: 10BTreg24

tag: donor id


title: BT245-KO1-r2_H3K27me1

description: According to manufacturer's protocol

tag: cell line

tag: genotype


title: singleCell_spheroid_plate1_H9_S41

tag: cell type


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G9_AD002

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G9_AD001


title: singleCell_spheroid_plate1_H8_S40

tag: differentiation id

tag: age (days)


title: singleCell_spheroid_plate1_I13_S69


title: BT245-KO1_H3K27me3

description: According to manufacturer's protocol

tag: chip antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G7_AD006

tag: tissue


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_H10_AD001


title: BT245-KO1_Input

description: According to manufacturer's protocol


title: 10BTreg22

tag: age at procedure

tag: date of procedure

tag: year diagnosed

tag: bmi

tag: Sex


title: 10BTreg21

tag: height (cm)

tag: weight (kg)

tag: donor group


title: singleCell_spheroid_plate1_H7_S39


title: 10BTreg20

tag: donor id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G7_AD004

tag: strain

tag: age

tag: source

tag: target


title: 10BTreg19


title: singleCell_spheroid_plate1_H5_S37

tag: cell type

tag: cell line

tag: differentiation id


title: BT245-KO1-r2_H3K27me2

description: According to manufacturer's protocol

tag: chip antibody

tag: genotype


title: BT245-K27M2_H3K27me3

description: According to manufacturer's protocol

value: H3K27me3 (Cell Signaling Technology, #3737)


title: singleCell_spheroid_plate1_I10_S66

tag: age (days)


title: singleCell_spheroid_plate1_H4_S36


title: 10BTreg23

tag: tissue

tag: age at procedure

tag: date of procedure

tag: year diagnosed


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G7_AD001

tag: gender


title: BT245-K27M2_SUZ12

description: According to manufacturer's protocol


title: 10BTreg17

tag: height (cm)

tag: weight (kg)

tag: bmi

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G6_AD006

tag: strain

tag: age

tag: source

tag: target


title: singleCell_spheroid_plate1_H3_S35

tag: cell type

tag: cell line

tag: differentiation id


title: BT245-K27M2_Input

description: According to manufacturer's protocol

tag: chip antibody

tag: genotype


title: 10BTreg18

tag: donor id

tag: tissue

tag: age at procedure

tag: date of procedure


title: 10BTreg16

tag: year diagnosed

tag: height (cm)

tag: weight (kg)


title: BT245-K27M3-DMSO_Input

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G6_AD004

tag: gender


title: singleCell_spheroid_plate1_H6_S38

tag: age (days)


title: singleCell_spheroid_plate1_H2_S34


title: BT245-K27M2_H3K9me3

description: According to manufacturer's protocol


title: BT245-KO2_Input

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G7_AD002

tag: strain

tag: age


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G6_AD002

tag: source

tag: target


title: 10BTreg15

tag: bmi

tag: Sex

tag: donor group


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G6_AD001


title: BT245-K27M3-DMSO_H3K27me2

description: According to manufacturer's protocol

tag: cell line

tag: chip antibody

tag: genotype


title: 10BTreg13

tag: donor id

tag: tissue

tag: age at procedure


title: singleCell_spheroid_plate1_H23_S55

tag: cell type

tag: differentiation id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G5_AD006

tag: gender


title: 10BTreg14

tag: date of procedure

tag: year diagnosed

tag: height (cm)

tag: weight (kg)


title: BT245-K27M2_H3K36me2

description: According to manufacturer's protocol

value: H3K36me2 (Cell Signaling Technology, #2901)


title: BT245-K27M2_H3K27me2

description: According to manufacturer's protocol

value: H3K27me2 (Cell Signaling Technology, #9728)


title: singleCell_spheroid_plate1_H22_S54

tag: age (days)


title: singleCell_spheroid_plate1_H21_S53


title: BT245-K27M2_H3K27me1

description: According to manufacturer's protocol


title: bulk_spheroid_SY15_D75_H20961


title: 10BTreg12

tag: bmi


title: bulk_spheroid_SY15_D50_H20961


title: 10BTreg11

tag: Sex


title: singleCell_spheroid_plate1_H20_S52


title: bulk_spheroid_SY15_D25_H20961


title: 10BTreg10

tag: donor group


title: singleCell_spheroid_plate1_H1_S33

tag: cell line


title: 10BTreg09


title: singleCell_spheroid_plate1_H18_S50


title: RNA-hNeuronMat-H9-UTXKO replicate 1

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (v24lift37) (Harrow et al., 2012).
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: raw reads count by HTSEQ

source_name: Cell Line

growth_protocol: H7/WA07 (WiCell) and H9/WA09 cells (WiCell) were grown on Matrigel with reduced growth  factors (ThermoFisher Scientific, #354230) in mTeSR1 medium (STEMCELL Technologies,  #85850) at 37°C and 5% CO2. For neural differentiation, ES cells were seeded onto  AggreWell800 plates (STEMCELL Technologies, #34811) and fed with neural induction medium  (STEMCELL Technologies, #05835) to form uni-sized embryoid bodies (EBs).

extract_protocol:
RNA was purified with the GeneJET RNA purification kit (ThermoFisher Scientific, K0732). The cDNA was reverse transcribed from 300 ng of RNA, using SuperScript IV reverse transcriptase (ThermoFisher Scientific, #18090050) with random hexamers. RT reactions were performed in triplicate to minimize variability.
total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)

treatment_protocol: On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation (STEMCELL  Technologies, #08500) started from day 11 to day 16. On day 17, cells were treated with  Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium  (STEMCELL Technologies, #08510) till days 22–24. For Neurosphere, Human NSCs were treated with accutase (STEMCELL Technologies, Cat. No. 07920),  dissociated into single cells, and plated in low-attachment 6-well plates (Fisher Scientific,  #CLS3471) at 10,000-25,000 cells/6-well densities. For serial passages, neurospheres after 6-8  days of culturing were dissociated to single cells with accutase treatment and plated in neural  expansion media.

value: Human Neuronal Maturation Cell H9 UTXKO


title: singleCell_spheroid_plate1_H24_S56


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G4_AD006

tag: strain

tag: age

tag: source

value: PTLp

tag: target


title: 10BTreg06

tag: donor id

tag: tissue

tag: age at procedure


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G4_AD002

tag: gender


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G5_AD004


title: singleCell_spheroid_plate1_H16_S48

tag: cell type

tag: differentiation id


title: 10BTreg08

tag: date of procedure

tag: year diagnosed

tag: height (cm)


title: singleCell_spheroid_plate1_H17_S49

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G4_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G5_AD002


title: 10BTreg07

tag: weight (kg)

tag: bmi

tag: Sex


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G3_AD006

tag: strain


title: 10BTreg05

tag: donor group


title: RNA-hESC-H9-UTXKO replicate 3

value: Human Embryonic Stem Cell H9 UTXKO


title: singleCell_spheroid_plate1_H15_S47

tag: cell line


title: RNA-hESC-H9-UTXKO replicate 1


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G5_AD001

tag: age

tag: source

tag: target


title: 10BTreg04

tag: donor id

tag: tissue

tag: age at procedure


title: RNA-hESC-H9-UTXKO replicate 2

tag: cell type


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G4_AD001

tag: gender


title: RNA-hNeuronMat-H9-WT replicate 1

value: Human Neuronal Maturation Cell H9


title: singleCell_spheroid_plate1_H19_S51

tag: differentiation id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G3_AD004


title: RNA-hESC-H7-UTXKO replicate 4

value: Human Embryonic Stem Cell H7 UTXKO


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G3_AD002


title: 10BTreg03

value: Blood

tag: date of procedure

tag: year diagnosed

tag: height (cm)

value: M


title: ATAC-hNSC-H9-WT replicate 2

data_processing:
Basecalls performed using CASAVA
2x100bp paired-end reads obtained from all samples were trimming for Nextera adapter by cutadapt(version 1.9, paired-end mode, default parameter with “-m 6 -O 20”) and aligned to human genome hg19(GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter). Duplicated reads were then marked with Picard(version 2.6.0-SNAPSHOT) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). After adjustment of Tn5 shift (reads were offset were offset by +4 bp for the sense strand and -5 bp for the antisense strand), we separated reads into nucleosome free, mononucleosome, dinucleosome, trinucleosome as described in Buenrostro et.al by fragment size and generated bigwig files by using the center 80bp of fragments and scale to 30M nucleosome free reads. We observed reasonable nucleosome free peaks and pattern of mono-, di-, tri-nucleosome on IGV (version 2.4.13) and all samples have about 10M nucleosome free reads so we conclude the data qualities are good and have enough depth.
Next we merged each 2 replicates to enhance peak calling on nucleosome free reads by MACS2(version 2.1.1.20160309 default parameters with “--extsize 200 --nomodel "). To assure the replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one merged sample and at least called with lower cutoff(macs2 -q 0.5) in the other merged sample. Then reproducible peaks were further merged between groups to create a final set of reference  chromatin accessible regions.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig

extract_protocol:
Libraries were generated from isolated nuclei using a standard protocol.
Libraries are prepared and sequenced at the St. Jude Hartwell Center.

treatment_protocol: On day 5, EBs were re-plated onto Matrigel-treated 6-well plates. Neural differentiation (STEMCELL  Technologies, #08500) started from day 11 to day 16. On day 17, cells were treated with  Accutase® (STEMCELL Technologies) and seeded and fed with neuronal maturation medium  (STEMCELL Technologies, #08510) till days 22–24.

value: Human Neural Stem Cells H9

tag: chip antibody


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G3_AD001

value: brain


title: 10BTreg02

tag: weight (kg)

tag: bmi

tag: Sex


title: ATAC-hNSC-H9-WT replicate 1


title: singleCell_spheroid_plate1_H12_S44

tag: cell line

tag: age (days)


title: 10BTreg01

tag: donor group


title: ATAC-hNSC-H9-UTXKO replicate 2

value: Human Neural Stem Cells H9 UTXKO


title: singleCell_spheroid_plate1_H11_S43


title: singleCell_spheroid_plate1_H10_S42


title: HA5529_OA

data_processing:
Reads were pseuoaligned with Kallisto v0.46.0 to the Ensembl v96 human transcripome
Transcript TPMs were aggregated and summed for gene-level analysis, and then log2-transformed; non-protein-coding transcripts were excluded
Genome_build: GRCh38.96
Supplementary_files_format_and_content: kallisto transcript abundance estimates in tsv format

source_name: Tregs sorted from peripheral blood

extract_protocol: Cells were harvested and RNA was isolated using RNeasy Micro Kit (QIAGEN), and immediately processed for cDNA preparation. Illumina TruSeq Stranded mRNA kit was used for library prep, and sequenced with a 2 X 100 bp paired-end protocol on the HiSeq 2000 Sequencing System (Illumina).

treatment_protocol: CD4+CD25hiCD127lo/neg Treg cells from healthy donors were sorted by FACS and cultured with 10 µM oleic acid, 10 µM arachidonic acid, or none (control) in the presence of anti-human CD3 (UCHT1) (1 µg/ml), soluble anti-human CD28 (28.2) (1 µg/ml) (BD Bioscience), and human IL-2 (50 U/ml) for three days.

value: Tregs sorted from peripheral blood

tag: batch

value: C

tag: treatment

value: Oleic acid


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G1_AD006

tag: strain

tag: age

tag: tissue

tag: source

tag: target

value: STR

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G1_AD004

tag: gender


title: ATAC-hNSC-H9-UTXKO replicate 1

tag: cell type


title: singleCell_spheroid_plate1_G9_S17

value: iPSC-derived cortical spheroid

tag: differentiation id


title: HA5529_ctrl

value: Vehicle

tag: donor id


title: ATAC-hNSC-H7-WT replicate 2

value: Human Neural Stem Cells H7

tag: chip antibody


title: singleCell_spheroid_plate1_H14_S46


title: HA5529_AA

value: Arachidonic acid


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G1_AD001

value: PTLp

value: female


title: ATAC-hNSC-H7-WT replicate 1


title: singleCell_spheroid_plate1_G8_S16


title: singleCell_spheroid_plate1_G7_S15


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G12_AD006


title: singleCell_spheroid_plate1_H13_S45


title: HA5528_OA


title: HA5528_ctrl


title: singleCell_spheroid_plate1_G6_S14


title: HA5528_AA


title: ATAC-hNSC-H7-UTXKO replicate 1

value: Human Neural Stem Cells H7 UTXKO


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G12_AD002


title: PFC_sc_Rep1_10X

city: New York

first: Anoushka

last: Joglekar

state: NY

address: 413 E 69th St

department: Dept. of Neurogenetics

institute: Weill Cornell Medicine

data_processing:
Illumina basecaller
PacBio IsoSeq basecaller
Oxford Nanopore Guppy basecaller
10X sequencing output processed with 10X cellranger v3
Cellranger output analyzed with Seurat v3
PacBio long read mapping done with STARlong
ONT long read mapping done with minimap2
Long read output processed with custom pipelines - Github
website with downloadable plots of the processed data: www.isoformAtlas.com
github repository with code: https://github.com/noush-joglekar/scisorseqr/
Genome_build: mm10
Supplementary_files_format_and_content: cellranger output for single-cell expression data
Supplementary_files_format_and_content: PacBio gff files: files were generated by mapping and aligning reads to the reference genome, and each line refers to an exon for a specific read. We selected reads that were uniquely mapped, spliced, and had consensus splice-sites. The files include 'hg19' but were  from mm10 alignment.

source_name: Prefrontal cortex

extract_protocol: As per recommendations of each individual platform

value: Brain

tag: brain region

value: Prefrontal cortex

tag: developmental stage


title: HA5527_OA


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G1_AD002


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G12_AD001


title: HA5527_ctrl


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G11_AD006


title: singleCell_spheroid_plate1_G3_S11

tag: cell line


title: 2019-9285: Ri4_IP

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Aligned to moouse genome (mm10) using STAR spliced read aligner
Count reads using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation and differential expression analysis using Bioconductor packages
FPKM values
Genome_build: mm10

source_name: R6/2 +hM4Di

extract_protocol:
Total RNA was extracted using RNeazy kit (Qiagen) accordance with the prescribed protocol provided with the kit.
Libraries prepared using the Illumina TruSeq Stranded RNA (100 ng) + RiboZero Gold Library Prep Kit  and sequenced on an Illumina HiSeq4000 sequencer using strand-specific

treatment_protocol: We overexpressed Rpl22-HA specially in the mouse striatal astrocytes by RiboTag AAV for three weeks before RNA extraction. To ablate MSNs, quinolinic acid (QA) was injected into the striatum 2 weeks before RNA extraction; to induce neuroinflammation, lipopolysaccharide (LPS) was i.p. injected 24h before; to reduce potassium current, AAV-GfaABC1D-Cre was injected with RiboTag AAV into Kir4.1 floxed mice; to activate Gs-GPCR signaling pathway, AAV-GfaABC1D-rM3D was injected with RiboTag AAV and CNO was i.p. injected 2h before RNA extraction. After tissue homogenization, RNA was purified from (i) cleared lysate as the input sample, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag as the IP sample.

value: striatal astrocytes

tag: condition

tag: rna-sample type

value: IP


title: 2019-9285: Ri4_input

value: Input


title: HIPP_sc_Rep1_10X

source_name: Hippocampus

value: Hippocampus


title: HA5527_AA

value: Tregs sorted from peripheral blood

tag: batch

value: C


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G11_AD002

value: brain

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G12_AD004

value: male


title: ATAC-hNSC-H7-UTXKO replicate 2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G11_AD001


title: singleCell_spheroid_plate1_G24_S32

value: iPSC-derived cortical spheroid

tag: age (days)


title: singleCell_spheroid_plate1_G23_S31


title: HA5526_OA

tag: treatment

value: Oleic acid


title: 2019-9285: Ri3_input

tag: strain


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G10_AD006

tag: age

tag: tissue


title: 2019-9285: Ri3_IP


title: HA5526_AA

value: Arachidonic acid


title: singleCell_spheroid_plate1_G5_S13


title: singleCell_spheroid_plate1_G22_S30


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G10_AD004

tag: source

value: PTLp

tag: target


title: HA5233_OA

tag: cell type

value: B


title: singleCell_spheroid_plate1_G21_S29

tag: differentiation id


title: 2019-9285: Ri2_IP


title: singleCell_spheroid_plate1_G2_S10


title: 2019-9285: Ri2_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G11_AD004

tag: gender


title: singleCell_spheroid_plate1_G4_S12


title: HA5233_ctrl

value: Vehicle

tag: donor id


title: singleCell_spheroid_plate1_G20_S28


title: 2019-9285: Ri1_IP


title: singleCell_spheroid_plate1_G1_S9


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G10_AD002

value: female


title: HA5233_AA


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_G10_AD001


title: HA5526_ctrl


title: 2019-9285: Ri1_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F9_AD006


title: HA5232_OA


title: singleCell_spheroid_plate1_G19_S27


title: singleCell_spheroid_plate1_G18_S26


title: 2019-9285: RC4_IP

source_name: R6/2 +Control cargo

value: Control


title: HA5232_ctrl


title: 2019-9285: RC4_input

value: striatal astrocytes


title: HA5232_AA


title: singleCell_spheroid_plate1_G17_S25


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F9_AD002


title: 2019-9285: RC3_IP

value: IP


title: HA5231_OA


title: singleCell_spheroid_plate1_G16_S24


title: 2019-9285: RC2_IP


title: 2019-9285: RC3_input

value: Input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F9_AD001


title: HA5231_ctrl


title: singleCell_spheroid_plate1_G15_S23


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F7_AD004


title: HA5231_AA


title: singleCell_spheroid_plate1_G14_S22


title: singleCell_spheroid_plate1_G13_S21


title: S146_OA

value: A


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F9_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F7_AD002


title: S146_ctrl

value: Tregs sorted from peripheral blood


title: 2019-9285: RC1_IP


title: singleCell_spheroid_plate1_G12_S20


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F7_AD001


title: singleCell_spheroid_plate1_G11_S19


title: S146_AA


title: 2019-9285: RC1_input


title: 2019-9247: JS8720_IP_KO

source_name: SAPAP3 knockout, replicate 4


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F6_AD006


title: singleCell_spheroid_plate1_G10_S18


title: S143_OA


title: 2019-9247: JS8720_In_KO


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F6_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F7_AD006


title: 2019-9285: RC2_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F6_AD002


title: S143_ctrl


title: singleCell_spheroid_plate1_F9_S293


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F5_AD006


title: singleCell_spheroid_plate1_F8_S292


title: S143_AA


title: 2019-9247: JS8719_IP_KO

source_name: SAPAP3 knockout, replicate 3


title: singleCell_spheroid_plate1_F7_S291


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F5_AD004


title: 2019-9247: JS8719_In_KO


title: HSJ019-K27M2_Input

description: According to manufacturer's protocol

tag: chip antibody

tag: genotype


title: HSJ019-K27M2_H3K36me3

description: According to manufacturer's protocol

tag: cell line

value: H3K36me3 (Active Motif, #61021)


title: singleCell_spheroid_plate1_F6_S290


title: 2019-9247: JS8715_IP_WT

source_name: Wild-type littermate, replicate 4

tag: condition

value: WT


title: 2019-9247: JS8715_In_WT

tag: rna-sample type


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F5_AD001

value: brain

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F5_AD002


title: G477-K27R1_Input

description: According to manufacturer's protocol

value: H3.3 (H3F3A) K27R overexpression


title: singleCell_spheroid_plate1_F5_S289

value: iPSC-derived cortical spheroid


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F3_AD006

value: male


title: singleCell_spheroid_plate1_F4_S288


title: G477-K27M1_Input

description: According to manufacturer's protocol

value: H3.3 (H3F3A) K27M overexpression


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F3_AD004

value: PTLp


title: 2019-9247: JS8487.9_In_WT

source_name: Wild-type littermate, replicate 3


title: 2019-9247: JS8487.9_IP_WT


title: singleCell_spheroid_plate1_F3_S287


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F1_AD006


title: 2019-9247: JS8486_IP_WT

source_name: Wild-type littermate, replicate 2


title: singleCell_spheroid_plate1_F2_S286


title: 2019-9247: JS8486_In_WT


title: G477-WT_H3K36me3

description: According to manufacturer's protocol

value: H3 wild-type


title: singleCell_spheroid_plate1_F24_S8


title: 2019-9247: JS8485_IP_KO

source_name: SAPAP3 knockout, replicate 2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F1_AD004


title: DIPGXIII-K27M3_SUZ12

description: According to manufacturer's protocol

value: SU-DIPGXIII

value: SUZ12 (Cell Signaling Technology, #3737)


title: G477-WT_Input

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F1_AD002

value: female


title: singleCell_spheroid_plate1_F23_S7


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F1_AD001


title: 2019-9247: JS8485_In_KO

value: striatal astrocytes


title: singleCell_spheroid_plate1_F22_S6


title: singleCell_spheroid_plate1_F21_S5


title: 2019-9247: JS8483_In_KO

source_name: SAPAP3 knockout, replicate 1

value: Input


title: DIPGXIII-K27M3_Input

description: According to manufacturer's protocol


title: 2019-9247: JS8483_IP_KO

value: IP


title: DIPGXIII-K27M2_Input

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F11_AD004


title: G477-WT_SUZ12

description: According to manufacturer's protocol


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F11_AD006


title: DIPGXIII-K27M2_H3K36me3

description: According to manufacturer's protocol


title: DIPGXIII-K27M1_H3K27me2

description: According to manufacturer's protocol

value: H3K27me2 (Cell Signaling Technology, #9728)


title: singleCell_spheroid_plate1_F20_S4


title: 2019-9247: JS8272_IP_WT

source_name: Wild-type littermate, replicate 1


title: DIPGXIII-K27M1_Input

description: According to manufacturer's protocol


title: singleCell_spheroid_plate1_F1_S285


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F11_AD002

source_name: C57BL/6J P56 Mouse Brain


title: 2019-9247: JS8272_In_WT


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F11_AD001


title: singleCell_spheroid_plate1_F19_S3

source_name: iPSC-derived cortical spheroid


title: DIPGXIII-K27M1_H3K27me3

description: According to manufacturer's protocol

source_name: brain tumor derived cell line & S2 cells (spike in)

value: H3K27me3 (Cell Signaling Technology, #9733)


title: 2018-9061: Y630_input

source_name: MPTP (20 mg/kg, 4 doses) microinjected into the striatum, replicate 4

value: MPTP

value: input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F10_AD006

value: brain

value: STR


title: 2018-9061: Y629_IP

source_name: MPTP (20 mg/kg, 4 doses) microinjected into the striatum, replicate 3


title: DIPGXIII-K27M1_H3K27me1

description: According to manufacturer's protocol

value: H3K27me1 (Active Motif, #61015)


title: singleCell_spheroid_plate1_F17_S1

value: iPSC-derived cortical spheroid


title: singleCell_spheroid_plate1_F18_S2


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F10_AD004

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F10_AD002

value: PTLp


title: singleCell_spheroid_plate1_F16_S300


title: 2018-9061: Y629_input


title: singleCell_spheroid_plate1_F15_S299


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_F10_AD001


title: 2018-9061: Y628_IP

source_name: MPTP (20 mg/kg, 4 doses) microinjected into the striatum, replicate 2


title: BT245-K27M4_Input

description: According to manufacturer's protocol


title: BT245-K27M5_Input

description: According to manufacturer's protocol


title: 2018-9061: Y627_input


title: singleCell_spheroid_plate1_F14_S298


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E9_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E9_AD004


title: singleCell_spheroid_plate1_F13_S297


title: 2018-9061: Y626_IP

source_name: MPTP (20 mg/kg, 4 doses) microinjected into the striatum, replicate 1


title: 2018-9061: Y630_IP


title: BT245-K27M4_H3K36me3

description: According to manufacturer's protocol

value: H3K36me3 (Active Motif, #61021)


title: BT245-K27M1_H3K27me3

description: According to manufacturer's protocol


title: singleCell_spheroid_plate1_F12_S296


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E9_AD002


title: 2018-9061: Y626_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E9_AD001


title: 2018-9061: Y625_IP

source_name: Vehicle microinjected into the striatum, replicate 4

value: Control


title: BT245-K27M5_SUZ12

description: According to manufacturer's protocol

value: SUZ12 (Cell Signaling Technology, #3737)


title: singleCell_spheroid_plate1_F11_S295


title: BT245-K27M1_H3K27me2

description: According to manufacturer's protocol


title: 2018-9061: Y625_input


title: BT245-K27M1_Input

description: According to manufacturer's protocol


title: singleCell_spheroid_plate1_F10_S294


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E7_AD006


title: singleCell_spheroid_plate1_E9_S269


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E7_AD004


title: BT245-K27M1_H3K9me3

description: According to manufacturer's protocol

value: H3K9me3 (Abcam, #ab8898)


title: 2018-9061: Y624_IP

source_name: Vehicle microinjected into the striatum, replicate 3

value: striatal astrocytes


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E7_AD002

value: female


title: singleCell_spheroid_plate1_E8_S268


title: 2018-9061: Y624_input


title: BT245-K27M1_H3K27me1

description: According to manufacturer's protocol


title: singleCell_spheroid_plate1_E7_S267


title: INPUT-hNSC-forUTX

description: UTX-hNSC.SICER.bed.gz

data_processing:
Basecalls performed using CASAVA
Single-end reads of 50bp were mapped human genome hg19(GRCh37-lite) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with Picard(version  2.6.0-SNAPSHOT) and only non-duplicated reads have been kept by samtools (parameter “-q  1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control of our data. For peak calling of H3K27ac, H3K4me3, we used MACS2(version 2.1.1.20160309). To assure the  replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one sample and at least called with lower  cutoff(macs2 -q 0.5) in the other sample. Peaks for H3K27me3 were called by reproducible peaks between SICER(V1.1) and MACS2. Correlation plots indicated the libraries are  reproducible between biological replicates.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: Peaks

source_name: Cell Line

extract_protocol:
Cells were harvested in PBS. Cytoplasmic fractions were extracted using buffer A with 1×  protease inhibitors and 1 mM DTT. Nuclear pellets were cross-linked by 1.1% formaldehyde in  buffer B with 1× protease inhibitors and 1 mM DTT; washed; and lysed in lysis buffer 3 with 1×  protease inhibitors, 1 mM DTT, and 1 mM PMSF. The fixed and lysed nuclear extract was  sonicated with Bioruptor® Pico (Diagenode) 10 times for 15 s each, with 45-s intervals.  Chromatin was added to Dynabeads™ (Life Technologies) prebound with 4 μg of antibodies.  For UTX chromatin immunoprecipitation (ChIP), chromatin and antibodies were incubated  overnight, followed by 4 h of recapture with Dynabeads™ the next day.
After incubation, beads were washed and immunoprecipitates were eluted. DNA from eluates was recovered by the  GeneJET FFPE DNA purification kit (ThermoFisher Scientific, #K0882).Libraries are prepared and sequenced at the St. Jude Hartwell Center.

value: Human Neural Stem Cells H9


title: 2018-9061: Y623_IP

source_name: Vehicle microinjected into the striatum, replicate 2

value: IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E6_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E7_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E6_AD004


title: singleCell_spheroid_plate1_E6_S266


title: 2018-9061: Y621_IP

source_name: Vehicle microinjected into the striatum, replicate 1


title: Erl resistant combo 2

city: Rehovot

first: Yosef

last: Yarden

address: Herzl St 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

description:
Lung cancer xenograft
bulk MARS-Seq

data_processing:
Data filtering: cutadapt
Read alignment software: STAR
Abundance measurement: HTSeq-count
Quantification: DESeq2
Genome_build: Hg38 (Gencode v34)
Supplementary_files_format_and_content: Regularized log transformed data

source_name: PC9 xenograft

growth_protocol: All animal studies were approved by our institutional board and they were performed in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
QIAGEN miRNeasy Mini Kit
Libraries for RNA-seq were prepared using a modified version of TranSeq, as described (Jaitin et al., 2014). Briefly, RNA was reversed transcribed with MARS-seq barcoded RT primers in a 10 µl volume with the Affinity Script kit (Agilent). Reverse transcription was analyzed by qRT-PCR and samples with a similar CT were pooled (up to eight samples per pool). Each pool was treated with Exonuclease I (NEB) for 30 min at 37°C and cleaned by 1.2× volumes of SPRI beads (Beckman Coulter). Next, the cDNA was converted to double-stranded DNA with a second strand synthesis kit (NEB) in a 20 ml reaction, incubating for 2 h at 16 °C. The product was purified with 1.4× volumes of SPRI beads, eluted in 8 µl and in vitro transcribed (with the beads) at 37 °C overnight for linear amplification using the T7 High Yield RNA polymerase IVT kit (NEB). Following IVT, the DNA template was removed with Turbo DNase I (Ambion) 15 min at 37 °C and the amplified RNA (aRNA) purified with 1.2 volumes of SPRI beads. The aRNA was fragmented by incubating min at 70 °C in Zn 621 2+ RNA fragmentation reagents (Ambion) and purified with 2× volumes of SPRI beads. The aRNA was ligated to the MARS-seq ligation adapter with T4 RNA Ligase I (NEB).  The reaction was incubated at 22 °C for 2 h. After 1.5× SPRI cleanup, the ligated product was reverse transcribed using Affinity Script RT enzyme (Agilent) and a primer complementary to the ligated adapter. The reaction was  incubated for 2 min at 42°C, 45 min at 50°C, and 5 min at 85°C. The cDNA was purified with 1.5× volumes of SPRI beads. The library was completed and amplified through a nested PCR reaction with 0.5 mM of P5_Rd1 and P7_Rd2 primers and PCR ready mix  (Kappa Biosystems). The amplified pooled library was purified with 0.7× volumes of SPRI beads to remove primer leftovers. Library concentration was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a TapeStation instrument. RNA-seq libraries were sequenced using the Illumina NextSeq® 500 High Output v2 Kit (75 cycles).

treatment_protocol: PC9 cells (3X106/mouse) were subcutaneously injected in the flanks of 13 CD1-nu/nu mice. When tumors reached 500 mm3, mice were treated daily with erlotinib (50 mg/kg). Once started relapsing and reached 800 mm3, we switched to a combination of 2XmAbs (Cetuximab + Trastuzumab) plus erlotinib (50 mg/kg)

tag: host strain

value: CD1 nude

value: lung cancer

value: Erlotinib 50 mg/kg cetuximab 0.1 mg traztuzumab 0.1 mg


title: 2018-9061: Y623_input

value: input


title: Erl resistant combo 1

description:
Lung cancer xenograft
bulk MARS-Seq


title: 2018-9061: Y621_input


title: Erl resistant 2

description:
Lung cancer xenograft
bulk MARS-Seq

value: Erlotinib 50 mg/kg


title: Erl resistant 3

description:
Lung cancer xenograft
bulk MARS-Seq


title: singleCell_spheroid_plate1_E3_S263

tag: age (days)


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E6_AD002

value: brain

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E6_AD001


title: Heart, LN5.22

city: Indianapolis

first: Andrea

last: Bonetto

state: IN

address: 980 W. Walnut Street, R3-C522

institute: Indiana University School of Medicine

data_processing:
The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control
Then all sequenced libraries were mapped to the mouse genome (mm10) using STAR RNA-seq aligner
The reads distribution across the genome was assessed using bamutils
Genes with read count per million (CPM) < 0.5 in more than 4 of the samples were removed.
Differential expression analysis was performed using edgeR
Genome_build: UCSC Mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts, normalized counts for each sample

source_name: Heart

extract_protocol:
RNA extraction and purification from tissue snap frozen in liquid nitrogen was done via homogenization in Trizol and the Qiagen miRNeasy Mini Kit (heart).
Five microliters of 2 nM pooled libraries per lane will then be denatured, neutralized and applied to the cBot for flow cell deposition and cluster amplification, before loading to HiSeq 4000 for 75b paired-end sequencing (Illumina, Inc.). Approximately 30M reads per library is generated

treatment_protocol: RNA isolation, sequencing for all heart samples were done at one time.

value: NSG

value: Heart

tag: Sex

value: Male

tag: tumor

value: splenic HCT116+ACVR2B/Fc


title: singleCell_spheroid_plate1_E2_S262

value: iPSC-derived cortical spheroid


title: Erl resistant 1

description:
Lung cancer xenograft
bulk MARS-Seq

tag: treatment


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E5_AD006

tag: strain

tag: age

tag: tissue

value: PTLp

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E5_AD002

tag: source

tag: target

value: female


title: Heart, LN5.21


title: Erl responding 3

description:
Lung cancer xenograft
bulk MARS-Seq

tag: cell type


title: singleCell_spheroid_plate1_E24_S284

tag: differentiation id


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E5_AD001

tag: gender


title: Erl responding 2

description:
Lung cancer xenograft
bulk MARS-Seq


title: singleCell_spheroid_plate1_E22_S282


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E4_AD004


title: singleCell_spheroid_plate1_E5_S265


title: Erl responding 1

description:
Lung cancer xenograft
bulk MARS-Seq


title: Heart, LN5.12

value: splenic HCT116


title: singleCell_spheroid_plate1_E21_S281


title: Control 5

description:
Lung cancer xenograft
bulk MARS-Seq

value: Untreated


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E1_AD006


title: singleCell_spheroid_plate1_E4_S264


title: Control 4

description:
Lung cancer xenograft
bulk MARS-Seq

value: CD1 nude


title: Heart, LN5.5

value: Sham


title: Heart, LN5.11


title: singleCell_spheroid_plate1_E20_S280


title: Control 3

description:
Lung cancer xenograft
bulk MARS-Seq

value: lung cancer


title: Heart, LN5.3


title: singleCell_spheroid_plate1_E19_S279


title: Control 2

description:
Lung cancer xenograft
bulk MARS-Seq


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E1_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E1_AD002


title: singleCell_spheroid_plate1_E23_S283


title: Control 1

description:
Lung cancer xenograft
bulk MARS-Seq


title: Heart, LN5.15


title: singleCell_spheroid_plate1_E18_S278


title: Heart, LN5.20


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 4

description:
2016-9188
Y318_IP

extract_protocol:
Total RNA was extracted using RNeazy kit (Qiagen) accordance with the prescribed protocol provided with the kit.  Mouse anti-HA monoclonal antibody used in the study,   manufacturer is Covance, catalog number is MMS-101R,   and lot/batch number is D13FF01557
Libraries prepared using the Illumina TruSeq Stranded RNA (100 ng) + RiboZero Gold Library Prep Kit  and sequenced on an Illumina HiSeq4000 sequencer using strand-specific

value: IP

tag: strain/genotype

value: striatal astrocytes


title: singleCell_spheroid_plate1_E17_S277

tag: cell line


title: input: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 4

description:
2016-9188
Y318_input

value: input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E12_AD004

value: brain

value: STR


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E1_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E12_AD002


title: singleCell_spheroid_plate1_E16_S276


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 3

description:
2016-9188
Y316_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E12_AD001


title: singleCell_spheroid_plate1_E15_S275


title: singleCell_spheroid_plate1_E1_S261


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E11_AD006


title: Heart, LN5.2

value: NSG

value: Heart


title: input: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 3

description:
2016-9188
Y316_input


title: Scramble_2

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

data_processing:
Library strategy: Ψ-seq
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina NextSeq500
CASAVA BclToFastq was used to export fastq files
Reads were mapped using Bowtie2 to ribosomal RNA retrieved from modomics server (https://iimcb.genesilico.pl/modomics/).
For each site with pseudouridylation annotation in MODOMICS (Machnicka et al., 2013), a Ψ-ratio was calculated, capturing the number of reads beginning at the position (that is, reflecting termination of reverse transcriptase) divided by the number of reads overlapping it. For technical reasons of the method the calculation needs conducted on the nucleotide which follows the position of the actual modification by +1.
Genome_build: human ribosomal RNA downloaded from https://iimcb.genesilico.pl/modomics/
Supplementary_files_format_and_content: The processed file contains columns of Ψ-ratios for each sample.

extract_protocol: Ψ-seq was performed on total RNA as described (Schwartz et al., 2014). Briefly, RNA was chemically fragmented, subjected to FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific), followed by 3′ ligation of an RNA adaptor using T4 ligase (New England Biolabs). Ligated RNA was reverse transcribed, and cDNA was subjected to 3′ ligation with a second adaptor using T4 ligase. The single-stranded cDNA product was amplified for 9-12 cycles in a PCR reaction. Libraries were sequenced on Illumina NextSeq500 with paired end reads (38 bp for read1 and 28 bp for read2).

tag: sample type

value: cell line with CTRL guide RNA


title: NOP10KO_2

value: cell line with NOP10 knock out


title: NOP10KO_4


title: 262T

source_name: parafﬁn-embedded NSCLC tissue sample

value: tumor


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E12_AD006

value: PTLp

value: male


title: Scramble_1


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 2

description:
2016-9188
Y315_IP

tag: rna-sample type


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E11_AD002

value: female


title: singleCell_spheroid_plate1_E12_S272

value: iPSC-derived cortical spheroid


title: singleCell_spheroid_plate1_E14_S274


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E11_AD001


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 1

description:
2016-9188
Y313_IP


title: 242T


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E10_AD006


title: input: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 1

description:
2016-9188
Y313_input


title: singleCell_spheroid_plate1_E11_S271


title: singleCell_spheroid_plate1_E10_S270


title: IP: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 4

description:
2016-9188
Y319_IP


title: singleCell_spheroid_plate1_D9_S245


title: input: CNO (1 mg/kg) i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 2

description:
2016-9188
Y315_input


title: singleCell_spheroid_plate1_E13_S273


title: singleCell_spheroid_plate1_D8_S244


title: 215N

value: normal


title: IP: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 3

description:
2016-9188
Y317_IP


title: singleCell_spheroid_plate1_D7_S243


title: input: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 4

description:
2016-9188
Y319_input


title: 262N


title: singleCell_spheroid_plate1_D6_S242


title: input: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 3

description:
2016-9188
Y317_input


title: 215T


title: 222N


title: 242N


title: IP: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 2

description:
2016-9188
Y314_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E10_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D9_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D9_AD002


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D9_AD004


title: input: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 2

description:
2016-9188
Y314_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D9_AD001


title: 206T


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E10_AD002


title: 206N


title: singleCell_spheroid_plate1_D4_S240


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_E10_AD004


title: IP: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 1

description:
2016-9188
Y312_IP


title: 222T


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D7_AD006


title: singleCell_spheroid_plate1_D3_S239


title: input: Vehicle i.p. injected into mice expressing hM3Dq in striatal astrocytes, replicate 1

description:
2016-9188
Y312_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D7_AD004


title: pAD052S6_S8

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

description: 6 hours after saline pre vitamin D

data_processing:
RNA-seq data was aligned to GRCh38 genome assembly using hisat2 using the parameters --known-splicesite-infile and --dta
Samtools was used to select for reads with paired mates.
Stringtie was used for transcriptome assembly and gene counts.
Gene level FPKM (Fragments Per Kilobase of transcript per Million) was estimated with Ballgown.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file; gene count

source_name: skin biopsy

extract_protocol:
Skin biopsy specimens were collected from the injection site 72 hours after injection with VZV antigen or 6 hour after normal saline injection. Normal (uninjected) skin from the same site was collected as a control. This was done before and after vitamin D supplementation within the same individuals. Frozen tissue was homogenized, and total RNA was extracted from bulk tissue homogenates by using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
Kappa Hyperprep kit (Roche Diagnostics)

tag: supplementation

value: pre vitamin D

value: 6 hours after saline

value: skin


title: singleCell_spheroid_plate1_D5_S241

tag: age (days)


title: singleCell_spheroid_plate1_D2_S238


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D7_AD002


title: input: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 4

description:
2018-9272
Y556_input

value: striatal astrocytes


title: pAD052N_S7

description: unmanipulated skin pre vitamin D

value: unmanipulated skin


title: singleCell_spheroid_plate1_D24_S260


title: pAD049S6_S14

description: 6 hours after saline pre vitamin D


title: pAD049N_S13

description: unmanipulated skin pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D6_AD006

value: brain


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 4

description:
2018-9272
Y556_IP

value: IP


title: pAD052D2_S9

description: Day2 after VZV pre vitamin D

value: Day2 after VZV


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 3

description:
2018-9272
Y555_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D7_AD001

value: STR


title: singleCell_spheroid_plate1_D23_S259


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D6_AD002


title: pAD047S6_S10

description: 6 hours after saline pre vitamin D


title: singleCell_spheroid_plate1_D22_S258


title: pAD047N_S9

description: unmanipulated skin pre vitamin D


title: IP: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 4

description:
2018-9272
Y554_IP


title: singleCell_spheroid_plate1_D21_S257


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D5_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D5_AD004


title: singleCell_spheroid_plate1_D20_S256


title: singleCell_spheroid_plate1_D1_S237


title: IP: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 3

description:
2018-9272
Y553_IP


title: pAD045S6_S2

description: 6 hours after saline pre vitamin D


title: input: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 3

description:
2018-9272
Y553_input

value: input


title: singleCell_spheroid_plate1_D19_S255


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D5_AD001


title: input: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 3

description:
2018-9272
Y555_input


title: singleCell_spheroid_plate1_D17_S253


title: singleCell_spheroid_plate1_D16_S252


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 1

description:
2018-9272
Y551_IP


title: pAD045N_S1

description: unmanipulated skin pre vitamin D


title: singleCell_spheroid_plate1_D18_S254


title: pAD040S6_S16

description: 6 hours after saline pre vitamin D


title: input: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 4

description:
2018-9272
Y554_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D1_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D1_AD004


title: singleCell_spheroid_plate1_D15_S251


title: pAD040D2_S13

description: Day2 after VZV pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D1_AD002


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D1_AD001


title: singleCell_spheroid_plate1_D14_S250


title: pAD040N_S15

description: unmanipulated skin pre vitamin D


title: IP: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 2

description:
2018-9272
Y550_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D12_AD006


title: pAD047D2_S11

description: Day2 after VZV pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D5_AD002


title: IP: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 2

description:
2018-9272
Y552_IP


title: pAD038S6_S4

description: 6 hours after saline pre vitamin D


title: pAD045D2_S3

description: Day2 after VZV pre vitamin D


title: singleCell_spheroid_plate1_D13_S249


title: pAD038N_S3

description: unmanipulated skin pre vitamin D


title: input: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 2

description:
2018-9272
Y550_input


title: IP: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 1

description:
2018-9272
Y549_IP


title: input: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 2

description:
2018-9272
Y552_input


title: input: CNO (1 mg/kg) i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 1

description:
2018-9272
Y551_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D12_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D12_AD001


title: singleCell_spheroid_plate1_D12_S248


title: IP: Wild-type littermate, replicate 4

description:
2018-9292
Y579_IP

source_name: Wild-type littermate, replicate 4

value: WT


title: pAD037N_S1

description: unmanipulated skin pre vitamin D


title: pAD037S6_S5

description: 6 hours after saline pre vitamin D


title: pAD037D2_S3

description: Day2 after VZV pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D11_AD006

source_name: C57BL/6J P56 Mouse Brain


title: pAD038D2_S5

description: Day2 after VZV pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D12_AD002


title: singleCell_spheroid_plate1_D11_S247

source_name: iPSC-derived cortical spheroid


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D11_AD002


title: singleCell_spheroid_plate1_C7_S219


title: input: Wild-type littermate, replicate 3

description:
2018-9292
Y577_input

source_name: Wild-type littermate, replicate 3


title: singleCell_spheroid_plate1_D10_S246


title: input: Vehicle i.p. injected into mice expressing rM3Ds in striatal astrocytes, replicate 1

description:
2018-9272
Y549_input


title: pAD033N_S7

description: unmanipulated skin pre vitamin D


title: IP: Wild-type littermate, replicate 2

description:
2018-9292
Y525_IP

source_name: Wild-type littermate, replicate 2


title: singleCell_spheroid_plate1_C8_S220


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D11_AD004


title: input: Wild-type littermate, replicate 4

description:
2018-9292
Y579_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D10_AD006


title: IP: Wild-type littermate, replicate 3

description:
2018-9292
Y577_IP


title: singleCell_spheroid_plate1_C9_S221


title: singleCell_spheroid_plate1_C4_S216


title: singleCell_spheroid_plate1_C5_S217


title: input: Wild-type littermate, replicate 2

description:
2018-9292
Y525_input


title: singleCell_spheroid_plate1_C6_S218


title: IP: IP3R2 knockout, replicate 4

description:
2018-9292
Y522_IP

source_name: IP3R2 knockout, replicate 4

value: KO


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D11_AD001

value: PTLp


title: pAD033S6_S8

description: 6 hours after saline pre vitamin D


title: pAD033D2_S9

description: Day2 after VZV pre vitamin D


title: pAD029N_S7

description: unmanipulated skin pre vitamin D


title: input: IP3R2 knockout, replicate 4

description:
2018-9292
Y522_input


title: singleCell_spheroid_plate1_C3_S215


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D10_AD001


title: pAD029D2_S9

description: Day2 after VZV pre vitamin D


title: singleCell_spheroid_plate1_C2_S214


title: IP: IP3R2 knockout, replicate 3

description:
2018-9292
Y520_IP

source_name: IP3R2 knockout, replicate 3


title: pAD028S6_S12

description: 6 hours after saline pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C9_AD006

value: male


title: singleCell_spheroid_plate1_C24_S236


title: input: IP3R2 knockout, replicate 3

description:
2018-9292
Y520_input


title: pAD028D2_S13

description: Day2 after VZV pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C9_AD004


title: pAD028N_S11

description: unmanipulated skin pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C9_AD002

value: female


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D10_AD004


title: IP: IP3R2 knockout, replicate 2

description:
2018-9292
Y519_IP

source_name: IP3R2 knockout, replicate 2


title: singleCell_spheroid_plate1_C23_S235

value: iPSC-derived cortical spheroid


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_D10_AD002


title: input: IP3R2 knockout, replicate 2

description:
2018-9292
Y519_input


title: pAD029S6_S8

description: 6 hours after saline pre vitamin D


title: pAD025N_S5

description: unmanipulated skin pre vitamin D


title: singleCell_spheroid_plate1_C20_S232


title: singleCell_spheroid_plate1_C22_S234


title: pAD025D2_S7

description: Day2 after VZV pre vitamin D


title: IP: IP3R2 knockout, replicate 1

description:
2018-9292
Y518_IP

source_name: IP3R2 knockout, replicate 1


title: singleCell_spheroid_plate1_C19_S231


title: pAD025S6_S6

description: 6 hours after saline pre vitamin D


title: IP: Wild-type littermate, replicate 1

description:
2018-9292
Y517_IP

source_name: Wild-type littermate, replicate 1


title: singleCell_spheroid_plate1_C1_S213


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C9_AD001


title: singleCell_spheroid_plate1_C21_S233


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C7_AD002


title: input: IP3R2 knockout, replicate 1

description:
2018-9292
Y518_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C7_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C7_AD006


title: singleCell_spheroid_plate1_C18_S230


title: pAD023S6_S2

description: 6 hours after saline pre vitamin D


title: input: Wild-type littermate, replicate 1

description:
2018-9292
Y517_input


title: pAD023N_S1

description: unmanipulated skin pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C7_AD001


title: input: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 4

description:
2018-9291
Y575_input

value: Cre


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C6_AD002


title: IP: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 4

description:
2018-9291
Y575_IP


title: pAD018S6_S14

description: 6 hours after saline pre vitamin D

value: pre vitamin D


title: singleCell_spheroid_plate1_C16_S228


title: IP: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 3

description:
2018-9291
Y574_IP


title: singleCell_spheroid_plate1_C15_S227


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C6_AD006


title: pAD023D2_S3

description: Day2 after VZV pre vitamin D


title: input: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 3

description:
2018-9291
Y574_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C4_AD001


title: pAD018N_S13

description: unmanipulated skin pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C6_AD001


title: singleCell_spheroid_plate1_C14_S226


title: IP: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 4

description:
2018-9291
Y573_IP

value: Control


title: pAD018D2_S1

description: Day2 after VZV pre vitamin D

value: skin


title: pAD012S6_S14

description: 6 hours after saline pre vitamin D

value: 6 hours after saline


title: singleCell_spheroid_plate1_C13_S225


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C12_AD006


title: input: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 4

description:
2018-9291
Y573_input

value: striatal astrocytes


title: pAD012N_S13

description: unmanipulated skin pre vitamin D

value: unmanipulated skin


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C12_AD004

value: brain


title: singleCell_spheroid_plate1_C12_S224


title: IP: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 3

description:
2018-9291
Y572_IP

value: IP


title: singleCell_spheroid_plate1_C17_S229


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C12_AD002

value: STR


title: singleCell_spheroid_plate1_C11_S223


title: input: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 3

description:
2018-9291
Y572_input

value: input


title: pAD011S6_S8

description: 6 hours after saline pre vitamin D


title: pAD012D2_S15

description: Day2 after VZV pre vitamin D

value: Day2 after VZV


title: singleCell_spheroid_plate1_C10_S222


title: pAD011N_S7

description: unmanipulated skin pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C12_AD001


title: singleCell_spheroid_plate1_B9_S197


title: input: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 2

description:
2018-9291
Y539_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C10_AD006


title: pAD011D2_S9

description: Day2 after VZV pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C10_AD004


title: singleCell_spheroid_plate1_B8_S196


title: pAD010S6_S2

description: 6 hours after saline pre vitamin D


title: singleCell_spheroid_plate1_B7_S195


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C10_AD002


title: IP: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 1

description:
2018-9291
Y538_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_C10_AD001


title: input: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 1

description:
2018-9291
Y538_input


title: singleCell_spheroid_plate1_B6_S194


title: IP: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 2

description:
2018-9291
Y537_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B9_AD006


title: pAD009S6_S8

description: 6 hours after saline pre vitamin D


title: input: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 2

description:
2018-9291
Y537_input


title: singleCell_spheroid_plate1_B4_S192


title: IP: AAV5-GfaABC1D-Cre microinjected into the striatum, replicate 2

description:
2018-9291
Y539_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B9_AD004


title: pAD010D2_S3

description: Day2 after VZV pre vitamin D


title: IP: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 1

description:
2018-9291
Y536_IP


title: input: AAV5-GfaABC1D-TdTomato microinjected into the striatum, replicate 1

description:
2018-9291
Y536_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B9_AD002


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B9_AD001


title: pAD009N_S7

description: unmanipulated skin pre vitamin D


title: IP: LPS (5 mg/kg) i.p. injected, replicate 4

description:
2016-9257
Y367_IP

value: LPS


title: pAD010N_S1

description: unmanipulated skin pre vitamin D


title: pAD009D2_S9

description: Day2 after VZV pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B7_AD006

value: PTLp


title: singleCell_spheroid_plate1_B3_S191


title: singleCell_spheroid_plate1_B24_S212


title: input: LPS (5 mg/kg) i.p. injected, replicate 4

description:
2016-9257
Y367_input


title: pAD006S6_S2

description: 6 hours after saline pre vitamin D


title: singleCell_spheroid_plate1_B2_S190


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B7_AD004

value: male


title: pAD006N_S1

description: unmanipulated skin pre vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B7_AD002

value: female


title: singleCell_spheroid_plate1_B5_S193

value: iPSC-derived cortical spheroid


title: singleCell_spheroid_plate1_B23_S211


title: IP: LPS (5 mg/kg) i.p. injected, replicate 3

description:
2016-9257
Y366_IP


title: input: LPS (5 mg/kg) i.p. injected, replicate 3

description:
2016-9257
Y366_input


title: AD052S6_S11

description: 6 hours after saline post vitamin D

value: post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B7_AD001


title: pAD006D2_S3

description: Day2 after VZV pre vitamin D

value: pre vitamin D


title: singleCell_spheroid_plate1_B22_S210


title: singleCell_spheroid_plate1_B21_S209


title: AD052N_S10

description: unmanipulated skin post vitamin D


title: IP: LPS (5 mg/kg) i.p. injected, replicate 2

description:
2016-9257
Y365_IP


title: input: LPS (5 mg/kg) i.p. injected, replicate 2

description:
2016-9257
Y365_input


title: AD052D2_S12

description: Day2 after VZV post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B6_AD006


title: singleCell_spheroid_plate1_B20_S208


title: singleCell_spheroid_plate1_B1_S189


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B6_AD002


title: singleCell_spheroid_plate1_B19_S207


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B6_AD001


title: IP: Vehicle i.p. injected, replicate 4

description:
2016-9257
Y357_IP

source_name: Vehicle i.p. injected, replicate 4

value: Control


title: AD047S6_S13

description: 6 hours after saline post vitamin D

value: skin


title: singleCell_spheroid_plate1_B18_S206


title: input: Vehicle i.p. injected, replicate 3

description:
2016-9257
Y356_input

source_name: Vehicle i.p. injected, replicate 3


title: input: Vehicle i.p. injected, replicate 4

description:
2016-9257
Y357_input


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B5_AD006


title: AD049N_S15

description: unmanipulated skin post vitamin D


title: IP: Vehicle i.p. injected, replicate 3

description:
2016-9257
Y356_IP


title: singleCell_spheroid_plate1_B17_S205


title: AD047D2_S14

description: Day2 after VZV post vitamin D


title: singleCell_spheroid_plate1_B15_S203


title: AD047N_S12

description: unmanipulated skin post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B5_AD001


title: singleCell_spheroid_plate1_B16_S204


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B5_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B5_AD002


title: input: Vehicle i.p. injected, replicate 2

description:
2016-9257
Y353_input

source_name: Vehicle i.p. injected, replicate 2


title: singleCell_spheroid_plate1_B14_S202


title: AD045S6_S6

description: 6 hours after saline post vitamin D

value: 6 hours after saline


title: AD049S6_S16

description: 6 hours after saline post vitamin D


title: IP: Vehicle i.p. injected, replicate 1

description:
2016-9257
Y352_IP

source_name: Vehicle i.p. injected, replicate 1

value: striatal astrocytes


title: AD045N_S4

description: unmanipulated skin post vitamin D

value: unmanipulated skin


title: singleCell_spheroid_plate1_B13_S201


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B12_AD006

value: brain


title: input: Vehicle i.p. injected, replicate 1

description:
2016-9257
Y352_input


title: singleCell_spheroid_plate1_B12_S200


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B12_AD004


title: AD045D2_S5

description: Day2 after VZV post vitamin D


title: IP: LPS (5 mg/kg) i.p. injected, replicate 1

description:
2016-9257
Y351_IP

value: IP


title: AD040S6_S15

description: 6 hours after saline post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B12_AD002

value: STR


title: IP: Vehicle i.p. injected, replicate 2

description:
2016-9257
Y353_IP


title: singleCell_spheroid_plate1_B11_S199


title: AD040N_S14

description: unmanipulated skin post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B12_AD001


title: IP: Vehicle microinjected into the striatum, replicate 4

description:
2018-9199
Y513_IP


title: singleCell_spheroid_plate1_B10_S198


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B4_AD002


title: AD040D2_S16

description: Day2 after VZV post vitamin D


title: input: Vehicle microinjected into the striatum, replicate 4

description:
2018-9199
Y513_input

value: input


title: singleCell_spheroid_plate1_A8_S172


title: singleCell_spheroid_plate1_A9_S173


title: singleCell_spheroid_plate1_A7_S171


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B11_AD006


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B11_AD001


title: AD038D2_S8

description: Day2 after VZV post vitamin D

value: Day2 after VZV


title: singleCell_spheroid_plate1_A6_S170


title: input: QA (30 nM) microinjected into the striatum, replicate 4

description:
2018-9199
Y511_input

value: QA


title: AD037S6_S2

description: 6 hours after saline post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B11_AD004

value: PTLp


title: singleCell_spheroid_plate1_A5_S169


title: input: LPS (5 mg/kg) i.p. injected, replicate 1

description:
2016-9257
Y351_input

value: LPS


title: IP: QA (30 nM) microinjected into the striatum, replicate 3

description:
2018-9199
Y508_IP


title: input: QA (30 nM) microinjected into the striatum, replicate 3

description:
2018-9199
Y508_input


title: AD037N_S4

description: unmanipulated skin post vitamin D


title: singleCell_spheroid_plate1_A4_S168


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B10_AD006

value: male


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B10_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B10_AD002

value: female


title: AD038S6_S7

description: 6 hours after saline post vitamin D

value: post vitamin D


title: input: QA (30 nM) microinjected into the striatum, replicate 2

description:
2018-9199
Y507_input


title: IP: QA (30 nM) microinjected into the striatum, replicate 4

description:
2018-9199
Y511_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B10_AD001


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_B11_AD002


title: AD038N_S6

description: unmanipulated skin post vitamin D


title: AD033S6_S11

description: 6 hours after saline post vitamin D


title: singleCell_spheroid_plate1_A2_S166

value: iPSC-derived cortical spheroid


title: singleCell_spheroid_plate1_A24_S188


title: IP: QA (30 nM) microinjected into the striatum, replicate 1

description:
2018-9199
Y506_IP


title: AD033N_S10

description: unmanipulated skin post vitamin D


title: AD033D2_S12

description: Day2 after VZV post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A9_AD002


title: input: Vehicle microinjected into the striatum, replicate 3

description:
2018-9199
Y505_input

value: Control


title: IP: QA (30 nM) microinjected into the striatum, replicate 2

description:
2018-9199
Y507_IP


title: singleCell_spheroid_plate1_A23_S187


title: input: QA (30 nM) microinjected into the striatum, replicate 1

description:
2018-9199
Y506_input


title: AD029S6_S11

description: 6 hours after saline post vitamin D

value: skin


title: AD029N_S10

description: unmanipulated skin post vitamin D


title: singleCell_spheroid_plate1_A22_S186


title: AD037D2_S6

description: Day2 after VZV post vitamin D


title: singleCell_spheroid_plate1_A3_S167


title: singleCell_spheroid_plate1_A21_S185


title: AD029D2_S12

description: Day2 after VZV post vitamin D


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A7_AD006


title: IP: Vehicle microinjected into the striatum, replicate 2

description:
2018-9199
Y504_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A9_AD006


title: singleCell_spheroid_plate1_A20_S184


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A7_AD002


title: singleCell_spheroid_plate1_A1_S165


title: AD028S6_S1

description: 6 hours after saline post vitamin D

value: 6 hours after saline


title: IP: Vehicle microinjected into the striatum, replicate 1

description:
2018-9199
Y503_IP

value: striatal astrocytes


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A7_AD001


title: AD028N_S14

description: unmanipulated skin post vitamin D

value: unmanipulated skin


title: singleCell_spheroid_plate1_A19_S183


title: IP: Vehicle microinjected into the striatum, replicate 3

description:
2018-9199
Y505_IP


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A6_AD006

value: brain


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A9_AD001


title: AD028D2_S2

description: Day2 after VZV post vitamin D


title: singleCell_spheroid_plate1_A18_S182


title: input: Vehicle microinjected into the striatum, replicate 1

description:
2018-9199
Y503_input


title: singleCell_spheroid_plate1_A17_S181


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A6_AD004


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A6_AD002


title: KO 6

city: Houaton

first: Ali

middle: J

last: Marian

state: Texas

address: 6770 Bertner Ave DAC C900a

department: Centre for Cardiovascular Genetics

institute: UTHSC, Houston

data_processing:
Fastq files where trimmed using TrimGalore!.
Trimmed files were aligned using HISAT2.
Genes were quantified using featureCount.
Genome_build: GRCM38
Supplementary_files_format_and_content: The processed data file is in a comma seperated format and contains the final featureCount generated count matrix.

source_name: Freshly isolated Cardiac Myocytes

extract_protocol:
RNA-Sequencing (RNA-Seq):  Total RNA was isolated from cardiac myocytes of 2-week old WT and Myh6-Cre:LmnaF/F mice. RNA-seq was performed on the on ribosome-depleted RNA.
Samples with a RNA Integrity Number (RIN) read out of more than 8 were used to prepare sequencing library using the Illumina TruSeq stranded total RNA library preparation kit. The samples were sequenced on the Illumina HiSeq 4000 instrument using the paired-end sequencing reagents to generate 100 base pair runs.

value: Freshly isolated Cardiac Myocytes

tag: genotype

value: Myocyte-Specific Lamin A/C Null Mice (Myh6-cre:LmnaF/F)


title: KO 5


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A7_AD004

value: STR


title: AD025S6_S9

description: 6 hours after saline post vitamin D


title: input: Vehicle microinjected into the striatum, replicate 2

description:
2018-9199
Y504_input

value: input


title: AD025N_S8

description: unmanipulated skin post vitamin D


title: singleCell_spheroid_plate1_A15_S179


title: 180313_CEMBA_mm_P56_P63_RS2_180313_P5_180313_P6_A5_AD006