title: 16BTreg31


title: 16BTreg33

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

tag: Sex

value: F

tag: donor group

value: HC


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD012

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: SSp

tag: target

value: Pons

tag: gender

value: female


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A3_AD002

value: MOp


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A3_AD007

value: male


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD008


title: 16BTreg30


title: 16BTreg46


title: 16BTreg32


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD007


title: 16BTreg27


title: 16BTreg38


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD004


title: 16BTreg35


title: 16BTreg26


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD010


title: 16BTreg23


title: 16BTreg24


title: 16BTreg25


title: 16BTreg22


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD002


title: 16BTreg34


title: 16BTreg20


title: 16BTreg21


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A1_AD006


title: 16BTreg28


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD006


title: 16BTreg17


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A1_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A1_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A12_AD012


title: 16BTreg16


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A12_AD008


title: 16BTreg14


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A12_AD007


title: 16BTreg12


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A12_AD006


title: 16BTreg11


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A12_AD002


title: 16BTreg19


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A1_AD002


title: 16BTreg09


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A3_AD006


title: 16BTreg08


title: 16BTreg15


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A11_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A11_AD008


title: 16BTreg06


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A11_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A11_AD004


title: 16BTreg05


title: 16BTreg04


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A10_AD012


title: 16BTreg13


title: 16BTreg03


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A10_AD007


title: 16BTreg01


title: 16BTreg10


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A12_AD001


title: 15FTreg96

value: Fat


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A10_AD004


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_H9_AD012

value: TH


title: 16BTreg07


title: 15FTreg92


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A10_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_H9_AD006


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_H7_AD006


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title: 15FTreg73


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_H6_AD012


title: 16BTreg18


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P3_180419_P4_A12_AD010


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title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G7_AD012


title: 15FTreg04


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G9_AD007


title: 15FTreg05


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G7_AD008


title: 15FTreg02


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G7_AD006


title: 15BTreg96


title: 15BTreg95


title: 15FTreg10


title: 15BTreg93


title: 15BTreg94


title: 15FTreg01


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G6_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G6_AD006


title: 15BTreg92


title: 15BTreg91


title: 15BTreg90


title: 15BTreg89


title: 15BTreg88


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G5_AD010


title: 15BTreg87


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G7_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G5_AD008


title: 15FTreg03


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G5_AD006


title: 15BTreg85


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G7_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G5_AD004


title: 15BTreg84


title: 15BTreg83


title: 15BTreg82


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G5_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G5_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G5_AD002


title: 15BTreg81


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G4_AD006


title: 15BTreg79


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G4_AD012


title: 15BTreg80


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G6_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G4_AD001


title: 15BTreg77


title: 15BTreg78


title: 15BTreg76


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G3_AD010


title: 15BTreg75


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G3_AD008


title: 15BTreg72


title: 15BTreg73


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G3_AD002


title: 15BTreg71


title: 15BTreg74


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G2_AD008


title: 15BTreg68


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G2_AD007


title: 15BTreg67


title: 15BTreg66


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G2_AD006


title: 15BTreg64


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G3_AD012


title: 15BTreg65


title: 15BTreg63


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G1_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G1_AD010


title: 15BTreg62


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G1_AD007


title: 15BTreg61


title: 15BTreg59


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G1_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G3_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G1_AD001


title: 15BTreg58


title: 15BTreg69


title: 15BTreg86


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G2_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G12_AD006


title: 15BTreg55


title: 15BTreg57


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G12_AD002


title: 15BTreg70


title: 15BTreg54


title: 15BTreg53


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G11_AD008


title: 15BTreg52


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G11_AD006


title: 15BTreg51


title: 15BTreg60


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G11_AD004


title: 15BTreg50


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G11_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G10_AD008


title: 15BTreg56


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G12_AD010


title: 15BTreg48


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F9_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G11_AD012


title: 15BTreg45


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G10_AD007


title: 15BTreg47


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G10_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F9_AD008


title: 15BTreg43


title: 15BTreg40


title: 15BTreg39


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F9_AD004


title: 15BTreg49


title: 15BTreg41


title: 15BTreg38


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_G10_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F9_AD001


title: 15BTreg36


title: 15BTreg35


title: 15BTreg46


title: 15BTreg44


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F8_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F8_AD008


title: 15BTreg42


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F8_AD006


title: 15BTreg31


title: 15BTreg34


title: 15BTreg32


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F8_AD004


title: 15BTreg30


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F8_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F8_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD010


title: 15BTreg28


title: 15BTreg37


title: 15BTreg29


title: 15BTreg27


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F8_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD004


title: 15BTreg24


title: 15BTreg26


title: 15BTreg25


title: 15BTreg23


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F7_AD002


title: 15BTreg22


title: 15BTreg33


title: 15BTreg21


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F6_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F6_AD012


title: 15BTreg19


title: 15BTreg20


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F6_AD001


title: 15BTreg18


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F6_AD004


title: 15BTreg16


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F5_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F5_AD012


title: 15BTreg17


title: 15BTreg15


title: 15BTreg14


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F5_AD007


title: 15BTreg13


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F5_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F5_AD006


title: 15BTreg08


title: 15BTreg12


title: 15BTreg11


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD010


title: 15BTreg09


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F3_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F4_AD001


title: 15BTreg05


title: 15BTreg06


title: 15BTreg04


title: 15BTreg03


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F3_AD008


title: 15BTreg07


title: 14FTreg96


title: 15BTreg02


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F5_AD001


title: 15BTreg01


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F3_AD004


title: 15BTreg10


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F3_AD006


title: 14FTreg95


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F3_AD002


title: 14FTreg94


title: 14FTreg92


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD008


title: 14FTreg93


title: 14FTreg90


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD004


title: 14FTreg89


title: 14FTreg88


title: 14FTreg87


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD002


title: 14FTreg86


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F1_AD010


title: 14FTreg84


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F1_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F2_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F1_AD008


title: 14FTreg85


title: 14FTreg82


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F1_AD006


title: 14FTreg80


title: 14FTreg83


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F1_AD004


title: 14FTreg81


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F1_AD002


title: 14FTreg78


title: 14FTreg79


title: 14FTreg77


title: 14FTreg75


title: 14FTreg76


title: 14FTreg91


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD007


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD012


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD002


title: 14FTreg73


title: 14FTreg74


title: 14FTreg72


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F12_AD001


title: 14FTreg71


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F11_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F11_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F11_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F11_AD004


title: 14FTreg70


title: 14FTreg67


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F10_AD012


title: 14FTreg66


title: 14FTreg68


title: 14FTreg69


title: 14FTreg65


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F10_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F10_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F10_AD007


title: 14FTreg64


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F10_AD002


title: 14FTreg63


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_F10_AD001


title: 14FTreg62


title: 14FTreg61


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD008


title: 14FTreg56


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD007


title: 14FTreg58


title: 14FTreg60


title: 14FTreg55


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD012


title: 14FTreg59


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD004


title: 14FTreg57


title: 14FTreg52


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E8_AD012


title: 14FTreg54


title: 14FTreg53


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E8_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E9_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E8_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E8_AD004


title: 14FTreg49


title: 14FTreg51


title: 14FTreg50


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E7_AD008


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E7_AD006


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E8_AD002


title: 14FTreg48


title: 14FTreg45


title: 14FTreg47


title: 14FTreg44


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E7_AD001


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E7_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E7_AD002


title: 14FTreg43


title: 14FTreg46


title: 14FTreg38


title: 14FTreg41


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E6_AD010


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E6_AD001


title: 14FTreg42


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E6_AD002


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E6_AD004


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E6_AD012


title: 14FTreg37


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E5_AD010


title: 14FTreg39


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E5_AD012


title: 14FTreg40


title: 180419_CEMBA_mm_P56_P63_RS2_180419_P1_180419_P2_E5_AD007


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title: singleCell_spheroid_plate2_P9_S137

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)

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