title: 180822_P7-180822_P8-B3-AD001


title: 180822_P7-180822_P8-B2-AD004

status: Public on May 02 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

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 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
Assembly: mm10
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
Library strategy: snmC-seq2 & 3

molecule: genomic DNA

organism: Mus musculus

source_name: 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-seq (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.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The 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, 2x1012 to 1x1013 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: tissue

value: brain

tag: source

value: PAL

tag: target

value: TH

tag: Sex

value: female


title: 180822_P7-180822_P8-B12-AD008

value: P

value: male


title: 180822_P7-180822_P8-B2-AD012


title: 180822_P7-180822_P8-B11-AD012


title: 180822_P7-180822_P8-B11-AD010


title: 180822_P7-180822_P8-B12-AD001


title: 180822_P7-180822_P8-B3-AD007


title: 180822_P7-180822_P8-B11-AD008


title: 180822_P7-180822_P8-B11-AD001


title: 180822_P7-180822_P8-B10-AD012


title: 180822_P7-180822_P8-B11-AD007


title: 180822_P7-180822_P8-B12-AD002


title: 180822_P7-180822_P8-B10-AD008


title: 180822_P7-180822_P8-B10-AD007


title: 180822_P7-180822_P8-B10-AD010


title: 180822_P7-180822_P8-B2-AD007


title: 180822_P7-180822_P8-B10-AD006


title: 180822_P7-180822_P8-B2-AD008


title: 180822_P7-180822_P8-B10-AD004


title: 180822_P7-180822_P8-B1-AD010


title: 180822_P7-180822_P8-B1-AD007


title: 180822_P7-180822_P8-B1-AD012


title: 180822_P7-180822_P8-B10-AD001


title: 180822_P7-180822_P8-B1-AD008


title: 180822_P7-180822_P8-B1-AD001


title: 180822_P7-180822_P8-A9-AD010


title: 180822_P7-180822_P8-A9-AD012


title: 180822_P7-180822_P8-A9-AD008


title: 180822_P7-180822_P8-A9-AD002


title: 180822_P7-180822_P8-A8-AD012


title: 180822_P7-180822_P8-A8-AD008


title: 180822_P7-180822_P8-A8-AD007


title: 180822_P7-180822_P8-A8-AD002


title: 180822_P7-180822_P8-A7-AD004


title: 180822_P7-180822_P8-A8-AD001


title: 180822_P7-180822_P8-A7-AD012


title: 180822_P7-180822_P8-A7-AD002


title: 180822_P7-180822_P8-A7-AD008


title: 180822_P7-180822_P8-A7-AD001


title: 180822_P7-180822_P8-A6-AD010


title: 180822_P7-180822_P8-A6-AD012


title: 180822_P7-180822_P8-A6-AD008


title: 180822_P7-180822_P8-A6-AD007


title: 180822_P7-180822_P8-B1-AD002


title: 180822_P7-180822_P8-A6-AD001


title: 180822_P7-180822_P8-A5-AD012


title: 180822_P7-180822_P8-A5-AD007


title: 180822_P7-180822_P8-A5-AD008


title: 180822_P7-180822_P8-A9-AD007


title: 180822_P7-180822_P8-A9-AD006


title: 180822_P7-180822_P8-A5-AD010


title: 180822_P7-180822_P8-A4-AD007


title: 180822_P7-180822_P8-A3-AD012


title: 180822_P7-180822_P8-A4-AD001


title: 180822_P7-180822_P8-A3-AD007


title: 180822_P7-180822_P8-A3-AD002


title: 180822_P7-180822_P8-A3-AD010


title: 180822_P7-180822_P8-A2-AD012


title: 180822_P7-180822_P8-A3-AD001


title: 180822_P7-180822_P8-A2-AD007


title: 180822_P7-180822_P8-A2-AD010


title: 180822_P7-180822_P8-A2-AD008


title: 180822_P7-180822_P8-A2-AD001


title: 180822_P7-180822_P8-A12-AD008


title: 180822_P7-180822_P8-A12-AD012


title: 180822_P7-180822_P8-A12-AD007


title: 180822_P7-180822_P8-A2-AD002


title: 180822_P7-180822_P8-A12-AD004


title: 180822_P7-180822_P8-A12-AD002


title: 180822_P7-180822_P8-A10-AD010


title: 180822_P7-180822_P8-A10-AD012


title: 180822_P7-180822_P8-A12-AD001


title: 180822_P7-180822_P8-A5-AD002


title: 180822_P7-180822_P8-A4-AD008


title: 180822_P7-180822_P8-A10-AD007


title: 180822_P7-180822_P8-A10-AD008


title: 180822_P7-180822_P8-A10-AD004


title: 180822_P7-180822_P8-A10-AD006


title: 180822_P7-180822_P8-A1-AD008


title: 180822_P7-180822_P8-A10-AD002


title: 180822_P7-180822_P8-A1-AD010


title: 180822_P7-180822_P8-A10-AD001


title: 180822_P7-180822_P8-A1-AD001


title: 180822_P5-180822_P6-H9-AD002

value: SC


title: 180822_P5-180822_P6-H9-AD010

value: STR


title: 180822_P5-180822_P6-H9-AD007


title: 180822_P5-180822_P6-H9-AD006


title: 180822_P5-180822_P6-H9-AD001


title: 180822_P5-180822_P6-H8-AD012


title: 180822_P5-180822_P6-H8-AD008


title: 180822_P5-180822_P6-H7-AD008


title: 180822_P5-180822_P6-H8-AD004


title: 180822_P5-180822_P6-H8-AD002


title: 180822_P5-180822_P6-H8-AD006


title: 180822_P5-180822_P6-H7-AD001


title: 180822_P5-180822_P6-H6-AD010


title: 180822_P5-180822_P6-H6-AD008


title: 180822_P5-180822_P6-H7-AD006


title: 180822_P5-180822_P6-H6-AD007


title: 180822_P5-180822_P6-H6-AD006


title: 180822_P7-180822_P8-A1-AD012


title: 180822_P7-180822_P8-A1-AD002


title: 180822_P5-180822_P6-H6-AD001


title: 180822_P5-180822_P6-H9-AD004


title: 180822_P5-180822_P6-H5-AD012


title: 180822_P5-180822_P6-H6-AD004


title: 180822_P5-180822_P6-H9-AD012


title: 180822_P5-180822_P6-H4-AD006


title: 180822_P5-180822_P6-H5-AD006


title: 180822_P5-180822_P6-H4-AD012


title: 180822_P5-180822_P6-H5-AD010


title: 180822_P5-180822_P6-H5-AD002


title: 180822_P5-180822_P6-H5-AD004


title: 180822_P5-180822_P6-H5-AD008


title: 180822_P5-180822_P6-H5-AD007


title: 180822_P5-180822_P6-H4-AD002


title: 180822_P5-180822_P6-H5-AD001


title: 180822_P5-180822_P6-H7-AD004


title: 180822_P5-180822_P6-H3-AD002


title: 180822_P5-180822_P6-H3-AD004


title: 180822_P5-180822_P6-H2-AD007


title: 180822_P5-180822_P6-H3-AD007


title: 180822_P5-180822_P6-H3-AD006


title: 180822_P5-180822_P6-H2-AD008


title: 180822_P5-180822_P6-H3-AD001


title: 180822_P5-180822_P6-H4-AD001


title: 180822_P5-180822_P6-H2-AD002


title: 180822_P5-180822_P6-H3-AD008


title: 180822_P5-180822_P6-H2-AD004


title: 180822_P5-180822_P6-H2-AD006


title: 180822_P5-180822_P6-H4-AD007


title: 180822_P5-180822_P6-H12-AD006


title: 180822_P5-180822_P6-H12-AD008


title: 180822_P5-180822_P6-H12-AD010


title: 180822_P5-180822_P6-H12-AD004


title: 180822_P5-180822_P6-H12-AD002


title: 180822_P5-180822_P6-H11-AD012


title: 180822_P5-180822_P6-H10-AD006


title: 180822_P5-180822_P6-H11-AD007


title: 180822_P5-180822_P6-H11-AD001


title: 180822_P5-180822_P6-H11-AD004


title: 180822_P5-180822_P6-H10-AD004


title: 180822_P5-180822_P6-H10-AD002


title: 180822_P5-180822_P6-H1-AD001


title: 180822_P5-180822_P6-H1-AD002


title: 180822_P5-180822_P6-H1-AD004


title: 180822_P5-180822_P6-H10-AD001


title: 180822_P5-180822_P6-H1-AD006


title: 180822_P5-180822_P6-G9-AD008


title: 180822_P5-180822_P6-G9-AD006


title: 180822_P5-180822_P6-G9-AD004


title: 180822_P5-180822_P6-G9-AD002


title: 180822_P5-180822_P6-G8-AD004


title: 180822_P5-180822_P6-G8-AD008


title: 180822_P5-180822_P6-G8-AD006


title: 180822_P5-180822_P6-G8-AD002


title: 180822_P5-180822_P6-G8-AD010


title: 180822_P5-180822_P6-G8-AD012


title: 180822_P5-180822_P6-H11-AD006


title: 180822_P5-180822_P6-H12-AD001


title: 180822_P5-180822_P6-G8-AD001


title: 180822_P5-180822_P6-H11-AD002


title: 180822_P5-180822_P6-G6-AD010


title: 180822_P5-180822_P6-G7-AD008


title: 180822_P5-180822_P6-G7-AD007


title: 180822_P5-180822_P6-G7-AD001


title: 180822_P5-180822_P6-G7-AD006


title: 180822_P5-180822_P6-H2-AD001


title: 180822_P5-180822_P6-G7-AD012


title: 180822_P5-180822_P6-G7-AD004


title: 180822_P5-180822_P6-G9-AD001


title: 180822_P5-180822_P6-G6-AD007


title: 180822_P5-180822_P6-G6-AD004


title: 180822_P5-180822_P6-G6-AD001


title: 180822_P5-180822_P6-G6-AD008


title: 180822_P5-180822_P6-G6-AD002


title: 180822_P5-180822_P6-G6-AD006


title: 180822_P5-180822_P6-G5-AD012


title: 180822_P5-180822_P6-G5-AD008


title: 180822_P5-180822_P6-G5-AD010


title: 180822_P5-180822_P6-G5-AD001


title: 180822_P5-180822_P6-G4-AD006


title: 180822_P5-180822_P6-G5-AD007


title: 180822_P5-180822_P6-G5-AD004


title: 180822_P5-180822_P6-G4-AD008


title: 180822_P5-180822_P6-G4-AD004


title: 180822_P5-180822_P6-G4-AD002


title: 180822_P5-180822_P6-G4-AD001


title: 180822_P5-180822_P6-G3-AD012


title: 180822_P5-180822_P6-G3-AD004


title: 180822_P5-180822_P6-G2-AD007


title: 180822_P5-180822_P6-G2-AD008


title: 180822_P5-180822_P6-G3-AD001


title: 180822_P5-180822_P6-G2-AD012


title: 180822_P5-180822_P6-G3-AD006


title: 180822_P5-180822_P6-G5-AD002


title: 180822_P5-180822_P6-G2-AD006


title: 180822_P5-180822_P6-G2-AD002


title: 180822_P5-180822_P6-G3-AD002


title: 180822_P5-180822_P6-G12-AD012


title: 180822_P5-180822_P6-G12-AD002


title: 180822_P5-180822_P6-G12-AD007


title: 180822_P5-180822_P6-G2-AD004


title: 180822_P5-180822_P6-G12-AD001


title: 180822_P5-180822_P6-G11-AD004


title: 180822_P5-180822_P6-G11-AD006


title: 180822_P5-180822_P6-G10-AD010


title: 180822_P5-180822_P6-G10-AD012


title: 180822_P5-180822_P6-G11-AD008


title: 180822_P5-180822_P6-G11-AD001


title: 180822_P5-180822_P6-G10-AD006


title: 180822_P5-180822_P6-G10-AD008


title: 180822_P5-180822_P6-G10-AD002


title: 180822_P5-180822_P6-G10-AD004


title: 180822_P5-180822_P6-G10-AD001


title: 180822_P5-180822_P6-G1-AD002


title: 180822_P5-180822_P6-G1-AD004


title: 180822_P5-180822_P6-G2-AD001


title: 180822_P5-180822_P6-F9-AD010


title: 180822_P5-180822_P6-F9-AD012


title: 180822_P5-180822_P6-F9-AD004


title: 180822_P5-180822_P6-F9-AD001


title: 180822_P5-180822_P6-F8-AD008


title: 180822_P5-180822_P6-F8-AD010


title: 180822_P5-180822_P6-F8-AD006


title: 180822_P5-180822_P6-F8-AD001


title: 180822_P5-180822_P6-F7-AD010


title: 180822_P5-180822_P6-F7-AD008


title: 180822_P5-180822_P6-F7-AD007


title: 180822_P5-180822_P6-G10-AD007


title: 180822_P5-180822_P6-F6-AD007


title: 180822_P5-180822_P6-F7-AD004


title: 180822_P5-180822_P6-F7-AD002


title: 180822_P5-180822_P6-F8-AD004


title: 180822_P5-180822_P6-F6-AD006


title: 180822_P5-180822_P6-F7-AD001


title: 180822_P5-180822_P6-G1-AD006


title: 180822_P5-180822_P6-F6-AD002


title: 180822_P5-180822_P6-F5-AD012


title: 180822_P5-180822_P6-F5-AD004


title: 180822_P5-180822_P6-F9-AD002


title: 180822_P5-180822_P6-F5-AD002


title: 180822_P5-180822_P6-F5-AD006


title: 180822_P5-180822_P6-F5-AD001


title: 180822_P5-180822_P6-F4-AD012


title: 180822_P5-180822_P6-F4-AD004


title: 180822_P5-180822_P6-F4-AD002


title: 180822_P5-180822_P6-F4-AD001


title: 180822_P5-180822_P6-F9-AD006


title: 180822_P5-180822_P6-F3-AD004


title: 180822_P5-180822_P6-F3-AD002


title: 180822_P5-180822_P6-F2-AD010


title: 180822_P5-180822_P6-F3-AD001


title: 180822_P5-180822_P6-F4-AD006


title: 180822_P5-180822_P6-F2-AD007


title: 180822_P5-180822_P6-F2-AD006


title: 180822_P5-180822_P6-F2-AD004


title: 180822_P5-180822_P6-F12-AD007


title: 180822_P5-180822_P6-F2-AD001


title: 180822_P5-180822_P6-F2-AD002


title: 180822_P5-180822_P6-F12-AD004


title: 180822_P5-180822_P6-F12-AD001


title: 180822_P5-180822_P6-F12-AD002


title: 180822_P5-180822_P6-F3-AD006


title: 180822_P5-180822_P6-F11-AD008


title: 180822_P5-180822_P6-F12-AD006


title: 180822_P5-180822_P6-F2-AD008


title: 180822_P5-180822_P6-F11-AD004


title: 180822_P5-180822_P6-F10-AD002


title: 180822_P5-180822_P6-F11-AD001


title: 180822_P5-180822_P6-F1-AD012


title: 180822_P5-180822_P6-F11-AD002


title: 180822_P5-180822_P6-F10-AD007


title: 180822_P5-180822_P6-F1-AD008


title: 180822_P5-180822_P6-F7-AD006


title: 180822_P5-180822_P6-F1-AD007


title: 180822_P5-180822_P6-E9-AD008


title: 180822_P5-180822_P6-E9-AD010


title: 180822_P5-180822_P6-F11-AD010


title: 180822_P5-180822_P6-E9-AD004


title: 180822_P5-180822_P6-F11-AD006


title: 180822_P5-180822_P6-E9-AD007


title: 180822_P5-180822_P6-E9-AD002


title: 180822_P5-180822_P6-E8-AD012


title: 180822_P5-180822_P6-E8-AD008


title: 180822_P5-180822_P6-F10-AD006


title: 180822_P5-180822_P6-E8-AD006


title: 180822_P5-180822_P6-E8-AD004


title: 180822_P5-180822_P6-E8-AD002


title: 180822_P5-180822_P6-F1-AD004


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title: 180822_P5-180822_P6-E7-AD002


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title: 180822_P5-180822_P6-E4-AD001


title: 180822_P5-180822_P6-E4-AD006


title: 180822_P5-180822_P6-E3-AD004


title: 180822_P5-180822_P6-E2-AD012


title: 180822_P5-180822_P6-E3-AD002


title: 180822_P5-180822_P6-E2-AD004


title: 180822_P5-180822_P6-E2-AD006


title: 180822_P5-180822_P6-E2-AD002


title: 180822_P5-180822_P6-E12-AD008


title: 180822_P5-180822_P6-E12-AD006


title: 180822_P5-180822_P6-E12-AD004


title: 180822_P5-180822_P6-E2-AD001


title: 180822_P5-180822_P6-E12-AD012


title: 180822_P5-180822_P6-E5-AD008


title: 180822_P5-180822_P6-E12-AD002


title: 180822_P5-180822_P6-E5-AD006


title: 180822_P5-180822_P6-E11-AD010


title: 180822_P5-180822_P6-E5-AD002


title: 180822_P5-180822_P6-E12-AD001


title: 180822_P5-180822_P6-E11-AD006


title: 180822_P5-180822_P6-E11-AD007


title: 180822_P5-180822_P6-E10-AD012


title: 180822_P5-180822_P6-E10-AD004


title: 180822_P5-180822_P6-E11-AD002


title: 180822_P5-180822_P6-E11-AD001


title: 180822_P5-180822_P6-E11-AD004


title: 180822_P5-180822_P6-E10-AD002


title: 180822_P5-180822_P6-E12-AD007


title: 180822_P5-180822_P6-D9-AD006


title: 180822_P5-180822_P6-D9-AD002


title: 180822_P5-180822_P6-D9-AD004


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title: 180822_P5-180822_P6-D9-AD010


title: 180822_P5-180822_P6-E1-AD004


title: 180822_P5-180822_P6-D9-AD012


title: 180822_P5-180822_P6-D9-AD007


title: 180822_P5-180822_P6-D9-AD001


title: 180822_P5-180822_P6-E1-AD006


title: 180822_P5-180822_P6-D8-AD012


title: 180822_P5-180822_P6-D8-AD006


title: 180822_P5-180822_P6-D8-AD004


title: 180822_P5-180822_P6-D8-AD010


title: 180822_P5-180822_P6-D8-AD007


title: 180822_P5-180822_P6-D8-AD002


title: 180822_P5-180822_P6-E10-AD010


title: 180822_P5-180822_P6-D7-AD010


title: 180822_P5-180822_P6-E10-AD006


title: 180822_P5-180822_P6-D7-AD002


title: 180822_P5-180822_P6-E10-AD001


title: 180822_P5-180822_P6-D7-AD007


title: 180822_P5-180822_P6-E1-AD010


title: 180822_P5-180822_P6-D6-AD007


title: 180822_P5-180822_P6-D7-AD006


title: 180822_P5-180822_P6-D6-AD008


title: 180822_P5-180822_P6-D7-AD004


title: 180822_P5-180822_P6-D7-AD001


title: 180822_P5-180822_P6-D6-AD006


title: 180822_P5-180822_P6-D4-AD007


title: 180822_P5-180822_P6-D5-AD012


title: 180822_P5-180822_P6-D6-AD004


title: 180822_P5-180822_P6-D4-AD001


title: 180822_P5-180822_P6-D5-AD008


title: 180822_P5-180822_P6-D5-AD006


title: 180822_P5-180822_P6-D4-AD008


title: 180822_P5-180822_P6-D3-AD008


title: 180822_P5-180822_P6-D3-AD010


title: 180822_P5-180822_P6-D3-AD007


title: 180822_P5-180822_P6-D5-AD004


title: 180822_P5-180822_P6-D4-AD002


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title: 180822_P5-180822_P6-D2-AD004


title: 180822_P5-180822_P6-D2-AD006


title: 180822_P5-180822_P6-D2-AD002


title: 180822_P5-180822_P6-D6-AD002


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title: 180822_P5-180822_P6-D3-AD002


title: 180822_P5-180822_P6-D12-AD012


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title: 180822_P5-180822_P6-D5-AD010


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title: 180822_P5-180822_P6-D12-AD001


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title: 180822_P5-180822_P6-D1-AD006


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title: 180822_P5-180822_P6-B11-AD006


title: 180822_P5-180822_P6-B12-AD002


title: 180822_P5-180822_P6-B11-AD012


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title: 180822_P5-180822_P6-B3-AD010


title: 180822_P5-180822_P6-B10-AD012


title: 180822_P5-180822_P6-B11-AD004


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title: 180822_P5-180822_P6-A9-AD012


title: 180822_P5-180822_P6-B2-AD002


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title: 180822_P5-180822_P6-A9-AD007


title: 180822_P5-180822_P6-A9-AD004


title: 180822_P5-180822_P6-A8-AD008


title: 180822_P5-180822_P6-B11-AD001


title: 180822_P5-180822_P6-A8-AD010


title: 180822_P5-180822_P6-A8-AD007


title: 180822_P5-180822_P6-B2-AD004


title: 180822_P5-180822_P6-A8-AD002


title: 180822_P5-180822_P6-A8-AD006


title: 180822_P5-180822_P6-B1-AD002


title: 180822_P5-180822_P6-A8-AD004


title: 180822_P5-180822_P6-A8-AD001


title: 180822_P5-180822_P6-A7-AD002


title: 180822_P5-180822_P6-A6-AD007


title: 180822_P5-180822_P6-A6-AD004


title: 180822_P5-180822_P6-A9-AD001


title: 180822_P5-180822_P6-A7-AD004


title: 180822_P5-180822_P6-A7-AD001


title: 180822_P5-180822_P6-A5-AD012


title: 180822_P5-180822_P6-A6-AD006


title: 180822_P5-180822_P6-A5-AD006


title: 180822_P5-180822_P6-A5-AD004


title: 180822_P5-180822_P6-A8-AD012


title: 180822_P5-180822_P6-A5-AD010


title: 180822_P5-180822_P6-A5-AD002


title: 180822_P5-180822_P6-A4-AD010


title: 180822_P5-180822_P6-A4-AD008


title: 180822_P5-180822_P6-A4-AD006


title: 180822_P5-180822_P6-A4-AD001


title: 180822_P5-180822_P6-A4-AD002


title: 180822_P5-180822_P6-A4-AD004


title: 180822_P5-180822_P6-A3-AD007


title: 180822_P5-180822_P6-A3-AD006


title: 180822_P5-180822_P6-A3-AD012


title: 180822_P5-180822_P6-A6-AD002


title: 180822_P5-180822_P6-A4-AD012


title: 180822_P5-180822_P6-B1-AD006


title: 180822_P5-180822_P6-A3-AD004


title: 180822_P5-180822_P6-A3-AD001


title: 180822_P5-180822_P6-A2-AD002


title: 180822_P5-180822_P6-A2-AD004


title: 180822_P5-180822_P6-A12-AD010


title: 180822_P5-180822_P6-A2-AD006


title: 180822_P5-180822_P6-A5-AD001


title: 180822_P5-180822_P6-A12-AD006


title: 180822_P5-180822_P6-A12-AD004


title: 180822_P5-180822_P6-A4-AD007


title: 180822_P5-180822_P6-A11-AD004


title: 180822_P5-180822_P6-A11-AD010


title: 180822_P5-180822_P6-A11-AD012


title: 180822_P5-180822_P6-A11-AD006


title: 180822_P5-180822_P6-A11-AD001


title: 180822_P5-180822_P6-A10-AD012


title: 180822_P5-180822_P6-A12-AD001


title: 180822_P5-180822_P6-A10-AD004


title: 180822_P5-180822_P6-A2-AD012


title: 180822_P5-180822_P6-A10-AD006


title: 180822_P5-180822_P6-A1-AD006


title: 180822_P5-180822_P6-A1-AD004


title: 180822_P5-180822_P6-A1-AD001


title: 180822_P5-180822_P6-A12-AD002


title: 180822_P5-180822_P6-A1-AD002


title: 180822_P5-180822_P6-A10-AD008


title: 180822_P5-180822_P6-A10-AD002


title: 180822_P3-180822_P4-H9-AD012

value: THp


title: 180822_P3-180822_P4-H9-AD002

value: THm

value: SSp


title: 180822_P3-180822_P4-H9-AD001


title: 180822_P3-180822_P4-H8-AD010


title: 180822_P3-180822_P4-H8-AD012


title: 180822_P3-180822_P4-H8-AD008

value: THl


title: 180822_P3-180822_P4-H8-AD002


title: 180822_P3-180822_P4-H7-AD012


title: 180822_P5-180822_P6-A10-AD010


title: 180822_P5-180822_P6-A11-AD002


title: 180822_P3-180822_P4-H7-AD008


title: 180822_P3-180822_P4-H7-AD007


title: 180822_P3-180822_P4-H7-AD010


title: 180822_P3-180822_P4-H7-AD004

value: ACA


title: 180822_P3-180822_P4-H7-AD002


title: 180822_P3-180822_P4-H6-AD012


title: 180822_P3-180822_P4-H6-AD010


title: 180822_P3-180822_P4-H7-AD001


title: 180822_P3-180822_P4-H6-AD008


title: 180822_P3-180822_P4-H6-AD002


title: 180822_P3-180822_P4-H6-AD007


title: 180822_P3-180822_P4-H5-AD010


title: 180822_P3-180822_P4-H6-AD001


title: 180822_P3-180822_P4-H5-AD012


title: 180822_P3-180822_P4-H5-AD007


title: SHSY5Y ,WT, Biol rep 2

city: Philadelphia

first: Alessandro

last: Gardini

state: PA

address: 3601 Spruce St, Room 230

institute: The Wistar Institute

library_source: transcriptomic

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment: STAR
tag density files: deepTools package was used to generate BigWiggle files
gene counts:  FeatureCounts (Liao et al., 2014)
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization). Tab delimited gene count files were generated with FeatureCounts.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: iPSCs were cultured on Geltrex-coated plates and maintained in StemMACS™ iPS-Brew XF (Miltenyi Biotec, cat#130-104-368). NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement. Neurons were differentiated from NPCs neuronal differentiation medium ( Neurobasal Meida (ThermoFisher Scientific, cat#21103049), B27 (ThermoFisher Scientific,cat#A3353501), GlutaMAX (ThermoFisher Scientific, cat#35050061), nonessential animal acids (ThermoFisher Scientific, cat#11140050), 20 ng/ml brain-derived neurotrophic factor (BDNF) (Peprotech, cat#450-02) and 20 ng/ml glial cell-derived neurotrophic factor (GDNF)(Peprotech, cat#450-10) for 21 days and then mainted in this media.  SHSY5Y cells were maintained in the basal medium (45% of Minimum Essential Medium (MEM) (Corning, cat#10009CV), 45% of Nutrient Mixture F-12 Ham (Sigma-Aldrich, Cat#N4888) and 10% of fetal bovine serum (Corning, cat#35010CV)). ReNcells were maintained in ReNcell proliferation medium (5 ml of 100X Glutmax, 10 ml of B27, 1 ml of Heparin (1 mg/ml) and 484 ml of DMEM/F12) that supplemented with bFGF ( 20ng/ml) and EGF (20ng/ml). To start the differentiation, ReN cells were plated in Laminin-coated 6-well plates with ReN proliferation medium at 30-40% confluency (Day 0). On the next day (Day 1), remove the medium and feed the cells with fresh ReN differentiation medium (without bFGF and EGF). Cells were fed with fresh ReN differentiation medium every 2-3 days.

extract_protocol:
RNA was extracted using the Zymo RNA Miniprep kitand then used to make sequencing libraries.
QuantSeq 3' - mRNA Seq Library Prep Kit for Illumina (Lexogen)
QuantSeq 3' - mRNA Seq

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs or SH-SY5Y were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Singel cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared. ReN and SH-SY5Y cells after selection with puromycin for 48 hours were trypsinized and plated into 10 cm tissue culture dishes. Single cells were maintained in the basal medium supplemented with 0.5 ug/ml of puromycin for the next 2-3 weeks until cell colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened by PCR initially ( Primers: INTS10-F, 5'- TATACCAGTGGCCTCTTGTC - 3', INTS10-R, 5' - CGTCTTCCTTTATCCATCTGCC - 3') and verified by Western Blot and Sanger sequencing.

tag: cell line

tag: cell type

value: neuroblastoma

tag: genotype

value: WT

tag: treatment

value: No treatment


title: 180822_P3-180822_P4-H5-AD002


title: 180822_P3-180822_P4-H5-AD008


title: 180822_P3-180822_P4-H4-AD012


title: 180822_P3-180822_P4-H8-AD001


title: 180822_P3-180822_P4-H4-AD008


title: SHSY5Y ,INTS10KOC37, Biol rep 2


title: 180822_P3-180822_P4-H4-AD010


title: SHSY5Y ,WT, Biol rep 1


title: SHSY5Y ,INTS10KOC24, Biol rep 2


title: SHSY5Y ,INTS10KOC37, Biol rep 1


title: SHSY5Y ,INTS10KOC24, Biol rep 1


title: 180822_P3-180822_P4-H4-AD007


title: 180822_P3-180822_P4-H4-AD002


title: 180822_P3-180822_P4-H4-AD001


title: 180822_P3-180822_P4-H3-AD012


title: 180822_P3-180822_P4-H3-AD010


title: 180822_P3-180822_P4-H3-AD007


title: SHSY5Y ,INTS10KOC10, Biol rep 1


title: ReN ,shLUC, Biol rep 1

source_name: ReN

value: ReN

value: neuronal progenitor

value: WT (shLUC)

value: shLUC


title: ReN ,shINTS10_2, Biol rep 1


title: 180822_P3-180822_P4-H3-AD004

value: brain


title: ReN ,WT, Biol rep 2


title: 180822_P3-180822_P4-H3-AD002

value: female


title: ReN ,INTS10HET1, Biol rep 2


title: NPC_p3 ,WT, Biol rep 2

value: neuronal progenitor cell differentated from pluripotent stem cells


title: 180822_P3-180822_P4-H2-AD012

value: P


title: NPC_p3 ,WT, Biol rep 3


title: NPC_p3 ,WT, Biol rep 1


title: SHSY5Y ,INTS10KOC10, Biol rep 2


title: 180822_P3-180822_P4-H2-AD010

value: male


title: NPC_p3 ,shSOX2, Biol rep 1


title: 180822_P3-180822_P4-H2-AD002


title: 180822_P3-180822_P4-H2-AD007


title: NPC_p3 ,shSOX2, Biol rep 4


title: 180822_P3-180822_P4-H2-AD001


title: ReN ,shLUC, Biol rep 2


title: 180822_P3-180822_P4-H2-AD008


title: 180822_P3-180822_P4-H12-AD012

value: THp


title: ReN ,INTS10HET1, Biol rep 1


title: 180822_P3-180822_P4-H3-AD001

value: THm


title: ReN ,shINTS10_2, Biol rep 2


title: NPC_p3 ,shLUC, Biol rep 4


title: NPC_p3 ,shLUC, Biol rep 1


title: 180822_P3-180822_P4-H3-AD008


title: 180822_P3-180822_P4-H12-AD010


title: NPC_p3 ,INTS10HET2, Biol rep 4


title: ReN ,WT, Biol rep 1


title: NPC_p3 ,INTS10HET2, Biol rep 3


title: 180822_P3-180822_P4-H12-AD008


title: 180822_P3-180822_P4-H12-AD007


title: NPC_p3 ,INTS10HET2, Biol rep 2


title: 180822_P3-180822_P4-H12-AD002

value: SSp


title: 180822_P3-180822_P4-H12-AD001


title: 180822_P3-180822_P4-H11-AD012


title: NPC_p3 ,INTS10HET1, Biol rep 3


title: NPC_p0 ,INTS10HET2, Biol rep 2


title: NPC_p0 ,WT, Biol rep 3


title: NPC_p0 ,INTS10HET1, Biol rep 3


title: NPC_p0 ,WT, Biol rep 1


title: NPC_p0 ,INTS10HET2, Biol rep 3


title: NPC_p3 ,INTS10HET1, Biol rep 1


title: NPC_p0 ,INTS10HET2, Biol rep 1


title: 180822_P3-180822_P4-H11-AD010


title: NPC_p3 ,INTS10HET1, Biol rep 2


title: NPC_p0 ,WT, Biol rep 4


title: 180822_P3-180822_P4-H11-AD007

value: THl


title: 180822_P3-180822_P4-H11-AD008


title: 180822_P3-180822_P4-H11-AD002


title: NPC_p0 ,INTS10HET1, Biol rep 2


title: 180822_P3-180822_P4-H10-AD007


title: 180822_P3-180822_P4-H11-AD001


title: 180822_P3-180822_P4-H10-AD012


title: 180822_P3-180822_P4-H10-AD006

value: ACA


title: NPC_p0 ,INTS10HET1, Biol rep 1


title: Neuron ,WT, Biol rep 2

source_name: Neuron

value: Neuron

value: cortical neurons differentated from pluripotent stem cells


title: Neuron ,WT, Biol rep 3

value: WT

value: No treatment


title: 180822_P3-180822_P4-H10-AD002


title: 180822_P3-180822_P4-H1-AD010


title: 180822_P3-180822_P4-H1-AD008


title: Neuron ,WT, Biol rep 1


title: 180822_P3-180822_P4-H10-AD010


title: 180822_P3-180822_P4-H10-AD008


title: 180822_P3-180822_P4-H1-AD007


title: Neuron ,INTS10HET2, Biol rep 3


title: 180822_P3-180822_P4-G9-AD008


title: 180822_P3-180822_P4-G9-AD010


title: Neuron ,INTS10HET1, Biol rep 2


title: iPSC ,WT, Biol rep 4

source_name: iPSC

value: iPSC

value: pluripotent stem cell


title: Neuron ,INTS10HET2, Biol rep 2


title: Neuron ,INTS10HET2, Biol rep 1


title: 180822_P3-180822_P4-G8-AD008


title: iPSC ,WT, Biol rep 1


title: 180822_P3-180822_P4-G8-AD012


title: Neuron ,INTS10HET1, Biol rep 3


title: 180822_P3-180822_P4-G9-AD002


title: iPSC ,INTS10HET2, Biol rep 4


title: 180822_P3-180822_P4-G9-AD007


title: iPSC ,INTS10HET2, Biol rep 3


title: 180822_P3-180822_P4-G9-AD001


title: 180822_P3-180822_P4-G8-AD010


title: iPSC ,INTS10HET1, Biol rep 4


title: 180822_P3-180822_P4-G8-AD007


title: iPSC ,WT, Biol rep 3


title: iPSC ,INTS10HET2, Biol rep 1


title: 180822_P3-180822_P4-G8-AD002


title: iPSC ,INTS10HET1, Biol rep 3


title: 180822_P3-180822_P4-G7-AD012


title: 180822_P3-180822_P4-G9-AD012


title: 180822_P3-180822_P4-G8-AD001


title: 180822_P3-180822_P4-H1-AD001


title: iPSC ,INTS10HET1, Biol rep 1


title: Neuron ,INTS10HET1, Biol rep 1


title: 180822_P3-180822_P4-H1-AD002


title: 180822_P3-180822_P4-G7-AD010


title: 180822_P3-180822_P4-G7-AD008


title: NPC, INTS10HET2, SOX2, biol rep3

description: SOX2ChIP-seq in INTS10HET2 NPCs

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment (ChIPseq): BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: NPC

growth_protocol: iPSCs were cultured on Geltrex-coated plates and maintained in StemMACS™ iPS-Brew XF (Miltenyi Biotec, cat#130-104-368). NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement. Neurons were differentiated from NPCs neuronal differentiation medium ( Neurobasal Meida (ThermoFisher Scientific, cat#21103049), B27 (ThermoFisher Scientific,cat#A3353501), GlutaMAX (ThermoFisher Scientific, cat#35050061), nonessential animal acids (ThermoFisher Scientific, cat#11140050), 20 ng/ml brain-derived neurotrophic factor (BDNF) (Peprotech, cat#450-02) and 20 ng/ml glial cell-derived neurotrophic factor (GDNF)(Peprotech, cat#450-10) for 21 days and then mainted in this media.  SHSY5Y cells were maintained in the basal medium (45% of Minimum Essential Medium (MEM) (Corning, cat#10009CV), 45% of Nutrient Mixture F-12 Ham (Sigma-Aldrich, Cat#N4888) and 10% of fetal bovine serum (Corning, cat#35010CV)).

extract_protocol:
Lysates were clarified from sonicated nuclei (Covaris S220), and protein-DNA complexes were isolated with antibody-conjugated Dynabeads
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Inc.)

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs or SH-SY5Y were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Singel cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared. SH-SY5Y cells after selection with puromycin for 48 hours were trypsinized and plated into 10 cm tissue culture dishes. Single cells were maintained in the basal medium supplemented with 0.5 ug/ml of puromycin for the next 2-3 weeks until cell colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened by PCR initially ( Primers: INTS10-F, 5'- TATACCAGTGGCCTCTTGTC - 3', INTS10-R, 5' - CGTCTTCCTTTATCCATCTGCC - 3') and verified by Western Blot and Sanger sequencing.

value: NPC

tag: chip antibody

value: SOX2 (cell signaling 23064S)


title: 180822_P3-180822_P4-G7-AD001

value: brain


title: NPC, WT, SOX2, biol rep3

description: SOX2ChIP-seq in WT NPCs

value: neuronal progenitor cell differentated from pluripotent stem cells

value: wt


title: NPC, INTS10HET2, SOX2, biol rep2

description: SOX2ChIP-seq in INTS10HET2 NPCs


title: NPC, INTS10HET2, SOX2, biol rep1

description: SOX2ChIP-seq in INTS10HET2 NPCs


title: NPC, WT, HiC, biol rep1

description: HiC in WT NPCs

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment: HiCPro
Loop files (.arc): FitHiC
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: .cool files and .arcs files

growth_protocol: iPSCs were cultured on Geltrex-coated plates and maintained in StemMACS™ iPS-Brew XF (Miltenyi Biotec, cat#130-104-368). NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement.

extract_protocol:
In situ HiC was performed on wildtype and INTS10 heterzygote NPCs (HET2)  using the Arima HiC+ kit (Arima Genomics). Briefly, according to the standard input protocol, 5 million cells were crosslinked then flash-frozen in aliquots of 1 million cells. After quantifying the DNA from 1 million cells, we used two aliquots of cells per condition to meet the amount of DNA (500ng-5ug) required to proceed with the HiC reaction. Digestion and proximity ligation steps were done according to the kit protocol. Proximally ligated DNA underwent quality control checks for ligation efficiency then they were sonicated with the Covaris ME220 sonicator and size selected with DNA purification beads (AMPure XP Beads) to obtain a fragment size distribution of 200-600bp prior to the biotin enrichment step. Finally, libraries were prepared by end repair, dA-tailing, and adaptor ligation using the NEB Next Ultra II DNA Library Prep kit for Illumina, following a protocol tailored for Arima HiC DNA.
NEB Next Ultra II DNA Library Prep kit for Illumina, following a protocol tailored for Arima HiC DNA.

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs  were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Singel cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared.


title: NPC, WT, SOX2, biol rep2

description: SOX2ChIP-seq in WT NPCs


title: NPC, WT, SOX2, biol rep1

description: SOX2ChIP-seq in WT NPCs


title: 180822_P3-180822_P4-G6-AD010

value: P

value: male


title: 180822_P3-180822_P4-G6-AD012

value: THp

value: female


title: 180822_P3-180822_P4-G6-AD001

value: THm

value: SSp


title: 180822_P3-180822_P4-G6-AD007

value: THl


title: 180822_P3-180822_P4-G6-AD002


title: 180822_P3-180822_P4-G6-AD008


title: iPSC, WT, SOX2, biol rep1

description: SOX2ChIP-seq in WT iPSCs


title: 180822_P3-180822_P4-G5-AD012


title: 180822_P3-180822_P4-G5-AD008


title: 180822_P3-180822_P4-G5-AD007


title: 180822_P3-180822_P4-G5-AD010


title: Neuron, WT, H3K4me1, biol rep1

description: H3K4me1ChIP-seq in WT Neurons

value: Neuron

value: cortical neurons differentated from pluripotent stem cells

value: H3K4me1(abcam ab8895)


title: NPC, INTS10HET2, H3K27me3, biol rep1

description: H3K27me3ChIP-seq in INTS10HET2 NPCs

value: No treatment

value: H3K27me3 (abcam ab6002)


title: NPC, INTS10HET2, H3K4me1, biol rep2

description: H3K4me1ChIP-seq in INTS10HET2 NPCs

value: NPC


title: NPC, INTS10HET2, HiC, biol rep1

description: HiC in INTS10HET2 NPCs


title: 180822_P3-180822_P4-G7-AD002


title: Neuron, WT, H3K4me1, biol rep2

description: H3K4me1ChIP-seq in WT Neurons


title: 180822_P3-180822_P4-G5-AD002


title: iPSC, WT, SOX2, biol rep2

description: SOX2ChIP-seq in WT iPSCs

value: iPSC

value: pluripotent stem cell

value: SOX2 (cell signaling 23064S)


title: 180822_P3-180822_P4-G5-AD001

value: brain


title: NPC, INTS10HET2, H3K4me1, biol rep1

description: H3K4me1ChIP-seq in INTS10HET2 NPCs

value: neuronal progenitor cell differentated from pluripotent stem cells


title: 180822_P3-180822_P4-G4-AD012

value: P


title: NPC, WT, H3K4me1, biol rep1

description: H3K4me1ChIP-seq in WT NPCs

value: wt


title: 180822_P3-180822_P4-G4-AD010

value: THp

value: male


title: NPC, WT, H3K4me1, biol rep2

description: H3K4me1ChIP-seq in WT NPCs


title: iPSC, INTS10HET2, H3K4me1, biol rep2

description: H3K4me1ChIP-seq in INTS10HET2 iPSCs


title: iPSC, INTS10HET2, H3K4me1, biol rep1

description: H3K4me1ChIP-seq in INTS10HET2 iPSCs


title: iPSC, WT, H3K4me1, biol rep2

description: H3K4me1ChIP-seq in WT iPSCs


title: NPC, WT, H3K27me3, biol rep1

description: H3K27me3ChIP-seq in WT NPCs


title: iPSC, WT, H3K4me1, biol rep1

description: H3K4me1ChIP-seq in WT iPSCs


title: 180822_P3-180822_P4-G4-AD007


title: 180822_P3-180822_P4-G4-AD001

value: THm

value: SSp


title: Neuron, WT, H3K27ac, biol rep2

description: H3K27ac ChIP-seq in WT Neurons

value: Neuron

value: H3K27ac (abcam ab4729)


title: Neuron, WT, H3K27ac, biol rep1

description: H3K27ac ChIP-seq in WT Neurons

value: cortical neurons differentated from pluripotent stem cells


title: 180822_P3-180822_P4-G3-AD012

value: female


title: 180822_P3-180822_P4-G3-AD010


title: NPC, INTS10HET2, H3K27ac, biol rep2

description: H3K27ac ChIP-seq in INTS10HET2 NPCs

value: No treatment


title: NPC, INTS10HET2, H3K27ac, biol rep1

description: H3K27ac ChIP-seq in INTS10HET2 NPCs

value: NPC


title: NPC, WT, H3K27ac, biol rep2

description: H3K27ac ChIP-seq in WT NPCs


title: 180822_P3-180822_P4-G3-AD007

value: THl


title: 180822_P3-180822_P4-G3-AD002


title: 180822_P3-180822_P4-G3-AD001


title: 180822_P3-180822_P4-G3-AD008


title: 180822_P3-180822_P4-G3-AD006

value: ACA


title: iPSC, INTS10HET2, H3K27ac, biol rep2

description: H3K27ac ChIP-seq in INTS10HET2 iPSCs

value: iPSC

value: pluripotent stem cell


title: NPC, WT, H3K27ac, biol rep1

description: H3K27ac ChIP-seq in WT NPCs

value: neuronal progenitor cell differentated from pluripotent stem cells


title: 180822_P3-180822_P4-G4-AD008

value: brain

value: P


title: iPSC, INTS10HET2, H3K27ac, biol rep1

description: H3K27ac ChIP-seq in INTS10HET2 iPSCs


title: 180822_P3-180822_P4-G2-AD010

value: THp


title: 180822_P3-180822_P4-G2-AD012


title: 180822_P3-180822_P4-G2-AD007

value: male


title: 180822_P3-180822_P4-G2-AD008


title: SHSY5Y, WT, RNAPII, biol rep2

description: RNAPII ChIP-seq in WT SHSY5Ys

value: neuroblastoma

value: wt

value: RNAPII (Barbieri et al., Mol Cell, 2018, 71, 103-116 e107.)


title: iPSC, WT, H3K27ac, biol rep1

description: H3K27ac ChIP-seq in WT iPSCs

value: H3K27ac (abcam ab4729)


title: iPSC, WT, H3K27ac, biol rep2

description: H3K27ac ChIP-seq in WT iPSCs


title: 180822_P3-180822_P4-G2-AD001

value: THm

value: SSp


title: 180822_P3-180822_P4-G12-AD012

value: female


title: 180822_P3-180822_P4-G12-AD010


title: Neuron, WT, RNAPII, biol rep1

description: RNAPII ChIP-seq in WT Neurons

value: Neuron

value: cortical neurons differentated from pluripotent stem cells

value: No treatment


title: SHSY5Y, WT, RNAPII, biol rep1

description: RNAPII ChIP-seq in WT SHSY5Ys


title: Neuron, WT, RNAPII, biol rep2

description: RNAPII ChIP-seq in WT Neurons


title: 180822_P3-180822_P4-G12-AD008

value: THl


title: NPC, INTS10HET2, RNAPII, biol rep3

description: RNAPII ChIP-seq in INTS10HET2 NPCs

value: NPC


title: NPC, INTS10HET2, RNAPII, biol rep1

description: RNAPII ChIP-seq in INTS10HET2 NPCs

value: neuronal progenitor cell differentated from pluripotent stem cells


title: 180822_P3-180822_P4-G12-AD006

value: brain

value: ACA


title: 180822_P3-180822_P4-G12-AD002


title: 180822_P3-180822_P4-G12-AD007

value: P


title: NPC, WT, RNAPII, biol rep1

description: RNAPII ChIP-seq in WT NPCs


title: NPC, WT, RNAPII, biol rep2

description: RNAPII ChIP-seq in WT NPCs


title: 180822_P3-180822_P4-G11-AD012

value: THp


title: iPSC, INTS10HET2, RNAPII, biol rep1

description: RNAPII ChIP-seq in INTS10HET2 iPSCs

value: iPSC

value: pluripotent stem cell


title: iPSC, INTS10HET2, RNAPII, biol rep2

description: RNAPII ChIP-seq in INTS10HET2 iPSCs

value: RNAPII (Barbieri et al., Mol Cell, 2018, 71, 103-116 e107.)


title: 180822_P3-180822_P4-G11-AD008


title: 180822_P3-180822_P4-G11-AD010

value: male


title: 180822_P3-180822_P4-G11-AD007


title: 180822_P3-180822_P4-G11-AD002

value: THm


title: 180822_P3-180822_P4-G11-AD001

value: SSp


title: SHSY5Y, WT, INTS13, biol rep2

description: INTS13 ChIP-seq in WT SHSY5Ys

value: neuroblastoma

value: wt

value: INTS13 (bethyl A303-575A)


title: 180822_P3-180822_P4-G10-AD008

value: female


title: Neuron, WT, INTS13, biol rep2

description: INTS13 ChIP-seq in WT Neurons

value: Neuron

value: cortical neurons differentated from pluripotent stem cells

value: No treatment


title: Neuron, WT, INTS13, biol rep1

description: INTS13 ChIP-seq in WT Neurons


title: iPSC, WT, RNAPII, biol rep2

description: RNAPII ChIP-seq in WT iPSCs


title: SHSY5Y, WT, INTS13, biol rep1

description: INTS13 ChIP-seq in WT SHSY5Ys


title: 180822_P3-180822_P4-G10-AD002

value: brain


title: 180822_P3-180822_P4-G10-AD006

value: ACA


title: 180822_P3-180822_P4-G10-AD007

value: THl

value: P


title: 180822_P3-180822_P4-G10-AD001


title: 180822_P3-180822_P4-G1-AD012

value: THp


title: 180822_P3-180822_P4-G10-AD012


title: NPC, WT, INTS13, biol rep2

description: INTS13 ChIP-seq in WT NPCs

value: NPC

value: neuronal progenitor cell differentated from pluripotent stem cells


title: 180822_P3-180822_P4-G1-AD010

value: male


title: iPSC, INTS10HET2, INTS13, biol rep1

description: INTS13 ChIP-seq in INTS10HET2 iPSCs

value: iPSC

value: pluripotent stem cell


title: NPC, INTS10HET2, INTS13, biol rep1

description: INTS13 ChIP-seq in INTS10HET2 NPCs


title: iPSC, INTS10HET2, INTS13, biol rep2

description: INTS13 ChIP-seq in INTS10HET2 iPSCs


title: iPSC, WT, INTS13, biol rep1

description: INTS13 ChIP-seq in WT iPSCs


title: iPSC, WT, INTS13, biol rep2

description: INTS13 ChIP-seq in WT iPSCs


title: 180822_P3-180822_P4-G1-AD004

value: THm


title: iPSC, WT, RNAPII, biol rep1

description: RNAPII ChIP-seq in WT iPSCs

value: wt

value: RNAPII (Barbieri et al., Mol Cell, 2018, 71, 103-116 e107.)


title: 180822_P3-180822_P4-G1-AD001

value: SSp


title: 180822_P3-180822_P4-F9-AD012

value: female


title: NPC, INTS10HET2, INTS13, biol rep2

description: INTS13 ChIP-seq in INTS10HET2 NPCs

value: INTS13 (bethyl A303-575A)


title: Neuron, WT, INTS11, biol rep2

description: INTS11 ChIP-seq in WT Neurons

value: Neuron

value: cortical neurons differentated from pluripotent stem cells

value: No treatment

value: INTS11 (bethyl A301-274A)


title: SHSY5Y, WT, INTS11, biol rep1

description: INTS11 ChIP-seq in WT SHSY5Ys

value: neuroblastoma


title: 180822_P3-180822_P4-F9-AD010

value: brain

value: THp

value: P


title: NPC, INTS10HET2, INTS11, biol rep2

description: INTS11 ChIP-seq in INTS10HET2 NPCs

value: NPC

value: neuronal progenitor cell differentated from pluripotent stem cells


title: 180822_P3-180822_P4-F9-AD008

value: THl


title: NPC, WT, INTS13, biol rep1

description: INTS13 ChIP-seq in WT NPCs


title: NPC, INTS10HET2, INTS11, biol rep1

description: INTS11 ChIP-seq in INTS10HET2 NPCs


title: 180822_P3-180822_P4-F9-AD004

value: THm

value: ACA

value: male


title: NPC, WT, INTS11, biol rep2

description: INTS11 ChIP-seq in WT NPCs

value: wt


title: 180822_P3-180822_P4-F9-AD007


title: NPC, WT, INTS11, biol rep1

description: INTS11 ChIP-seq in WT NPCs


title: 180822_P3-180822_P4-F9-AD001

value: SSp


title: 180822_P3-180822_P4-G1-AD002

value: female


title: 180822_P3-180822_P4-F8-AD012


title: 180822_P3-180822_P4-F8-AD007


title: iPSC, INTS10HET2, INTS11, biol rep1

description: INTS11 ChIP-seq in INTS10HET2 iPSCs

value: iPSC

value: pluripotent stem cell


title: 180822_P3-180822_P4-F8-AD010


title: 180822_P3-180822_P4-F8-AD008


title: iPSC, WT, INTS11, biol rep2

description: INTS11 ChIP-seq in WT iPSCs

value: No treatment


title: iPSC, WT, INTS11, biol rep1

description: INTS11 ChIP-seq in WT iPSCs

value: INTS11 (bethyl A301-274A)


title: SHSY5Y, WT, INTS10, biol rep2

description: INTS10 ChIP-seq in WT SHSY5Ys

value: neuroblastoma

value: INTS10 (proteintech 15271-1-AP)


title: Neuron, WT, INTS11, biol rep1

description: INTS11 ChIP-seq in WT Neurons

value: Neuron

value: cortical neurons differentated from pluripotent stem cells


title: 180822_P3-180822_P4-F8-AD002

value: brain


title: Neuron, WT, INTS10, biol rep1

description: INTS10 ChIP-seq in WT Neurons


title: SHSY5Y, WT, INTS10, biol rep1

description: INTS10 ChIP-seq in WT SHSY5Ys


title: Neuron, WT, INTS10, biol rep2

description: INTS10 ChIP-seq in WT Neurons


title: 180822_P3-180822_P4-F8-AD006


title: NPC, WT, INTS10, biol rep2

description: INTS10 ChIP-seq in WT NPCs

value: NPC

value: neuronal progenitor cell differentated from pluripotent stem cells


title: NPC, INTS10HET2, INTS10, biol rep1

description: INTS10 ChIP-seq in INTS10HET2 NPCs


title: NPC, INTS10HET2, INTS10, biol rep2

description: INTS10 ChIP-seq in INTS10HET2 NPCs


title: 180822_P3-180822_P4-F8-AD001

value: THm


title: NPC, WT, INTS10, biol rep1

description: INTS10 ChIP-seq in WT NPCs


title: 180822_P3-180822_P4-F7-AD010

value: THp

value: P


title: 180822_P3-180822_P4-F7-AD002


title: 180822_P3-180822_P4-F7-AD008

value: THl


title: 180822_P3-180822_P4-F7-AD012


title: SHSY5Y, WT, INTS11, biol rep2

description: INTS11 ChIP-seq in WT SHSY5Ys

value: wt


title: iPSC, WT, INTS10, biol rep1

description: INTS10 ChIP-seq in WT iPSCs


title: iPSC, INTS10HET2, INTS10, biol rep2

description: INTS10 ChIP-seq in INTS10HET2 iPSCs


title: iPSC, INTS10HET2, INTS10, biol rep1

description: INTS10 ChIP-seq in INTS10HET2 iPSCs


title: 180822_P3-180822_P4-F9-AD002

value: SSp

value: female


title: NPC, INTS10HET2, ATAC, biol rep2

description: ATAC in INTS10HET2 NPCs

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment: BWA-MEM
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

extract_protocol:
Omni ATAC-seq was performed on wildtype iPSCs and both wildtype and INTS10 heterzygote NPCs (HET2) according to Corces et al 2017. Briefly, 50,000 cells were washed in  ATAC-resuspension buffer (RSB)  with 0.1% Tween-20 and then lysed by incubated on ice for 3 minutes in RSB with 0.1% NP-40 and 0.1% Tween-20. Lysis was washed out in RSB 0.1% Tween-20 and nuclei was pelleted by centrifugation at 600g/4°C/5 minutes. Nuclei were then incubated in transposition mixture for 30 minutes at 37°C while shaking at 1000rpm. DNA was then purified using Zymo DNA clean and concentrator-5 Kit (cat# D4014). DNA was then amplified for 5 cycles with ATAC index primers and NEBNext Ultra II Q5 Master Mix (NEB #M0544). Additional amplification cycles were then determined by qPCR using 5uL of original amplification with PerfeCTa SYBR Green FastMix Reaction Mixes (Quantabio 95072-012). After additional amplification cycles with remaining 15uL DNA was then purified using Zymo DNA clean and concentrator-5 Kit (cat# D4014) and quantified by QUBIT.
Omni-ATAC-seq (Corces et al. 2017)

treatment_protocol: Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLentiCRISPR v2-INTS10 gRNA3 (Target sequence: TTCTGAGAGCTACGTTTGCT). iPSCs  were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, iPSC colonies were disassociated with Accutase and passed through a 40 uM cell stainer to to generate single cells. Single cell suspension with 10 μM of ROCK inhibitor and 0.5 ug/ml of puromycin were seeded in Geltrex-coated 10 cm dishes.  ROCK inhibitor was removed 24 hours after the seeding. Single cells were cultured in iPSC medium with 0.5 ug/ml of puromycin for the next 2-3 weeks until iPSC colonies appeared.


title: 180822_P3-180822_P4-F6-AD002


title: 180822_P3-180822_P4-F6-AD012


title: NPC, INTS10HET2, ATAC, biol rep1

description: ATAC in INTS10HET2 NPCs


title: 180822_P3-180822_P4-F6-AD008


title: 180822_P3-180822_P4-F7-AD007

value: male


title: 180822_P3-180822_P4-F5-AD012


title: 180822_P3-180822_P4-F6-AD001


title: 180822_P3-180822_P4-F5-AD008


title: NPC, WT, ATAC, biol rep2

description: ATAC in WT NPCs

value: No treatment


title: 180822_P3-180822_P4-F5-AD010


title: 180822_P3-180822_P4-F5-AD007


title: iPSC, WT, ATAC, biol rep1

description: ATAC in WT iPSCs

value: iPSC

value: pluripotent stem cell


title: 180822_P3-180822_P4-F6-AD010


title: 180822_P3-180822_P4-F5-AD001


title: NPC, wt, H3K4me1, biol rep1

description: H3K27me3 CUT&TAG in WT SHSY5Y

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
Base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality control: FastQC
Adapter trimming: Trim Galore!
Alignment: bowtie2
Tag density files: deepTools bamCoverage
Genome_build: GRCh37/hg19
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

growth_protocol: iPSCs were cultured on Geltrex-coated plates and maintained in StemMACS™ iPS-Brew XF (Miltenyi Biotec, cat#130-104-368). NPCs were differentiated from iPSCs using Neural Induction Medium (98% Neurobasal Meida (ThermoFisher, cat#21103049) and 2% Neuronal Induction Supplementd) for 7 days and maintained in Neural Expansion Medium (49% Neurobasal Meida (ThermoFisher, cat#21103049), 49% Advanced DMEM/F12 (ThermoFisher, cat#12634010) and 2% Neuronal Induction Supplement.  SHSY5Y cells were maintained in the basal medium (45% of Minimum Essential Medium (MEM) (Corning, cat#10009CV), 45% of Nutrient Mixture F-12 Ham (Sigma-Aldrich, Cat#N4888) and 10% of fetal bovine serum (Corning, cat#35010CV)).

extract_protocol:
Profiling of histone markers in SH-SY5Y cells was performed with CUTANA™ CUT&Tag kit (Epicypher, cat#14-1101) following the manufacturer's protocol. Briefly, desired Concanavalin A (ConA) coated magnetic beads (Bangs Laboratories, cat#BP531) for all planned CUT&Tag reactions (11 μL per reaction) were processed together and activated in cold Bead Activation Buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 10 ul of activated ConA beads were aliquoted into each 8-strip PCR tubes for individual reactions and kept cold until needed. WT and INTS10 KO SH-SY5Y cells were harvest, counted and centrifuged for 3 min at 600⨉g at room temperature in two individual 1.5 mL tubes. Total desired amount of WT and INTS10 KO cells (200, 000 cells per experiment) were washed once with PBS at room temperature. To isolate nuclei, cell pellets were resuspended in cold Nulcear Extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine, 1 x Protease inhibitor), incubated for 10 min on ice and centrifuged for 3 minutes at 600⨉g at 4 °C to remove the supernatant. Fluffy nuclei pellets were resuspended in 100 μL/reaction cold NE buffer and aliquoted into 8-strip PCR tubes containing 10 μL of activated ConA beads. Nuclei-beads slurry were vortex gently to mix and incubated for 10 minutes at room temperature. 50 μL cold Antibody150 Buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 2 mM EDTA, 1X protease inhibitor ) containing 0.5 ug of H3K4me1 or H3K27ac antibody was added immediately to the beads after the removal of the supernant and vortex gently and thoroughly. The reactions were incubated on nutator overnight at 4 °C . On the next day, anti-rabbit secondary antibody master mix was prepared first by diluting secondary antibodies in cold Digitonin 150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 1X Protease inhibitor). After removing the supernatant from the beads slurry, 50 μL/reaction cold secondary antibody master mix was added to each reaction and mixed well by gentle vortexing. The reactions were incubated on nutator for 30 minutes at room temperature. After two washes with cold Digitonin 150 buffer (), 50 μL/reaction cold Digitonin 300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1 X protease inhibitor, 0.01% Digitonin ) containing 2.5 μL pAG-Tn5 was added to the beads slurry. Beads were thoroughly resuspened by gentle vortexing and incubated on nutator for 1 hour at room temperature. After two washes with 200 μL/reaction cold Digitonin 300 buffer, 50 μL/reaction cold Tagmentation buffer (Digitonin300 Buffer, 10 mM MgCl2 ) was added to each reaction and the tubes were incubated for 1 hour at 37 °C in a thermocycle. 50 μL/reaction RT TAPS buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA) was then used to wash the reactions and 5 μL/reaction RT SDS Release buffer (10 mM TAPS, pH 8.5, 0.1% SDS) was added to quench the tagmentation reaction. 15 μL/reaction RT SDS Quench buffer (0.67% Triton-X 100 in Molecular grade H2O) was then used to neutralize SDS, which inhibits PCR. Library amplification was performed directly on the entire reaction mixture by adding dual primers and CUTANATM High Fidelity 2x PCR Master Mix. After PCR, the library DNA was purified using AMPure XP beads (ThermoFisher, cat#A63881) and quantified by Qubit.
CUT&TAG (Kaya-Okur et al. 2020)

value: neuroblastoma

tag: cut&tag antibody


title: 180822_P3-180822_P4-F4-AD012


title: iPSC, WT, INTS10, biol rep2

description: INTS10 ChIP-seq in WT iPSCs

value: INTS10 (proteintech 15271-1-AP)


title: NPC, wt, H3K4me1, biol rep2

description: H3K27me3 CUT&TAG in WT SHSY5Y


title: 180822_P3-180822_P4-F4-AD010


title: NPC, wt, H3K27me3, biol rep1

description: H3K4me1 CUT&TAG in WT SHSY5Y


title: NPC, wt, H3K27me3, biol rep2

description: H3K4me1 CUT&TAG in WT SHSY5Y


title: 180822_P3-180822_P4-F4-AD008


title: 180822_P3-180822_P4-F4-AD007


title: 180822_P3-180822_P4-F4-AD002


title: NPC, wt, H3K27ac, biol rep1

description: H3K27ac CUT&TAG in WT SHSY5Y


title: NPC, wt, H3K27ac, biol rep2

description: H3K27ac CUT&TAG in WT SHSY5Y


title: NPC, INTS10KO_C10, H3K27me3, biol rep2

description: H3K27me3 CUT&TAG in INTS10KO_C10 SHSY5Y


title: 180822_P3-180822_P4-F3-AD008


title: NPC, INTS10KO_C10, H3K4me1, biol rep1

description: H3K4me1 CUT&TAG in INTS10KO_C10 SHSY5Y


title: 180822_P3-180822_P4-F3-AD012


title: 180822_P3-180822_P4-F4-AD001


title: NPC, WT, ATAC, biol rep1

description: ATAC in WT NPCs


title: NPC, INTS10KO_C10, H3K27me3, biol rep1

description: H3K27me3 CUT&TAG in INTS10KO_C10 SHSY5Y


title: 180822_P3-180822_P4-F3-AD007


title: NPC, INTS10KO_C10, H3K4me1, biol rep4

description: H3K4me1 CUT&TAG in INTS10KO_C10 SHSY5Y


title: NPC, INTS10KO_C10, H3K27ac, biol rep1

description: H3K27ac CUT&TAG in INTS10KO_C10 SHSY5Y


title: 180822_P3-180822_P4-F3-AD010


title: 180822_P3-180822_P4-F5-AD002


title: NPC, INTS10KO_C10, H3K27ac, biol rep4

description: H3K27ac CUT&TAG in INTS10KO_C10 SHSY5Y


title: NPC, shSOX2, H3K4me1, biol rep1

description: H3K4me1 CUT&TAG in shSOX2 NPCs


title: 180822_P3-180822_P4-F3-AD002


title: NPC, shSOX2, H3K27ac, biol rep2

description: H3K27ac CUT&TAG in shSOX2 NPCs


title: 180822_P3-180822_P4-F3-AD001


title: 180822_P3-180822_P4-F2-AD007


title: NPC, shSOX2, H3K4me1, biol rep2

description: H3K4me1 CUT&TAG in shSOX2 NPCs


title: 180822_P3-180822_P4-F2-AD012


title: 180822_P3-180822_P4-F2-AD008


title: iPSC, INTS10HET2, INTS11, biol rep2

description: INTS11 ChIP-seq in INTS10HET2 iPSCs

value: INTS11 (bethyl A301-274A)


title: NPC, shLUC, H3K4me1, biol rep2

description: H3K4me1 CUT&TAG in shLUC NPCs

value: shLUC


title: 180822_P3-180822_P4-F2-AD010

value: brain


title: 180822_P3-180822_P4-F2-AD006

value: ACA


title: 180822_P3-180822_P4-F2-AD002

value: THm


title: NPC, shLUC, H3K4me1, biol rep1

description: H3K4me1 CUT&TAG in shLUC NPCs

value: NPC

value: neuronal progenitor cell differentated from pluripotent stem cells


title: 180822_P3-180822_P4-F12-AD012

value: THp

value: P


title: NPC, shLUC, H3K27ac, biol rep2

description: H3K27ac CUT&TAG in shLUC NPCs

value: wt


title: NPC, shLUC, H3K27ac, biol rep1

description: H3K27ac CUT&TAG in shLUC NPCs


title: 180822_P3-180822_P4-F12-AD010


title: 180822_P3-180822_P4-F2-AD001

value: SSp


title: NPC, shSOX2, H3K27ac, biol rep1

description: H3K27ac CUT&TAG in shSOX2 NPCs


title: 180822_P3-180822_P4-F12-AD007

value: THl

value: male


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide NT, replicate C, bulk RNA-seq

city: Cambridge

first: Jorge Diego

last: Martin Rufino

state: MA

address: 415 Main Street

institute: Harvard University / Broad Institute of MIT and Harvard / Boston Children's Hospital

description:
Smart-seq v4
GATA1_c220_2TC_NT_d2_repC_RNA_seq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: h5 files, contains gene expression matrices and cropseq transcript matrices, and barcoded antibody matrices (if applicable)

source_name: Hematopoietic system

extract_protocol:
Following final FACS enrichment to remove debris and purify transduced cells, 5-mL PBS-BSA coated tubes described above were spun down at 400 x g for 5 minutes at 4ºC. The entire supernatant was carefully removed and 1mL of PBS_0.05% BSA was added. Cells were then counted twice using an automated Countess 2 cell counter (Thermo Fisher, I-CACC2). Cell viability as determined by Trypan Blue was always >95%. Cells were again washed with 5mL PBS_0.05% BSA and resuspended at a final concentration of 1,000 cells / µL and kept on ice.
Single-cells were immediately processed using v3.1 Chemistry Dual Index kits according to manufacturer’s instructions (10X Genomics), using 20µL of cell suspension and 23.2 µL of water on the cell suspension loading step. Libraries were sequenced using a 28 base pair (Read 1), 10 base pair (Index 1), 10 base pair (Index 2), 90 base pair (Read 2) configuration on Nextseq 500, Nextseq 2000 or Novaseq S2/S4 instruments.

value: Differentiated hematopoietic stem and progenitor cells

value: Hematopoietic system

tag: library type

value: mRNA (bulk RNA-sequencing)

tag: antibodies/tags


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide NT, replicate A, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_NT_d1_repA_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide NT, replicate B, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_NT_d2_repB_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide NT, replicate B, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_NT_d1_repB_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide NT, replicate C, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_NT_d1_repC_RNA_seq


title: 180822_P3-180822_P4-F12-AD002

value: female


title: 180822_P3-180822_P4-F11-AD012


title: 180822_P3-180822_P4-F12-AD001


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide 2, replicate A, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g2_d2_repA_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide 2, replicate B, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g2_d2_repB_RNA_seq


title: 180822_P3-180822_P4-F11-AD010


title: 180822_P3-180822_P4-F11-AD002


title: 180822_P3-180822_P4-F11-AD007


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide 2, replicate B, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g2_d1_repB_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide 2, replicate C, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g2_d1_repC_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide 2, replicate A, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g2_d1_repA_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide NT, replicate A, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_NT_d2_repA_RNA_seq


title: 180822_P3-180822_P4-F12-AD008


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide 1, replicate B, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g1_d2_repB_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide 1, replicate C, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g1_d2_repC_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide 1, replicate A, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g1_d2_repA_RNA_seq


title: 180822_P3-180822_P4-F11-AD001


title: 180822_P3-180822_P4-F10-AD012


title: Differentiated HSPCs day 9 post-electroporation, donor 2, edited with c220_2T>C guide 2, replicate C, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g2_d2_repC_RNA_seq


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide 1, replicate C, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g1_d1_repC_RNA_seq


title: 180822_P3-180822_P4-F10-AD007


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep32, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep32_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep32

library_source: transcriptomic single cell

value: mRNA (enrichment PCR)


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide 1, replicate B, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g1_d1_repB_RNA_seq


title: 180822_P3-180822_P4-F10-AD004


title: 180822_P3-180822_P4-F11-AD008


title: 180822_P3-180822_P4-F10-AD002


title: 180822_P3-180822_P4-F10-AD001


title: Differentiated HSPCs day 9 post-electroporation, donor 1, edited with c220_2T>C guide 1, replicate A, bulk RNA-seq

description:
Smart-seq v4
GATA1_c220_2TC_g1_d1_repA_RNA_seq


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep31, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep31_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep31


title: 180822_P3-180822_P4-F1-AD008


title: 180822_P3-180822_P4-F1-AD012


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep30, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep30_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep30


title: 180822_P3-180822_P4-F1-AD007


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep29, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep29_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep29


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep28, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep28_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep28


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep27, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep27_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep27


title: 180822_P3-180822_P4-F10-AD010


title: 180822_P3-180822_P4-F1-AD001


title: 180822_P3-180822_P4-E9-AD012


title: 180822_P3-180822_P4-E9-AD010


title: 180822_P3-180822_P4-E9-AD008


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep24, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep24_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep24


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep26, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep26_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep26


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep23, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep23_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep23


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep22, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep22_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep22


title: 180822_P3-180822_P4-E9-AD004


title: 180822_P3-180822_P4-E9-AD001


title: Differentiated HSPCs day 9 erythroid, GATA1 library, rep25, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep25_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep25


title: 180822_P3-180822_P4-E9-AD002


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep21, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep21_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep21


title: 180822_P3-180822_P4-E8-AD012


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep20, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep20_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep20


title: 180822_P3-180822_P4-E8-AD010


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep19, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep19_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep19


title: 180822_P3-180822_P4-E8-AD008


title: 180822_P3-180822_P4-E8-AD006


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep17, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep17_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep17


title: 180822_P3-180822_P4-E8-AD004


title: Differentiated HSPCs day 4 erythroid, GATA1 library, rep15, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep15_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep15


title: 180822_P3-180822_P4-E8-AD001


title: 180822_P3-180822_P4-E9-AD007


title: 180822_P3-180822_P4-E7-AD010


title: Differentiated HSPCs day 4 erythroid, GATA1 library, rep13, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep13_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep13


title: Differentiated HSPCs day 4 erythroid, GATA1 library, rep12, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep12_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep12


title: Differentiated HSPCs day 4 erythroid, GATA1 library, rep11, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep11_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep11


title: 180822_P3-180822_P4-E7-AD012


title: 180822_P3-180822_P4-E7-AD008


title: Differentiated HSPCs day 4 erythroid, GATA1 library, rep10, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep10_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep10


title: 180822_P3-180822_P4-E7-AD006


title: 180822_P3-180822_P4-E7-AD007


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep8, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep8_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep8


title: 180822_P3-180822_P4-E7-AD002


title: Differentiated HSPCs day 7 erythroid, GATA1 library, rep18, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep18_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep18


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep7, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep7_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep7


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep6, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep6_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep6


title: 180822_P3-180822_P4-E6-AD012


title: 180822_P3-180822_P4-E6-AD008


title: 180822_P3-180822_P4-E6-AD010


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep5, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep5_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep5


title: Differentiated HSPCs day 4 erythroid, GATA1 library, rep14, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep14_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep14


title: 180822_P3-180822_P4-E6-AD006


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep4, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep4_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep4


title: 180822_P3-180822_P4-E6-AD002


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep2, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep2_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep2


title: 180822_P3-180822_P4-E8-AD002


title: 180822_P3-180822_P4-E6-AD007


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep3, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep3_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep3


title: Differentiated HSPCs day 2 erythroid, GATA1 library, rep1, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep1_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep1


title: 180822_P3-180822_P4-E6-AD001


title: HSPC-derived erythroblasts, edited with HBG1/2 library, rep8, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep8_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep8


title: 180822_P3-180822_P4-E5-AD012


title: 180822_P3-180822_P4-E5-AD008


title: 180822_P3-180822_P4-E5-AD002


title: HSPC-derived erythroblasts, edited with HBG1/2 library, rep7, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep7_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep7


title: HSPC-derived erythroblasts, edited with HBG1/2 library, rep8, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep8_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep8

value: mRNA


title: Differentiated HSPCs day 4 erythroid, GATA1 library, rep9, enrichment PCR

description:
10x Genomics
perturb_BE_seq_GATA1_rep9_filtered_feature_bc_matrix.h5
perturb_BE_seq_GATA1_enrichment_pcr_rep9


title: HSPC-derived erythroblasts, edited with HBG1/2 library, rep7, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep7_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep7


title: HSPC-derived erythroblasts, HBG1/2 library, rep6, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep6_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep6


title: 180822_P3-180822_P4-E4-AD012

value: brain


title: 180822_P3-180822_P4-E5-AD001


title: HSPC-derived erythroblasts, HBG1/2 library, rep5, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep5_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep5


title: 180822_P3-180822_P4-E4-AD010


title: HSPC-derived erythroblasts, HBG1/2 library, rep5, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep5_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep5


title: 180822_P3-180822_P4-E4-AD002


title: HSPC-derived erythroblasts, HBG1/2 library, rep4, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep4_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep4


title: 180822_P3-180822_P4-E4-AD007


title: 180822_P3-180822_P4-E4-AD001


title: HSPC-derived erythroblasts, HBG1/2 library, rep3, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep3_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep3


title: 180822_P3-180822_P4-E3-AD012


title: HSPC-derived erythroblasts, HBG1/2 library, rep4, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep4_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep4


title: 180822_P3-180822_P4-E3-AD010


title: HSPC-derived erythroblasts, HBG1/2 library, rep2, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep2_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep2


title: 180822_P3-180822_P4-E3-AD008


title: 180822_P3-180822_P4-E3-AD004

value: ACA


title: 180822_P3-180822_P4-E3-AD002

value: THm


title: Differentiated HSPCs, 4 arrayed lentiviruses, rep 2, enrichment PCR

description:
10x Genomics
perturb_seq_CD33_rep1_filtered_feature_bc_matrix.h5

extract_protocol:
Following final FACS enrichment to remove debris and purify transduced cells, 5-mL PBS-BSA coated tubes described above were spun down at 400 x g for 5 minutes at 4ºC. The entire supernatant was carefully removed and 1mL of PBS+0.05% BSA was added. Cells were then counted twice using an automated Countess 2 cell counter (Thermo Fisher, I-CACC2). Cell viability as determined by Trypan Blue was always >95%. Cells were again washed with 5mL PBS+0.05% BSA and resuspended at a final concentration of 1,000 cells / µL and kept on ice.
Single-cells were immediately processed using v3.1 Chemistry Dual Index kits according to manufacturer’s instructions (10X Genomics), using 20µL of cell suspension and 23.2 µL of water on the cell suspension loading step. Libraries were sequenced using a 28 base pair (Read 1), 10 base pair (Index 1), 10 base pair (Index 2), 90 base pair (Read 2) configuration on Nextseq 500, Nextseq 2000 or Novaseq S2/S4 instruments.


title: HSPC-derived erythroblasts, HBG1/2 library, rep1, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep1_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep1


title: Differentiated HSPCs, 4 arrayed lentiviruses, rep 1, enrichment PCR


title: 180822_P3-180822_P4-E3-AD001


title: HSPC-derived erythroblasts, HBG1/2 library, rep2, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep2_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep2


title: HSPC-derived erythroblasts, HBG1/2 library, rep6, scRNA-seq

description:
10x Genomics
perturb_BE_seq_HbF_rep6_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_gex_rep6


title: 180822_P3-180822_P4-E2-AD010


title: 180822_P3-180822_P4-E4-AD008


title: HSPC-derived erythroblasts, HBG1/2 library, rep3, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep3_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep3


title: 180822_P3-180822_P4-E2-AD008


title: 180822_P3-180822_P4-E2-AD007


title: 180822_P3-180822_P4-E2-AD001


title: 180822_P3-180822_P4-E12-AD012


title: 180822_P3-180822_P4-E12-AD010


title: HSPC-derived erythroblasts, HBG1/2 library, rep1, enrichment PCR

description:
10x Genomics
perturb_BE_seq_HbF_rep1_filtered_feature_bc_matrix.h5
perturb_BE_seq_HbF_enrichment_pcr_rep1


title: 180822_P3-180822_P4-E2-AD012


title: 180822_P3-180822_P4-E12-AD007


title: 180822_P3-180822_P4-E12-AD008


title: 180822_P3-180822_P4-E12-AD002


title: Control 3

type: RNA

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

description:
Wild Type Control
SAMPLE 3

data_processing:
We normalized using the SignArraysR analysis tool from (Any Genes, Paris, France).
mRNA expression was calculated using the recommended 2-ΔΔCt method

label: not provided

molecule: total RNA

source_name: Control 3

label_protocol: The expression of 84 mature mRNAs was analyzed using Array Template (AnyGenes)

growth_protocol: RNA from brain of 5XFAD were converted to cDNA thorugh a reverse transcription reaction using using StaRT Reverse Transcriptase kit (StaRT-50)

extract_protocol: Total RNA was isolated from liver by using the Trizol® reagent (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer’s instructions. NucleoSpin RNA Clean-Up (Macherey-Nagel, Düren, Germany) was used for RNA purification. RNA concentration was determined by measuring absorbance at 260 nm, and the absorbance ratio 260/280 nm was used to analyze RNA quality

treatment_protocol: Brain extraction by using Trizol Reagent

value: Wild Type

tag: agent

tag: age


title: 5XFAD Control 1

description:
5XFAD Control
SAMPLE 4

source_name: 5XFAD Control 1


title: 5XFAD Treated UB-ALT-EV 2

description:
5XFAD Treated
SAMPLE 8

source_name: 5XFAD Treated UB-ALT-EV 2

value: UB-ALT-EV


title: 5XFAD Treated UB-ALT-EV 1

description:
5XFAD Treated
SAMPLE 7

source_name: 5XFAD Treated UB-ALT-EV 1


title: 5XFAD Control 2

description:
5XFAD Control
SAMPLE 5

source_name: 5XFAD Control 2


title: Control 2

description:
Wild Type Control
SAMPLE 2

source_name: Control 2


title: 5XFAD Treated UB-ALT-EV 3

description:
5XFAD Treated
SAMPLE 9

source_name: 5XFAD Treated UB-ALT-EV 3


title: Control 1

description:
Wild Type Control
SAMPLE 1

source_name: Control 1


title: 180822_P3-180822_P4-E11-AD012

value: THp


title: 180822_P3-180822_P4-E12-AD001


title: 180822_P3-180822_P4-E11-AD010

value: P


title: Liver, sh951 (RNA-seq)

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

data_processing:
Mapping and quantification of RNA-seq reads was done with STAR aligner (v.2.7.0f) against MesAur 1.0 genome reference (gene annotation from Ensembl release 96)
Count data for all samples obtained by alignment with STAR.
Assembly: MesAur1.0
Supplementary files format and content: Count data

organism: Mesocricetus auratus

source_name: Liver

extract_protocol:
Liver was flushed with physiological salt solution, removed and snap-frozen in liquid nitrogen and stored at −80 °C.
Total RNA was extracted from liver tissue samples of three animals per hibernation phase using Nucleospin (Machery Nagel, Düren, Germany). Concentrations were measured using Nanodrop and processed for RNA sequencing (RNAseq) by NXTGNT (www.nxtgnt.com). RNA quality was checked using a Bioanalyzer RNA 6000 nano chip assay and Ribogreen assay (Invitrogen, Carlsbad, CA, USA). 437ng RNA per sample was used for further analysis. cDNA libraries were prepared for sequencing using Truseq stranded mRNA library prep (Illumina, San Diego, CA. USA) according to protocol. Sequencing was performed on a NextSeq500 High output flow cell, generating single-end 75bp reads.

treatment_protocol: All hibernating animals were kept in darkness until euthanization. Arousal was induced at > 3 days of torpor by gentle handling. The animal's activity pattern accurately identified torpor bouts of hamsters, as evidenced by mouth temperature (Tm) at euthanization, being 9.0±0.9°C and 35.0±2.1°C for TL and AE, respectively, whereas SE animals had a Tm of 35.7±0.5°C.

value: Liver

tag: sample id

tag: hibernation stage

value: arousal early

tag: hibernation stage abbr

value: AE


title: Liver, sh959 (RNA-seq)

tag: tissue


title: Liver, sh974 (RNA-seq)

value: summer euthermic

value: SE


title: 180822_P3-180822_P4-E11-AD008

tag: source

value: THl


title: Liver, sh973 (RNA-seq)


title: 180822_P3-180822_P4-E11-AD007

tag: target

value: male


title: 5XFAD Control 3

description:
5XFAD Control
SAMPLE 6

source_name: 5XFAD Control 3


title: Liver, sh931 (RNA-seq)

value: torpor late

value: TL


title: 180822_P3-180822_P4-E11-AD002

value: SSp

tag: Sex

value: female


title: Liver, sh970 (RNA-seq)


title: 180822_P3-180822_P4-E10-AD012

value: brain


title: Liver, sh939 (RNA-seq)


title: 180822_P3-180822_P4-E10-AD010


title: Liver, sh929 (RNA-seq)


title: 180822_P3-180822_P4-E10-AD004

value: THm

value: ACA


title: Liver, sh920 (RNA-seq)


title: Serum, patient 650, BRCA Mutated

city: Łódź

first: Zuzanna

last: Nowicka

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Łódź

description: QIAseq

data_processing:
All miRNA sequencing data were mapped to the reference miRNA database (miRBase version 22.1) using nf-core/smrnaseq version 1.1.0.
The sequencing protocol was set as QIAseq, Illumina or Nextflex, as appropriate for each sample. All parameters of the pipeline were kept at the default values recommended by the code authors.
After voom normalization and mean variance trend removal (model formula used for voom: ~0 + brcaStatus + havingOvaries + group), ComBat was used to combine data from all subject groups, with the UPenn group serving as reference (model formula used for ComBat: ~brcaStatus + havingOvaries)
miRNAs were filtered for species detected in at least 33% of the samples in each group at a minimum detection threshold of >=10 transcripts per million (TPM).
Assembly: Reads unmapped to miRbase were subsequently mapped to human genome GRCh38.
Supplementary files format and content: processed_raw.xlsx - spreadsheet containing raw miRNA counts of all samples
Supplementary files format and content: processed_log2tpm.xlsx -spreadsheet containing log2(TPM)-transformed miRNA counts of all samples

source_name: Serum

extract_protocol:
Libraries were prepared using NEBNEXT library generation kit (New England Biolabs Inc.) according to the manufacturer’s instructions.
Total RNA was extracted from serum using the miRCURY™ RNA isolation kit - biofluids.

value: Serum

tag: brca1/2 mutation_status

value: Mutated

tag: control type

value: Breast cancer in the future

value: Female

tag: menopausal status

value: Postmenopausal

tag: having ovaries_at_testing

value: yes

tag: platform

value: ILLUMINA


title: Serum, patient 653, BRCA Wild-type

description: QIAseq

value: Wild-type

value: Healthy

value: Premenopausal


title: Serum, patient 649, BRCA Mutated

description: QIAseq


title: Serum, patient 652, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-E10-AD006

source_name: brain


title: 180822_P3-180822_P4-E1-AD008

value: THl

value: P


title: Serum, patient 647, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-E10-AD008


title: Serum, patient 648, BRCA Mutated

description: QIAseq


title: Serum, patient 646, BRCA Mutated

description: QIAseq


title: 180822_P3-180822_P4-E1-AD012

value: THp


title: 180822_P3-180822_P4-E1-AD007

value: male


title: 180822_P3-180822_P4-E10-AD001

value: brain

value: SSp


title: Serum, patient 645, BRCA Mutated

description: QIAseq


title: Serum, patient 651, BRCA Mutated

description: QIAseq


title: Serum, patient 644, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-E1-AD001

value: THm


title: 180822_P3-180822_P4-E10-AD002

value: female


title: 180822_P3-180822_P4-E1-AD002


title: 180822_P3-180822_P4-E1-AD004

value: ACA


title: Serum, patient 643, BRCA Mutated

description: QIAseq

value: Serum

value: Mutated


title: Serum, patient 642, BRCA Mutated

description: QIAseq

value: Female


title: 180822_P3-180822_P4-D9-AD012


title: 180822_P3-180822_P4-D9-AD010


title: 180822_P3-180822_P4-E1-AD010


title: 180822_P3-180822_P4-D9-AD008


title: Serum, patient 640, BRCA Mutated

description: QIAseq

value: yes


title: Serum, patient 638, BRCA Mutated

description: QIAseq

value: ILLUMINA


title: Serum, patient 637, BRCA Mutated

description: QIAseq


title: Serum, patient 639, BRCA Mutated

description: QIAseq

value: Other cancer in the future

value: Postmenopausal


title: Serum, patient 636, BRCA Mutated

description: QIAseq

value: Healthy


title: Serum, patient 634, BRCA Mutated

description: QIAseq

value: Breast cancer in the future


title: Serum, patient 633, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-D9-AD007

value: THl

value: P


title: Serum, patient 632, BRCA Wild-type

description: QIAseq

value: Premenopausal


title: 180822_P3-180822_P4-D9-AD001

value: brain

value: SSp

value: male


title: 180822_P3-180822_P4-D9-AD006

value: THm

value: ACA

value: female


title: 180822_P3-180822_P4-D8-AD008


title: Serum, patient 631, BRCA Wild-type

description: QIAseq

value: Serum

value: Female


title: Serum, patient 630, BRCA Wild-type

description: QIAseq

value: yes

value: ILLUMINA


title: 180822_P3-180822_P4-D8-AD010

value: THp


title: 180822_P3-180822_P4-D8-AD012


title: 180822_P3-180822_P4-D8-AD006


title: 180822_P3-180822_P4-D8-AD007


title: 180822_P3-180822_P4-D8-AD002


title: Serum, patient 629, BRCA Wild-type

description: QIAseq

value: Healthy


title: 180822_P3-180822_P4-D7-AD012


title: Serum, patient 641, BRCA Mutated

description: QIAseq

value: Mutated

value: Postmenopausal


title: 180822_P3-180822_P4-D7-AD010


title: 180822_P3-180822_P4-D7-AD008

value: THl


title: Serum, patient 627, BRCA Wild-type

description: QIAseq

value: Wild-type


title: 180822_P3-180822_P4-D7-AD007

value: P


title: Serum, patient 635, BRCA Mutated

description: QIAseq

value: Breast cancer in the future

value: Premenopausal


title: 180822_P3-180822_P4-D9-AD002

value: brain

value: SSp


title: Serum, patient 626, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-D7-AD002

value: THm


title: Serum, patient 624, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-D6-AD012

value: female


title: 180822_P3-180822_P4-D7-AD001

value: male


title: Serum, patient 623, BRCA Wild-type

description: QIAseq

value: Serum

value: Female


title: Serum, patient 622, BRCA Wild-type

description: QIAseq

value: yes

value: ILLUMINA


title: 180822_P3-180822_P4-D6-AD010

value: THp


title: 180822_P3-180822_P4-D6-AD002


title: Serum, patient 620, BRCA Mutated

description: QIAseq

value: Mutated

value: Healthy


title: 180822_P3-180822_P4-D6-AD001


title: 180822_P3-180822_P4-D5-AD012


title: Serum, patient 621, BRCA Wild-type

description: QIAseq


title: Serum, patient 628, BRCA Wild-type

description: QIAseq


title: 180822_P3-180822_P4-D6-AD008

value: THl


title: 180822_P3-180822_P4-D6-AD007


title: Serum, patient 617, BRCA Mutated

description: QIAseq


title: Serum, patient 615, BRCA Mutated

description: QIAseq


title: Serum, patient 618, BRCA Mutated

description: QIAseq


title: Serum, patient 616, BRCA Wild-type

description: QIAseq

value: Wild-type