title: J1 mcSCRB/KAPAHiFi GTTCGA

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GTTCGA
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi GGGATT

status: Public on Jul 26 2018

type: SRA

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GGGATT
processed data file:
J1.KAPA_UMIcounts.txt

library_source: transcriptomic

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Human Genome (hg38) or Mouse genome (mm10) with STAR 2.5.3
Quantification was done with ENSEMBL gene models (GRCh38.84/GRCm38.75)
Genome_build: Human: hg38, Ensembl 84; Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table

molecule: polyA RNA

organism: Mus musculus

source_name: J1 embryonic stem cell

extract_protocol:
Cells were FACS sorted into lysis buffer
The Universal Human Reference RNA was obtained from Agilent (catalog number 740000).
Libraries were constructed using various developments of the SCRB-seq protocol, see sample description for more details

tag: protocol

value: mcSCRB-seq (KAPA HiFi)

tag: cell type/rna source

value: J1 embryonic stem cell


title: J1 mcSCRB/KAPAHiFi CGGTGG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: CGGTGG
processed data file:
J1.KAPA_UMIcounts.txt


title: A9_noPEG_Mouse

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
Mouse mcSCRB noPEG ACTTTA
processed data file: Species_mixing_counts.txt

molecule: total RNA

source_name: JM8 embryonic stem cell

extract_protocol:
Cells were FACS sorted into lysis buffer
Libraries were constructed using various developments of the SCRB-seq protocol, see sample description for more details

value: mcSCRB-seq without PEG

tag: tissue

value: JM8 embryonic stem cell


title: J1 mcSCRB/KAPAHiFi ATTACT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: ATTACT
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi CCCCGT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: CCCCGT
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi GGCGTC

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: GGCGTC
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi CCCACG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: CCCACG
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi CCCTGG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: CCCTGG
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi AAAGTT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: AAAGTT
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi AAGATT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: AAGATT
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi ATATAG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: ATATAG
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi ATGAAT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: ATGAAT
processed data file:
J1.KAPA_UMIcounts.txt


title: J1_ERCC_mcSCRB_TTTCTT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TTTCTT
processed data file:
J1.ERCC_UMIcounts.txt

value: mcSCRB-seq


title: J1_ERCC_mcSCRB_TTTTGA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TTTTGA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi AAATTG

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: AAATTG
processed data file:
J1.KAPA_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi ATCAAA

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: ATCAAA
processed data file:
J1.KAPA_UMIcounts.txt


title: J1_ERCC_mcSCRB_TATAGA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TATAGA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GTACCG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GTACCG
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_TTTACA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TTTACA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_TAGTAA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TAGTAA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1 mcSCRB/KAPAHiFi AAAACT

description:
Libraries were constructed with molecular crowding reverse transcription and KAPA HiFi Polymerase
barcode: AAAACT
processed data file:
J1.KAPA_UMIcounts.txt


title: J1_ERCC_mcSCRB_TACTAT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TACTAT
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_TTGAAA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TTGAAA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GCCCTC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GCCCTC
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GGTGGC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGTGGC
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GGGCAG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGGCAG
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GGGGAC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGGGAC
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GCACGG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GCACGG
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GGGTCG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGGTCG
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GCCAGG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GCCAGG
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_CGCCCT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGCCCT
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_CGAGGC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGAGGC
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_GAGCGG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GAGCGG
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_CCTGGC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CCTGGC
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_CCGTCG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CCGTCG
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_TATGAA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: TATGAA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_ATTCTA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: ATTCTA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_CAAATA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CAAATA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_ATTTCA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: ATTTCA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_ACCGGC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: ACCGGC
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_AATACA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: AATACA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_ACAATA

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: ACAATA
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_CATTAT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CATTAT
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_AATTCT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: AATTCT
processed data file:
J1.ERCC_UMIcounts.txt


title: J1_ERCC_mcSCRB_AATCTT

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: AATCTT
processed data file:
J1.ERCC_UMIcounts.txt


title: JM8_mcSCRB_48_H10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTCCCGC
processed data file:
JM8_UMIcounts.txt


title: J1_ERCC_mcSCRB_ACGGGG

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: ACGGGG
processed data file:
J1.ERCC_UMIcounts.txt


title: JM8_mcSCRB_48_H11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTCGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_H9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGTGCGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_G10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGCGAGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_G12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGCGGTC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_H8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGGTGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_G9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGCCGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_H7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGGGTCG
processed data file:
JM8_UMIcounts.txt


title: J1_ERCC_mcSCRB_CCAACC

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CCAACC
processed data file:
J1.ERCC_UMIcounts.txt


title: JM8_mcSCRB_48_G8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGCCCTC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_G7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGCCAGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_H12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTGGCCG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_F9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCGCGCA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_F10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCGCTGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_F12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCGGGCT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_F11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCGGCCA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_F7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCGAGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_E12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCAGGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_F8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCGCCCT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_E11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCACGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_E10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTAGGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_D12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCTAGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_D11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCCACAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_D10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCACCAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_E9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTAGCGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_D8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTTTTGA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_E7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTACCGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_C9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTATTGT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_C11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTCTTAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_G11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGCGCTG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_D9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTAGACCT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_D7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTTTCTT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_B11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGATAAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_B10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCTTTAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_B12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTGTAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_B9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCTATAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_B7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCAAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_B8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTCATTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_C8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTTATGAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_E8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTACGGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_A12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTATACAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_A11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTATAAAC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_A7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTAATTCT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_A9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTACTTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_H11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTCGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_A8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTACAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_H9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGTGCGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_48_A10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: CGGAGCCTAGATTA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_H8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGGTGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_H7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGGGTCG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_H10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTCCCGC
processed data file:
JM8_UMIcounts.txt


title: B_12d-2

city: Oeiras

first: Daniel

last: Simão

address: Av. República, Qta. do Marquês, Estação Agronómica Nacional, Edificio IBET/ITQB

country: Portugal

institute: iBET, Instituto de Biologia Experimental e Biológica

description: hiPSC-NSC_3D diff_processed.txt

data_processing:
The raw sequences were mapped to the Ensembl Human Genome Assembly GRCh38.p10 using StrangNGS software (http://www.strand-ngs.com/).
After mapping and counting, the data were normalized using quantile using StrandNGS.
Genome_build: Ensembl Human Genome Assembly GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Homo sapiens

source_name: Neural progenitor cells

growth_protocol: Expansion of hiPSC-NPC was performed on poly-L-ornithine-laminin (PLOL)-coated surfaces. PLOL coating was prepared by performing a 3 hour incubation at 37°C with 0.16 mg/mL solution of poly-L-ornithine in PBS (with Ca2+ and Mg2+), followed by a washing step and a 3 hour incubation at 37°C with 1 μg/mL solution of laminin in PBS (with Ca2+ and Mg2+). hiPSC-NPC were cultured in expansion medium (EM), composed of DMEM/F12 media with Glutamax (Life Technologies) supplemented with 1% N2 supplement (Life Technologies), 0.1% B27 supplement (Life Technologies), 1.6 μg/mL glucose (Sigma-Aldrich), 20 μg/mL insulin (Sigma-Aldrich), 20 ng/mL rhu-bFGF (Peprotech), 20 ng/mL rhu-EGF (Sigma-Aldrich). Cells were split typically every 4-5 days at 90-100% confluence. Cells were dislodged through incubation with 0.05% Trypsin-EDTA for 1-2 minutes. Cells were ressuspended in DMEM supplemented with 10% FBS (Life Technologies), sedimented by centrifugation and the resultant pellet ressuspended in EM. Cell concentration and viability were determined by the trypan blue exclusion method in a Fuchs-Rusenthal hemocytometer. The cell suspension was used to inoculate PLOL-coated T-flasks, at a cell density of 3 x 104 cell/cm2. A 50 % media exchange was performed at day 2 of culture. Cells were maintained under humidified atmosphere, in a multi-gas cell incubator (Sanyo), with 5 % CO2 and 3 % O2, at 37 °C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions and quantified using a NanoDrop 2000c (Thermo Scientific)
Libraries were prepared using the TruSeq RNA Sample Preparation v2 kit (Illumina).

treatment_protocol: hiPSC-NPC were expanded and dislodged with trypsin into a cell suspension, as described above. This cell suspension was passed through a 70 µm nylon strainer (Millipore) prior to bioreactor inoculation, in order to eliminate cell clumps. The obtained single cell suspension was diluted for a cell density of 4x105 cell/mL in aggregation medium (AM), with the same composition as EM, except for reduced EGF/FGF concentration (5 ng/mL) and the addition of 5 μM Y-27632. Cells were then inoculated into software-controlled stirred-tank DASGIP® Bioblock bioreactor system (Eppendorf). Culture conditions were set to maintain cells under 3 % dissolved oxygen (15 % of air with 21 % of oxygen), pH 7.4, 37 ºC and a stirring rate of 70 rpm. In order to control the aggregate size and avoid aggregate fusion, the stirring rate was gradually increased up to 90 rpm with 10 rpm steps, based on visual inspection of the culture. After 48 hours of culture, perfusion operation mode was activated, with a dilution rate of 0.33 day-1 (i.e., 33 % working volume exchange per day) under gravimetric control. To prevent the loss of aggregates through the outlet perfusion line, a metallic filter of 20 μm pore size was adopted as cell retention device. After a 7 day aggregation period with AM, differentiation was induced by replacing the perfusion medium with differentiation medium (DM), maintain the culture for further 23 days (total of 30 days). DM was prepared by supplementing DMEM/F12 with Glutamax with 2 % B27 supplement, 1.6 μg/mL glucose, 10 μg/mL insulin, 10 μg/mL putrescin, 63 ng/mL progesterone, 50 μg/mL apotransferrin, 50 ng/mL sodium selenium (all from Sigma-Aldrich) and 200 mM ascorbic acid (Wako).

tag: cell type

value: hiPSC-derived neural progenitor cells

tag: cell subtype

value: neural spheroids, day 12

tag: cell line

value: hiPSC-NPC B


title: B_30d-2

description: hiPSC-NSC_3D diff_processed.txt

value: neural spheroids, day 30


title: B_0d-2

description: hiPSC-NSC_3D diff_processed.txt

value: monolayer, day 0


title: JM8_mcSCRB_96_H6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGGGGAC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_H5

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGGGCAG
processed data file:
JM8_UMIcounts.txt


title: B_30d-1

description: hiPSC-NSC_3D diff_processed.txt


title: B_0d-1

description: hiPSC-NSC_3D diff_processed.txt


title: B_12d-1

description: hiPSC-NSC_3D diff_processed.txt


title: JM8_mcSCRB_96_H2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGGAGCC
processed data file:
JM8_UMIcounts.txt


title: A_30d-2

description: hiPSC-NSC_3D diff_processed.txt

value: hiPSC-NPC A


title: JM8_mcSCRB_96_H1

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCTCGC
processed data file:
JM8_UMIcounts.txt


title: A_30d-1

description: hiPSC-NSC_3D diff_processed.txt


title: A_0d-2

description: hiPSC-NSC_3D diff_processed.txt


title: A_0d-1

description: hiPSC-NSC_3D diff_processed.txt


title: A_12d-1

description: hiPSC-NSC_3D diff_processed.txt


title: JM8_mcSCRB_96_G11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCGCTG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCGGTC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCGAGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G5

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGAGCGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G3

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCTGCGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCCCTC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCCGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCGTGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCACGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCGGGCT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G1

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCGGTGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCGCTGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCCTGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F5

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCCGTCG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCGGCCA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCGCGCA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_H12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTGGCCG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F1

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCCCACG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCCCCGT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F4

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCCGGAC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACACGGGG
processed data file:
JM8_UMIcounts.txt


title: A_12d-2

description: hiPSC-NSC_3D diff_processed.txt


title: JM8_mcSCRB_96_E10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAGGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCACGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACACCGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGTACCG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAGCGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCCAGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGGGATT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E3

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGTTCGA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E4

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTCTGCA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_G4

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGACCGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCGAGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCTAGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCACCAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAGACCT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCCACAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_E1

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGCTAGA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D5

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTTGAAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_F3

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCCCTGG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTTTCTT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTTTTGA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTCTTAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTTTACA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTCATAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_D2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTTAATC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTATTGT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTATGAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C4

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTAATGA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C3

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTAAGAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTGATTT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTATAGA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C1

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGTTTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTAGTAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGTAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACGATAAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCTTTAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B4

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACATTACT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACATTTCA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B3

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACATGAAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCTATAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACATCAAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACCAAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A11

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACATAAAC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A8

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACACAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A10

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAGATTA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A12

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACATACAA
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A9

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACACTTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A7

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAATTCT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A3

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAAATTG
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A4

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAAGATT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A6

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAATCTT
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A5

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAATACA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_H10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATCCCGC
processed data file:
JM8_UMIcounts.txt

value: SCRB-seq (Ziegenhain et al., 2017)


title: JM8_SCRB_48_H8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGGTGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_C2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACTAAAGT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_H11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATCGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_H12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATGGCCG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_G11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGCGCTG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_H7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGGGTCG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_G12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGCGGTC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_F10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACGCTGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_F8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACGCCCT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_G10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGCGAGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_B1

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACATATAG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_G9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGCCGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_F12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACGGGCT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_F11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACGGCCA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_G7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGCCAGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_G8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGCCCTC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A2

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAAAGTT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_F7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACGAGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_mcSCRB_96_A1

description:
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
barcode: GGAGCTACAAAACT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_E12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACAGGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_E11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACACGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_H9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGTGCGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_D11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACCACAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_E7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAACCGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_D8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATTTTGA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_D10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACACCAA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_D9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAAGACCT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_D7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATTTCTT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_C12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATGATTT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_C9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATATTGT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_E10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAAGGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_C10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATCATAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_A9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAACTTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_B12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGTAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_A7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAAATTCT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_B8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACATTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_A12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAATACAA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_B11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAGATAAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_B9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACTATAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_E9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAAGCGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_A8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAACAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_B7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACAAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_E8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAACGGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_C7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATATAGA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_D12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACTAGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_A10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTAAGATTA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_H12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATGGCCG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_H6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGGGGAC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_H3

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGGCCAC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGCGGTC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_F9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTACGCGCA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_H2

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGGAGCC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGCCCTC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGCGAGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_48_C8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: ACTCGCTATATGAA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGCGCTG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGCCGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G5

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGAGCGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G4

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGACCGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_H11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATCGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G3

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACTGCGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G2

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACGTGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACGCCCT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACGCTGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACGGGCT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G1

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACGGTGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACGGCCA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACGCGCA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACCTGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F2

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACCCCGT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F5

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACCGTCG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F1

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACCCACG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_F4

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACCGGAC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_G6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGCACGG
processed data file:
JM8_UMIcounts.txt


title: PCL2plus_Ter119plus_PCL2

city: Ottawa

first: William

last: Stanford

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

library_source: genomic

data_processing:
Bowtie v2.2.3 and MACS 1.3.7 were used for alignments and peak calling, respectively.
Genome_build: mm9
Supplementary_files_format_and_content: Bowtie generated alignments and MACS generated peak calling files for ChIPSeq data

molecule: genomic DNA

source_name: embryonic fetal liver

growth_protocol: Gene targeted mouse C57Bl/6 ES cells were obtained through EUCOMM and were aggregated with CD1 blastocysts to form chimeras.

extract_protocol:
FL cells from e14.5 Pcl2+/+ and Pcl2-/- mice were isolated and CD71+Ter119-/lo and CD71+Ter119high fractions were sorted using a MoFlo sorter
For ChIP-seq, sorted cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Samples were sheared using a Covaris sonicator until DNA reached a final size of 75-700bp. 10ug of antibody (anti-Pcl2, Genway; anti-H3K27me3, Millipore) was bound to pre-blocked Protein A magnetic beads (Millipore), combined with sonicated DNA and incubated overnight.  After incubation, beads were collected and DNA-antibody complexes were eluted at 65oC.  Crosslinks were reversed overnight at 65oC. Samples were treated with Proteinase K and RNase A and DNA was purified using phenol-chloroform. 500,000 cells per sample were used for both IP and control (IgG, SantaCruz).

tag: strain background

tag: genotype/variation

value: WT

tag: developmental stage

tag: tissue source

value: embryonic fetal liver

tag: sorted fraction

value: Ter119plus; CD71+Ter119high

tag: chip antibody

value: Pcl2 (also known as Mtf2/M96) antibody

tag: chip antibody vendor

value: GenwayGWB

tag: chip antibody cat.#

tag: chip antibody lot #


title: JM8_SCRB_96_E11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACACGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAGGGGC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAGCGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E5

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACCAACC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGTACCG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAACGGGG
processed data file:
JM8_UMIcounts.txt


title: PCL2plus_Ter119neg_IgG

value: Ter119minus; CD71+Ter119-/lo

value: Rabbit IgG

value: Santa Cruz


title: PCL2plus_Ter119plus_H3K27me3

value: H3K27me3 Antibody

value: Millipore


title: PCL2minus_Ter119plus_IgG


title: PCL2plus_Ter119neg_H3K27me3


title: PCL2plus_Ter119neg_PCL2


title: JM8_SCRB_96_E3

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGTTCGA
processed data file:
JM8_UMIcounts.txt

value: JM8 embryonic stem cell


title: JM8_SCRB_96_D12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACTAGTG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_D11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACCACAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_D10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACACCAA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E2

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGGGATT
processed data file:
JM8_UMIcounts.txt


title: PCL2plus_Ter119plus_IgG


title: JM8_SCRB_96_D8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATTTTGA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_D6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATTTACA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_D5

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATTGAAA
processed data file:
JM8_UMIcounts.txt


title: PCL2minus_Ter119plus_H3K27me3


title: PCL2minus_Ter119neg_H3K27me3


title: 548Bminus-Ter119minus

description: processed data files: 548B_Ter119+-gene_exp.diff; 560I548B_Ter119-gene_exp.diff

data_processing:
TopHat v1.4.1 and Cuffdiff v1.3.0 (73) were used to map reads to mm9 and determine expression differences against the Ensembl release 67 gene model. Significant fold changes were determined using Benjamini-Hochberg corrected p value of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: cuffdif v1.3.0 (73) output files

growth_protocol: Gene targeted mouse C57Bl/6 ES cells were obtained through EUCOMM and were aggregated with CD1 blastocysts to form chimeras. Germline transmission was confirmed using PCR-based genotyping (primers listed in Table S1) and all future breeding was done on the C57Bl6/J strain to maintain this background.

extract_protocol:
FL cells from e14.5 Pcl2+/+ and Pcl2-/- mice were isolated and CD71+Ter119-/lo and CD71+Ter119high fractions were sorted using a MoFlo sorter
RNA was isolated (Arcturus PicoPure Kit, LifeTech) and rDNase treated (Qiagen). Quality of RNA was determined using a Bioanalyzer. Library preparation was performed using 150ng of high-quality RNA (TruSeq Library Prep Kit, Illumina)

value: Pcl -/-

value: fetal liver


title: 560Iplus-Ter119minus

description: processed data files: 560I_Ter119+-gene_exp.diff; 560I548B_Ter119-gene_exp.diff


title: 548Bminus-Ter119plus

description: processed data files: 548B_Ter119+-gene_exp.diff; 560I548B_Ter119+gene_exp.diff


title: JM8_SCRB_96_D3

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATTAGTT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACAGGGG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_D1

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATGTTTA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_C11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATCTTAA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_C9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATATTGT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_C8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATATGAA
processed data file:
JM8_UMIcounts.txt


title: PCL2minus_Ter119neg_IgG


title: JM8_SCRB_96_C7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATATAGA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_E1

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGCTAGA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_C6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATAGTAA
processed data file:
JM8_UMIcounts.txt


title: 560Iplus-Ter119plus

description: processed data files: 560I_Ter119+-gene_exp.diff; 560I548B_Ter119+gene_exp.diff


title: JM8_SCRB_96_B11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGATAAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACTTTAA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACTATAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACAAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAATTTCA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B5

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAATTCTA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B4

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAATTACT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A7

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAATTCT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAACAATA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A11

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAATAAAC
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B2

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAATCAAA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B1

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAATATAG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A9

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAACTTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_B3

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAATGAAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_C10

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATCATAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A5

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAATACA
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A6

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAATCTT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A4

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAAGATT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_C1

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGTTTAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A3

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAAATTG
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_C3

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATAAGAT
processed data file:
JM8_UMIcounts.txt


title: JM8_SCRB_96_A2

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAAAAGTT
processed data file:
JM8_UMIcounts.txt


title: WT2_kidney_1

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

country: China

institute: Institute of Zoology,CAS

data_processing:
Basecalls performed by Casava using default settings
The clean reads were mapped to the macFas5 genome and assembled using HISAT, version 0.1.6-beta.
Each read with a unique genomic location in the bam format was retained for a gene expression calculation using Cufflinks (version 2.0.2) with the option “--GTF”.
The gene annotation was downloaded from NCBI (GCF_000364345.1), and only exon annotation for mRNA and other ncRNAs were used .
Genes with at least 1 FPKM (Fragments Per Kilobase of exon per Million fragments mapped) in at least one sample were used for the differentially expressed gene analyses
Genome_build: macFas5
Supplementary_files_format_and_content: FPKM files estimated by Cufflinks

organism: Macaca fascicularis

growth_protocol: The tissue samples of cynomolgus monkeys (Macaca fascicularis)at a gestation period of 2, 4 month of embryonic monkey and newborn stage.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Monkey tissues were homogenized in liquid nitrogen, then RNA were extracted using TRIzol reagent protocol, and purified using RNeasy Mini Kit (Qiagen) according to the manuals. After quantification of RNA by Fragment Analyzer (Advanced Analytical), 1.5 μg of total RNA was used to construct sequencing libraries by TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s standard protocol. The libraries were sequenced on the HiSeq X Ten platform.

tag: Stage

value: Newborn

value: kidney

tag: genotype

value: wild-type


title: WT3_kidney_1


title: WT3_kidney_2


title: WT2_kidney_2


title: JM8_SCRB_96_B8

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGACATTAT
processed data file:
JM8_UMIcounts.txt

tag: protocol

value: SCRB-seq (Ziegenhain et al., 2017)


title: KO3_kidney_2

value: SIRT6 mutant


title: KO2_kidney_2


title: KO3_kidney_1


title: KO2_kidney_1


title: WT3_lung_2

value: lung


title: WT3_lung_1


title: WT2_lung_2


title: WT2_lung_1


title: KO3_lung_1


title: WT3_heart_1

value: heart


title: WT3_heart_2


title: KO2_lung_2


title: KO2_lung_1


title: WT2_heart_2


title: WT2_heart_1


title: KO3_heart_1


title: KO3_heart_2


title: KO2_heart_2


title: KO2_heart_1


title: WT3_liver_1

value: liver


title: WT2_liver_1


title: WT2_liver_2


title: KO2_liver_2


title: WT3_liver_2


title: KO3_liver_1


title: KO2_liver_1


title: WT3_thymus_2

value: thymus


title: KO3_lung_2


title: KO3_liver_2


title: KO3_thymus_1


title: WT2_thymus_1


title: WT3_thymus_1


title: WT2_thymus_2


title: KO2_thymus_1


title: KO2_thymus_2


title: WT3_brain_2

value: brain


title: WT2_brain_2


title: KO3_brain_2


title: KO2_brain_2


title: KO2_brain_1


title: WT3_brain_1


title: KO3_brain_1


title: WT2_muscle_2

value: muscle


title: WT3_muscle_1


title: WT3_muscle_2


title: KO3_thymus_2


title: T4M_brain_2

value: Gestation period of 4 month


title: WT2_muscle_1


title: KO3_muscle_1


title: T4M_brain_1


title: KO2_muscle_2


title: T2M_brain_2

value: Gestation period of 2 month


title: T4M_muscle_2


title: T4M_muscle_1


title: T2M_brain_1


title: WT2_brain_1


title: JM8_SCRB_96_H4

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGAGGCGTC
processed data file:
JM8_UMIcounts.txt

tag: cell type/rna source


title: T2M_muscle_2

tag: tissue


title: T2M_muscle_1


title: 3WL_fatbody_ORC2_Rep2

status: Public on Jul 25 2018

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

address: 455 Main Street

country: USA

institute: Whitehead Institute

description:
Male OrR late-third wandering larval fat body ORC2 ChIP
3WL_fatbody_ORC2_Rep2
Processed data file: 3WL_ORC2_IDR_peaks.bed
Processed data file: 3WL_ORC2_all_peaks_Rep1_Rep2_merge.bed

data_processing:
Reads were mapped using Bowtie2 with "-L 22" and other default settings.
Peaks were called using MACS2, with sample inputs as controls and "--nomodel", setting "--extsize" based on Phantompeakqualtools' cross-correlation analysis.
High confidence peaks were called between biological replicates using an irreproducibility discovery rate (IDR) threshold of 0.1.
Peaks within 1 kb were treated as overlapping.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: *ORC2_all_peaks_Rep1_Rep2_merge.bed: BED file with the chromosomal locations of each peak called by MACS2 with peaks from biological replicates merged.
Supplementary_files_format_and_content: *ORC2_IDR_peaks.bed: BED file with the chromosomal locations of each peak called by the IDR method.

organism: Drosophila melanogaster

source_name: Male OrR late-third wandering larval fat body tissue, ORC2 ChIP

growth_protocol: OregonR flies were raised on standard cornmeal, molasses, and agar media at 25C.

extract_protocol:
Fat body tissue was dounced homogenized and then sonicated using a Bioruptor 300 (Diagenode) prior to ChIP with anti-ORC2 antibody.
Libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (Part # E7645S) according to manufacturer's recommendations with indexing primers for multiplexing.

treatment_protocol: Embryos were collected for 1hr and aged at 25C. Male larvae were picked 67-68hrs and 91-92hrs after egg laying in addition to male third-wandering larvae until 60-120 larvae were collected for each developmental stage. Whole larvae were dissected in Ephrussi-Beadle Ringer solution and fixed in 2% formaldehyde. Fat body tissue was isolated by hand dissection and testes were removed.

tag: strain/background

value: OregonR

tag: Sex

value: male

value: fat body

value: Late-third wandering larvae

value: anti-ORC2 (Steve Bell lab, MIT)


title: 92hr_fatbody_Input_Rep2

description:
Male OrR 92hr AEL larval fat body input
92hr_fatbody_Input_Rep2

source_name: Male OrR 92hr AEL larval fat body tissue, input

value: 92hr after egg laying (AEL) - Mid-3rd instar larvae


title: 3WL_fatbody_ORC2_Rep1

description:
Male OrR late-third wandering larval fat body ORC2 ChIP
3WL_fatbody_ORC2_Rep1
Processed data file: 3WL_ORC2_IDR_peaks.bed
Processed data file: 3WL_ORC2_all_peaks_Rep1_Rep2_merge.bed

value: wild-type


title: 92hr_fatbody_ORC2_Rep2

description:
Male OrR 92hr AEL larval fat body ORC2 ChIP
92hr_fatbody_ORC2_Rep2
Processed data file: 92hr_ORC2_IDR_peaks.bed
Processed data file: 92hr_ORC2_all_peaks_Rep1_Rep2_merge.bed

source_name: Male OrR 92hr AEL larval fat body tissue, ORC2 ChIP


title: 3WL_fatbody_Input_Rep2

description:
Male OrR late-third wandering larval fat body input
3WL_fatbody_Input_Rep2

source_name: Male OrR late-third wandering larval fat body tissue, input


title: 3WL_fatbody_Input_Rep1

description:
Male OrR late-third wandering larval fat body input
3WL_fatbody_Input_Rep1


title: 92hr_fatbody_ORC2_Rep1

description:
Male OrR 92hr AEL larval fat body ORC2 ChIP
92hr_fatbody_ORC2_Rep1
Processed data file: 92hr_ORC2_IDR_peaks.bed
Processed data file: 92hr_ORC2_all_peaks_Rep1_Rep2_merge.bed


title: 68hr_fatbody_ORC2_Rep2

description:
Male OrR 68hr AEL larval fat body ORC2 ChIP
68hr_fatbody_ORC2_Rep2
Processed data file: 68hr_ORC2_IDR_peaks.bed
Processed data file: 68hr_ORC2_all_peaks_Rep1_Rep2_merge.bed

source_name: Male OrR 68hr AEL larval fat body tissue, ORC2 ChIP

value: 68hr after egg laying (AEL) - Mid-2nd instar larvae


title: 68hr_fatbody_Input_Rep2

description:
Male OrR 68hr AEL larval fat body input
68hr_fatbody_Input_Rep2

source_name: Male OrR 68hr AEL larval fat body tissue, input


title: 68hr_fatbody_ORC2_Rep1

description:
Male OrR 68hr AEL larval fat body ORC2 ChIP
68hr_fatbody_ORC2_Rep1
Processed data file: 68hr_ORC2_IDR_peaks.bed
Processed data file: 68hr_ORC2_all_peaks_Rep1_Rep2_merge.bed


title: 68hr_fatbody_Input_Rep1

description:
Male OrR 68hr AEL larval fat body input
68hr_fatbody_Input_Rep1


title: 92hr_fatbody_mRNA_Rep2

description:
Male OrR 92hr AEL larval fat body mRNA-seq
92hr_fatbody_mRNA_Rep2
cDNA

data_processing:
Reads were mapped using TopHat with default settings.
FPKM values were calculated using Cufflinks.
Biological replicates were summarized by taking the mean value for the two FPKM values for each transcript.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *.fkpm_tracking.txt: Tab-delimited text files include FPKM values.

source_name: Male OrR 92hr AEL larval fat body tissue

extract_protocol:
Total mRNA was extracted in Trizol and mRNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Part# E7490S).
Libraries were constructed using the NEBNext mRNA Library Prep Reagent Set for Illumina (Part# E6100S).

treatment_protocol: Embryos were collected for 1hr and aged at 25C. Male larvae were picked 67-68hrs and 91-92hrs after egg laying in addition to male third-wandering larvae until 30 larvae were collected for each developmental stage. Whole larvae were dissected in Ephrussi-Beadle Ringer solution and fixed in 2% formaldehyde. Fat body tissue was isolated by hand dissection and testes were removed.


title: KO2_muscle_1

value: Newborn

value: SIRT6 mutant


title: KO3_muscle_2


title: 92hr_fatbody_mRNA_Rep1

description:
Male OrR 92hr AEL larval fat body mRNA-seq
92hr_fatbody_mRNA_Rep1
cDNA


title: MOC2

city: Malaga

first: Alejandro

last: Labella

state: Malaga

address: Boulevard Louis Pasteur campus teatinos Faculty of Sciences

department: Microbiology

country: Spain

institute: University of Malaga

description:
Processed data file: MOC_allgenes_edgeR.txt
Processed data file: MOC_Normalized_counts_edgeR.txt
Processed data file: MOC_DEgenes_edgeR.txt

data_processing:
RNA-Seq was performed using the Illumina HiSeq™ 2000 platform. Stranded mRNA-Seq application was selected obtaining >40 million paired-ended (PE) reads per sample with 2 x 75 bp reads length.
Pre-processing of raw reads was performed using SeqtrimNEXT (v2.0.60).
For the mapping and assembly of pre-processed FASTQ reads, we used the script Bowtie2 (v2.2.9) using reference transcriptome (Solea senegalensis v.4.1 2014-01-23).
To convert SAM mapping results to reference sequence counts, the script sam2counts (v20131126) was used.
Bioconductor project tools (EdgeR, DESeq2, and limma) were used for the analysis and comprehension of high-throughput transcriptomic data.
Genome_build: Solea senegalensis v.4.1 2014-01-23 (SoleaDB: http://www.juntadeandalucia.es/agriculturaypesca/ifapa/soleadb_ifapa/assemblies/46?tab=inf)
Supplementary_files_format_and_content: *_edgeR.txt: Tab-delimited text files include abundance measurements.

organism: Solea senegalensis

source_name: Eye-brain, mutant reassortant strain

extract_protocol:
Organs were removed, flash frozen on liquid nitrogen and then passed to -80 ºC. RNA was harvested combining Trizol reagent and Qiagen RNeasy mini kit.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.

tag: experimental group

value: Eye-brain

tag: infection

value: Betanodaviruses mutant reassortant strain


title: MOC1


title: L15OC3

description:
Processed data file: VOC_allgenes_edgeR.txt
Processed data file: VOC_Normalized_counts_edgeR.txt
Processed data file: VOC_DEgenes_edgeR.txt
Processed data file: MOC_allgenes_edgeR.txt
Processed data file: MOC_Normalized_counts_edgeR.txt
Processed data file: MOC_DEgenes_edgeR.txt

source_name: Eye-brain, control

value: L15-Leivobitz medium


title: VOC1

description:
Processed data file: VOC_allgenes_edgeR.txt
Processed data file: VOC_Normalized_counts_edgeR.txt
Processed data file: VOC_DEgenes_edgeR.txt

source_name: Eye-brain, wild reassortant strain

value: Betanodavirus wild reassortant strain


title: VOC2


title: VOC3


title: MOC3


title: 68hr_fatbody_mRNA_Rep1

description:
Male OrR 68hr AEL larval fat body mRNA-seq
68hr_fatbody_mRNA_Rep1
cDNA

source_name: Male OrR 68hr AEL larval fat body tissue

tag: genotype/variation


title: 68hr_fatbody_mRNA_Rep2

description:
Male OrR 68hr AEL larval fat body mRNA-seq
68hr_fatbody_mRNA_Rep2
cDNA

tag: developmental stage


title: L15OC2


title: L15OC1


title: 92hr_fatbody_Input_Rep1

description:
Male OrR 92hr AEL larval fat body input
92hr_fatbody_Input_Rep1


title: MR3

description:
Processed data file: MR_allgenes_edgeR.txt
Processed data file: MR_Normalized_counts_edgeR.txt
Processed data file: MR_DEgenes_edgeR.txt

source_name: Head-Kidney, mutant reassortant strain

value: Head-Kidney


title: MR1


title: MR2


title: L15R3

description:
Processed data file: VR_allgenes_edgeR.txt
Processed data file: VR_Normalized_counts_edgeR.txt
Processed data file: VR_DEgenes_edgeR.txt
Processed data file: MR_allgenes_edgeR.txt
Processed data file: MR_Normalized_counts_edgeR.txt
Processed data file: MR_DEgenes_edgeR.txt

source_name: Head-Kidney, control


title: VR2

description:
Processed data file: VR_allgenes_edgeR.txt
Processed data file: VR_Normalized_counts_edgeR.txt
Processed data file: VR_DEgenes_edgeR.txt

source_name: Head-Kidney, wild reassortant strain


title: VR1


title: L15R2


title: VR3


title: L15R1


title: HE8W_STR1_sc90

status: Public on Jul 24 2018

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

description: mRNA with polyA tail

data_processing:
For data from Illumina, Illumina CASAVA version 1.8 were used to the basecalling
Read 2 was used to obtain the cell barcodes to further split the reads according to the cell IDs (barcode) and the same time recorded the UMI sequences
Read 1 was picked in each cell and these raw reads were trimmed to remove TSO or polyA sequence
Adaptor contamination and low-quality reads were discarded from the trimmed Read 1 raw data
TopHat(version 2.0.14) with default settings were used for sequence alignment and uniquely mapped reads were kept.
Genome_build: Reference sequence and transcript annotation files were from UCSC genome assembly hg19
Supplementary_files_format_and_content: TPM (transcripts-per-million mapped reads) data was calculated as the total UMIs for a genes to be divided by the sum of UMIs from each cell and then multiply by 1,000,000

source_name: Stromal cell of Week 8

extract_protocol:
Chrion were scraped from human  placenta and the remaining villi were collected and minced into small pieces. The tissue were digested with an enzyme cocktail (0.125% trypsin 0.04% Dnase and 0.05% type Ⅳcollagenase) for 8 min twice at 37 ℃. Cell suspension were collected by filtering the ezyme mixture with 70 μm cell strainer and the enzyme reaction were stopped by addition of 5% DMEM. cells were centrifuged at 1200 g at 4 ℃ on a percoll gradient (7 layers: 10%, 20%, 30%, 40%, 50%, 60% and 70%) and cells from 30% - 50% percoll gradient were collected and washed with DMEM. EVT and CTB were sorted with MACS with PE-conjucted HLA-G and CDH1 antibody combined with anti-PE beads,STB were purified with mouth pipette based on their big size from the cell population and the remaning HLA-G and CDH1 double negative cells were stromal cells. For isolation of EVT from the basal plate of the 24 w placenta, basal plate were scaped from the placenta, minced and  digested with the method as described above,finally 24 w EVT were purified by MACs with HLA-G antibody.
the single cells were picked into 2ul cell lysis buffer using mouse pipet, then the transcriptome was amplified by modified smart-seq2 protocol which added in barcode for each cell. the amplified cDNAs were sheared into 300bp  fragments, the 3' end of the cDNAs were enriched to build library with KAPA Hyper Prep Kits for Illumina

treatment_protocol: human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h

tag: cell type

value: Stromal cell

tag: cell population

value: Week 8


title: HE8W_STR1_sc87

description: mRNA with polyA tail


title: HE8W_STR1_sc85

description: mRNA with polyA tail


title: HE8W_STR1_sc89

description: mRNA with polyA tail


title: HE8W_STR1_sc88

description: mRNA with polyA tail


title: HE8W_STR1_sc9

description: mRNA with polyA tail


title: HE8W_STR1_sc84

description: mRNA with polyA tail


title: HE8W_STR1_sc86

description: mRNA with polyA tail


title: HE8W_STR1_sc83

description: mRNA with polyA tail


title: HE8W_STR1_sc82

description: mRNA with polyA tail


title: HE8W_STR1_sc80

description: mRNA with polyA tail


title: HE8W_STR1_sc81

description: mRNA with polyA tail


title: HE8W_STR1_sc8

description: mRNA with polyA tail


title: HE8W_STR1_sc79

description: mRNA with polyA tail


title: HE8W_STR1_sc78

description: mRNA with polyA tail


title: HE8W_STR1_sc76

description: mRNA with polyA tail


title: HE8W_STR1_sc77

description: mRNA with polyA tail


title: HE8W_STR1_sc73

description: mRNA with polyA tail


title: HE8W_STR1_sc74

description: mRNA with polyA tail


title: HE8W_STR1_sc72

description: mRNA with polyA tail


title: HE8W_STR1_sc75

description: mRNA with polyA tail


title: HE8W_STR1_sc7

description: mRNA with polyA tail


title: HE8W_STR1_sc69

description: mRNA with polyA tail


title: HE8W_STR1_sc70

description: mRNA with polyA tail


title: HE8W_STR1_sc65

description: mRNA with polyA tail


title: HE8W_STR1_sc64

description: mRNA with polyA tail


title: HE8W_STR1_sc61

description: mRNA with polyA tail


title: HE8W_STR1_sc62

description: mRNA with polyA tail


title: HE8W_STR1_sc63

description: mRNA with polyA tail


title: HE8W_STR1_sc60

description: mRNA with polyA tail


title: HE8W_STR1_sc6

description: mRNA with polyA tail


title: HE8W_STR1_sc59

description: mRNA with polyA tail


title: HE8W_STR1_sc58

description: mRNA with polyA tail


title: HE8W_STR1_sc57

description: mRNA with polyA tail


title: HE8W_STR1_sc56

description: mRNA with polyA tail


title: HE8W_STR1_sc54

description: mRNA with polyA tail


title: HE8W_STR1_sc55

description: mRNA with polyA tail


title: HE8W_STR1_sc50

description: mRNA with polyA tail


title: HE8W_STR1_sc52

description: mRNA with polyA tail


title: HE8W_STR1_sc71

description: mRNA with polyA tail


title: HE8W_STR1_sc51

description: mRNA with polyA tail


title: HE8W_STR1_sc53

description: mRNA with polyA tail


title: HE8W_STR1_sc5

description: mRNA with polyA tail


title: HE8W_STR1_sc67

description: mRNA with polyA tail


title: HE8W_STR1_sc46

description: mRNA with polyA tail


title: HE8W_STR1_sc47

description: mRNA with polyA tail


title: HE8W_STR1_sc48

description: mRNA with polyA tail


title: HE8W_STR1_sc49

description: mRNA with polyA tail


title: HE8W_STR1_sc44

description: mRNA with polyA tail


title: HE8W_STR1_sc45

description: mRNA with polyA tail


title: HE8W_STR1_sc43

description: mRNA with polyA tail


title: HE8W_STR1_sc66

description: mRNA with polyA tail


title: HE8W_STR1_sc68

description: mRNA with polyA tail


title: HE8W_STR1_sc42

description: mRNA with polyA tail


title: HE8W_STR1_sc40

description: mRNA with polyA tail


title: HE8W_STR1_sc41

description: mRNA with polyA tail


title: HE8W_STR1_sc4

description: mRNA with polyA tail


title: HE8W_STR1_sc38

description: mRNA with polyA tail


title: 8hpf_wt_Plate4.1

city: mainz

first: lucas

last: kaaij

address: ackermannweg 4

department: RNA silencing

institute: IMB

data_processing:
After sequencing, read 1 was aligned to the Zv9 ensemblezebrafish transcriptome downloaded from the UCSC genome browser (Meyer et al., 2013, Junker et al 2015) using bwa (Li and Durbin, 2010) with default parameters. Read 2 contains a barcode identifying the sample from which the read originated. CEL-seq only sequences the most 3’ prime end of a transcript and generates one read per transcript.
Genome_build: zv9
Supplementary_files_format_and_content: The sc_fdata file contains all cells (at least 1100 transcripts) en transcripts that pass the filtering criteria. Transcripts are normalized by downsampling.

organism: Danio rerio

source_name: Germ cells

growth_protocol: Zebrafish were maintained under standard conditions.

extract_protocol:
mRNA was extracted from single cells by Trizol extraction
The RNA was extracted using chloroform and precipitated with iso-propanol. The RNA-pellet was then processed using the CEL-seq protocol (Hashimshony et al., 2012) and sequenced on an Illumina Nextseq using 75bp paired end sequencing.

tag: cell line

value: Primary cells

value: wildtype

value: CEL-seq (Hashimshony et al., Cell reports 2012)


title: HE8W_STR1_sc37

description: mRNA with polyA tail


title: 8hpf_wt_Plate3.1


title: HE8W_STR1_sc36

description: mRNA with polyA tail


title: 8hpf_wt_Plate2.1


title: 8hpf_wt_Plate1.1


title: 8hpf_Tdrd6a-:-_Plate4.1


title: 8hpf_Tdrd6a-:-_Plate2.1


title: HE8W_STR1_sc31

description: mRNA with polyA tail


title: 8hpf_Tdrd6a-:-_Plate3.1


title: HE8W_STR1_sc3

description: mRNA with polyA tail


title: HE8W_STR1_sc33

description: mRNA with polyA tail


title: HE8W_STR1_sc30

description: mRNA with polyA tail


title: HE8W_STR1_sc35

description: mRNA with polyA tail


title: HE8W_STR1_sc32

description: mRNA with polyA tail


title: 3.5hpf_wt_Plate5.1


title: 3.5hpf_wt_Plate4.1


title: HE8W_STR1_sc29

description: mRNA with polyA tail


title: HE8W_STR1_sc28

description: mRNA with polyA tail


title: 8hpf_Tdrd6a-:-_Plate1.1


title: HE8W_STR1_sc27

description: mRNA with polyA tail


title: 3.5hpf_wt_Plate3.1


title: HE8W_STR1_sc39

description: mRNA with polyA tail


title: HE8W_STR1_sc26

description: mRNA with polyA tail


title: 3.5hpf_wt_Plate2.1


title: 3.5hpf_Tdrd6a-:-_Plate5.1


title: 3.5hpf_Tdrd6a-:-_Plate4.1


title: HE8W_STR1_sc22

description: mRNA with polyA tail


title: 3.5hpf_Tdrd6a-:-_Plate3.1


title: 8and24hpf_wt_Plate1.1


title: 3.5hpf_Tdrd6a-:-_Plate2.1


title: HE8W_STR1_sc21

description: mRNA with polyA tail


title: HE8W_STR1_sc2

description: mRNA with polyA tail


title: 3.5hpf_Tdrd6a-:-_Plate1.1


title: HE8W_STR1_sc17

description: mRNA with polyA tail


title: 2wpf_wt_1


title: HE8W_STR1_sc20

description: mRNA with polyA tail


title: HE8W_STR1_sc18

description: mRNA with polyA tail


title: 24hpf_wt_Plate3.1


title: HE8W_STR1_sc19

description: mRNA with polyA tail


title: 24hpf_wt_Plate5.1


title: 3.5hpf_wt_Plate1.1


title: 24hpf_wt_Plate1.1


title: HE8W_STR1_sc25

description: mRNA with polyA tail


title: 24hpf_wt_Plate4.1


title: HE8W_STR1_sc14

description: mRNA with polyA tail


title: 24hpf_Tdrd6a-:-_Plate3.1


title: HE8W_STR1_sc16

description: mRNA with polyA tail


title: HE8W_STR1_sc12

description: mRNA with polyA tail


title: HE8W_STR1_sc15

description: mRNA with polyA tail


title: 24hpf_Tdrd6a-:-_Plate2.1


title: HE8W_STR1_sc24

description: mRNA with polyA tail


title: 24hpf_Tdrd6a-:-_Plate1.1


title: HE8W_STR1_sc13

description: mRNA with polyA tail


title: HE8W_STR1_sc1

description: mRNA with polyA tail


title: HE8W_STR1_sc10

description: mRNA with polyA tail


title: HE8W_STR1_sc11

description: mRNA with polyA tail


title: HE8W_EVT4_sc9

description: mRNA with polyA tail

source_name: Extravillous trophoblast of Week 8

value: Extravillous trophoblast

value: HLA-G+


title: HE8W_EVT4_sc90

description: mRNA with polyA tail


title: 24hpf_wt_Plate2.1


title: HE8W_EVT4_sc88

description: mRNA with polyA tail


title: HE8W_EVT4_sc89

description: mRNA with polyA tail


title: HE8W_EVT4_sc87

description: mRNA with polyA tail


title: HE8W_EVT4_sc86

description: mRNA with polyA tail


title: HE8W_EVT4_sc84

description: mRNA with polyA tail


title: HE8W_EVT4_sc85

description: mRNA with polyA tail


title: HE8W_EVT4_sc83

description: mRNA with polyA tail


title: HE8W_EVT4_sc82

description: mRNA with polyA tail


title: HE8W_EVT4_sc81

description: mRNA with polyA tail


title: HE8W_EVT4_sc79

description: mRNA with polyA tail


title: HE8W_EVT4_sc80

description: mRNA with polyA tail


title: HE8W_EVT4_sc75

description: mRNA with polyA tail


title: HE8W_EVT4_sc76

description: mRNA with polyA tail


title: HE8W_EVT4_sc78

description: mRNA with polyA tail


title: HE8W_EVT4_sc73

description: mRNA with polyA tail


title: HE8W_EVT4_sc7

description: mRNA with polyA tail


title: HE8W_EVT4_sc69

description: mRNA with polyA tail


title: HE8W_EVT4_sc70

description: mRNA with polyA tail


title: HE8W_EVT4_sc68

description: mRNA with polyA tail


title: HE8W_EVT4_sc71

description: mRNA with polyA tail


title: HE8W_EVT4_sc67

description: mRNA with polyA tail


title: HE8W_EVT4_sc65

description: mRNA with polyA tail


title: HE8W_EVT4_sc66

description: mRNA with polyA tail


title: HE8W_EVT4_sc6

description: mRNA with polyA tail


title: HE8W_EVT4_sc62

description: mRNA with polyA tail


title: HE8W_EVT4_sc63

description: mRNA with polyA tail


title: HE8W_EVT4_sc61

description: mRNA with polyA tail


title: JM8_SCRB_96_C12

description:
Libraries were constructed using the SCRB-seq protocol using KAPA HiFi Polymerase (see Ziegenhain et al., 2017)
barcode: GCTCATGATGATTT
processed data file:
JM8_UMIcounts.txt

source_name: JM8 embryonic stem cell

value: SCRB-seq (Ziegenhain et al., 2017)

value: JM8 embryonic stem cell


title: HE8W_EVT4_sc8

description: mRNA with polyA tail


title: HE8W_EVT4_sc60

description: mRNA with polyA tail


title: HE8W_EVT4_sc74

description: mRNA with polyA tail


title: HE8W_EVT4_sc72

description: mRNA with polyA tail


title: HE8W_EVT4_sc58

description: mRNA with polyA tail


title: HE8W_EVT4_sc57

description: mRNA with polyA tail


title: HE8W_EVT4_sc56

description: mRNA with polyA tail


title: HE8W_EVT4_sc54

description: mRNA with polyA tail


title: HE8W_EVT4_sc59

description: mRNA with polyA tail


title: HE8W_EVT4_sc77

description: mRNA with polyA tail


title: HE8W_EVT4_sc55

description: mRNA with polyA tail


title: HE8W_EVT4_sc52

description: mRNA with polyA tail


title: HE8W_EVT4_sc51

description: mRNA with polyA tail


title: HE8W_EVT4_sc5

description: mRNA with polyA tail


title: HE8W_EVT4_sc64

description: mRNA with polyA tail


title: HE8W_EVT4_sc47

description: mRNA with polyA tail


title: HE8W_EVT4_sc45

description: mRNA with polyA tail


title: HE8W_EVT4_sc48

description: mRNA with polyA tail


title: HE8W_EVT4_sc46

description: mRNA with polyA tail


title: HE8W_EVT4_sc53

description: mRNA with polyA tail


title: HE8W_EVT4_sc49

description: mRNA with polyA tail


title: HE8W_EVT4_sc50

description: mRNA with polyA tail


title: HE8W_EVT4_sc41

description: mRNA with polyA tail


title: HE8W_EVT4_sc43

description: mRNA with polyA tail


title: HE8W_EVT4_sc4

description: mRNA with polyA tail


title: HE8W_EVT4_sc39

description: mRNA with polyA tail


title: HE8W_EVT4_sc42

description: mRNA with polyA tail


title: HE8W_EVT4_sc40

description: mRNA with polyA tail


title: HE8W_EVT4_sc38

description: mRNA with polyA tail


title: HE8W_EVT4_sc37

description: mRNA with polyA tail


title: HE8W_EVT4_sc32

description: mRNA with polyA tail


title: HE8W_EVT4_sc3

description: mRNA with polyA tail


title: HE8W_EVT4_sc35

description: mRNA with polyA tail


title: HE8W_EVT4_sc30

description: mRNA with polyA tail


title: HE8W_EVT4_sc31

description: mRNA with polyA tail


title: HE8W_EVT4_sc28

description: mRNA with polyA tail


title: HE8W_EVT4_sc29

description: mRNA with polyA tail


title: HE8W_EVT4_sc26

description: mRNA with polyA tail


title: HE8W_EVT4_sc25

description: mRNA with polyA tail


title: HE8W_EVT4_sc24

description: mRNA with polyA tail


title: HE8W_EVT4_sc22

description: mRNA with polyA tail


title: HE8W_EVT4_sc19

description: mRNA with polyA tail


title: HE8W_EVT4_sc21

description: mRNA with polyA tail


title: HE8W_EVT4_sc20

description: mRNA with polyA tail


title: HE8W_EVT4_sc18

description: mRNA with polyA tail


title: HE8W_EVT4_sc17

description: mRNA with polyA tail


title: HE8W_EVT4_sc36

description: mRNA with polyA tail


title: HE8W_EVT4_sc14

description: mRNA with polyA tail


title: HE8W_EVT4_sc1

description: mRNA with polyA tail