title: 1001000289.F6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E3 (single cell)

status: Public on Jul 31 2017

type: SRA

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

country: USA

institute: Emory University

description:
hCS-derived cell
Single cell

library_source: transcriptomic

data_processing:
Short read trimming: Prinseq to remove short reads (-min_len 30) trim the first 10 bp on the 5’-end (-trim_left 10), trim reads with low quality on the 3’-end (-trim_qual_right 25) and filter low complexity reads (-lc_method entropy \-lc_threshold 65).  We used FASTQC to determine overrepresented sequences and removed those using cutadapt (-e 0.15 –m 30). We then used Prinseq to remove orphan pairs less than 30bp in length followed by removal of nextera adapters using Trim Galore  (--stringency 1).
Read alignment: reads were aligned to the hg19 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using HTSeq (-m intersection-nonempty \-s no).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: human cortical spheroid-derived cell

extract_protocol:
single-cell sorting in 96-well plates followed by cDNA preparation using Smart-seq2
Smart-Seq2 for preparation of cDNA followed by library preparation using Nextera XT
Nextera tagmentation according to the standard protocol for single cell RNA-seq following Smart-Seq2

tag: plate id

tag: well

tag: tissue

value: hCS

tag: age

value: Day 130

tag: selection type

value: HEPACAM

tag: cell type

value: glia

tag: glial cluster


title: 1001000289.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E4 (single cell)

description:
hCS-derived cell
Single cell

value: neuron


title: 1001000289.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.D3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.G1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.A6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.F4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.F1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.F6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.B7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.F9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.D2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.C7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.E3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000213.H11 (single cell)

description:
hCS-derived cell
Single cell

value: Day 450

value: Unselected


title: 1001000212.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000212.H9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.G1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000288.A4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.D2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.H11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.D1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.C11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.D10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.F5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.C6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.C10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.G7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.E10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.G8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.B6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000289.C4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.E6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000210.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.E4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.B12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.D5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.D9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.G7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.F4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000209.H9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.H4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.F1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000062.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.H10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.H8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.H7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.E12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.B7 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Mid-gestation 3

city: West Haven

first: Gunter

last: Wagner

state: CT

address: 300 Heffernan Drive, ISTC 108

department: Systems Biology Institute, EEB

institute: Yale University

data_processing:
Basecalls performed using CASAVA
mRNA-seq reads were aligned to the rabbit (OryCun2.0), opossum (MonDom5.69) mouse (Mus38.69) and armadillo (DasNov3.0) cDNA builds using Tophat2
Number of reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: Genome_build: rabbit (OryCun2.0), opossum (MonDom5.69) mouse (Mus38.69) and armadillo (DasNov3.0)
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Comma-delimited csv files include read counts for each sample.

organism: Oryctolagus cuniculus

source_name: cervix

extract_protocol:
Tissues were harvested and kept in RNAlater until extraction of RNA using Qiagen RNeasy extraction kit.
RNA libraries were prepared for sequencing using standard illumina protocols.

value: cervix

tag: gestation stage

value: Mid-gestation

tag: strain

value: New Zealand White


title: 1001000061.D5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.F6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G8 (single cell)

description:
hCS-derived cell
Single cell

value: Day 175


title: 1001000084.F4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000061.G4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.D4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.C3 (single cell)

description:
hCS-derived cell
Single cell


title: WT-25

city: Tehran

first: Ali

last: Sharifi-Zarchi

address: Royan Institute, Bani Hashem Sq.

country: Iran

institute: Royan Institute for Stem Cell Biology and Technology

description:
Nascent RNA
WT-25N.wig,WT-25P.wig
GRO-seq data of wild-type yeast

data_processing:
Trimming the data using cutadapt version 1.7.1
Aligning reads to the sacCer3 reference genome using bowtie2
Aligning reads to the sacCer3 reference genome using Aryana
Computing strand-specific normalized signal over the genome using custom R scripts
Processing of the alignment results using custom R scripts
Genome_build: sacCer3, April 2011, www.yeastgenome.org
Supplementary_files_format_and_content: RAW data: fastq.gz, Processed data: wig.gz, genomic signal

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: BY4734 Wild type cells

growth_protocol: Cells were grown at permissive temperature and shifted to non-permissive temperature for two hours.

extract_protocol:
Total RNA was isolated by Trizol method and then nascent Br-UTP RNA was paffinity purified.
Nascent Br-UTP-labelled RNA was converted into cDNA and library was constructed using ScriptSeq-TM complete kit from 'Epicenter'.

treatment_protocol: Nascent RNA was labelled by growing cells in Br-UTP

tag: temperature

value: 25 degrees C

tag: genotype/variation

value: Wild-type

tag: replicate


title: TS-37-R1

description:
Nascent RNA
TS-37N.wig,TS-37P.wig
GRO-seq data of mutant yeast

source_name: Clp1 mutant cells

value: 37 degrees C

value: Mutant


title: 1001000061.B6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.E3 (single cell)

description:
hCS-derived cell
Single cell


title: TS-25-R3

description:
Nascent RNA
TS-25N.wig, TS-25P.wig
GRO-seq data of mutant yeast


title: WT-37

description:
Nascent RNA
WT-37N.wig,WT-37P.wig
GRO-seq data of wild-type yeast


title: TS-37-R3


title: TS-25-R2


title: TS-37-R2


title: 1001000084.G1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.D1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.B1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 20YoungWT4Cork

city: Sault Sainte Marie

first: Isabel

last: Molina

state: Ontario

address: 1520 Queen Street East, CC403 Essar Bldg.

department: Biology

country: Canada

institute: Algoma University

data_processing:
Base calls are made using the Illumina CASAVA pipeline.
Read trimming and clipping of adapters. Reads are trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters are removed from the reads, and all reads are required to have a length of at least 32bp. Trimming and clipping are done with the Trimmomatic software .
Aligning the reads to the reference sequence. The filtered reads are aligned to a reference genome. The genome used in the analysis is Populus trichocarpa v3. The alignment is done with the combination of tophat/bowtie software[2] . It generates a Binary Alignment Map file (.bam).
Generating FPKM values. The Cufflinks program is used to assemble aligned RNA-Seq reads into transcripts and to estimate their abundance (FPKM). In RNA-Seq experiments, cDNA fragments are sequenced and mapped back to genes and ideally, individual transcripts. Properly normalized, the RNA-Seq fragment counts can be used as a measure of the relative abundance of transcripts, and Cufflinks measures transcript abundances in Fragments Per Kilobase of exon per Million fragments mapped (FPKM), which is analagous to single-read "RPKM". In paired-end RNA-Seq experiments, fragments are sequenced from both ends, providing two reads for each fragment. To estimate isoform-level abundances, one must assign fragments to individual transcripts, which may be difficult because a read may align to multiple isoforms of the same gene. Cufflinks uses a statistical model of paired-end sequencing experiments to derive a likelihood for the abundances of a set of transcripts given a set of fragments. Once transcripts have been assembled and their corresponding FPKM estimated, these transcript are annotated with the known reference set of transcripts obtained from the Ensembl database.
Generating wiggle graphs/tracks. Wiggles track Format file are generated from the aligned reads using BedGraphToBigWig. This file is a representation of read alignments that can be easily downloaded in browsers like IGV or UCSC (for UCSC some name conventions and/or coordinate limits may cause some problems, in this case please contact us for file formating).
Genome_build: Populus trichocarpa v3.0
Supplementary_files_format_and_content: Differential gene analysis. The results of the differential gene expression analysis were generated using DESeq and edgeR Bioconductor package. Raw read counts generated by HTSeq were used as input. The first column is the gene id, the second column is the gene symbol, the third column is the log2 fold change of the level of expression of each gene, the fourth column is the nominal p-value of the test and the fifth column is the FDR adjusted p-value of the test.
Supplementary_files_format_and_content: Raw data matrix: The count data are obtained using HTSeq and are represented as a Table which reports, for each sample (columns), the number of reads that have been assigned to a given gene (rows).

organism: Populus tremula x Populus alba

source_name: Poplar outer bark

growth_protocol: P. tremula x P. alba hybrid poplar clone INRA 717-1B4 trees were grown at the Ontario Forest Research Institute in Sault Ste. Marie, Ontario, in greenhouse conditions and moved outside during the growing season only (May-September)

extract_protocol:
Total RNA was extracted from 1 g tissue from each. Each sample was mechanically ground in liquid nitrogen until a fine powder was obtained. To this tissue 3 % insoluble polyvinylpyrrolidinone (PVPP) was added and further ground in an extraction buffer containing 2% hexadecyltrimethylammonium bromide (CTAB), 2.0 M sodium chloride, 0.5 g/L spermidine, 100 mM Tris-HCl, 25 mM EDTA and 3% ß-mercaptoethanol pre-warmed to 65 °C. The mixture was then incubated at 65 °C for 10 minutes before extraction with 24:1 chloroform:isoamyl alcohol. The RNA was precipitated by the addition of ¼ volume 10 M LiCl, incubation at 4 °C for 6 hours followed by incubation at -20 °C overnight. The RNA was then harvested by centrifugation (10 000 x g) at 4 °C for one hour, removing aqueous phase, and washing in 70 % ethanol. Pellets were dried, re-dissolved in RNase- free water, and stored at -80 °C until use.
Unstranded RNA protocol

tag: stem diameter

tag: tissue type

value: phellem + phellogen

tag: bark layer

value: outer

tag: stem age

value: young


title: 16YoungWT1Cork


title: 1001000084.E9 (single cell)

description:
hCS-derived cell
Single cell

value: hCS


title: 1001000084.A10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.C7 (single cell)

description:
hCS-derived cell
Single cell


title: 9YoungWT4Control

source_name: Poplar inner bark

value: secondary phloem + vascular meristem

value: inner


title: 17YoungWT2Control


title: 1001000061.E2 (single cell)

description:
hCS-derived cell
Single cell

value: Day 130

value: glia


title: 15YoungWT1Control


title: 8WT4Cork

value: old


title: 1001000084.D11 (single cell)

description:
hCS-derived cell
Single cell

value: Unselected

value: neuron


title: 1001000084.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G12 (single cell)

description:
hCS-derived cell
Single cell


title: 6WT3Cork


title: 1001000084.A12 (single cell)

description:
hCS-derived cell
Single cell


title: TS-25-R1


title: 1001000084.H7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 2WT1Cork


title: 7WT4Control


title: 1001000084.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 5WT3Control


title: 1001000084.C12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 18YoungWT2Cork


title: 1001000084.F3 (single cell)

description:
hCS-derived cell
Single cell


title: 1WT1Control


title: 1001000084.H9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.H2 (single cell)

description:
hCS-derived cell
Single cell


title: Opossum Non-pregnant 2

organism: Monodelphis domestica

value: cervix

value: Non-pregnant


title: 4WT2Cork


title: 1001000084.A4 (single cell)

description:
hCS-derived cell
Single cell

value: Day 175


title: 1001000084.H11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.E4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.H4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.C1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.D3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.D9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 3WT2Control


title: 1001000084.E10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.H6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.D12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.A1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.H8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.F12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.G9 (single cell)

description:
hCS-derived cell
Single cell

value: HEPACAM


title: 1001000081.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.F11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.G3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.D2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.B5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000084.A6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.F7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.G4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.F9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.B8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.F2 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Late-gestation 3

value: Late-gestation

value: New Zealand White


title: 1001000081.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.A5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.E6 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Late-gestation 1


title: 1001000081.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H11 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Mid-gestation 2

value: Mid-gestation


title: 1001000084.A8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.B12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.A4 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Mid-gestation 1


title: 1001000081.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.G1 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Non-pregnant 2


title: Rabbit Non-pregnant 3


title: 1001000081.G11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.F11 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Non-pregnant 1


title: 1001000081.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.F8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.E1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F1 (single cell)

description:
hCS-derived cell
Single cell

value: Day 100


title: 1001000078.A4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.D11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.F1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.C3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.D4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.D6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A8 (single cell)

description:
hCS-derived cell
Single cell


title: Rabbit Late-gestation 2


title: 1001000078.F3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.C5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.C6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.C11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.D8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.D10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.D12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.C9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F4 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A9 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F2 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.G6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H8 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F6 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E12 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.B10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000081.C11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.C7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.D7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E5 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E11 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.F10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.A7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G10 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G7 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.G1 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.H3 (single cell)

description:
hCS-derived cell
Single cell


title: 1001000078.E3 (single cell)

description:
hCS-derived cell
Single cell


title: hT2-2D/FOXA1 RNA-Seq (rep2)

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference mouse (mm9) or human (hg19) genome assembly with Tophat, and rpkm values were calucated with Cufflink
Genome_build: mm9 and hg19

source_name: hT2-2D/FOXA1 cells

growth_protocol: Mouse/human PDA organoids or cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted using Trizol reagent
Libraries were made following the instructions of Illumina TruSeq RNA sample prep kit v2

treatment_protocol: For cDNA overepxression, cDNAs were retrovirally introduced and selected with G418. For shRNA expression, shRNAs were retrovirally introduced and selected with puromycin. For sgRNA expression, sgRNAs were lentivirally introduced and GFP-sorted with FACS.

value: PDA patient

value: Monolayer-cultured cells established from PDX-derived primary tumor organoid

tag: peturbation

value: Transduced with MSCV/FOXA1 retrovirus

tag: biological replicate


title: hT2-2D/FOXA1 RNA-Seq (rep1)


title: 1001000078.C10 (single cell)

description:
hCS-derived cell
Single cell

tag: plate id

tag: well

value: hCS


title: hT2-2D/emp RNA-Seq (rep2)

source_name: hT2-2D/emp cells

value: Transduced with MSCV/emp retrovirus


title: hT2-2D/emp RNA-Seq (rep1)


title: 1001000078.G4 (single cell)

description:
hCS-derived cell
Single cell

tag: tissue

tag: age

value: glia


title: 1001000078.A5 (single cell)

description:
hCS-derived cell
Single cell

tag: selection type

tag: cell type


title: hT2-2D/FOXA1 Ipt ChIP-Seq

library_source: genomic

data_processing:
Raw reads were mapped to the reference mouse (mm9) or human (hg19) genome assembly using Bowtie allowing two-mismatches for only unique alignment; -v 2 -m 1 -best --strata. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net).
HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

extract_protocol:
Lysates were prepared from ~1 millon single cell dissociated of organoid cultures, or ~5 million of monolayer cultures. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with apporiate antibodies.
Libraries were prepared according to Illumina's instructions of TruSeq ChIP Sample Prep kit.

tag: antibody

value: Ipt genomic DNA


title: hT2-2D/emp Ipt ChIP-Seq

tag: strain


title: hT2-2D/emp H3K27ac ChIP-Seq

value: H3K27ac (ab4729; Abcam)


title: hT3 Ipt ChIP-Seq

source_name: hT3 organoid

value: Patient-derived PDA primary tumor organoid (hT3)


title: hT1 Ipt ChIP-Seq

source_name: hT1 organoid

value: Patient-derived PDA primary tumor organoid (hT1)


title: 1001000078.E8 (single cell)

description:
hCS-derived cell
Single cell

value: Unselected

tag: glial cluster


title: XG7 RASSF4 control vector

city: Montpellier

first: Jerome

last: Moreaux

address: 80 Av. Augustin Fliche

department: Biological Hematology

country: France

institute: CHRU Montpellier

data_processing:
RNA-seq read pairs were mapped to the reference human GRCh37 genome using the STAR aligner. All statistical analyses were performed with the statistics software R and R packages developed by BioConductor project. The expression level of each gene was summarized and normalized using DESeq2 R/Bioconductor package. Differential expression analysis were performed using DESeq2 pipeline. P values were adjusted to control the global FDR across all comparisons with the default option of the DESeq2 package. Genes were considered differentially expressed if they had an adjusted p-value of 0.05 and a fold change of 1.5.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts as provided by DESeq2.

source_name: Human Multiple Myeloma Cell Lines

extract_protocol:
RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany) according to manufactures’ instructions.
The RNA sequencing library preparation was done with 150ng of input RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit. Paired-end RNA-seq were performed with illumina NextSeq sequencing instrument.

value: Multiple Myeloma

tag: cell line


title: RNA mock rep1

city: Berlin

first: Benedikt

last: Obermayer

address: Chariteplatz 1

department: Core Unit Bioinformatics

country: Germany

institute: Berlin Institute of Health

description: total RNA, mock infection

data_processing:
3 rounds of adapter removal using flexbar and the adapter sequence AGATCGGAAGAGCACACGTCT
in silico rRNA depletion using bowtie2 and a rRNA database from ARB silva and refseq
map against combined reference (hg19 and PR8 H1N1 genome) with STAR and gencode v19 annotation
count reads over exons using featureCounts and gencode v19 annotation
Genome_build: hg19; GCF_000865725.1
Supplementary_files_format_and_content: txt file; featureCounts output

source_name: A549 epithelial cells

growth_protocol: A549 cells were grown in a 15cm dish in culture medium

extract_protocol:
12 hours post infection, cells were harvested.
Library preparation proceeded according to manufacturer's protocol using the TruSeq Ribo Profile for Mammalian kit. Depletion of ribosomal RNA was performed using the Ribo-Zero rRNA Removal Kit (H/M/R).

treatment_protocol: Cells were infected with PR8 or PR8∆NS1 as described (Talon et al. ASM 74:7989, 2000). Control cells were not subject to any media changes, while mock infected cells were washed with PBS, rocked in 4mL's of DMEM without any supplements for 1 hour, then washed with PBS, followed by the addition of culture medium

tag: infection

value: mock

value: A549 cells

tag: molecule

value: total RNA


title: RPF control rep1

description: ribosome profiling, control

data_processing:
Library strategy: ribo-seq
3 rounds of adapter removal using flexbar and the adapter sequence AGATCGGAAGAGCACACGTCT
in silico rRNA depletion using bowtie2 and a rRNA database from ARB silva and refseq
map against combined reference (hg19 and PR8 H1N1 genome) with STAR and gencode v19 annotation
count reads over exons using featureCounts and gencode v19 annotation
Genome_build: hg19; GCF_000865725.1
Supplementary_files_format_and_content: txt file; featureCounts output

value: control

value: RPF


title: RPF mock rep1

description: ribosome profiling, mock infection


title: RNA mock rep2

description: total RNA, mock infection


title: RNA control rep1

description: total RNA, control


title: JJN3 overexpressing RASSF4


title: XG7 overexpressing RASSF4


title: AMO1 overexpressing RASSF4


title: hT2-2D/FOXA1 H3K27ac ChIP-Seq

value: PDA patient


title: RNA control rep2

description: total RNA, control


title: RPF PR8 rep1

description: ribosome profiling, PR8 infection

organism:
Homo sapiens
Influenza A virus (A/reassortant/NIBRG-121(California/07/2009 x PR8)(H1N1))

value: H1N1 PR8


title: JJN3 RASSF4 control vector


title: RPF mock rep2

description: ribosome profiling, mock infection


title: RPF PR8[delta]NS1 rep1

description: ribosome profiling, PR8∆NS1 infection

value: H1N1 PR8[delta]NS1


title: RPF control rep2

description: ribosome profiling, control


title: ADT: CD8_high_Dropseq

city: New York

first: Marlon

last: Stoeckius

state: New York

address: 101 Avenue of the Americas

department: Innovation Lab

institute: New York Genome Center

description:
CITE-seq using Dropseq of sorted CD8 cells to validate to flow cytometry (data for Figure 2)
read1 file: ~ cell barcode and UMI
read2 file: ~ Antibody Derived Tag reads

data_processing:
Library strategy: CITE-seq
Drop-seq data was processed with the standard pipeline (Drop-seq tools version 1.12 from McCarroll lab). 10x data from the species mixing experiment was processed using Cell Ranger 1.2 using default parameters.
RNA Reads were aligned to the human reference sequence GRCh37/hg19 (CD8a FACS comparison), or an hg19 and mouse reference mm10 concatenation (species mixing experiment, CBMCs).
Antibody Tags and cell barcodes were directly extracted from the reads in the ADT fastq files.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: csv files with cell barcodes, transcript counts and antibody tag counts.

molecule: other

source_name: cord blood

extract_protocol:
Cord blood mononuclear cells (CBMCs) were isolated from cord blood as described in Breton et al. 2015.
Library was constructed as described in the protocol of the manufacturer (10x Genomics Single Cell) or for Dropseq (Macosko et al., 2015) with the modifications described in Stoeckius et al. 2017

value: blood mononuclear cells


title: RNA PR8[delta]NS1 rep1

description: total RNA, PR8∆NS1 infection


title: RNA PR8 rep2

description: total RNA, PR8 infection


title: ADT: CD8_low_Dropseq


title: ADT: CD8_intermediate_Dropseq


title: hT3 H3K27ac ChIP-Seq


title: hT1 H3K27ac ChIP-Seq


title: RNA: CD8_low_Dropseq

description:
CITE-seq using Dropseq of sorted CD8 cells to validate to flow cytometry (data for Figure 2)
read1 file: ~ cell barcode and UMI
read2 file: ~ transcript


title: RNA PR8[delta]NS1 rep2

description: total RNA, PR8∆NS1 infection


title: RNA: CD8_high_Dropseq


title: ADT: CD8_off_Dropseq


title: RNA: PBMC_vs_flow_10x

description:
Validation CITE-seq dataset. Using 10x containing 8000 PBMCs. Used for quantification comarison to mulitcolor flow cytometry using (data for Figure 2).
read1 file: ~ cell barcode and UMI
read2 file: ~ transcript

source_name: peripheral blood


title: RPF PR8[delta]NS1 rep2

description: ribosome profiling, PR8∆NS1 infection


title: ADT: PBMC_vs_flow_10x

description:
Validation CITE-seq dataset. Using 10x containing 8000 PBMCs. Used for quantification comarison to mulitcolor flow cytometry using (data for Figure 2).
read1 file: ~ cell barcode and UMI
read2 file: ~ Antibody Derived Tag reads


title: RNA: CBMC_8K_13AB_10x

description:
Large CITE-seq dataset with 8000 CBMCs and 13 antibodies (data for Figure 3).
read1 file: ~ cell barcode and UMI
read2 file: ~ transcript


title: ADT: CBMC_8K_13AB_10x

description:
Large CITE-seq dataset with 8000 CBMCs and 13 antibodies (data for Figure 3).
read1 file: ~ cell barcode and UMI
read2 file: ~ Antibody Derived Tag reads


title: RNA PR8 rep1

description: total RNA, PR8 infection


title: AMO1 RASSF4 control vector


title: DeltaRing_R12_2

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

country: Japan

institute: RIKEN

description: Ribosome Profiling

data_processing:
library strategy: ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.0.6
Alignment with TopHat v2.0.7 to reporter plasmid p416GPDp-GFP-R12-FLAG-HIS3
Read quantitation using custom scripts
Genome_build: p416GPDp-GFP-R12-FLAG-HIS3
Supplementary_files_format_and_content: text files contain following columns: 1.distance from start codon [nt] ;2-36. total or 13 to 36 nucleotides long reads at the given position. Asite positions of the reads are asigned.

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction
Trizol and following Direct-zol kit (Zymo scientific).
RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification

tag: genetic background

value: MATa ade2 his3 leu2 trp1 ura3 can1, hel2<delta>::natMX4, p415-HEL2<delta>RING

value: hel2<delta>, p415-HEL2<delta>RING

tag: treated with


title: us10kr_R12_2

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1, rps20::natMX4, p415-rps20K6/8R

value: rps20<delta>, p415-RpS20K6/8R


title: rqt2_R12_2

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1, rqt2<delta>::natMX4


title: rqt1_R12_2

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1, hel2<delta>::natMX4


title: DeltaRing_R12_1

description: Ribosome Profiling


title: rqt2_R12_1

description: Ribosome Profiling


title: us10kr_R12_1

description: Ribosome Profiling


title: GL_M_3

city: Nanjing

first: yuqiu

last: lu

state: Jiangsu

address: 305 East Zhongshan Road

country: China

institute: National Clinical Research Center for Kidney Disease

description: Processed data file: fpkm_data_M.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.74 whole genome using Tophat v2.0.12 with parameters mismatch=2.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) were calculated using a protocol from Trapnell, Cole, et al., 2010. HTSeq v0.6.1 was used with parameters -m union
Genome_build: GRCm38.74
Supplementary_files_format_and_content: fpkm_data_M.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Mus musculus

source_name: Mixed glomerular mesangial and endothelial cells

extract_protocol:
We isolated mouse glomeruli with Dana-beads/magnetic concentration and dissociated them into single cells using enzymes. The cell suspension was then loaded onto a Fluidigm C1 Single-Cell Auto Prep System, which separated the single cells and lysed them for RNA extraction in individual wells. Then, we performed qPCR analyses of glomerular cell markers to determine the identity of each sample. Fifteen mesangial cells and 15 endothelial cells' cDNA samples were mixed and then divided into 3 aliquots, followed by sequencing library construction.
cDNA libraries were made automatically in the Fluidigm C1 platform.

tag: strain/background

tag: genotype/variation

value: wild type

tag: gender

value: male

value: 8 weeks

value: kidney/glomeruli

value: mixed glomerular mesangial and endothelial cells


title: GL_M_2

description: Processed data file: fpkm_data_M.txt


title: GL_M_1

description: Processed data file: fpkm_data_M.txt


title: RNA: CD8_off_Dropseq


title: us10kr_R12

description: Ribosome Profiling

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA alignment with bowtie2 v2.0.6
Alignment with TopHat v2.0.7 to reporter plasmid p416GPDp-GFP-FLAG-HIS3 or p416GPDp-GFP-R12-FLAG-HIS3
Read quantitation using custom scripts
Genome_build: p416GPDp-GFP-FLAG-HIS3 and p416GPDp-GFP-R12-FLAG-HIS3
Supplementary_files_format_and_content: text files contain following columns: 1.distance from start codon [nt] ;2-36. total or 13 to 36 nucleotides long reads at the given position. Asite positions of the reads are asigned.

source_name: Saccharomyces cerevisiae

extract_protocol:
RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification
Ribosome profiling

tag: treatment

value: rps20-delta, p415-RpS20K6/8R

tag: extracted molecule

value: total RNA

value: Rnase I footprinting, ribosome pelleting, RNA extraction


title: wt_R12_2

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1


title: us10kr_control2

description: Ribosome Profiling


title: us10kr_control1

description: Ribosome Profiling


title: RPF PR8 rep2

description: ribosome profiling, PR8 infection

value: H1N1 PR8

value: A549 cells

value: RPF


title: rqt2_control2

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1, rqt2∆::natMX4


title: rqt2_R12

description: Ribosome Profiling


title: rqt2_control1

description: Ribosome Profiling


title: rqt1_R12_1

description: Ribosome Profiling


title: rqt1_R12

description: Ribosome Profiling

value: MATa ade2 his3 leu2 trp1 ura3 can1, hel2∆::natMX4


title: GL_P_83

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using Tophat v2.0.12 with parameters mismatch=2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008. HTSeq v0.6.1 was used with parameters -m union
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited excel files include RPKM values for each Sample

source_name: Glomerular podocytes

extract_protocol:
We isolated mouse glomeruli with Dana-beads/magnetic concentration and dissociated them into single cells using enzymes,The cell suspension was then loaded onto a Fluidigm C1TM Single-Cell Auto Prep System, which separated the single cells and lysed them for RNA extraction in individual wells.
cDNA libraroes were made automatically in the Fluidigm C1 platform.

tag: tissue

value: kindey/glomeruli

tag: celltype

value: podocyte

value: 8 week

tag: genotype


title: rqt1_control1

description: Ribosome Profiling


title: GL_P_69

tag: age

value: wild type


title: GL_P_67


title: rqt1_control2

description: Ribosome Profiling


title: GL_P_70


title: GL_P_62


title: wt_R12_1

description: Ribosome Profiling


title: GL_P_71


title: GL_P_93


title: wt_R12

description: Ribosome Profiling


title: GL_P_50


title: wt_control2

description: Ribosome Profiling


title: GL_P_45


title: GL_P_38


title: wt_control1

description: Ribosome Profiling


title: Armadillo Late-gestation 1

organism: Dasypus novemcinctus

value: cervix

tag: gestation stage

value: Late-gestation


title: Armadillo Mid-gestation 5

value: Mid-gestation

tag: strain


title: 1001000078.D9 (single cell)

description:
hCS-derived cell
Single cell

source_name: human cortical spheroid-derived cell

tag: plate id

tag: well

value: hCS

value: Day 100

tag: selection type

value: Unselected

tag: cell type

value: glia

tag: glial cluster


title: Armadillo Mid-gestation 4

source_name: cervix


title: GL_P_42


title: GL_P_73


title: GL_P_32


title: GL_P_23


title: Armadillo Mid-gestation 2


title: GL_P_21


title: Armadillo Mid-gestation 1


title: GL_P_54


title: GL_P_18


title: Armadillo Non-pregnant 3

value: Non-pregnant


title: GL_P_17


title: GL_P_10


title: GL_P_9


title: Armadillo Non-pregnant 1


title: Armadillo Non-pregnant 2


title: Hela990_10_Pfx2

city: Curitiba

first: Christian

middle: Macagnan

last: Probst

state: PR

address: Rua Professor Algacyr Munhoz Mader, 3775

country: Brazil

institute: Instituto Carlos Chagas

description: Oligo-ME aRNA

data_processing:
Reads were aligned using the SHRIMP2 v2.2.2, with default parameter, except –strata -h 80% --max-alignments 1000
Sample read count normalization was performed by edgeR v. 3.12.0, Bioconductor suite, R v 3.2.3
Genome_build: MBSY00000000
Supplementary_files_format_and_content: Normalized read count for each Trypanosoma cruzi Dm28c gene cluster (SgdmA)

organism: Trypanosoma cruzi

source_name: HeLa lineage cell + Epimastigote stage

growth_protocol: Parasite culture: T. cruzi Dm28c epimastigotes [32] were cultured at 28°C in LITB medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) as previously described [33]. Tissue culture-derivedCell derived trypomastigote forms were obtained by infection of cultured Vero cell (ATCC® CCL-81™) at 37ºC in a humidified 5% CO2 atmosphere using a multiplicity of infection (MOI) of 10 parasites per host cell. Cell derived tTrypomastigotes were recovered after 4 days of infection, in the cell burst peak. HeLa culture: the human derived epithelial cell ATCC® CCL-2™ were grownth in 75 cm2 culture bottles at 37ºC in a humidified 5% CO2 atmosphere using DMEM medium supplemented with 10% FBS. When confluent, cells were detached from the culture flask by enzymatic treatment (0.01% trypsin, 0.1% EDTA in PBS), washed in PBS and passed to new bottles at cell density of 106 HeLa cells for each 75 cm2 culture bottle.

extract_protocol:
Total RNA was extracted from T. cruzi epimastigote and trypomastigote forms (5 × 108 cells) and from confluent HeLa cells with the RNeasy kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions, with an additional on-column DNase digestion step. Total RNA from HeLa cells were obtained from MessageAmpTM II aRNA Amplification Kit from Life Technologies® (#AMB1751-5). RNA integrity was assessed on an Agilent 2100 Bioanalyzer with RNA 6000 Nano LabChip kit, according to the manufacturer’s instructions. Polyadenylated RNA were purified from at least 50 µg of total RNA using PolyA+Track® mRNA Isolation System III from Promega® (#Z5300), according to the manufacturer's instructions. Polyadenylated RNA were purified from at least 50 µg of total RNA using PolyA+Track® mRNA Isolation System III from Promega® (#Z5300), according to the manufacturer's instructions. All mRNA amplification reactions were done using reagents from MessageAmpTM II aRNA Amplification Kit from Life Technologies® (#AMB1751-5). For classic Eberwine amplification method, first-strand cDNA was synthesized using a T7oligo(dT) primer that contains a T7 RNA polymerase promoter upstream to the poly-T tract; this promoter will further direct the in vitro mRNA synthesis (amplification). First, 100 ng of total RNA (in 11 µl) were mixed with first-strand cDNA reaction mix containing 1 µl of T7oligo(dT) primer, 2 µl first-strand buffer, 4 µl dNTPs, 1 µl RNase inhibitor and 1 µl ArrayScript Reverse Transcriptase and incubated for 2 hours at 42ºC. Second-strand cDNA was then synthesized for 2 hours at 16ºC using the total 20 µl first-strand product plus 80 µl of second strand mix containing 63 µl water, 10 µl second-strand buffer, 4 µl dNTPs, 2 µl DNA Polymerase and 1 µl of RNase H. Double-strand cDNA was then purified using PureLink® PCR Micro Kit from Life Technologies (#K310250) according manufacturer’s instructions. Eluted cDNA was adjusted to 16 µl and used as template for amplification reaction in a total volume of 40 µl containing 16 µl NTPs, 4 µl amplification buffer and 4 µl of T7 RNA polymerase; in vitro transcription took 14 hours at 37ºC. Amplified RNA (aRNA) was then purified using RNeasy MinElute CleanUp Kit (Qiagen, #74204), according to the manufacturer’s instructions. For specific amplification of spliced leader containing mRNA, we used a custom designed primer complementary to the last 21 bases of T. cruzi spliced leader (in bold) with an upstream T7 RNA polymerase promoter (in gray) (5'-GGCCAGTGAATTGTAATACG ACTCACTATAGGGAGGCGGTACAGTTTCTGTACTATATTG-3'), which we named T7SL. In this case, T7SL was used for second-strand cDNA synthesis, while first-strand cDNA was produced using random primers, accordingly to the second round amplification protocol of MessageAmpTM II aRNA Kit. Template total RNA was adjusted to 10 µl, mixed with 2 µl of "second round primers" (random primers) and incubated at 70ºC for 10 minutes followed by snap cool on ice to allow annealing of random primers to RNA. Then, 8 µl of reverse transcription master mix was added and first-strand cDNA synthesized at 42ºC for 2 hours. RNase H was added (1 µl) and sample incubated at 37ºC for 30 minutes to specifically degrade the remaining RNA. T7SL primer was added to a final concentration of 1 µM and the sample was incubated at 70ºC for 10 minutes and then placed on ice. Second-strand cDNA master mix without RNase H was added (74 µl) and the reaction incubated for 2 hours at 16ºC. Double-strand cDNA purification, in vitro transcription and aRNA purification was performed as described above.
Total RNA-Seq Kit (Life Technologies, #4445374) was used accordingly to manufacturer instructions. Briefly, RNA was fragmented using RNase III and cleaned up with Invitrogen RiboMinus™ Concentration Module. Strand-specific adaptors were hybridized and ligated to both extremities of RNA in an overnight reaction, followed by first-strand cDNA synthesis with reverse transcriptase. cDNA was purified using MinElute® PCR Purification Kit (Qiagen) and gel-based selected for size using a Novex TBE-Urea 6% gel (#EC6865bOX). On-gel cDNA was amplified by PCR using SOLiDTM RNA barcoding kit primers (Life Technologies, #4427046 and #4453189) and purified with Invitrogen PureLink® PCR Micro Kit. Amplified DNA was quantified with Qubit® dsDNA HS Assay Kit on a Qubit® 2.0 Fluorometer. Equal masses of each sample, containing specific barcodes, were pooled together and the mixture used as DNA template for emulsion PCR on Applied Biosystems SOLiD® EZ Bead™ E80 system  (#4453095). After 3' end modification with terminal transferase, template beads were deposited onto glass slides and libraries sequenced on a SOLiDTM 4 system using multiplex fragment sequencing protocol that generates about 700 millions 50 bases short reads per run.

treatment_protocol: No treatment

tag: Stage

value: epimastigote

tag: mixture

value: yes

tag: mrna quantity (t. cruzi / human)


title: Hela4995_5_Pfx1

description: Oligo-ME aRNA


title: Hela4995_5_Pfx2

description: Oligo-ME aRNA


title: Armadillo Non-pregnant 4


title: Hela9990_10_Pfx1

description: Oligo-ME aRNA


title: Hela9990_10_Pfx2

description: Oligo-ME aRNA


title: Mouse Late-gestation 3


title: RNA: CD8_intermediate_Dropseq

value: blood mononuclear cells


title: Mouse Late-gestation 2


title: NT-siKMT1A-1

city: Yangling

first: Jingcheng

last: Zhang

address: Taicheng Road NO.3

institute: Northwest A&F University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UMD3.1 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM of each gene was calculated using Cufflinks (http://cufflinks.cbcb.umd.edu).
Genome_build: UMD3.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Bos taurus

source_name: embryos

extract_protocol:
Twenty 8-cell embryos for control and si-KMT1A injected group were directly lysed and used for cDNA synthesis using the SMARTer® v4 Ultra™ Low RNA Kit for Illumina® sequencing (Clontech)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Holstein

value: embryos

tag: developmental stage

value: 8 cell

tag: genotype/variation

value: KMT1A knockdown


title: NT-siKMT1A-3

tag: tissue


title: Mouse Late-gestation 1


title: NT-siKMT1A-2


title: Mouse Mid-gestation 3

value: Mid-gestation (E15)


title: Hela900_100_Pfx2

description: Oligo-ME aRNA


title: Hela990_10_Pfx1

description: Oligo-ME aRNA


title: Armadillo Mid-gestation 3


title: Hela900_100_Pfx1

description: Oligo-ME aRNA


title: NT-3

value: control


title: 3208_24_cyt_7_5h_2rep

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: polyadenylated cytoplasmic RNA

data_processing:
Basecalling and filtering was performed using standard software of  the illumina hiSeq 2500
Reads were aligned to the drosophila genome, BDGP5, using TopHat (version 2.0.12)  and bowtie (version 1.0.0), using default settings and a model annotation file (Drosophila_melanogaster.BDGP5_77.txt)
FPKM values per gene were generated using Cufflinks, using default settings
Supplementary_files_format_and_content: FPKM values, generated by CuffLinks

organism: Drosophila melanogaster

source_name: pre-existing cytoplasmic mRNA from cell line kc167

growth_protocol: Drosophila kc167 cells were routinely cultured in 10cm dishes using  the medium of M3+BPYE+10% FCS.

treatment_protocol: Samples 1-24 were labelled with 300μM 4-Thiouridine for the indicated duration of time, subjected to hypotonic fractionation and spun down. Samples 13-24 were the supernatant representing the cytoplasmic fraction and samples 1-12 were the pellet representing the nuclear fraction. TRISure (BIO-38032) were spiked-in with 100ng/ml total RNA of S. Cecrevisae and applied to sample 1-24. Total RNA is extracted and proceed with reaction with HPDP-Biotin (Thermo Fisher 21341).  Total RNA were precipitated and the biotinylated fractions was pulled out by streptavidin T1 beads (Thermo Fisher 65601). The remaining unlabeled fractions were subjected to the following Illumina TruSeq RNA preparation protocol.

tag: barcode

value: GTGAAAC

tag: cell line

tag: treatment

tag: time of treatment


title: Mouse Mid-gestation 2

value: cervix

tag: gestation stage

tag: strain


title: 3208_23_cyt_5_0h_2rep

description: polyadenylated cytoplasmic RNA

extract_protocol: Illumina TruSeq RNA preparation protocol

value: GTCCGCA


title: NT-2


title: Mouse Non-pregnant 3


title: 3208_22_cyt_3_0h_2rep

description: polyadenylated cytoplasmic RNA

value: CCGTCCC


title: 3208_21_cyt_1_5h_2rep

description: polyadenylated cytoplasmic RNA

value: ATGTCAG


title: NT-1


title: EpiBsort_ME2

description: Oligo-ME aRNA

source_name: Epimastigote stage

value: no

tag: method

value: amplification and oligo-ME T7


title: EpiA3_ME1

description: Oligo-ME aRNA

tag: mrna quantity


title: EpiBsort_ME1

description: Oligo-ME aRNA


title: EpiA6_ME1

description: Oligo-ME aRNA


title: EpiA3_ME2

description: Oligo-ME aRNA


title: 3208_20_cyt_0_5h_2rep

description: polyadenylated cytoplasmic RNA

value: AGTTCCG


title: 3208_18_nuc_7_5h_2rep

description: polyadenylated cytoplasmic RNA

source_name: pre-existing nuclear mRNA from cell line kc167

value: CTTGTAA


title: 3208_15_nuc_1_5h_2rep

description: polyadenylated cytoplasmic RNA

value: ACAGTGA


title: 3208_16_nuc_3_0h_2rep

description: polyadenylated cytoplasmic RNA

value: GCCAATA


title: 3208_14_nuc_0_5h_2rep

description: polyadenylated cytoplasmic RNA

value: TGACCAA


title: 3208_17_nuc_5_0h_2rep

description: polyadenylated cytoplasmic RNA

value: CAGATCA


title: 3208_13_nuc_0_0h_2rep

description: polyadenylated cytoplasmic RNA

value: CGATGTA


title: EpiA12_ME1

description: Oligo-ME aRNA

value: epimastigote


title: EpiA12_ME2

description: Oligo-ME aRNA


title: EpiA25_ME2

description: Oligo-ME aRNA


title: 3208_12_cyt_7_5h_1rep

description: polyadenylated nuclear RNA

molecule: nuclear RNA

value: ATTCCTT


title: Hela0_100_Pfx2

description: Oligo-ME aRNA


title: 3208_19_cyt_0_0h_2rep

description: polyadenylated cytoplasmic RNA

value: AGTCAAC


title: EpiA50_ME2

description: Oligo-ME aRNA


title: 3208_11_cyt_5_0h_1rep

description: polyadenylated nuclear RNA

value: ACTGATA


title: Hela0_100_Pfx1

description: Oligo-ME aRNA


title: EpiA50_ME1

description: Oligo-ME aRNA


title: 3208_10_cyt_3_0h_1rep

description: polyadenylated nuclear RNA

value: GAGTGGA


title: EpiA100_ME2

description: Oligo-ME aRNA


title: EpiBsort_ME3

description: Oligo-ME aRNA


title: EpiA25_ME1

description: Oligo-ME aRNA


title: 3208_9_cyt_1_5h_1rep

description: polyadenylated nuclear RNA

value: CGTACGT


title: TrpB_ME1

description: Oligo-ME aRNA

source_name: Trypomastigote stage

value: trypomastigote


title: EpiA100_ME1

description: Oligo-ME aRNA


title: TrpB_ME2

description: Oligo-ME aRNA


title: 3208_5_nuc_5_0h_1rep

description: polyadenylated nuclear RNA

value: TAGCTTA


title: 3208_6_nuc_7_5h_1rep

description: polyadenylated nuclear RNA

value: GGCTACA


title: 3208_3_nuc_1_5h_1rep

description: polyadenylated nuclear RNA

value: ACTTGAA


title: EpiB_ME2

description: Oligo-ME aRNA

value: no

value: amplification and oligo-ME T7


title: EpiA_ME2

description: Oligo-ME aRNA


title: EpiB_ME1

description: Oligo-ME aRNA


title: TrpA_ME1

description: Oligo-ME aRNA


title: EpiA_ME1

description: Oligo-ME aRNA


title: TrpA_dT2

description: Oligo-dTT7 aRNA

value: oligo-dT T7


title: TrpB_dT2

description: Oligo-dTT7 aRNA


title: 3208_1_nuc_0_0h_1rep

description: polyadenylated nuclear RNA

value: ATCACGA


title: TrpB_dT1

description: Oligo-dTT7 aRNA


title: EpiB_dT2

description: Oligo-dTT7 aRNA


title: TrpA_dT1

description: Oligo-dTT7 aRNA


title: EpiA_dT2

description: Oligo-dTT7 aRNA


title: 3208_8_cyt_0_5h_1rep

description: polyadenylated nuclear RNA

value: GTTTCGG


title: 3208_7_cyt_0_0h_1rep

description: polyadenylated nuclear RNA

value: GTGGCCT


title: EpiA_dT1

description: Oligo-dTT7 aRNA


title: EpiB_dT1

description: Oligo-dTT7 aRNA


title: ZC3H18_rep3

city: Aarhus

first: Evdoxia

last: Karadoulama

address: C.F. Møllers Alle 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
The RNA-Seq data was quality controled and trimmed using FastQC and Trimomomatics respectively.
The data was mapped using HISAT against hg19.
Uniquely mapped and properly paired reads were used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using Bedtools and bedGraphtoBigWig. The score represents strand specific per base genome coverage.

source_name: ZC3H18 total RNA replicate 3

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNA was extracted with Trizol and PureLink RNA Mini Kits (Thermo Scientific) and using on-column DNase I (PureLink DNase; Thermo Scientific) digestion according to the manufacturer’s manual.
Libraries were prepared, after rRNA-depletion using Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat; Illumina), using Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: siRNA transfections were performed targeting EGFP(control), ARS2, ZC3H18

tag: cell type

value: HeLa Kyoto

tag: transfection


title: TrpB_PolA

description: polyA+ purified mRNA

tag: Stage

value: poly-A purification


title: 3208_4_nuc_3_0h_1rep

description: polyadenylated nuclear RNA

value: GATCAGA


title: 3208_2_nuc_0_5h_1rep

description: polyadenylated nuclear RNA

value: TTAGGCA


title: EpiA_PolA

description: polyA+ purified mRNA

value: epimastigote

tag: mixture


title: ZC3H18_rep1

source_name: ZC3H18 total RNA replicate 1


title: EpiB_PolA

description: polyA+ purified mRNA


title: ARS2_rep3

source_name: ARS2 total RNA replicate 3


title: Wildtype, high CO2, 24 h after shift back to HC H24_3

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.8 software used for basecalling.
Illumina reads were mapped to the Ensembl release of the C. merolae transcriptome (ASM9120v1.30.gtf) using RSEM and BOWTIE2.
The resulting raw read counts were used for downstream analyses.
RNAseq data were statistically evaluated using edgeR on raw read counts as implemented in Bioconductor. Genes were called significantly differentially expressed if the FDR (q) value was below 0.01.
Transcripts per million (TPM) were reported for all transcripts. TPM values were averaged for the replicates of each condition.
Supplementary_files_format_and_content: Excel sheet (Table S3.xls) file including gene name (ID), closest homolog in Arabidopsis thaliana (AGI, Blast.p), functional description, Mapman category, assigned cluster, raw counts, gene length, TPM for each sample and mean TPM for biological replicates, log2 fold-changes between HC 0 h and LC 3 h, HC 0 h and LC 24 h, and HC 0 h and HC 24 h, and edgeR results (q-values) of differential gene expression analysis comparing HC 0 h  versus  the different time points after shift.

organism: Cyanidioschyzon merolae strain 10D

source_name: whole cell

growth_protocol: C. merolae cells were grown in batch cultures (Multi-Cultivator MC 1000-OD system) under controlled conditions (90 µmol photons m-2 s-1, 30 °C, 5% CO2 in air, start OD750=0.7).

extract_protocol:
Cells were harvested and immediately frozen in liquid nitrogen. RNA was isolated ffrom the cells using the EURx GeneMatrix Universal RNA Purification Kit (Roboclon, Berlin, Germany). Residues of DNA were removed with RNase-free DNase I (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared from 1 µg RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed and sequenced in paired-end mode (100 bp read length) on an Illumina HiSeq 2000 platform.

treatment_protocol: After 24 h growth under standard conditions, three independent biological replicates with a start OD750=0.7 were shifted by changing the CO2 concentration from 5% CO2 (high CO2, HC) to 0.04% CO2 (low CO2, LC) in the airation for 24 h to LC conditions and then shifted back to HC conditions for a 24 h recovery phase. RNA samples were harvested before the shift to LC (HC 0 h), 3 h and 24 h after the shift to LC (LC 3 h, LC 24 h), and 24 h after a shift back to HC conditions (HC 24 h). Besides the change in CO2 conditions all other growth parameters were kept constant.

tag: genotype

value: Wildtype

tag: co2 condition

value: high CO2, 24 h after shift back to HC


title: Wildtype, high CO2, 24 h after shift back to HC H24_2


title: ARS2_rep2

source_name: ARS2 total RNA replicate 2


title: Wildtype, high CO2, 24 h after shift back to HC H24_1


title: EGFP_rep3

source_name: EGFP(control) total RNA replicate 3

value: EGFP(control)


title: ARS2_rep1

source_name: ARS2 total RNA replicate 1


title: Wildtype, low CO2, 24 h after shift to LC L24_3

value: low CO2, 24 h after shift to LC


title: Wildtype, low CO2, 24 h after shift to LC L24_1


title: Wildtype, low CO2, 24 h after shift to LC L24_2


title: EGFP_rep2

source_name: EGFP(control) total RNA replicate 2


title: 15Z3P5 (RNA-seq)

city: Taiyuan

first: Ruifeng

last: Liu

state: Shanxi

address: No. 1 Dong San Dao Xiang

department: Institute of Dermatology

institute: Taiyuan City Centre Hospital

description: Skin-derived Mesenchymal stem cells

data_processing:
RNA-seq reads were mapped to human genome by hisat2 software. Cuffdiff2 software was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Mesenchymal stem cells

growth_protocol: Skin derived mesenchymal stem cells were cultured in DMDM/F12 medium and adherent cultured

extract_protocol:
Total RNA from each sample was used to prepare the RNA sequencing library
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). 10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

value: Skin

value: Skin-derived Mesenchymal stem cells

tag: disease status

value: Normal


title: TrpA_PolA

description: polyA+ purified mRNA

value: trypomastigote

value: no


title: 15Y29P5 (RNA-seq)

description: Skin-derived Mesenchymal stem cells

value: Psoriasis


title: Wildtype, low CO2, 3 h after shift to LC L3_1

value: low CO2, 3 h after shift to LC


title: Wildtype, low CO2, 3 h after shift to LC L3_3


title: 15Y26P5 (RNA-seq)

description: Skin-derived Mesenchymal stem cells


title: Wildtype, high CO2, 0 h before shift to LC H0_3

value: high CO2, 0 h before shift to LC


title: Wildtype, low CO2, 3 h after shift to LC L3_2


title: Wildtype, high CO2, 0 h before shift to LC H0_2


title: ZC3H18_rep2

source_name: ZC3H18 total RNA replicate 2

value: HeLa Kyoto


title: 14Z70P5 (RNA-seq)

description: Skin-derived Mesenchymal stem cells


title: Wildtype, high CO2, 0 h before shift to LC H0_1


title: 15Y15P5 (RNA-seq)

description: Skin-derived Mesenchymal stem cells


title: 14Z66P5 (RNA-seq)

description: Skin-derived Mesenchymal stem cells