title: p4-2_H04

description: SMART Seq2 with few modification


title: p4-2_H08

status: Public on Oct 26 2022

type: SRA

city: Daejeon

first: Hanseul

last: Yang

address: 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: SMART Seq2 with few modification

library_source: transcriptomic single cell

data_processing:
Sequencing reads from single-cell RNA-Seq libraries were aligned to the mouse reference genome (version mm10 from the UCSC) using Bowtie 2 (version 2.4.2) with default parameters for paired-end reads.
Supplementary files format and content: Expression values of each gene were quantified as TPM using RSEM (version 1.3.3)

molecule: polyA RNA

organism: Mus musculus

source_name: colon

extract_protocol:
Colonic epithelial cells were stained with eBioscience™ Fixable Viability Dye eFluor™ 506 (65-0866-14, Invitrogen) in a 1:1000 ratio for dead cell exclusion. Cells were Fc-blocked using Purified Rat Anti-Mouse CD16/CD32 (Clone 2.4G2, 553142, BD Pharmingen™) for 10 minutes and washed with FACS buffer (Ca2+ and Mg2+-free DPBS supplemented with 0.5% BSA and 0.3% sodium azide). For surface marker staining, PE Rat Anti-Mouse Siglec-F (Clone E50-2440, 552126, BD Pharmingen™) antibody and APC anti-mouse CD326 (EpCAM) antibody (clone G8.8, 118214, Biolegend) were used in a 1:50 and 1:100 dilution ratio, respectively. Antibody staining was performed for 30 minutes. All procedures were conducted at 4°C in the dark. Tuft cells were acquired by BD FACSAriaII (BD Biosciences)
Single-cell RNA-Seq libraries were prepared using the Smart-seq2 protocol with few modifications. Single-cells were sorted using a BD FACSAriaII (BD Biosciences) into 96 well PCR plates (Thermo Scientific) containing 2μl of lysis buffer (0.1% Triton X-100, 1U/μl RNase Inhibitor (Enzynomics), 0.25μM oligo-dT30VN primer) and stored at -80°C. The plates were thawed on ice and incubated for 3 min at 72 °C to lyse the cells. Revers transcription (40U/µl Maxima H minus transcriptase), template switching reaction and PCR pre-amplification (15 cycles) were performed according to the protocol. The PCR products in each well was cleaned up using 0.5X SPRI beads (2% Sera-Mag Speed Beads (Cytiva), 1M NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.01% NP40, 0.05% Sodium Azide, 22% w/v PEG 8000). To exclude empty wells and low-quality libraries, cDNA libraries were assessed by quantitative PCR with a primer pair of GAPDH, a housekeeping gene (forward: 5′-GTCGTGGAGTCTACTGGTGTCTTCAC-3′; reverse: 5′-GTTGTCATATTTCTCGTGGTTCACACCC-3′). Samples showing a high threshold cycle (Ct) value (>35 cycles) or no PCR amplification were discarded. 50–200 pg of each cDNA library were used to generate the Illumina sequencing library using EZ-Tera XT DNA library preparation kits (Enzynomics). After the final PCR amplification, samples were pooled and size-selected by SPRI beads (removing DNA bound to 0.3X beads and taking DNA bound to subsequent 0.6X beads). Pooled sequencing libraries were sequenced on an Illumina NextSeq 500 instrument using a 38-bp paired-end reads setting.

tag: tissue

value: colon

tag: age

value: 11 weeks old

tag: Sex

value: Female

tag: genotype

value: VillinCre;IPMKf/f

tag: cell type

value: tuft


title: p4-2_H03

description: SMART Seq2 with few modification


title: p4-2_H05

description: SMART Seq2 with few modification


title: p6-1_A08

description: SMART Seq2 with few modification

value: wt

value: epithelial


title: p4-2_H02

description: SMART Seq2 with few modification


title: p5-1_A08

description: SMART Seq2 with few modification


title: p4-2_G11

description: SMART Seq2 with few modification


title: p4-2_G10

description: SMART Seq2 with few modification


title: p4-2_G09

description: SMART Seq2 with few modification


title: p4-2_G08

description: SMART Seq2 with few modification


title: p4-2_G07

description: SMART Seq2 with few modification


title: p4-2_G04

description: SMART Seq2 with few modification


title: p4-2_G02

description: SMART Seq2 with few modification


title: p5-1_B01

description: SMART Seq2 with few modification


title: p4-2_F09

description: SMART Seq2 with few modification


title: p4-2_G12

description: SMART Seq2 with few modification


title: p4-2_F06

description: SMART Seq2 with few modification


title: p4-2_G03

description: SMART Seq2 with few modification


title: p4-2_F05

description: SMART Seq2 with few modification


title: p4-2_F11

description: SMART Seq2 with few modification


title: p4-2_F08

description: SMART Seq2 with few modification


title: p4-2_F12

description: SMART Seq2 with few modification


title: p4-2_F10

description: SMART Seq2 with few modification


title: p4-2_H07

description: SMART Seq2 with few modification


title: p4-2_F07

description: SMART Seq2 with few modification


title: p4-2_H01

description: SMART Seq2 with few modification


title: p4-2_G05

description: SMART Seq2 with few modification


title: p4-2_F01

description: SMART Seq2 with few modification


title: p4-2_E07

description: SMART Seq2 with few modification


title: p4-2_F04

description: SMART Seq2 with few modification


title: p4-2_E12

description: SMART Seq2 with few modification


title: p4-2_E06

description: SMART Seq2 with few modification


title: p4-2_E09

description: SMART Seq2 with few modification


title: p4-2_E05

description: SMART Seq2 with few modification


title: p4-2_G01

description: SMART Seq2 with few modification


title: p4-2_E11

description: SMART Seq2 with few modification


title: p4-2_E02

description: SMART Seq2 with few modification


title: p4-2_E04

description: SMART Seq2 with few modification


title: p4-2_D10

description: SMART Seq2 with few modification


title: p4-2_F02

description: SMART Seq2 with few modification


title: p4-2_D07

description: SMART Seq2 with few modification


title: p4-2_D09

description: SMART Seq2 with few modification


title: p4-2_E03

description: SMART Seq2 with few modification


title: p4-2_D04

description: SMART Seq2 with few modification


title: p4-2_D03

description: SMART Seq2 with few modification


title: p4-2_C10

description: SMART Seq2 with few modification


title: p4-2_C11

description: SMART Seq2 with few modification


title: p4-2_D02

description: SMART Seq2 with few modification


title: p4-2_C07

description: SMART Seq2 with few modification


title: p4-2_C04

description: SMART Seq2 with few modification


title: p4-2_C09

description: SMART Seq2 with few modification


title: p4-2_C08

description: SMART Seq2 with few modification


title: p4-2_C05

description: SMART Seq2 with few modification


title: p4-2_C03

description: SMART Seq2 with few modification


title: p4-2_C02

description: SMART Seq2 with few modification


title: p4-2_B10

description: SMART Seq2 with few modification


title: p4-2_C01

description: SMART Seq2 with few modification


title: p4-2_D12

description: SMART Seq2 with few modification


title: p4-2_D05

description: SMART Seq2 with few modification


title: p4-2_B09

description: SMART Seq2 with few modification


title: p4-2_D01

description: SMART Seq2 with few modification


title: p4-2_B05

description: SMART Seq2 with few modification


title: p4-2_B02

description: SMART Seq2 with few modification


title: p4-2_B04

description: SMART Seq2 with few modification


title: p4-2_B08

description: SMART Seq2 with few modification


title: p4-2_B03

description: SMART Seq2 with few modification


title: p4-2_B11

description: SMART Seq2 with few modification


title: p4-2_A12

description: SMART Seq2 with few modification


title: p4-2_A11

description: SMART Seq2 with few modification


title: p4-2_A10

description: SMART Seq2 with few modification


title: p4-2_A09

description: SMART Seq2 with few modification


title: p4-2_A08

description: SMART Seq2 with few modification


title: p4-2_E08

description: SMART Seq2 with few modification


title: p4-2_A07

description: SMART Seq2 with few modification


title: p4-2_A02

description: SMART Seq2 with few modification


title: p4-2_A06

description: SMART Seq2 with few modification


title: p4-2_A03

description: SMART Seq2 with few modification


title: p4-2_A01

description: SMART Seq2 with few modification


title: p4-2_D08

description: SMART Seq2 with few modification


title: p4-1_H12

description: SMART Seq2 with few modification


title: p4-1_H11

description: SMART Seq2 with few modification


title: p4-1_H09

description: SMART Seq2 with few modification


title: p4-1_H07

description: SMART Seq2 with few modification


title: p4-1_H06

description: SMART Seq2 with few modification


title: p4-1_H08

description: SMART Seq2 with few modification


title: p4-1_H05

description: SMART Seq2 with few modification


title: p4-1_H04

description: SMART Seq2 with few modification


title: p4-1_H03

description: SMART Seq2 with few modification


title: p4-1_H02

description: SMART Seq2 with few modification


title: p4-1_H01

description: SMART Seq2 with few modification


title: p4-1_G12

description: SMART Seq2 with few modification


title: p4-1_G11

description: SMART Seq2 with few modification


title: p4-1_G10

description: SMART Seq2 with few modification


title: p4-2_A04

description: SMART Seq2 with few modification


title: p4-1_G08

description: SMART Seq2 with few modification


title: p4-1_G07

description: SMART Seq2 with few modification


title: p4-1_G04

description: SMART Seq2 with few modification


title: p4-1_G05

description: SMART Seq2 with few modification


title: p4-1_G02

description: SMART Seq2 with few modification


title: p4-1_G03

description: SMART Seq2 with few modification


title: p4-1_G01

description: SMART Seq2 with few modification


title: p4-1_F10

description: SMART Seq2 with few modification


title: p4-1_F08

description: SMART Seq2 with few modification


title: p4-1_F07

description: SMART Seq2 with few modification


title: p4-1_G06

description: SMART Seq2 with few modification


title: p4-1_F06

description: SMART Seq2 with few modification


title: p4-1_F04

description: SMART Seq2 with few modification


title: p4-1_F03

description: SMART Seq2 with few modification


title: p4-1_G09

description: SMART Seq2 with few modification


title: p4-1_E12

description: SMART Seq2 with few modification


title: p4-1_F02

description: SMART Seq2 with few modification


title: p4-1_E11

description: SMART Seq2 with few modification


title: p4-1_E10

description: SMART Seq2 with few modification


title: p4-1_E09

description: SMART Seq2 with few modification


title: p4-1_E06

description: SMART Seq2 with few modification


title: p4-1_E08

description: SMART Seq2 with few modification


title: p4-1_F12

description: SMART Seq2 with few modification


title: p4-1_E02

description: SMART Seq2 with few modification


title: p4-1_E01

description: SMART Seq2 with few modification


title: p4-1_E03

description: SMART Seq2 with few modification


title: p4-1_D12

description: SMART Seq2 with few modification


title: p4-1_D11

description: SMART Seq2 with few modification


title: p4-1_D08

description: SMART Seq2 with few modification


title: p4-1_E05

description: SMART Seq2 with few modification


title: p4-1_F11

description: SMART Seq2 with few modification


title: p4-1_D07

description: SMART Seq2 with few modification


title: p4-1_D05

description: SMART Seq2 with few modification


title: p4-1_F05

description: SMART Seq2 with few modification


title: p4-1_C12

description: SMART Seq2 with few modification


title: p4-1_E07

description: SMART Seq2 with few modification


title: p4-1_D02

description: SMART Seq2 with few modification


title: p4-1_C10

description: SMART Seq2 with few modification


title: p4-1_C06

description: SMART Seq2 with few modification


title: p4-1_C11

description: SMART Seq2 with few modification


title: p4-1_C05

description: SMART Seq2 with few modification


title: p4-1_D01

description: SMART Seq2 with few modification


title: p4-1_C02

description: SMART Seq2 with few modification


title: p4-1_D09

description: SMART Seq2 with few modification


title: p4-1_B08

description: SMART Seq2 with few modification


title: p4-1_B12

description: SMART Seq2 with few modification


title: p4-1_B07

description: SMART Seq2 with few modification


title: p4-1_B06

description: SMART Seq2 with few modification


title: p4-1_C03

description: SMART Seq2 with few modification


title: p4-1_B05

description: SMART Seq2 with few modification


title: p4-1_A12

description: SMART Seq2 with few modification


title: p4-1_B04

description: SMART Seq2 with few modification


title: p4-1_A11

description: SMART Seq2 with few modification


title: p4-1_B03

description: SMART Seq2 with few modification


title: p4-1_A10

description: SMART Seq2 with few modification


title: p4-1_C07

description: SMART Seq2 with few modification


title: p4-1_A05

description: SMART Seq2 with few modification


title: p4-1_A08

description: SMART Seq2 with few modification


title: p4-1_C04

description: SMART Seq2 with few modification


title: p4-1_A09

description: SMART Seq2 with few modification


title: p4-1_A03

description: SMART Seq2 with few modification


title: p4-1_A02

description: SMART Seq2 with few modification


title: p4-1_A04

description: SMART Seq2 with few modification


title: p4-1_C01

description: SMART Seq2 with few modification


title: p4-1_B09

description: SMART Seq2 with few modification


title: p5-2_H07

description: SMART Seq2 with few modification


title: p3-2_H11

description: SMART Seq2 with few modification


title: p3-2_H10

description: SMART Seq2 with few modification


title: p3-2_H08

description: SMART Seq2 with few modification


title: p3-2_H09

description: SMART Seq2 with few modification


title: p3-2_H06

description: SMART Seq2 with few modification


title: p3-2_H03

description: SMART Seq2 with few modification


title: p3-2_H04

description: SMART Seq2 with few modification


title: p3-2_H05

description: SMART Seq2 with few modification


title: p3-2_G12

description: SMART Seq2 with few modification


title: p3-2_H01

description: SMART Seq2 with few modification


title: p3-2_G11

description: SMART Seq2 with few modification


title: p5-2_D03

description: SMART Seq2 with few modification


title: p3-2_H12

description: SMART Seq2 with few modification


title: p3-2_G05

description: SMART Seq2 with few modification


title: p3-2_G06

description: SMART Seq2 with few modification


title: p3-2_G08

description: SMART Seq2 with few modification


title: p3-2_G09

description: SMART Seq2 with few modification


title: p3-2_G10

description: SMART Seq2 with few modification


title: p3-2_G07

description: SMART Seq2 with few modification


title: p3-2_G04

description: SMART Seq2 with few modification


title: p3-2_G01

description: SMART Seq2 with few modification


title: p3-2_G02

description: SMART Seq2 with few modification


title: p3-2_G03

description: SMART Seq2 with few modification


title: p3-2_F10

description: SMART Seq2 with few modification


title: p3-2_F07

description: SMART Seq2 with few modification


title: p3-2_F08

description: SMART Seq2 with few modification


title: p3-2_F06

description: SMART Seq2 with few modification


title: p3-2_F03

description: SMART Seq2 with few modification


title: p3-2_F05

description: SMART Seq2 with few modification


title: p4-1_D10

description: SMART Seq2 with few modification


title: p3-2_F01

description: SMART Seq2 with few modification


title: p3-2_E10

description: SMART Seq2 with few modification


title: p3-2_E08

description: SMART Seq2 with few modification


title: p3-2_F11

description: SMART Seq2 with few modification


title: p3-2_E07

description: SMART Seq2 with few modification


title: p3-2_E05

description: SMART Seq2 with few modification


title: p3-2_E06

description: SMART Seq2 with few modification


title: p3-2_D07

description: SMART Seq2 with few modification


title: p3-2_E04

description: SMART Seq2 with few modification


title: p3-2_D05

description: SMART Seq2 with few modification


title: p3-2_D10

description: SMART Seq2 with few modification


title: p3-2_D04

description: SMART Seq2 with few modification


title: p3-2_D08

description: SMART Seq2 with few modification


title: p3-2_D11

description: SMART Seq2 with few modification


title: p3-2_E03

description: SMART Seq2 with few modification


title: p3-2_E02

description: SMART Seq2 with few modification


title: p3-2_E01

description: SMART Seq2 with few modification


title: p3-2_F04

description: SMART Seq2 with few modification


title: p3-2_D02

description: SMART Seq2 with few modification


title: p3-2_F02

description: SMART Seq2 with few modification


title: p3-2_E09

description: SMART Seq2 with few modification


title: p3-2_D12

description: SMART Seq2 with few modification


title: p3-2_C10

description: SMART Seq2 with few modification


title: p3-2_C12

description: SMART Seq2 with few modification


title: p3-2_D01

description: SMART Seq2 with few modification


title: p3-2_C08

description: SMART Seq2 with few modification


title: p3-2_C09

description: SMART Seq2 with few modification


title: p3-2_C05

description: SMART Seq2 with few modification


title: p3-2_C07

description: SMART Seq2 with few modification


title: p3-2_C04

description: SMART Seq2 with few modification


title: p3-2_C01

description: SMART Seq2 with few modification


title: p3-2_B11

description: SMART Seq2 with few modification


title: p3-2_B10

description: SMART Seq2 with few modification


title: p3-2_B08

description: SMART Seq2 with few modification


title: p3-2_B06

description: SMART Seq2 with few modification


title: p3-2_B05

description: SMART Seq2 with few modification


title: p3-2_B07

description: SMART Seq2 with few modification


title: p3-2_B04

description: SMART Seq2 with few modification


title: p3-2_B03

description: SMART Seq2 with few modification


title: p4-2_B01

description: SMART Seq2 with few modification


title: p3-2_A12

description: SMART Seq2 with few modification


title: p3-2_A11

description: SMART Seq2 with few modification


title: p3-2_B02

description: SMART Seq2 with few modification


title: p3-2_A02

description: SMART Seq2 with few modification


title: p3-2_A03

description: SMART Seq2 with few modification


title: p3-2_A09

description: SMART Seq2 with few modification


title: p3-1_H12

description: SMART Seq2 with few modification


title: p3-1_H11

description: SMART Seq2 with few modification


title: p3-2_A07

description: SMART Seq2 with few modification


title: p3-2_A06

description: SMART Seq2 with few modification


title: p3-2_A05

description: SMART Seq2 with few modification


title: p3-1_H07

description: SMART Seq2 with few modification


title: p3-1_H10

description: SMART Seq2 with few modification


title: p3-2_C02

description: SMART Seq2 with few modification


title: p3-1_H08

description: SMART Seq2 with few modification


title: p3-1_H05

description: SMART Seq2 with few modification


title: p3-1_H06

description: SMART Seq2 with few modification


title: p3-1_H03

description: SMART Seq2 with few modification


title: p3-1_H01

description: SMART Seq2 with few modification


title: p3-1_G11

description: SMART Seq2 with few modification


title: p3-1_G10

description: SMART Seq2 with few modification


title: p3-1_G09

description: SMART Seq2 with few modification


title: p3-1_G06

description: SMART Seq2 with few modification


title: p3-1_G07

description: SMART Seq2 with few modification


title: p3-1_G08

description: SMART Seq2 with few modification


title: p3-1_G05

description: SMART Seq2 with few modification


title: p3-2_B09

description: SMART Seq2 with few modification


title: p3-1_G03

description: SMART Seq2 with few modification


title: p3-1_G02

description: SMART Seq2 with few modification


title: p3-1_H04

description: SMART Seq2 with few modification


title: p3-1_F10

description: SMART Seq2 with few modification


title: p3-1_F05

description: SMART Seq2 with few modification


title: p3-1_F07

description: SMART Seq2 with few modification


title: p3-1_F12

description: SMART Seq2 with few modification


title: p3-1_F08

description: SMART Seq2 with few modification


title: p3-1_F04

description: SMART Seq2 with few modification


title: p3-1_F01

description: SMART Seq2 with few modification


title: p3-1_E11

description: SMART Seq2 with few modification


title: p3-1_E12

description: SMART Seq2 with few modification


title: p3-1_H02

description: SMART Seq2 with few modification


title: p3-1_F06

description: SMART Seq2 with few modification


title: p3-1_E10

description: SMART Seq2 with few modification


title: p5-1_H05

description: SMART Seq2 with few modification


title: p3-1_E08

description: SMART Seq2 with few modification


title: p3-1_E06

description: SMART Seq2 with few modification


title: p3-1_E07

description: SMART Seq2 with few modification


title: p3-1_G01

description: SMART Seq2 with few modification


title: p3-1_E02

description: SMART Seq2 with few modification


title: p3-1_E04

description: SMART Seq2 with few modification


title: p3-1_E05

description: SMART Seq2 with few modification


title: p3-1_E03

description: SMART Seq2 with few modification


title: p3-1_E01

description: SMART Seq2 with few modification


title: p3-1_D12

description: SMART Seq2 with few modification


title: p3-1_F03

description: SMART Seq2 with few modification


title: p3-1_F09

description: SMART Seq2 with few modification


title: p3-1_D10

description: SMART Seq2 with few modification


title: p3-1_D07

description: SMART Seq2 with few modification


title: p3-1_D08

description: SMART Seq2 with few modification


title: p3-1_D03

description: SMART Seq2 with few modification


title: p3-1_D06

description: SMART Seq2 with few modification


title: p3-1_D04

description: SMART Seq2 with few modification


title: p3-1_F11

description: SMART Seq2 with few modification


title: p3-1_D01

description: SMART Seq2 with few modification


title: p3-1_D05

description: SMART Seq2 with few modification


title: p3-1_C07

description: SMART Seq2 with few modification


title: p3-1_D02

description: SMART Seq2 with few modification


title: p3-1_C08

description: SMART Seq2 with few modification


title: p3-1_D11

description: SMART Seq2 with few modification


title: p3-1_C09

description: SMART Seq2 with few modification


title: p3-1_C06

description: SMART Seq2 with few modification


title: p3-1_C05

description: SMART Seq2 with few modification


title: p3-1_E09

description: SMART Seq2 with few modification


title: p3-1_C02

description: SMART Seq2 with few modification


title: p3-1_C04

description: SMART Seq2 with few modification


title: p3-1_B11

description: SMART Seq2 with few modification


title: p3-1_B09

description: SMART Seq2 with few modification


title: p3-1_C01

description: SMART Seq2 with few modification


title: p3-1_B07

description: SMART Seq2 with few modification


title: p3-1_B06

description: SMART Seq2 with few modification


title: p3-1_B08

description: SMART Seq2 with few modification


title: p3-1_B05

description: SMART Seq2 with few modification


title: p3-1_B04

description: SMART Seq2 with few modification


title: p3-1_C12

description: SMART Seq2 with few modification


title: p3-1_B02

description: SMART Seq2 with few modification


title: p3-1_B03

description: SMART Seq2 with few modification


title: p3-1_A11

description: SMART Seq2 with few modification


title: p3-1_B01

description: SMART Seq2 with few modification


title: p3-1_A06

description: SMART Seq2 with few modification


title: p3-1_A08

description: SMART Seq2 with few modification


title: p3-1_A05

description: SMART Seq2 with few modification


title: p2-2_G09

description: SMART Seq2 with few modification


title: p3-1_A10

description: SMART Seq2 with few modification


title: p3-1_A07

description: SMART Seq2 with few modification


title: p2-2_G08

description: SMART Seq2 with few modification


title: p2-2_G07

description: SMART Seq2 with few modification


title: p2-2_G06

description: SMART Seq2 with few modification


title: p3-1_A03

description: SMART Seq2 with few modification


title: small RNA-seq for chimpanzee iPS cells #1

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

library_source: transcriptomic

data_processing:
Cutadapt (DOI:10.14806/ej.17.1.200) was used to remove the adapter sequences.
the retained reads of 24 to 35 bp in length (corresponding to small RNAs of 24 to 35 nucleotides, which is the range for typical piRNAs) were mapped to the respective reference genomes (hg38 or panTro5) by Hisat2 (Kim et al. 2019) allowing multiple hits.
Reads originated from TE regions in the repeatmasker track were counted and normalized as RPM.  If a read was mapped to multiple candidate regions, all regions were used for read counting, using a weighted number, 1/n, where n is the number of mapped regions.
Assembly: hg38/panTro5
Supplementary files format and content: tab-separated files with TE names and RPM values (total, sense hits, and antisense hits)

molecule: total RNA

organism: Pan troglodytes

extract_protocol:
Total cellular RNAs were isolated from ~1×106 cells by using Isogen (TOYOBO) and Direct-ZolTM RNA (ZYMO RESEARCH) according to manufactures’ instructions.
After quality check by Agilent 2100 Bioanalyzer (Agilent Technologies), small RNA-seq libraries were prepared from approximately 0.5 μg of total RNA using NEBNext small RNA library kit (New England Biolabs).  After library amplification by PCR, products were run on 6% polyacrylamide gel electrophoresis, and a gel region corresponding to DNA sizes with 15 to 40 bp insertion were cut for DNA extraction.

tag: cell line

value: iPS cells

value: female

tag: origin of_ipscs

value: dermal fibroblasts


title: small RNA-seq for chimpanzee iPS cells #2


title: p2-2_G05

description: SMART Seq2 with few modification


title: Mixed intraerythrocytic stage total RNA

city: Khlong Nung

first: Pavita

last: Kaewprommal

state: Pathum Thani

department: NBT

country: Thailand

institute: NSTDA

data_processing:
Data were collected over 24 h runs using MinKnow software (Oxford Nanopore Technologies). The signals were converted to sequences in .fastq format using Scrappie basecalling software (Oxford Nanopore Technologies).
Cutadapt version 2.8 (Martin 2011) was used to identify cDNA reads containing both 5′ and 3′ cDNA adapter, trim adapters and reverse-complement first-strand cDNA reads. The settings used were: cutadapt --rc --discard-untrimmed -g CTACACGACGCTCTTCCGATCT...AAAAAAAAAGTACTCTGCGTTGATACCACTGCTT -e 0.2.
Preprocessed reads were aligned to the reference genome using the minimap2 tool (Li, 2018) in the spliced alignment mode guided by genome annotation with maximum intron 5 kb with settings: minimap2 -ax splice -uf -k14 -G 5k --secondary=no --junc-bed.
Candidate non-redundant isoform sequences were generated from the aligned reads using the TAMA collapse tool (Kuo et al 2020) with “low” settings: -x capped -rm low_mem -sj sj_priority -log log_off -lde 5 -sjt 20 -a 100 -z100 -m 20
Genome_build: Plasmodium falciparum 3D7 GCA_000002765.3
Supplementary_files_format_and_content: TAMA collapse output (isoform annotation) in .bed12 format

organism: Plasmodium falciparum 3D7

source_name: Intraerythrocytic parasites

growth_protocol: Plasmodium falciparum was cultured in vitro in human O+ erythrocytes and medium containing 8% pooled, heat inactivated human serum and buffered RPMI as described previously (Shaw et al., 2007).

extract_protocol:
The washed pellet of saponin-liberated parasites was suspended in Trizol™ reagent and RNA extracted according to the manufacturer’s instructions (Invitrogen).
10-30 ng of 5′ capped RNA sequin MixA (Hardwick et al., 2016) was added to P. falciparum total RNA. For purification of 5′ capped RNA, purified HseIF4E-eIF4G_x6His recombinant protein (50 µg) was immobilized on 40 µL of HisPur Ni-NTA Magnetic Beads (#88831, Thermo Scientific) equilibrated with RNase-free 1XPBS (Ambion). 50-100 µg of P. falciparum/spike-in RNA mixture was incubated with protein immobilized-beads for capture of 5′ capped RNA. Beads were washed thrice with 1 mL 1XPBS, and 5′ capped RNA was eluted in a solution of 1% SDS, 200 mM NaCl, 1 mM EDTA. 5′ capped RNA was purified by acidic phenol:chloroform extraction and ethanol precipitation. The 5′ capped RNA pellet was re-dissolved in 20 µL of nuclease-free water and genomic DNA was removed using a Turbo DNA-free kit following manufacturer’s instructions (Ambion).  First-strand cDNA synthesis reactions contained 100-300 ng of purified 5′ capped RNA spiked with RNA sequin as described above, primer (AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTVN) and Superscript IV (Thermo Scientific). RNA was removed by treatment with 0.2 N sodium hydroxide and first-strand cDNA was purified using 0.5x AMPure beads as recommended by the manufacturer (Beckman Coulter). A double-stranded 5′ adapter was made by annealing  adapter oligonucleotides (/5PHOS/AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT/3INVDT/ and ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNN). 5′ adapter was ligated to 50–100 ng cDNA using T4 DNA ligase (New England Biolabs). Excess adapter was removed and cDNA purified using 0.5x AMPure beads. Double-stranded cDNA was obtained by PCR amplification with primers  (/5PHOS/CTACACGACGCTCTTCCGATCT and /5PHOS/AAGCAGTGGTATCAACGCAGAGT) and KAPA HiFi HotStart Ready mix (Kapa Bioscience). The reaction conditions used were: 95°C 5 min; 15–20 cycles of 98°C 15 s, 62°C 5 min 30 s. DNA was purified using 0.5x AMPure beads and converted to Nanopore DNA sequencing library using a 1D ligation kit as recommended by the manufacturer (Oxford Nanopore Technologies). DNA sequencing library was quantified by QuantIT HS assay (Invitrogen) and agarose gel electrophoresis. Approximately 20 fmol of library DNA was sequenced on SpotON MkI flow cells (R9.4) in a Minion device (Oxford Nanopore Technologies).

treatment_protocol: Cultured parasites were liberated from the host cell by treatment with 0.1% (w/v) saponin. Parasite pellets were washed thrice with phosphate buffered saline (1x PBS; 137 mM NaCl, 2.7 mM KCl, 8 mM Na2HPO4, and 2 mM KH2PO4)  prior to extraction.

tag: Stage

value: Intraerythrocytic parasites


title: p2-2_G03

description: SMART Seq2 with few modification


title: p3-1_C03

description: SMART Seq2 with few modification


title: p2-2_G02

description: SMART Seq2 with few modification


title: T. ethanolicus, 60, stationary, biol rep 3

city: 't Horntje (Texel)

first: Diana

middle: X.

last: Sahonero-Canavesi

address: Landsdiep 4

country: Netherlands

institute: NIOZ

data_processing:
Adapter sequences and poor quality reads were removed with Trimmomatic v0.36 (parameter settings: Illuminaclip: TruSeq3-SE.fa:2:30:10, leading: 20, trailing: 20, sliding window: 5: 20 min length: 40);
Poly-G tails were removed using cutadapt v1.16 with the --nextseq-trim parameter set to 20
Gene counts were calculated using Salmon v1.3.0 with the mapping-based mode against the reference genome of T. ethanolicus JW200 (NCBI Reference Sequence: CP033580.1)
Quantification estimates were imported into R/Bioconductor with tximport and differential gene expression between growth phases and temperatures was assessed with DESeq2 v1.26.0 using the default values
Assembly: NCBI Reference Sequence: CP033580.1
Supplementary files format and content: tab-delimited text files include raw counts and TPM values for each sample

organism: Thermoanaerobacter ethanolicus

source_name: bacterial cell

growth_protocol: Thermoanaerobacter ethanolicus (strain JW2000, DMS 2246) was cultivated under anaerobic conditions in 80 ml batch cultures in 250 ml serum bottles. The media was composed of (per liter): (NH4)2SO4 1.3 g, KH2PO4 0.375 g, K2HPO4 0.75 g, MgCl2 x 6H2O 0.4 g, CaCl2 x 2H2O 0.13 g, FeSO4 x 7H2O (0.001% (w/v) in H2SO4 2 mM), yeast extract 4 g, resazurin standard stock solution 100x, and pH was adjusted to 6.7 with 5 M NaOH. Growth was monitored by measuring the optical density (OD) at 600 nm and by fluorescent microscopy. Cultures were grown at 45°C or 60°C for 1 sub-cultivation growth cycle to ensure acclimatization.

extract_protocol:
Cells cleared from medium were snap-frozen in dry-ice and stored at -80oC until usage. For RNA extraction the frozen cell pellets were resuspended in 4 ml RNA-later (Invitrogen) while maintained on ice. A 200 µl sample was taken from the cell suspension for RNA isolation. The cells were incubated at room temperature for 5 min. The cells were then pelleted for 10 min at 4700xg. The cell pellet was resuspended in 100 µl TE buffer pH 7.5. 500 µl TRIzol reagent was added and mixed. The subsequent suspension was transferred to a pre-cooled 2 ml screw-cap tube supplemented with 250 µl sterile 0.1 mm and 1 mm glass beads. Cells were lysed by beating 6 rounds of 25 sec pulse at 6500 rpm and 5 min pause on watery ice. Ice-cold chloroform (200 µl) was subsequently added and mixed by shaking. Two phases were produced by centrifugation for 15 min. at 12,000xg. The transparent aqueous phase was transferred to a new RNAse-free pre-cooled tube without disturbing the interphase. Ethanol was added at 1 volume and mixed. The isolate was transferred to an RNAeasy column and centrifuged 15 seconds at 8000 xg to bind nucleic acids to the column. The column was rinsed with 350 µl RLT buffer by centrifugation. An 80 µl RNAse-free DNAse reaction mixture was added to the column and incubated 20 min at 30oC to digest DNA contaminants. The column was rinsed with 350 µl RW1, incubated 5 min and centrifuged. The column was then washed with 700 µl RPE, centrifuged and washed with 80% ethanol. The column was dried by a 2 min spin at 21.000 xg. To elute the RNA, 35 µl nuclease-free water was added and eluted by 1 min centrifugation at 8,000 xg. For rRNA depletion, 18 µl (1 µg) of total RNA was hybridized with the Pan-Prokaryote riboPOOL 3' biotinylated probe following the depletion protocol and stored at -80°C until library preparation.
RNA libraries for RNA-seq were prepared using TruSeq RNA stranded kit following manufacturer's protocols and sequenced at the Utrecht Sequencing facility (USeq, The Netherlands)

tag: strain

value: bacterial cell

tag: growth phase

value: stationary

tag: growth temperature

value: 60° C


title: p3-1_F02

description: SMART Seq2 with few modification


title: T. ethanolicus, 60, stationary, biol rep 1


title: p2-2_G01

description: SMART Seq2 with few modification


title: p3-1_A01

description: SMART Seq2 with few modification


title: T. ethanolicus, 60, mid exp, biol rep 2

value: mid exponential


title: p2-2_F11

description: SMART Seq2 with few modification


title: p2-2_F10

description: SMART Seq2 with few modification


title: p2-2_F12

description: SMART Seq2 with few modification


title: T. ethanolicus, 60, mid exp, biol rep 1


title: p2-2_F09

description: SMART Seq2 with few modification


title: T. ethanolicus, 60, mid exp, biol rep 3


title: T. ethanolicus, 60, late exp, biol rep 3

value: late exponential


title: T. ethanolicus, 60, late exp, biol rep 1


title: T. ethanolicus, 60, late exp, biol rep 2


title: T. ethanolicus, 45, stationary, biol rep 2

value: 45° C


title: p2-2_F08

description: SMART Seq2 with few modification

value: colon


title: p2-2_F06

description: SMART Seq2 with few modification

value: 11 weeks old


title: T. ethanolicus, 45, mid exp, biol rep 3


title: T. ethanolicus, 45, stationary, biol rep 1


title: p2-2_F04

description: SMART Seq2 with few modification

value: Female


title: p2-2_F03

description: SMART Seq2 with few modification

value: VillinCre;IPMKf/f


title: p2-2_G04

description: SMART Seq2 with few modification

value: tuft


title: T. ethanolicus, 60, stationary, biol rep 2


title: p2-2_F02

description: SMART Seq2 with few modification


title: T. ethanolicus, 45, mid exp, biol rep 1


title: p2-2_F01

description: SMART Seq2 with few modification


title: T. ethanolicus, 45, late exp, biol rep 3


title: T. ethanolicus, 45, late exp, biol rep 2


title: p2-2_E06

description: SMART Seq2 with few modification


title: p2-2_E09

description: SMART Seq2 with few modification


title: p2-2_E12

description: SMART Seq2 with few modification


title: p2-2_E07

description: SMART Seq2 with few modification


title: T. ethanolicus, 45, stationary, biol rep 3


title: Delta82S26H4AC

city: Hanover

first: Bin

last: Wang

state: New Hampshire

address: Vail Loading Dock, Attn: 702 Remsen

department: MSB

country: USA

institute: Geisel School at Dartmouth

description: Ion Chef System

library_source: genomic

data_processing:
Samples were mapped to the Neurospora crassa genome (from GenBank) using TMAP (Ion 569 Software, https://github.com/iontorrent/TMAP)
Peaks were called using MACS2 (https://github.com/taoliu/MACS).
Peaks were annotated with ChIPseeker (Bioconductor, https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html).
In addition to MACS2, the SICER software (https://home.gwu.edu/~wpeng/Software.htm) was used to identify peaks and identify differentially abundant peaks between WT and mutant strains.
For comparison of WT vs. control in histone and acetylated histone, three runs apiece were performed with window sizes of 200, 400 and 600, and gap sizes of 600, 1,200 and 1,800, respectively.
Redundant peaks between the three runs (within 2,500 bp) were eliminated with a simple R script. Another script was used to identify genes within 1,000 bp from either border of the peaks.
Assembly: NC12
Supplementary files format and content: bedgraph

molecule: genomic DNA

organism: Neurospora crassa

source_name: Neurospora tissue

growth_protocol: 2% LCM medium, 25 degrees,  in the dark for 20 hrs for WT while 26 hrs for the mutant

extract_protocol:
Neurospora tissue was cross-linked with 3% formaldehyde for 15 min and quenched with 0.25 M glycine for 5 min. Tissue was then washed with PBS three times and vacuum-dried; 0.4 g was weighed, cut into 9 pieces, and each piece soaked in 0.5 ml SDS lysis buffer (50 mM Tris/HCL [pH 8.0], 1% SDS, 5 mM EDTA) containing Roche protease inhibitors (Sigma-Aldrich, Catalog # 11836170001). The soaked tissue was first sonicated for 8 sec for three times at 30% amplitude with a Bronson sonicator equipped with a microtip, and then further sonicated in a water bath sonicator 5 times for 5 min each with an interval of 30 sec on and 30 sec off.
The purified ChIP DNA was end-repaired and ligated to Ion-compatible barcode adapters using Ion XpressTM Plus Fragment kit (Catalog # 4471269) and Ion XpressTM Barcode Adapters (Catalog # 4471250). The final libraries were purified with two rounds of AMPure XP Bead capture to size select fragments between 160 to 340 bps in length. The emulsion clonal bead amplification to generate bead templates for the Ion Torrent platform was performed on the Ion Chef System (Thermo Fisher Scientific) with the Ion PI™ Hi-Q™ Chef Kit (Thermo Fisher Scientific, Catalog # A27198) and Ion PI™ Chip Kit v3 (Thermo Fisher Scientific, Catalog # A26771).

treatment_protocol: shaking

value: Neurospora tissue

tag: time

value: 26 hr

tag: chip antibody


title: p2-2_E08

description: SMART Seq2 with few modification


title: T. ethanolicus, 45, mid exp, biol rep 2


title: p2-2_E11

description: SMART Seq2 with few modification


title: 328_4D20_Input

description: Ion Chef System

value: WT

value: 20 hr


title: 328_4D20H4

description: Ion Chef System


title: T. ethanolicus, 45, late exp, biol rep 1


title: p2-2_D09

description: SMART Seq2 with few modification


title: p2-2_D10

description: SMART Seq2 with few modification


title: p2-2_E01

description: SMART Seq2 with few modification


title: p2-2_E04

description: SMART Seq2 with few modification


title: p2-2_D12

description: SMART Seq2 with few modification


title: p2-2_F05

description: SMART Seq2 with few modification


title: Delta82D26H4

description: Ion Chef System


title: Delta82D26_Input

description: Ion Chef System


title: p2-2_D08

description: SMART Seq2 with few modification


title: p2-2_D06

description: SMART Seq2 with few modification


title: ACC7.Plate7

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
scRNA-seq data were aligned to GRCh38 with STAR42 and counted with featureCounts.
Assembly: hg38
Supplementary files format and content: counts.txt (the beginning of the name of each cell corresponds to the sample it comes from)

organism: Homo sapiens

source_name: Adenoid cystic carcinoma tumor

extract_protocol:
Samples were minced and dissociated with a Human Tumor Dissociation Kit (Miltenyi Biotec) according to manufacturer guidelines. Single cell suspensions were filtered, and cells were resuspended in PBS with 1% bovine serum albumin (BSA; Sigma-Aldrich). Trypan blue (ThermoFisher Scientific) was used to confirm cell viability of > 90% in all samples. Cells were stained with CD45-vioblue (Miltenyi Biotec), as well as 1 μM calcein AM (ThermoFisher Scientific), and 0.22 μM TO-PRO-3 iodide (ThermoFisher Scientific) for viability prior to sorting. Fluorescence-activated cell sorting (FACS) was performed on FACSAria Fusion Special Order System (BD Biosciences) using 488 nm (calcein AM, 530/30 filter), 640 nm (TO-PRO-3, 670/14 filter), and 405 nm (Vioblue, 450/50 filter) lasers. We captured singlet viable cells using standard forward scatter height versus area criteria, as well as calceinhigh and TO-PROlow gates. Subsquently, CD45- cells were captured to enrich for cancer cells and deplete immune cells. Individual cells were sorted into TCL- buffer (QIAGEN) with 1% β-mercaptoethanol in 96-well plates. Plates were snap frozen and stored at -80oC before cDNA synthesis and library construction.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol, with the following modifications: Agencourt RNAClean XP beads (Beckman Coulter) was used to purify RNA prior to reverse transcription with Superscript II (ThermoFisher Scientific) or Maxima (ThermoFisher Scientific) reverse transcriptase. Whole transcriptome amplification was performed using the KAPA HiFi HotStart ReadyMix (KAPA Biosystems).

value: Adenoid cystic carcinoma tumor

tag: site

value: Right buccal mucosa

tag: histology

value: Tubular/solid

tag: ihc profile

tag: perineural invasion

value: Present

tag: lymphovascular invasion


title: ACC7.Plate3

tag: tissue


title: p2-2_E05

description: SMART Seq2 with few modification

tag: age

tag: Sex


title: p2-2_D07

description: SMART Seq2 with few modification

tag: genotype

tag: cell type


title: ACC7.Plate2


title: p2-2_D04

description: SMART Seq2 with few modification


title: ACC5.Plate4

value: Left parotid gland

value: Cribriform

value: MYB+

value: Absent


title: ACC7.Plate1


title: p2-2_D05

description: SMART Seq2 with few modification

value: colon


title: p2-2_D03

description: SMART Seq2 with few modification

value: 11 weeks old


title: ACC7.Plate13.LN

value: Right level 1 lymph node


title: 328_4D20H4AC

description: Ion Chef System


title: HMC_GVC

first: Hyo Min

last: Kim

address: 291 Daehak-ro

department: Department of Bio and Brain Engineering

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned to the human reference genome sequence (GRCh38, GENCODE v. 39) by using STAR version 2.7.10a program.
samtools sort method using BAM-aligned files sorted by coordinate and differentially expressed gene were determined based on counts from htseq
Expression data was normalized multi-sample comparison was performed by edgeR package
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were sorted
Assembly: version 39 of mouse reference genome GRCh38
Supplementary files format and content: tab-delimited text files include log2-transformation of counts per million (CPM) within calculated scaling factor using trimmed mean of the M-values (TMM)

source_name: human leptomeninges-derived fibroblast cells

growth_protocol: Specialty Medium (#1401, ScienCell) was used for culture medium for cells, adding the 2 % of fetal bovine serum (FBS), 1 % of antibiotic solution (P/S), and 1X meningeal cell growth supplement (MCGS). Cells were cultured in PLL (2 g/cm2) and type-I collagen (0.1 mg/mL)-coated T75 flask incubating with 5% CO2/95% air. 0.025 % Trypsin/EDTA solution was used to detach the cells for experiments and seeding density was 5 000 cells/cm2, subculturing when the culture reaches 90-95 % confluency. Culturing cells were followed by instructions from ScienCell until passage number 7. To adapt cells with type-I collagen, T75 flasks were coated with 2 g/cm2 of poly-L-lysine solution adding 0.1 mg/mL type-I collagen diluted in 0.1 % acetic acid solution. Cells were seeded at a density of 5 000 cells/cm2 and cultured for 3 days for all in vitro experiments.

extract_protocol:
As total RNA was isolated using Trizol method , QC validation and total RNA sequencing were all performed by ebiogen (Seoul, Korea).
For control and test RNAs, the construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions. In brief, each 500ng total RNA were prepared and an oligo-dT primer containing an Illumina-compatible sequence at its 5’ end was hybridized to the RNA and reverse transcription was performed.

value: wild-type

tag: condition

value: vitrified collagen membrane with glycation


title: HMC_VC

value: human leptomeninges-derived fibroblast cells

value: vitrified collagen membrane without glycation


title: p2-2_D01

description: SMART Seq2 with few modification

value: Female

value: VillinCre;IPMKf/f

value: tuft


title: p2-2_C12

description: SMART Seq2 with few modification


title: ACC5.Plate2

value: Adenoid cystic carcinoma tumor


title: ACC5.Plate1


title: p2-2_C11

description: SMART Seq2 with few modification


title: ACC22.Plate2

value: Left floor of mouth


title: p2-2_C09

description: SMART Seq2 with few modification


title: p2-2_C10

description: SMART Seq2 with few modification


title: p2-2_C08

description: SMART Seq2 with few modification


title: ACC22.Plate3

value: Present


title: ACC22.Plate12.LN

value: Left level 3 lymph node


title: ACC22.Plate1

value: Cribriform


title: ACC22.Plate11.LN

value: MYB+


title: p2-2_C07

description: SMART Seq2 with few modification


title: p2-2_C05

description: SMART Seq2 with few modification


title: p2-2_C02

description: SMART Seq2 with few modification


title: p2-2_C01

description: SMART Seq2 with few modification


title: ACC2.Plate4

value: Right preauricular

value: Tubular/cribriform

value: Absent


title: ACC21.Plate5

value: Right base of tongue


title: p2-2_C03

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old


title: ACC21.Plate1


title: p2-2_B11

description: SMART Seq2 with few modification


title: p2-2_B10

description: SMART Seq2 with few modification


title: ACC19.Plate3

value: Left parotid gland

value: Tubular/solid


title: ACC19.Plate1


title: ACC2.Plate2


title: p2-2_B09

description: SMART Seq2 with few modification

value: Female


title: p2-2_B08

description: SMART Seq2 with few modification

value: VillinCre;IPMKf/f


title: ACC2.Plate1


title: ACC19.Plate2


title: ACC15.Plate1

value: Right orbit


title: p2-2_B07

description: SMART Seq2 with few modification

value: tuft


title: p2-2_B05

description: SMART Seq2 with few modification


title: p2-2_B06

description: SMART Seq2 with few modification


title: p2-2_C04

description: SMART Seq2 with few modification


title: Control MDA-MB-231  [Tube_ctl_MDA_MB.231_S115]

city: New Delhi

first: Smriti

last: Chawla

address: Okhla Industrial Estate, Phase III, near Govind Puri Metro Station

country: India

institute: Indraprastha Institute of Information Technology,

data_processing:
RSEM index generated on hg19
Read data aligned to index using RSEM/bowtie
Quantified gene expression levels in counts using RSEM v1.2.44
Genomic mappings(GM) performed with TopHat 2 v2.0.135 and GM percentages calculated using resulting alignments
Raw sequencing read data aligned to the human rRNA sequences using bowtie 2 v2.2.46, and calculated percentage of reads aligned to rRNA as reads aligned to sequences divided by the total reads
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated csv files include RSEM TPM values for each Sample

growth_protocol: MDA-MB-231 cells (triple-negative breast carcinoma, ATCC® HTB-26 ™) were cultured using the DMEM (high modified) culture medium supplemented with 10% inactivated fetal bovine serum and 1% penicillin/streptomycin, replicating the culture every three days, keeping the culture at a confluence of 40% at the time of passage, at 37°C in a humid atmosphere at 5% CO2. The adherent cells were dissociated with the TrypLE reagent (Gibco) and resuspended in the complete culture medium. NK-92MI cells (human NK cells genetically modified to produce interleukin 2, ATCC® CRL-2408) were cultured using the AMEM (Alpha Minimum Essential medium) culture medium, plus 0.2 mM inositol, 0.1 mM mercaptoethanol, 0.02 mM folic acid, 12.5% fetal bovine serum and 12.5% horse serum. The cells were homogenized in order to separate the clusters of NKs prior to the replication of the culture into a new 25 cm² flask (1mL of cells cultured previously + 9mL new culture medium). Both cell lines were cultured separately for the subsequent cell-cell interaction experiment using the Polaris equipment (Fluidigm, South San Francisco, USA).

extract_protocol:
NA
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Preparation Kit (FC-131-1096), using the cDNA synthetized from total isolated RNA.

treatment_protocol: Activation was assessed after 24 and 48 hours of cell incubation in a proportion of 3 NK cells for each MDA-MB-231 by evaluating the markers (CD25, CD69, and CD314) expressed from cell-cell contact, using flow cytometry (Sony SH800S).

value: Pooled control cancer cell

tag: cell line


title: p2-2_B04

description: SMART Seq2 with few modification


title: ACC21.Plate4

value: Adenoid cystic carcinoma tumor

value: Present


title: Control NK-92MI  [Tube_ctl_NK92_S122]

value: Pooled control NK cell


title: p2-2_B12

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_48_S144]

value: Cancer cell


title: p2-2_B03

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_47_S145]


title: p2-2_B02

description: SMART Seq2 with few modification


title: p2-2_B01

description: SMART Seq2 with few modification


title: ACC5.Plate11.Recurr

value: Recurrance

value: Cribriform

value: MYB+


title: TU [chip8_1851022116_site_45_S141]


title: p2-2_A11

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_44_S142]


title: TU [chip8_1851022116_site_43_S143]


title: p2-2_A10

description: SMART Seq2 with few modification


title: p2-2_F07

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_42_S138]


title: ACC15.Plate5

value: Tubular/cribriform

value: Absent


title: TU [chip8_1851022116_site_41_S139]


title: p2-2_A08

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old


title: p2-2_A07

description: SMART Seq2 with few modification


title: p2-2_A04

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_39_S135]


title: TU [chip8_1851022116_site_38_S136]


title: p2-2_A05

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_37_S137]


title: TU [chip8_1851022116_site_40_S140]


title: p2-2_A02

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_35_S133]

value: Cancer-NK doublet


title: TU [chip8_1851022116_site_46_S146]


title: p2-2_A03

description: SMART Seq2 with few modification

value: Female


title: p2-1_H10

description: SMART Seq2 with few modification

value: VillinCre;IPMKf/f


title: TU-NK [chip8_1851022116_site_36_S132]


title: p2-2_A12

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_34_S134]


title: p2-2_A09

description: SMART Seq2 with few modification


title: p2-1_H08

description: SMART Seq2 with few modification


title: p2-1_H09

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_30_S126]


title: TU-NK [chip8_1851022116_site_31_S131]


title: TU-NK [chip8_1851022116_site_33_S129]


title: p2-1_H05

description: SMART Seq2 with few modification


title: p2-1_H07

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_32_S130]


title: p2-1_H04

description: SMART Seq2 with few modification


title: p2-2_A06

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_29_S127]


title: p2-1_H03

description: SMART Seq2 with few modification


title: p2-1_H06

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_26_S124]


title: p2-1_G12

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_25_S125]


title: p2-1_G09

description: SMART Seq2 with few modification


title: p2-1_G10

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_23_S120]


title: TU-NK [chip8_1851022116_site_27_S123]


title: p2-1_G08

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_21_S118]


title: p2-1_G07

description: SMART Seq2 with few modification


title: p2-1_G06

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_24_S121]


title: TU-NK [chip8_1851022116_site_28_S128]


title: p2-1_G05

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_19_S116]


title: p2-1_H02

description: SMART Seq2 with few modification


title: p2-1_G04

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_20_S117]


title: p2-1_H01

description: SMART Seq2 with few modification


title: p2-1_G02

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_18_S114]


title: TU [chip8_1851022116_site_17_S113]


title: p2-1_G03

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_15_S111]


title: TU [chip8_1851022116_site_16_S112]


title: p2-1_G01

description: SMART Seq2 with few modification


title: p2-1_F12

description: SMART Seq2 with few modification


title: TU [chip8_1851022116_site_14_S110]


title: TU-NK [chip8_1851022116_site_13_S109]


title: TU-NK [chip8_1851022116_site_22_S119]


title: Unknown [chip8_1851022116_site_12_S108]

source_name: Unknown

value: Unknown


title: p2-1_F11

description: SMART Seq2 with few modification

value: tuft


title: p2-1_F10

description: SMART Seq2 with few modification


title: NK [chip8_1851022116_site_11_S107]

value: NK cell


title: p2-1_F09

description: SMART Seq2 with few modification


title: Unknown [chip8_1851022116_site_10_S106]


title: p2-1_F07

description: SMART Seq2 with few modification


title: p2-1_F06

description: SMART Seq2 with few modification


title: NK [chip8_1851022116_site_08_S104]


title: p2-1_F05

description: SMART Seq2 with few modification


title: p2-1_F03

description: SMART Seq2 with few modification


title: NK [chip8_1851022116_site_06_S102]


title: p2-1_F02

description: SMART Seq2 with few modification


title: NK [chip8_1851022116_site_02_S98]


title: p2-1_F01

description: SMART Seq2 with few modification


title: TU-NK [chip8_1851022116_site_04_S100]


title: NK [chip8_1851022116_site_03_S99]


title: p2-1_E09

description: SMART Seq2 with few modification


title: p2-1_E11

description: SMART Seq2 with few modification


title: NK [chip8_1851022116_site_05_S101]


title: p2-1_E07

description: SMART Seq2 with few modification


title: p2-1_E06

description: SMART Seq2 with few modification


title: TU [chip6_1851027105_site_47_S95]


title: NK [chip8_1851022116_site_01_S97]


title: TU [chip6_1851027105_site_48_S94]


title: p2-1_E03

description: SMART Seq2 with few modification


title: TU [chip6_1851027105_site_46_S96]


title: p2-1_E02

description: SMART Seq2 with few modification


title: p2-1_F08

description: SMART Seq2 with few modification


title: p2-1_E01

description: SMART Seq2 with few modification


title: NK [chip8_1851022116_site_09_S105]


title: TU [chip6_1851027105_site_44_S92]


title: p2-1_D12

description: SMART Seq2 with few modification


title: TU [chip6_1851027105_site_45_S91]


title: TU [chip6_1851027105_site_43_S93]


title: NK [chip8_1851022116_site_07_S103]


title: TU [chip6_1851027105_site_42_S82]


title: p2-1_D11

description: SMART Seq2 with few modification


title: p2-1_D10

description: SMART Seq2 with few modification


title: TU [chip6_1851027105_site_41_S83]


title: TU [chip6_1851027105_site_40_S84]


title: p2-1_D09

description: SMART Seq2 with few modification


title: TU [chip6_1851027105_site_37_S81]


title: p2-1_D08

description: SMART Seq2 with few modification


title: p2-1_D06

description: SMART Seq2 with few modification


title: p2-1_D03

description: SMART Seq2 with few modification


title: p2-1_D07

description: SMART Seq2 with few modification


title: TU [chip6_1851027105_site_38_S80]


title: p2-1_D01

description: SMART Seq2 with few modification


title: TU-NK [chip6_1851027105_site_36_S70]


title: TU-NK [chip6_1851027105_site_34_S72]


title: TU-NK [chip6_1851027105_site_33_S67]


title: TU-NK [chip6_1851027105_site_35_S71]


title: TU-NK [chip6_1851027105_site_32_S68]


title: p2-1_C12

description: SMART Seq2 with few modification


title: p2-1_D05

description: SMART Seq2 with few modification


title: p2-1_C11

description: SMART Seq2 with few modification


title: p2-1_D02

description: SMART Seq2 with few modification


title: TU-NK [chip6_1851027105_site_30_S58]


title: p2-1_C09

description: SMART Seq2 with few modification


title: p2-1_C10

description: SMART Seq2 with few modification


title: TU [chip6_1851027105_site_39_S79]


title: TU-NK [chip6_1851027105_site_27_S55]


title: TU-NK [chip6_1851027105_site_25_S57]


title: p2-1_C05

description: SMART Seq2 with few modification


title: TU-NK [chip6_1851027105_site_28_S60]


title: TU-NK [chip6_1851027105_site_26_S56]


title: p2-1_C07

description: SMART Seq2 with few modification


title: p2-1_C06

description: SMART Seq2 with few modification


title: p2-1_C01

description: SMART Seq2 with few modification


title: p2-1_C03

description: SMART Seq2 with few modification


title: TU-NK [chip6_1851027105_site_21_S45]


title: TU-NK [chip6_1851027105_site_20_S44]


title: p2-1_B11

description: SMART Seq2 with few modification

value: epithelial


title: TU-NK [chip6_1851027105_site_24_S48]


title: TU-NK [chip6_1851027105_site_22_S46]


title: TU-NK [chip6_1851027105_site_19_S43]


title: p2-1_C04

description: SMART Seq2 with few modification


title: p2-1_B10

description: SMART Seq2 with few modification


title: p2-1_C02

description: SMART Seq2 with few modification


title: TU-NK [chip6_1851027105_site_23_S47]


title: p2-1_B08

description: SMART Seq2 with few modification


title: NK [chip6_1851027105_site_18_S36]


title: TU-NK [chip6_1851027105_site_16_S34]


title: TU-NK [chip6_1851027105_site_29_S59]


title: p2-1_B12

description: SMART Seq2 with few modification


title: p2-1_B07

description: SMART Seq2 with few modification


title: p2-1_B09

description: SMART Seq2 with few modification


title: p2-1_C08

description: SMART Seq2 with few modification


title: TU-NK [chip6_1851027105_site_31_S69]


title: TU-NK [chip6_1851027105_site_15_S33]


title: TU-NK [chip6_1851027105_site_13_S31]


title: TU-NK [chip6_1851027105_site_17_S35]


title: p2-1_B04

description: SMART Seq2 with few modification


title: NK [chip6_1851027105_site_12_S24]


title: p2-1_A12

description: SMART Seq2 with few modification


title: p2-1_B02

description: SMART Seq2 with few modification


title: p2-1_A06

description: SMART Seq2 with few modification


title: p2-1_A08

description: SMART Seq2 with few modification


title: p2-1_B03

description: SMART Seq2 with few modification


title: NK [chip6_1851027105_site_09_S21]


title: p2-1_A05

description: SMART Seq2 with few modification


title: Unknown [chip6_1851027105_site_10_S22]


title: Unknown [chip6_1851027105_site_11_S23]


title: NK [chip6_1851027105_site_04_S10]


title: NK [chip6_1851027105_site_07_S19]


title: NK [chip6_1851027105_site_06_S12]


title: p2-1_A11

description: SMART Seq2 with few modification


title: p2-1_A03

description: SMART Seq2 with few modification


title: NK [chip6_1851027105_site_08_S20]


title: NK [chip6_1851027105_site_03_S9]


title: p2-1_A02

description: SMART Seq2 with few modification


title: NK [chip6_1851027105_site_05_S11]


title: NK [chip6_1851027105_site_01_S7]


title: p2-1_B06

description: SMART Seq2 with few modification


title: p2-1_A04

description: SMART Seq2 with few modification


title: p2-1_A01

description: SMART Seq2 with few modification


title: TU-NK [chip6_1851027105_site_14_S32]


title: NK [chip6_1851027105_site_02_S8]


title: p2-1_B05

description: SMART Seq2 with few modification


title: TU [chip5_1851027101_site_48_S88]


title: p1-2_H11

description: SMART Seq2 with few modification

value: wt


title: p2-1_A10

description: SMART Seq2 with few modification


title: p1-2_H12

description: SMART Seq2 with few modification


title: p1-2_H10

description: SMART Seq2 with few modification


title: TU [chip5_1851027101_site_47_S89]


title: TU [chip5_1851027101_site_44_S86]


title: TU [chip5_1851027101_site_46_S90]


title: TU [chip5_1851027101_site_45_S85]


title: TU [chip5_1851027101_site_42_S76]


title: TU [chip5_1851027101_site_40_S78]


title: p1-2_H06

description: SMART Seq2 with few modification


title: p1-2_H09

description: SMART Seq2 with few modification


title: p1-2_H04

description: SMART Seq2 with few modification


title: TU [chip5_1851027101_site_39_S73]


title: p1-2_H07

description: SMART Seq2 with few modification


title: p1-2_H05

description: SMART Seq2 with few modification


title: p1-2_H03

description: SMART Seq2 with few modification


title: Unknown [chip5_1851027101_site_38_S74]


title: p1-2_H02

description: SMART Seq2 with few modification


title: p1-2_H01

description: SMART Seq2 with few modification


title: TU [chip5_1851027101_site_37_S75]


title: TU-NK [chip5_1851027101_site_36_S64]


title: p1-2_G12

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_35_S65]


title: p1-2_G10

description: SMART Seq2 with few modification


title: p1-2_G09

description: SMART Seq2 with few modification


title: p1-2_H08

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_33_S61]


title: TU-NK [chip5_1851027101_site_34_S66]


title: p1-2_G08

description: SMART Seq2 with few modification


title: p1-2_G06

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_32_S62]


title: TU-NK [chip5_1851027101_site_31_S63]


title: p1-2_G07

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_27_S49]


title: p1-2_G03

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_29_S53]


title: TU-NK [chip5_1851027101_site_28_S54]


title: TU-NK [chip5_1851027101_site_26_S50]


title: p1-2_F12

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_25_S51]


title: TU-NK [chip5_1851027101_site_24_S42]


title: p1-2_F11

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_23_S41]


title: p1-2_F09

description: SMART Seq2 with few modification


title: TU [chip5_1851027101_site_43_S87]


title: p1-2_F10

description: SMART Seq2 with few modification


title: TU [chip5_1851027101_site_41_S77]


title: p1-2_F08

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_30_S52]


title: TU-NK [chip5_1851027101_site_21_S39]


title: TU-NK [chip5_1851027101_site_19_S37]


title: p1-2_F07

description: SMART Seq2 with few modification


title: p1-2_F06

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_22_S40]


title: p1-2_G02

description: SMART Seq2 with few modification


title: p1-2_F05

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_18_S30]


title: TU-NK [chip5_1851027101_site_17_S29]


title: TU-NK [chip5_1851027101_site_15_S27]


title: p1-2_F02

description: SMART Seq2 with few modification


title: p1-2_F01

description: SMART Seq2 with few modification


title: p1-2_E11

description: SMART Seq2 with few modification


title: TU-NK [chip5_1851027101_site_16_S28]


title: NK [chip5_1851027101_site_13_S25]


title: NK [chip5_1851027101_site_12_S18]


title: p1-2_E09

description: SMART Seq2 with few modification


title: p1-2_E06

description: SMART Seq2 with few modification


title: NK [chip5_1851027101_site_11_S17]


title: p1-2_E07

description: SMART Seq2 with few modification


title: p1-2_E03

description: SMART Seq2 with few modification


title: NK [chip5_1851027101_site_10_S16]


title: NK [chip5_1851027101_site_09_S15]


title: p1-2_E02

description: SMART Seq2 with few modification


title: NK [chip5_1851027101_site_08_S14]


title: p1-2_E01

description: SMART Seq2 with few modification


title: p1-2_F03

description: SMART Seq2 with few modification


title: p1-2_D11

description: SMART Seq2 with few modification


title: NK [chip5_1851027101_site_06_S6]


title: p1-2_D12

description: SMART Seq2 with few modification


title: NK [chip5_1851027101_site_05_S5]


title: TU-NK [chip5_1851027101_site_14_S26]


title: NK [chip5_1851027101_site_04_S4]


title: p1-2_D10

description: SMART Seq2 with few modification


title: p1-2_D09

description: SMART Seq2 with few modification


title: NK [chip5_1851027101_site_02_S2]


title: p1-2_D07

description: SMART Seq2 with few modification


title: p1-2_D06

description: SMART Seq2 with few modification


title: NK [chip5_1851027101_site_01_S1]


title: Control MDA-MB-231  [Tube_MDA.MD.231_S194  ]

value: Pooled control cancer cell


title: TU [chip4_1851035024_site_48]

value: Cancer cell


title: p1-2_D05

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_47]


title: p1-2_D01

description: SMART Seq2 with few modification


title: p1-2_D02

description: SMART Seq2 with few modification


title: Unknown [chip4_1851035024_site_46]


title: p1-2_C12

description: SMART Seq2 with few modification


title: Severe dengue, 07

type: RNA

city: Bangkok

first: Umaporn

last: Limothai

state: Thailand

address: 1873 Rama IV Rd, Pathum Wan, Pathum Wan District, Faculty of Medicine, Chulalongkorn University

institute: Chulalongkorn University, Faculty of Medicine

hyb_protocol: Standard nanostring  nCounter miRNA Hybridization Protocol; The final hybridization reaction contained the following components: 10 μL Reporter CodeSet, 10 μL hybridization buffer, a 5 μL aliquot from the miRNA Sample Preparation Protocol, and 5 μL Capture ProbeSet.

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer for image capture (280 fields of view).

data_processing: The miRNA data analysis was performed using nSolver Analysis (version 4·0) software. Each miRNA count data was subtracted from the geometric mean of the negative controls. Profiling data were then normalized by the geometric mean of the positive controls and the geometric mean of the top 100 most highly-expressed microRNAs.

source_name: Severe dengue

label_protocol: Standard nanostring miRNA protocols (nCounter Human v3 miRNA Expression Assays (NanoString Technologies,Seattle, USA))

extract_protocol: Total RNA was extracted from 200 mL of serum sample using miRNeasy Serum/Plasma Kit (Qiagen, Gaithersburg, MD, USA) according to the manufacturer’s protocol.

tag: infection

value: dengue

value: severe dengue infection

value: Serum


title: TU [chip4_1851035024_site_45]


title: p1-2_C11

description: SMART Seq2 with few modification


title: Severe dengue, 06


title: Severe dengue, 05


title: Severe dengue, 03


title: Severe dengue, 04


title: NK [chip5_1851027101_site_07_S13]


title: TU [chip4_1851035024_site_44]


title: Severe dengue, 02


title: Severe dengue, 08


title: p1-2_D08

description: SMART Seq2 with few modification


title: Severe dengue, 01


title: TU [chip4_1851035024_site_43]


title: dengue with warning sign, 04

source_name: dengue with warning sign

value: non-severe dengue infection


title: dengue with warning sign, 06


title: p1-2_C09

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_42]


title: dengue with warning sign, 02


title: p1-2_C10

description: SMART Seq2 with few modification


title: dengue with warning sign, 05


title: p1-2_C07

description: SMART Seq2 with few modification


title: p1-2_C08

description: SMART Seq2 with few modification


title: dengue with warning sign, 01


title: dengue with warning sign, 03


title: TU [chip4_1851035024_site_41]


title: dengue infection, 04

source_name: dengue infection


title: p1-2_C06

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_40]


title: dengue infection, 01


title: TU [chip4_1851035024_site_38]


title: dengue infection, 03


title: p1-2_C05

description: SMART Seq2 with few modification


title: dengue infection, 02


title: TU [chip4_1851035024_site_37]


title: dengue infection, 05


title: p1-2_C03

description: SMART Seq2 with few modification


title: p1-2_C04

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_39]


title: p1-2_C02

description: SMART Seq2 with few modification


title: TU-NK [chip4_1851035024_site_36]


title: IgG-5

city: Hangzhou

first: Jianing

last: Chen

address: Qingchun Road 79#

country: China

institute: Zhejiang university

description:
otu_table.relative for antibody.xls
reletive abundance of OTUs

library_source: other

data_processing:
library strategy: 16S rDNA seq
Sequencing libraries were prepared and the library quality was evaluated
the library was sequenced and the paired-end reads were generated
The gene sequence data were processed with default parameters
Sequences with ≥97% similarity were assigned to the same operational taxonomic units
The representative sequence for each OTU was screened for further annotation. The output data was further analyzed using Statistical Analysis
Assembly: Not applicatable
Supplementary files format and content: Matrix table with relative abundance for every gene and every sample
Supplementary files format and content: RELATIVE-genome.xls: reletive abundance in kingdom, class, family, genus and species
Supplementary files format and content: otu-FMT.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for in vivo.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative. in vitro.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for antibody.xls: reletive abundance of OTUs
Supplementary files format and content: gene.description-TRANS.xls: gene information of transcriptome

molecule: other

organism: Bacteria

source_name: ileocecal contents

extract_protocol:
Total genome DNA from murine luminal samples from ileocecus was extracted for amplification
Sequencing libraries were prepared and the library quality was evaluated
DNA V3-V4 region or genome

value: ileocecal contents

value: bacteria

value: wild type

tag: treatment

value: high fat

tag: molecule type

value: rDNA


title: IgG-1


title: IgG-3


title: hab-opn-3

description:
otu_table.relative. in vitro.xls
reletive abundance of OTUs


title: IgG-4


title: hab-opn-2


title: hab-opn-1


title: IgG-2


title: hab-3


title: TU-NK [chip4_1851035024_site_34]

value: Cancer-NK doublet


title: p1-2_B12

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old

value: Female


title: hab-2


title: TU-NK [chip4_1851035024_site_33]


title: hab-1


title: KO REC-8

description:
otu_table.relative for in vivo.xls
reletive abundance of OTUs

value: nornal diet


title: p1-2_B11

description: SMART Seq2 with few modification

value: wt

value: tuft


title: KO REC-7


title: KO REC-6


title: TU-NK [chip4_1851035024_site_32]


title: NK [chip4_1851035024_site_35]

value: NK cell


title: p1-2_B10

description: SMART Seq2 with few modification


title: KO REC-5


title: KO REC-3


title: KO REC-4


title: TU-NK [chip4_1851035024_site_30]


title: p1-2_C01

description: SMART Seq2 with few modification


title: p1-2_B09

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_31]

value: Cancer cell


title: KO REC-2


title: p1-2_B08

description: SMART Seq2 with few modification


title: TU-NK [chip4_1851035024_site_29]


title: KO REC-1


title: WT REC-7


title: p1-2_G05

description: SMART Seq2 with few modification


title: WT REC-8


title: p1-2_B07

description: SMART Seq2 with few modification


title: WT REC-5


title: WT REC-6


title: TU-NK [chip4_1851035024_site_27]


title: p1-2_B05

description: SMART Seq2 with few modification


title: WT REC-3


title: WT REC-4


title: TU [chip4_1851035024_site_26]


title: TU-NK [chip5_1851027101_site_20_S38]


title: NK [chip4_1851035024_site_25]


title: WT REC-2


title: p1-2_B04

description: SMART Seq2 with few modification


title: TU-NK [chip4_1851035024_site_24]


title: KO MOT-5


title: KO MOT-3


title: p1-2_G04

description: SMART Seq2 with few modification


title: KO MOT-4


title: WT REC-1


title: p1-2_B02

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_28]


title: KO MOT-2


title: TU [chip4_1851035024_site_23]


title: p1-2_G01

description: SMART Seq2 with few modification


title: p1-2_A12

description: SMART Seq2 with few modification


title: Control NK-92MI  [Tube_NK.92_S193  ]

value: Pooled control NK cell


title: p1-2_B06

description: SMART Seq2 with few modification


title: WT MOT-5


title: TU-NK [chip4_1851035024_site_22]


title: WT MOT-3


title: p1-2_B03

description: SMART Seq2 with few modification


title: WT MOT-4


title: WT MOT-2


title: p1-2_A11

description: SMART Seq2 with few modification


title: WT MOT-1


title: p1-2_A10

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_21]


title: p1-2_A08

description: SMART Seq2 with few modification


title: KO-KO-4

description:
otu-FMT.xls
reletive abundance of OTUs

value: high fat diet


title: TU-NK [chip4_1851035024_site_20]


title: p1-2_A06

description: SMART Seq2 with few modification


title: KO-KO-2

description:
otu-FMT.xls
reletive abundance of OTUs


title: TU-NK [chip4_1851035024_site_19]


title: KO-KO-3

description:
otu-FMT.xls
reletive abundance of OTUs


title: TU-NK [chip4_1851035024_site_18]


title: KO-KO-5

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-2_A05

description: SMART Seq2 with few modification


title: KO MOT-1


title: KO-WT-4

description:
otu-FMT.xls
reletive abundance of OTUs


title: NK [chip5_1851027101_site_03_S3]


title: KO-KO-1

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-2_A04

description: SMART Seq2 with few modification


title: TU-NK [chip4_1851035024_site_17]


title: TU-NK [chip4_1851035024_site_16]


title: KO-WT-2

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-2_A03

description: SMART Seq2 with few modification


title: KO-WT-1

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT-KO-5

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-2_A02

description: SMART Seq2 with few modification


title: WT-KO-4

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-2_D03

description: SMART Seq2 with few modification


title: WT-KO-3

description:
otu-FMT.xls
reletive abundance of OTUs


title: TU-NK [chip4_1851035024_site_14]


title: p1-2_A01

description: SMART Seq2 with few modification


title: TU [chip4_1851035024_site_13]


title: TU-NK [chip4_1851035024_site_15]


title: KO-WT-5

description:
otu-FMT.xls
reletive abundance of OTUs


title: NK [chip4_1851035024_site_11]


title: WT-KO-1

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT-WT-3

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-1_H12

description: SMART Seq2 with few modification


title: KO-WT-3

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT-WT-4

description:
otu-FMT.xls
reletive abundance of OTUs


title: NK [chip4_1851035024_site_12]


title: p1-1_H11

description: SMART Seq2 with few modification


title: KO donor-10

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT-WT-2

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-1_H09

description: SMART Seq2 with few modification


title: p1-1_H10

description: SMART Seq2 with few modification


title: KO donor-11

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT-KO-2

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-1_H07

description: SMART Seq2 with few modification


title: KO donor-7

description:
otu-FMT.xls
reletive abundance of OTUs


title: NK [chip4_1851035024_site_08]


title: Unknown [chip4_1851035024_site_10]

value: Unknown


title: Unknown [chip4_1851035024_site_09]


title: KO donor-9

description:
otu-FMT.xls
reletive abundance of OTUs

value: ileocecal contents


title: KO donor-8

description:
otu-FMT.xls
reletive abundance of OTUs

value: bacteria


title: KO donor-6

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT-WT-5

description:
otu-FMT.xls
reletive abundance of OTUs

value: wild type


title: KO donor-5

description:
otu-FMT.xls
reletive abundance of OTUs


title: NK [chip4_1851035024_site_07]


title: p1-1_H06

description: SMART Seq2 with few modification


title: KO donor-4

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT-WT-1

description:
otu-FMT.xls
reletive abundance of OTUs


title: NK [chip4_1851035024_site_06]


title: p1-1_H04

description: SMART Seq2 with few modification


title: KO donor-2

description:
otu-FMT.xls
reletive abundance of OTUs


title: KO donor-12

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-1_H08

description: SMART Seq2 with few modification


title: WT donor-7

description:
otu-FMT.xls
reletive abundance of OTUs


title: Unknown [chip4_1851035024_site_05]


title: WT donor-8

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-1_H01

description: SMART Seq2 with few modification


title: WT donor-6

description:
otu-FMT.xls
reletive abundance of OTUs


title: p1-1_G12

description: SMART Seq2 with few modification


title: p1-1_G11

description: SMART Seq2 with few modification


title: WT donor-5

description:
otu-FMT.xls
reletive abundance of OTUs


title: NK [chip4_1851035024_site_02]


title: WT donor-2

description:
otu-FMT.xls
reletive abundance of OTUs


title: WT donor-1

description:
otu-FMT.xls
reletive abundance of OTUs


title: Unknown [chip3_1851035015_site_48]


title: p1-1_G08

description: SMART Seq2 with few modification


title: p1-1_G10

description: SMART Seq2 with few modification


title: WT donor-4

description:
otu-FMT.xls
reletive abundance of OTUs


title: Unknown [chip4_1851035024_site_01]


title: p1-1_G07

description: SMART Seq2 with few modification


title: KO donor-3

description:
otu-FMT.xls
reletive abundance of OTUs


title: CS11-e2

city: Beijing

first: Xiangxiang

last: Jiang

state: Beijing

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Raw fastq files were processed with Cell Ranger 3.1.0 with default mapping arguments.
Reads were mapped to the Macaca_fascicularis_5.0 genome
The cellranger aggr command was executed to adjust the sequencing depth of different samples to the same level.
Genome_build: Macaca_fascicularis_5.0

organism: Macaca fascicularis

source_name: embyo

extract_protocol:
Single cells were added to the 10x Chip channels. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs.
RNA libraries were prepared for sequencing using 10x Single Cell 3' Library & Gel Bead Kit v3  protocol

treatment_protocol: no treatment

tag: developmental stage

value: day 29


title: p1-1_G05

description: SMART Seq2 with few modification


title: CS11-e1

value: day 26


title: CS9-e2

value: day 23


title: Unknown [chip3_1851035015_site_47]


title: CS11-ys1

source_name: yolk sac


title: NK [chip4_1851035024_site_04]


title: NK [chip4_1851035024_site_03]


title: CS9-e1


title: Unknown [chip3_1851035015_site_46]


title: CS8-e2

value: day 20


title: Unknown [chip3_1851035015_site_45]


title: CS8-e1


title: p1-1_G02

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old


title: TU [chip3_1851035015_site_44]


title: mRNA-seq for chimpanzee iPS cells #1

data_processing:
Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was used to remove the adapter sequences and 3' nucleotides with low quality scores (Q < 30).
The retained reads were mapped to both the human (hg38) and chimpanzee (panTro5) reference genomes, using TopHat2 (Kim et al. 2013) with default parameters.
The reads were first mapped to panTro5 regardless of the species of mRNA origin, and only the mapped reads were then mapped to hg38.
The mapping data on hg38 was analyzed using the human genome annotation. Gene expression levels were analyzed using Cuffdiff (Trapnell et al. 2013).
Assembly: hg38
Supplementary files format and content: tab-separated files with gene names and FPKM values

extract_protocol:
Total cellular RNAs were isolated from ~1×106 cells by using Isogen (TOYOBO) and Direct-ZolTM RNA (ZYMO RESEARCH) according to manufactures’ instructions.
After quality check by Agilent 2100 Bioanalyzer (Agilent Technologies), PolyA-containing mRNAs were purified using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and used for the preparation of indexed mRNA-seq libraries using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). oligo(dT)-purified RNA-seq (stranded)

value: iPS cells

value: female

tag: origin of_ipscs

value: dermal fibroblasts


title: mRNA-seq for chimpanzee iPS cells #2


title: WT donor-3

description:
otu-FMT.xls
reletive abundance of OTUs

value: nornal diet

value: rDNA


title: TU [chip3_1851035015_site_43]

value: Cancer cell


title: H3K27me3  for chimpanzee iPS cells #2

data_processing:
Trim Galore! (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) was used to remove the adapter sequences and 3' nucleotides with low quality scores (Q < 30).
The retained reads were mapped to the human (hg38) or chimpanzee (panTro5) reference genomes, using Hisat2 with default parameters.
After de-duplication using samtools, the mapping reasults (in bam format) were used to generate read density files (in tdf format) using igvtools count.
Assembly: hg38 and panTro5
Supplementary files format and content: binary files for read density

extract_protocol:
MNase-digested chromatins were incubated with antibodies against H3K4me3 (Millipore, #07-473) and H3K27me3 (Cell Signaling Technology, #9733),  respectively.  Bound chromatins were collected using anti-IgG antibody-conjugated Dynabeads® M-280 (ThermoFisher).
Sequencing libraries were generated using NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England BioLabs).

tag: chip antibody

value: Cell Signaling Technology, #9733


title: H3K27me3 for chimpanzee iPS cells #1


title: p1-1_F11

description: SMART Seq2 with few modification

value: Female

value: wt

value: tuft


title: p1-1_F10

description: SMART Seq2 with few modification


title: H3K4me3  for chimpanzee iPS cells #2

value: Millipore, #07-473


title: p1-1_F12

description: SMART Seq2 with few modification


title: input control of H3K27me3  for chimpanzee iPS cells #2

value: none (input)


title: TU [chip3_1851035015_site_42]


title: input control of H3K27me3 for chimpanzee iPS cells #1


title: TU [chip3_1851035015_site_41]


title: Unknown [chip3_1851035015_site_40]

value: Unknown


title: p1-1_G04

description: SMART Seq2 with few modification


title: input control of H3K4me3  for chimpanzee iPS cells #2


title: p1-1_F08

description: SMART Seq2 with few modification


title: input control of H3K4me3 for chimpanzee iPS cells #1


title: NK [chip3_1851035015_site_39]

value: NK cell


title: p1-1_F06

description: SMART Seq2 with few modification


title: Vasc1

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

data_processing:
Low quality nucleotides were removed Illumina fastq filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner  using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENC
HTSeq-0.6.1p1  was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
Assembly: mm10
Supplementary files format and content: Tab-Delimited Gene-Wise Raw read counts text file

source_name: Adrenal Cortex

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

value: Adrenal Cortex

value: icosapent ethyl


title: p1-1_G01

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old


title: Vasc2


title: Vasc3


title: Vasc4


title: p1-1_F05

description: SMART Seq2 with few modification


title: ND7

value: Normal Diet


title: TU [chip3_1851035015_site_37]


title: ND6


title: ND5


title: p1-1_F03

description: SMART Seq2 with few modification


title: H3K4me3 for chimpanzee iPS cells #1

value: iPS cells

value: female

value: dermal fibroblasts


title: TU-NK [chip3_1851035015_site_36]

value: Cancer-NK doublet


title: HFD3

value: High-Fat Diet


title: HFD2


title: TU-NK [chip3_1851035015_site_34]


title: TU-NK [chip3_1851035015_site_35]


title: p1-1_F02

description: SMART Seq2 with few modification

value: Female


title: HFD4


title: HFD1


title: p1-1_F01

description: SMART Seq2 with few modification

value: wt


title: p1-1_E12

description: SMART Seq2 with few modification

value: tuft


title: TU-NK [chip3_1851035015_site_33]


title: KO donor-1

description:
otu-FMT.xls
reletive abundance of OTUs

value: ileocecal contents

value: bacteria

value: high fat diet

value: rDNA


title: p1-1_E11

description: SMART Seq2 with few modification


title: TU [chip3_1851035015_site_38]

value: Cancer cell


title: p1-1_E10

description: SMART Seq2 with few modification


title: T7296,VilgemA,T15,V1N

city: Columbus

first: Anna

last: Vilgelm

state: OH

address: 460 W 12th Ave

department: Pathology

institute: The Ohio State University

data_processing:
Individual FASTQ files were trimmed for adapter sequences and filtered for a minimum quality score of Q20 using AdapterRemoval v2.2.0.
Preliminary alignment using HISAT2 v2.0.6 was performed to a composite reference of rRNA, mtDNA, and PhiX bacteriophage sequences obtained from NCBI RefSeq. Reads aligning to these references were excluded in downstream analyses.
Primary alignment was performed against the mouse genome reference GRCm38p4 using HISAT2.
Gene expression values for genes described by the GENCODE Gene Transfer Format (GTF) release M14 (mouse) were quantified using the featureCounts tool of the Subread package v1.5.1 58 in stranded mode.
expression values in the processed data file were ‘sequencing depth normalized’ by DESeq2 package
Assembly: mm10
Supplementary files format and content: Excel spreadsheet includes raw normalized counts for each Sample

source_name: Tumor

growth_protocol: B16F10 cells were maintained in F12 -DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy@mini kit
libraries were generated with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext rRNA Depletion Kit (NEB #E7405) with an input amount of 100 ng total RNA per sample.

treatment_protocol: C57Bl/6 mice were injected subcutaineously with 50000 B16F10 cells and treated with with 100 mg/kg navitoclax (BCLi), 25 mg/kg of alisertib (AURKAi), a combination of both drugs (same doses), or drug vehicles for 11 days by daily oral gavage.

value: Tumor

value: Melanoma

value: Wild

value: Alisertib

tag: strain

value: C57Bl/6 mice


title: T7297,VilgemA,T16,V1N


title: T7295,VilgemA,T14,V1N


title: TU-NK [chip3_1851035015_site_31]


title: p1-1_E09

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old


title: TU-NK [chip3_1851035015_site_32]

value: Cancer-NK doublet


title: ND2

value: Adrenal Cortex

value: Normal Diet


title: T7294,VilgemA,T1,V1N

value: Navitoclax


title: p1-1_E08

description: SMART Seq2 with few modification

value: Female

value: wt

value: tuft


title: Aortic CD45+, WT and myeloid JAK2-V617F, GEX

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

source_name: Aorta

extract_protocol:
Jak2WT (n=5) and Jak2V617F MyC (n=5) mice under isoflurane anesthesia received 2µg of anti-CD45.2-APC (clone 104, BioLegend) i.v. 5 minutes before sacrifice to label circulating immune cells and were killed by cervical dislocation. Upon collection of the aorta using a stereomicroscope, aneurysm development was macroscopically detected in 2 Jak2V617F MyC mice. Aortas were collected and enzymatically digested in RPMI medium containing 450U/ml collagenase I (Sigma-Aldrich C0130), 125U/ml collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich H3506) and 60U/ml DNAse1 (Roche #11284932001) for 45 minutes at 37°C with agitation, washed in PBS+1% FCS and passed through a 70µm cell strainer. After washing in PBS+1%FCS, aortic cells were resuspended in erythrocyte lysis buffer (ACK buffer) for 5 minutes and washed again with PBS+1% FCS. Cells were plated in round bottom 96 well plates, and incubated for 10 minutes on ice with anti-CD16/32 (BioLegend, Clone 93, 10µg/ml in PBS+1% FCS) to block unspecific binding of antibodies to Fc receptors. Cells were subsequently labeled in a final volume of 60µl for 25 minutes at 4°C with a mix containing CITE-seq antibodies (TotalSeq-A, BioLegend), 1:1000 Fixable Viability Dye e780 (ThermoFisher Scientific 65-0865-14), 2µg/ml anti-CD45.2 BV421 (Jak2WT samples) or 2µg/ml anti-CD45.2 Alexa488 (Jak2V617F samples). Each unique sample was labeled with a specific Hashtag antibody for cell hashing (Hashtag 1 to 5: Jak2WT aortas, Hashtag 7 and 9: Jak2V617F MyC with aneurysm; Hashtag 6, 8 and 10: Jak2V617F MyC without aneurysm; final concentration 1:100, BioLegend TotalSeq-A). After labeling, cells were washed twice in PBS+1% FCS and pooled. Viable leukocytes were sorted with exclusion of contaminating circulating leukocytes (CD45.2-APC+) using a BD FACS Aria III with a 100µm nozzle. The amount of sorted cells was adjusted so that cells from Jak2WT (CD45.2-BV421+) and from Jak2V617F aortas (CD45.2-Alexa488+) each represented ~50% of the total sorted cells. Cells were sorted in PBS supplemented with 1% PBS, and washed twice post-sort in PBS+0.04% UltraPure BSA (ThermoFisher AM2616). Cells were counted in Trypan blue to assess viability (>80%). 20,000 cells were loaded at a concentration of 500 cells/µl in the 10x Genomics Chromium (Single Cell 3’ v3 reagents, 10x Genomics) and scRNA-seq, ADT and HTO libraries were prepared and sequenced.
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: Aorta

value: not applicable

value: WT and Myeloid JAK-V617F


title: Aortic CD45+, WT and myeloid JAK2-V617F, ADT

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

molecule: protein


title: Aortic CD45+, WT and myeloid JAK2-V617F, HTO

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)


title: NK [chip3_1851035015_site_30]

value: NK cell


title: T7293,VilgemA,T11,V1N

value: Tumor

value: Melanoma


title: T7292,VilgemA,T10,V1N

value: Wild


title: TU-NK [chip3_1851035015_site_29]


title: TU-NK [chip3_1851035015_site_28]


title: p1-1_E06

description: SMART Seq2 with few modification


title: p1-1_E05

description: SMART Seq2 with few modification


title: T7288,VilgemA,T4,V1N

value: Vehicle

value: C57Bl/6 mice


title: T7290,VilgemA,T7,V1N

value: Alisertib+Navitoclax


title: NK [chip3_1851035015_site_27]


title: T7287,VilgemA,T3,V1N


title: T7286,VilgemA,T2,V1N


title: p1-1_E04

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old


title: p1-1_E03

description: SMART Seq2 with few modification


title: T7289,VilgemA,T5,V1N


title: Th17_ROR_WT_1

city: Duarte

first: Xiancai

last: Zhong

state: CA

address: 1500 E Duarte Rd

department: Immunology & Theranostics

institute: Beckman Research Institute of City of Hope

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Novaseq output and RTA version was 3.4.4.
Files for each group are associated and subjected to data processing using Partek® Flow®.
ChIP-seq reads were aligned to the mm10 genome using BWA version 0.7.17.
Reads were filtered by removing unaligned reads, singletons, and duplicates. Files (BAMPE format) were then reformatted to BigWig files.
Peaks were called uing MACS2 v2.1.1 with the significance cut-off q-value <=0.05.
Sequence reads were quantified and normalized to fragments per kilobase million (FPKM).
Assembly: mm10
Supplementary files format and content: BigWig files showing binding peaks

source_name: Spleen

growth_protocol: ROR-KO CD4+ T cells isolated from mouse spleen were stimulated with 0.25 ug/mL anti-CD3 and 1 ug/mL anti-CD28 antibodies overnight in a 24-well plate coated with anti-hamster secondary antibody.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented using a ChIP-IT Express Enzymatic kit (Active motif).
ChIP-seq libraries were prepared using the KAPA DNA HyperPrep Library Preparation Kit complemented with xGen Stubby Adapter and Unique Dual Index Primer Pairs from IDT. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Flag-tagged WT or K256R mutated RORgt were retrovirally transduced to acitivated CD4+ T cells. Th17 differentiation was subsequenctly induced by the supplementation of 2 ng/mL TGF-beta, 20 ng/mL IL-6, and 20 ng/mL of IL-23 in the presence of 2 ug/mL anti-IL-4 and 2 ug/mL anti-IFN-gamma antibodies.

value: Spleen

value: CD4+ T cells

value: TGF-β, IL-6. IL-23

value: sigma F1804