title: SS2_17_154_K18_R1


title: SS2_17_154_J19_R1

status: Public on Jul 03 2020

type: SRA

city: Uppsala

first: Åsa

last: Wallén-Mackenzie

address: Norbyvägen 18A

country: Sweden

institute: Uppsala University

library_source: transcriptomic

data_processing:
All reads were aligned to the mouse (mm10) genome using STAR (Dobin et al., 29, 2013)
Non-uniquely mapped reads were removed
The expression values of merged RefSeq and Ensemble gene annotations were computed as described in Rämsköld et al. (PLoS Comput. Biol., 5,2013) , using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. PLoS One, 8, 2013)
Genome_build: mm10
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

molecule: polyA RNA

organism: Mus musculus

source_name: cDNA - brain / subthalamic nucleus

extract_protocol:
Snap frozen tissue was dissociated with lysis buffer+0.32Msucrose in 1ml dounce homogenizers. Homogenate was added over a 1.8Msucrose layer and centrifuged 2 h 20 min at 30,000 × g (Beckman J-25 centrifuge with a J13.1 rotor).  cDNA was generated from FACS sorted single nuclei using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer
Nextera XT DNA sample preparation index kit, 384 indices (Illumina)

tag: mouse strain

tag: age

value: postnatal day 28

tag: spike-in

value: ERCC


title: SS2_17_154_J18_R1


title: SS2_17_154_J15_R1


title: SS2_17_154_J14_R1


title: SS2_17_154_N16_R1


title: SS2_17_154_J11_R1


title: SS2_17_154_J16_R1


title: SS2_17_154_J13_R1


title: SS2_17_154_I8_R1


title: SS2_17_154_J17_R1


title: SS2_17_154_J12_R1


title: SS2_17_154_J5_R1


title: SS2_17_154_J10_R1


title: SS2_17_154_I9_R1


title: SS2_17_154_J2_R1


title: SS2_17_154_J23_R1


title: SS2_17_154_I7_R1


title: SS2_17_154_I5_R1


title: SS2_17_154_I6_R1


title: SS2_17_154_I4_R1


title: SS2_17_154_I3_R1


title: SS2_17_154_I22_R1


title: SS2_17_154_I2_R1


title: SS2_17_154_I1_R1


title: SS2_17_154_I19_R1


title: SS2_17_154_I21_R1


title: SS2_17_154_I20_R1


title: SS2_17_154_I18_R1


title: SS2_17_154_K23_R1


title: SS2_17_154_I11_R1


title: SS2_17_154_I13_R1


title: SS2_17_154_I12_R1


title: SS2_17_154_I15_R1


title: SS2_17_154_I10_R1


title: SS2_17_154_I14_R1


title: SS2_17_154_H9_R1


title: SS2_17_154_H8_R1


title: SS2_17_154_H6_R1


title: SS2_17_154_I24_R1


title: SS2_17_154_H5_R1


title: SS2_17_154_I23_R1


title: SS2_17_154_H7_R1


title: SS2_17_154_H3_R1


title: SS2_17_154_H4_R1


title: SS2_17_154_H20_R1


title: SS2_17_154_H24_R1


title: SS2_17_154_H2_R1


title: SS2_17_154_H18_R1


title: SS2_17_154_H15_R1


title: SS2_17_154_H17_R1


title: SS2_17_154_H19_R1


title: SS2_17_154_H23_R1


title: SS2_17_154_H21_R1


title: SS2_17_154_H22_R1


title: SS2_17_154_H16_R1


title: SS2_17_154_I16_R1


title: SS2_17_154_I17_R1


title: SS2_17_154_H1_R1


title: SS2_17_154_H14_R1


title: SS2_17_154_H12_R1


title: SS2_17_154_H10_R1


title: SS2_17_154_G9_R1


title: SS2_17_154_G8_R1


title: SS2_17_154_H11_R1


title: SS2_17_154_G7_R1


title: SS2_17_154_G6_R1


title: SS2_17_154_G3_R1


title: SS2_17_154_G2_R1


title: SS2_17_154_G24_R1


title: SS2_17_154_G23_R1


title: SS2_17_154_G21_R1


title: SS2_17_154_G22_R1


title: SS2_17_154_G4_R1


title: SS2_17_154_G1_R1


title: SS2_17_154_G19_R1


title: SS2_17_154_G15_R1


title: SS2_17_154_G13_R1


title: SS2_17_154_G16_R1


title: SS2_17_154_G17_R1


title: SS2_17_154_G12_R1


title: SS2_17_154_H13_R1


title: SS2_17_154_G10_R1


title: SS2_17_154_G14_R1


title: SS2_17_154_G18_R1


title: SS2_17_154_G11_R1


title: SS2_17_154_F9_R1


title: SS2_17_154_F8_R1


title: SS2_17_154_F5_R1


title: SS2_17_154_F2_R1


title: SS2_17_154_F3_R1


title: SS2_17_154_F7_R1


title: SS2_17_154_F24_R1


title: SS2_17_154_F23_R1


title: SS2_17_154_G20_R1


title: SS2_17_154_F21_R1


title: SS2_17_154_F22_R1


title: SS2_17_154_F20_R1


title: SS2_17_154_F19_R1


title: SS2_17_154_F16_R1


title: SS2_17_154_F15_R1


title: SS2_17_154_F14_R1


title: SS2_17_154_F18_R1


title: SS2_17_154_F13_R1


title: SS2_17_154_F11_R1


title: SS2_17_154_F17_R1


title: SS2_17_154_F12_R1


title: SS2_17_154_F10_R1


title: SS2_17_154_F4_R1


title: SS2_17_154_F6_R1


title: SS2_17_154_E4_R1


title: SS2_17_154_E8_R1


title: SS2_17_154_E6_R1


title: SS2_17_154_E9_R1


title: SS2_17_154_E7_R1


title: SS2_17_154_E3_R1


title: SS2_17_154_E24_R1


title: SS2_17_154_E23_R1


title: SS2_17_154_E22_R1


title: SS2_17_154_F1_R1


title: SS2_17_154_E20_R1


title: SS2_17_154_E21_R1


title: SS2_17_154_E19_R1


title: SS2_17_154_E1_R1


title: SS2_17_154_E18_R1


title: SS2_17_154_G5_R1


title: SS2_17_154_E16_R1


title: SS2_17_154_E17_R1


title: SS2_17_154_E5_R1


title: SS2_17_154_E14_R1


title: SS2_17_154_E15_R1


title: SS2_17_154_D8_R1


title: SS2_17_154_E13_R1


title: SS2_17_154_E12_R1


title: SS2_17_154_D9_R1


title: SS2_17_154_E2_R1


title: SS2_17_154_E11_R1


title: SS2_17_154_D15_R1


title: SS2_17_154_D13_R1


title: SS2_17_154_D16_R1


title: SS2_17_154_D14_R1


title: SS2_17_154_E10_R1


title: SS2_17_154_D12_R1


title: SS2_17_154_D4_R1


title: SS2_17_154_D18_R1


title: SS2_17_154_D17_R1


title: SS2_17_154_D3_R1


title: SS2_17_154_D19_R1


title: SS2_17_154_D22_R1


title: SS2_17_154_D2_R1


title: SS2_17_154_D7_R1


title: SS2_17_154_D24_R1


title: SS2_17_154_D1_R1


title: SS2_17_154_D20_R1


title: SS2_17_154_D6_R1


title: SS2_17_154_D5_R1


title: SS2_17_154_D23_R1


title: SS2_17_154_D11_R1


title: SS2_17_154_D10_R1


title: SS2_17_154_C8_R1


title: SS2_17_154_D21_R1


title: SS2_17_154_C6_R1


title: SS2_17_154_C9_R1


title: SS2_17_154_C7_R1


title: SS2_17_154_C5_R1


title: SS2_17_154_C4_R1


title: SS2_17_154_C3_R1


title: SS2_17_154_C24_R1


title: SS2_17_154_C2_R1


title: SS2_17_154_C23_R1


title: S2_17_154_C19_R1


title: SS2_17_154_B7_R1


title: SS2_17_154_C10_R1


title: SS2_17_154_C1_R1


title: SS2_17_154_B8_R1


title: SS2_17_154_C12_R1


title: SS2_17_154_C16_R1


title: SS2_17_154_B6_R1


title: SS2_17_154_C20_R1


title: SS2_17_154_C21_R1


title: SS2_17_154_C22_R1


title: SS2_17_154_C13_R1


title: SS2_17_154_C11_R1


title: SS2_17_154_B5_R1


title: SS2_17_154_B4_R1


title: SS2_17_154_C18_R1


title: SS2_17_154_B9_R1


title: SS2_17_154_B24_R1


title: SS2_17_154_B3_R1


title: SS2_17_154_C14_R1


title: SS2_17_154_B2_R1


title: SS2_17_154_C17_R1


title: SS2_17_154_B23_R1


title: SS2_17_154_B22_R1


title: SS2_17_154_B21_R1


title: SS2_17_154_B20_R1


title: SS2_17_154_C15_R1


title: SS2_17_154_B19_R1


title: SS2_17_154_B1_R1


title: SS2_17_154_B17_R1


title: SS2_17_154_B18_R1


title: SS2_17_154_B12_R1


title: SS2_17_154_B15_R1


title: SS2_17_154_B14_R1


title: SS2_17_154_B10_R1


title: SS2_17_154_B16_R1


title: SS2_17_154_A7_R1


title: SS2_17_154_A5_R1


title: SS2_17_154_A9_R1


title: SS2_17_154_A2_R1


title: SS2_17_154_A24_R1


title: SS2_17_154_B13_R1


title: SS2_17_154_B11_R1


title: SS2_17_154_A3_R1


title: SS2_17_154_A22_R1


title: SS2_17_154_A1_R1


title: SS2_17_154_A19_R1


title: SS2_17_154_A6_R1


title: SS2_17_154_A8_R1


title: SS2_17_154_A23_R1


title: SS2_17_154_A21_R1


title: SS2_17_154_A17_R1


title: SS2_17_154_A16_R1


title: SS2_17_154_A18_R1


title: SS2_17_154_A15_R1


title: SS2_17_154_A14_R1


title: SS2_17_154_A4_R1


title: SS2_17_154_A13_R1


title: SS2_17_154_A12_R1


title: SS2_17_154_A20_R1


title: SS2_17_154_A11_R1


title: SS2_17_039_P7_R1


title: SS2_17_039_P5_R1


title: SS2_17_039_P3_R1


title: SS2_17_039_P4_R1


title: SS2_17_039_P1_R1


title: SS2_17_039_P20_R1


title: SS2_17_039_P24_R1

source_name: empty well - just lysis buffer


title: SS2_17_039_P23_R1


title: SS2_17_039_P22_R1


title: SS2_17_039_P8_R1


title: SS2_17_039_P2_R1


title: SS2_17_039_P19_R1


title: SS2_17_039_P18_R1


title: SS2_17_039_P15_R1


title: SS2_17_039_P17_R1


title: SS2_17_039_P12_R1


title: SS2_17_039_P14_R1


title: SS2_17_039_P16_R1


title: SS2_17_039_P21_R1


title: SS2_17_039_P10_R1


title: SS2_17_039_P13_R1


title: SS2_17_039_P11_R1


title: SS2_17_039_O8_R1


title: SS2_17_039_O9_R1


title: SS2_17_039_P9_R1


title: SS2_17_039_P6_R1


title: SS2_17_154_A10_R1


title: SS2_17_039_O7_R1


title: SS2_17_039_O5_R1


title: SS2_17_039_O3_R1


title: SS2_17_039_O6_R1


title: SS2_17_039_O2_R1


title: SS2_17_039_O24_R1


title: SS2_17_039_O23_R1


title: SS2_17_039_O19_R1


title: SS2_17_039_O22_R1


title: SS2_17_039_O21_R1


title: SS2_17_039_O18_R1


title: SS2_17_039_O17_R1


title: SS2_17_039_O16_R1


title: SS2_17_039_O15_R1


title: SS2_17_039_O12_R1


title: SS2_17_039_O14_R1


title: SS2_17_039_O10_R1


title: SS2_17_039_N9_R1


title: SS2_17_039_N7_R1


title: SS2_17_039_N5_R1


title: SS2_17_039_N3_R1


title: SS2_17_039_N2_R1


title: SS2_17_039_N4_R1


title: SS2_17_039_N23_R1


title: SS2_17_039_O20_R1


title: SS2_17_039_N21_R1


title: SS2_17_039_N20_R1


title: SS2_17_039_N22_R1


title: SS2_17_039_N1_R1


title: SS2_17_039_O13_R1


title: SS2_17_039_O11_R1


title: SS2_17_039_N15_R1


title: SS2_17_039_N17_R1


title: SS2_17_039_N19_R1


title: SS2_17_039_N13_R1


title: SS2_17_039_N12_R1


title: SS2_17_039_N14_R1


title: SS2_17_039_N16_R1


title: SS2_17_039_N11_R1


title: SS2_17_039_O4_R1


title: SS2_17_039_N10_R1


title: SS2_17_039_M9_R1


title: SS2_17_039_N8_R1


title: SS2_17_039_N6_R1


title: SS2_17_039_M7_R1


title: SS2_17_039_N24_R1


title: SS2_17_039_M6_R1


title: SS2_17_039_M3_R1


title: SS2_17_039_M5_R1


title: SS2_17_039_M24_R1


title: SS2_17_039_M4_R1


title: SS2_17_039_N18_R1


title: SS2_17_039_M21_R1


title: SS2_17_039_M23_R1


title: SS2_17_039_M1_R1


title: SS2_17_039_M20_R1


title: SS2_17_039_M18_R1


title: SS2_17_039_M8_R1


title: SS2_17_039_M19_R1


title: SS2_17_039_M15_R1


title: SS2_17_039_M13_R1


title: SS2_17_039_L9_R1


title: SS2_17_039_M16_R1


title: SS2_17_039_M14_R1


title: SS2_17_039_L8_R1


title: SS2_17_039_L6_R1


title: SS2_17_039_L7_R1


title: SS2_17_039_M17_R1


title: SS2_17_039_M11_R1


title: SS2_17_039_M10_R1


title: SS2_17_039_M2_R1


title: SS2_17_039_L5_R1


title: SS2_17_039_M22_R1


title: SS2_17_039_L4_R1


title: SS2_17_039_L24_R1


title: SS2_17_039_L2_R1


title: SS2_17_039_L3_R1


title: SS2_17_039_L23_R1


title: SS2_17_039_L22_R1


title: SS2_17_039_L21_R1


title: SS2_17_039_L20_R1


title: SS2_17_039_L19_R1


title: SS2_17_039_L18_R1


title: SS2_17_039_L1_R1


title: SS2_17_039_L16_R1


title: SS2_17_039_L11_R1


title: SS2_17_039_L10_R1


title: SS2_17_039_L12_R1


title: SS2_17_039_K7_R1


title: SS2_17_039_K8_R1


title: SS2_17_039_K9_R1


title: SS2_17_039_L15_R1


title: SS2_17_039_K5_R1


title: SS2_17_039_K6_R1


title: SS2_17_039_L14_R1


title: SS2_17_039_K4_R1


title: SS2_17_039_K3_R1


title: SS2_17_039_K2_R1


title: SS2_17_039_K22_R1


title: SS2_17_039_K24_R1


title: SS2_17_039_K23_R1


title: SS2_17_039_K21_R1


title: SS2_17_039_K1_R1


title: SS2_17_039_K20_R1


title: SS2_17_039_K19_R1


title: SS2_17_039_L17_R1


title: SS2_17_039_K17_R1


title: SS2_17_039_K18_R1


title: SS2_17_039_K16_R1


title: SS2_17_039_K14_R1


title: SS2_17_039_K15_R1


title: SS2_17_039_L13_R1


title: SS2_17_039_K13_R1


title: SS2_17_039_K10_R1


title: SS2_17_039_J8_R1


title: SS2_17_039_J9_R1


title: SS2_17_039_J6_R1


title: SS2_17_039_J4_R1


title: SS2_17_039_J3_R1


title: SS2_17_039_J24_R1


title: SS2_17_039_J2_R1


title: SS2_17_039_J23_R1


title: SS2_17_039_J22_R1


title: SS2_17_039_J1_R1


title: SS2_17_039_J5_R1


title: SS2_17_039_J19_R1


title: SS2_17_039_J17_R1


title: SS2_17_039_J21_R1


title: SS2_17_039_J20_R1


title: SS2_17_039_J18_R1


title: SS2_17_039_J16_R1


title: SS2_17_039_J15_R1


title: SS2_17_039_J11_R1


title: SS2_17_039_J12_R1


title: SS2_17_039_J14_R1


title: SS2_17_039_K12_R1


title: SS2_17_039_K11_R1


title: SS2_17_039_J13_R1


title: SS2_17_039_J10_R1


title: SS2_17_039_I8_R1


title: SS2_17_039_I6_R1


title: SS2_17_039_I7_R1


title: SS2_17_039_O1_R1


title: SS2_17_039_I9_R1


title: SS2_17_039_J7_R1


title: SS2_17_039_I5_R1


title: SS2_17_039_I3_R1


title: SS2_17_039_I4_R1


title: SS2_17_039_I24_R1


title: SS2_17_039_I22_R1


title: SS2_17_039_I2_R1


title: SS2_17_039_I23_R1


title: SS2_17_039_I1_R1


title: SS2_17_039_I20_R1


title: SS2_17_039_I21_R1


title: SS2_17_039_I19_R1


title: SS2_17_039_I17_R1


title: SS2_17_039_I16_R1


title: SS2_17_039_I18_R1


title: SS2_17_039_I15_R1


title: SS2_17_039_I11_R1


title: SS2_17_039_I10_R1


title: SS2_17_039_H8_R1


title: SS2_17_039_H9_R1


title: SS2_17_039_H4_R1


title: SS2_17_039_H6_R1


title: SS2_17_039_I12_R1


title: SS2_17_039_H3_R1


title: SS2_17_039_H7_R1


title: SS2_17_039_H23_R1


title: SS2_17_039_H24_R1


title: SS2_17_039_H2_R1


title: SS2_17_039_H5_R1


title: SS2_17_039_H20_R1


title: SS2_17_039_H21_R1


title: SS2_17_039_I14_R1


title: non-atypical hepatocytes rep4

city: Itabashi-ku

first: Mitsuhiko

last: Moriyama

state: Tokyo

address: Oyaguchi Uemachi 30-1

country: Japan

institute: Nihon University School of Medicine

data_processing:
Torrent Suite software 4.4.2 (Thermo Fisher Scientific) software was used for basecalling.
AmpliSeq sequencing data were analyzed using the Ion Torrent Mapping Alignment Program (TMAP).
The raw read counts were calculated by ampliSeqRNA plugin (v4.4.0.4).
Calculation of rpkm (or RPM) was performed by ampliSeqRNA plugin (v4.4.0.4).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (raw count / RPM) for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: liver

extract_protocol:
RNA extraction from FFPE samples was performed with an RNeasy FFPE Kit (Qiagen, Tokyo, Japan) and TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) .
The Ion AmpliSeq Human Gene Expression Panel (Life Technologies Corp., Carlsbad, CA, USA) was used to generate target amplicon libraries.

tag: tissue

value: liver

tag: cell type

value: hepatocyte


title: SS2_17_039_H1_R1


title: non-atypical hepatocytes rep3


title: SS2_17_039_H17_R1


title: SS2_17_039_H18_R1


title: atypical hepatocytes rep3


title: non-atypical hepatocytes rep2


title: SS2_17_039_I13_R1


title: atypical hepatocytes rep2


title: SS2_17_039_H19_R1


title: atypical hepatocytes rep4


title: SS2_17_039_H15_R1


title: WT-PMN-003

city: Tampa

first: Dongliang

last: Du

state: FL

address: 12902 USF Magnolia Drive

country: USA

institute: Moffitt Cancer Center

data_processing:
Illumina NextSeq 500 pair-end reads from RNA-Seq libraries were first adaptor trimmed
STAR v2.5.3a was used for alignment to the reference genome.
HTSeq v0.6.1 was used for reads counting to estimate expression level of genes
Library size normalization was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: comma-delimited text file including read counts of each gene (in rows) for each sample (in columns)

source_name: Untreated PMN-MDSC

growth_protocol: Mice were given B16 tumors. Once tumors were established (>25mm2), one group of mice were given cyclophosphamide and fludarabine.

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy MiniKit according to the manufacturer’s instructions
Total RNA-seq libraries were generated from 100 ng of RNA using the NuGen Ovation Mouse RNA-seq System according to the manufacturer's protocol. rRNA transcripts were selectively reduced using the NuGen probe-based AnyDeplete strategy according to the protocol.

treatment_protocol: Spleens were collected from mice 7 days after treatment and MDSCs were sorted by FACS with >99% purity.

tag: strain

tag: treatment

value: Untreated

value: spleen

tag: genotype

value: WT

value: PMN-MDSCs


title: SS2_17_039_H22_R1


title: SS2_17_039_H14_R1


title: SS2_17_039_H13_R1


title: atypical hepatocytes rep1


title: SS2_17_039_H11_R1


title: SS2_17_039_H12_R1


title: WT-Mo-003

source_name: Untreated M-MDSC

value: M-MDSCs


title: WT-Mo-002


title: WT-PMN-001


title: non-atypical hepatocytes rep1


title: SS2_17_039_H10_R1


title: SS2_17_039_H16_R1


title: WT-Mo-001


title: SS2_17_039_M12_R1


title: WT-LD-PMN-003

source_name: Lymphodepleted PMN-MDSC

value: Lymphodepleted


title: SS2_17_039_G7_R1


title: WT-LD-PMN-002


title: SS2_17_039_G6_R1


title: WT-LD-PMN-001


title: SS2_17_039_G5_R1


title: WT-PMN-002


title: WT-LD-Mo-003

source_name: Lymphodepleted M-MDSC


title: WT-LD-Mo-001


title: SS2_17_039_G4_R1


title: IL6KO-PMN-003

source_name: IL6KO Untreated PMN-MDSC


title: WT-LD-Mo-002


title: SS2_17_039_G2_R1


title: SS2_17_039_G24_R1


title: IL6KO-PMN-002


title: SS2_17_039_G3_R1


title: SS2_17_039_G23_R1


title: SS2_17_039_G21_R1


title: 1051

city: Birmingham

first: Soniya

last: Bastola

state: AL

address: 1824 6th Ave S

department: Neurosurgery

institute: UAB

data_processing:
bcl2fastq version 1.8.4 software from Illumina to create the Fastq files
Raw FASTQ files were trimmed with TrimGalore! version 0.6.2 with parameters --paired --trim1
Trimmed FASTQ files were aligned with STAR version 2.5.4b with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated with HTSeq-count version ??? Using parameters -r pos; -t exon; -I gene_id; -a 10; -s no; -f bam
DESeq2 was used to normalize and perform pairwise differential expression using default parameters
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: tab-delimited Excel file containing Ensembl ID and raw counts for each sample

source_name: GBM

growth_protocol: Neurosphere primary cultures were established using freshly resected GBM samples. Tumors were dissociated and neurospheres were cultivated in DMEM/F12 medium containing 2% B27 supplement, 1% Penicillin-Streptomycin solution, 2.5 μg/ml heparin, 20 ng/ml basic fibroblast growth factor (bFGF), and 20 ng/ml epidermal growth factor (EGF). bFGF and EGF were added twice a week and the cultural medium was changed every 7 days. The data with neurospheres were obtained with cells cultivated for no longer than 40 passages.

extract_protocol:
RNA was isolated using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 500 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Neurosphere primary culture

tag: tumor region

value: Unknown

tag: phenotype

value: Edge-like


title: IL6KO-PMN-001


title: 101027 edge

value: Edge


title: SS2_17_039_G9_R1


title: SS2_17_039_G20_R1


title: SS2_17_039_G22_R1


title: 101027 core

value: Core


title: 28

value: Core-like


title: IL6KO-Mo-003

source_name: IL6KO Untreated M-MDSC


title: SS2_17_039_G19_R1


title: SS2_17_039_G18_R1


title: SS2_17_039_G1_R1


title: IL6KO-Mo-002


title: SS2_17_039_G8_R1


title: 157


title: SS2_17_039_G17_R1


title: IL6KO-Mo-001


title: 267


title: SS2_17_039_G15_R1


title: IL6KO-LD-PMN-003

source_name: IL6KO Lymphodepleted PMN-MDSC


title: SS2_17_039_G13_R1


title: N1085

value: Normal brain tissue


title: SS2_17_039_G14_R1

value: postnatal day 28


title: IL6KO-LD-PMN-002


title: SS2_17_039_G12_R1

value: ERCC


title: IL6KO-LD-PMN-001


title: N1032


title: SS2_17_039_F9_R1


title: SS2_17_039_G11_R1


title: IL6KO-LD-Mo-003

source_name: IL6KO Lymphodepleted M-MDSC


title: N1210


title: SS2_17_039_F8_R1


title: SS2_17_039_F7_R1


title: SS2_17_039_F6_R1


title: 1051 core


title: SS2_17_039_G10_R1


title: 1051 edge


title: SS2_17_039_F5_R1


title: IL6KO-LD-Mo-002


title: SS2_17_039_F4_R1


title: IL6KO-LD-Mo-001


title: PMN-MDSC-plus-LD-003

value: polymorphonuclear myeloid derived suppressor cells (PMN-MDSCs)

tag: treatement

value: LD


title: SS2_17_039_F3_R1


title: SS2_17_039_F2_R1


title: 1020


title: SS2_17_039_G16_R1


title: 1079


title: SS2_17_039_F24_R1


title: 1027


title: SS2_17_039_F23_R1


title: SS2_17_039_F22_R1


title: PMN-MDSC-plus-LD-001


title: SS2_17_039_F21_R1


title: 1053C

value: Tumor tissue


title: SS2_17_039_F20_R1


title: PMN-MDSC-Ctrl-002

value: spleen

value: Ctrl


title: SS2_17_039_F1_R1


title: SS2_17_039_F19_R1


title: 1051E


title: 0573C


title: SS2_17_039_F18_R1


title: SS2_17_039_F17_R1


title: 1053E


title: SS2_17_039_F15_R1


title: PMN-MDSC-Ctrl-001


title: SS2_17_039_F14_R1


title: M-MDSC-plus-LD-002

value: monocytic myeloid derived suppressor cells (M-MDSCs)


title: PMN-MDSC-plus-LD-002


title: SS2_17_039_F16_R1


title: 0573E


title: SS2_17_039_F11_R1


title: SS2_17_039_F10_R1


title: M-MDSC-plus-LD-001


title: SS2_17_039_F13_R1


title: SS2_17_039_F12_R1


title: 1005


title: PMN-MDSC-Ctrl-003


title: SS2_17_039_E7_R1


title: M-MDSC-Ctrl-003


title: SS2_17_039_E8_R1


title: CUTLL1.Cas9_sgGLI1.C

city: Padua

first: Erich

last: Piovan

address: via Gattamelata 64

department: Dep. Surgery, Oncology and Gastroenterology

institute: University of Padua

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. We followd GDC STAR-HTseq pipeline. step1: 2-pass STAR alignment, reads were mapped to hg19 whole genome using STAR v2.5.3a with parameters --alignIntronMin 20 --alignIntronMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignMatesGapMax 1000000  --chimJunctionOverhangMin 15 --chimMainSegmentMultNmax 1 --chimSegmentMin 15 --limitSjdbInsertNsj 1200000 --chimOutType SeparateSAMold SoftClip  --outFilterMatchNminOverLread 0.33 --outFilterScoreMinOverLread 0.33 --outFilterMismatchNoverLmax 0.1 --outFilterMismatchNmax 999 --outFilterMultimapNmax 20 --outFilterType BySJout --outSAMstrandField intronMotif
step2: HTseq v0.12.3  htseq-count with parameters: -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m intersection-nonempty --nonunique none --secondary-alignments score --supplementary-alignments score
Genome_build: hg19

source_name: lymphoma/leukemia cells

growth_protocol: Cells were grown in RPMI supplemented with 10% fetal bovine serum, 1% glutamine and 1% penicilin/streptomycin

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was subjected to  Dnase treatment (on-column) using  RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CUTLL1 T-ALL cell line was transduced with lentiviral particles containing  a single guide RNA (sgRNA) against GLI1 transcription factor and CAS9 (sgGLI1) or CAS9 only (CTLR). Cells were then selected for  5 days in complete  RPMI containing puromycin (1 µg/µl). Viable cells were collected on a Ficoll gradient and expanded for 3 days before being collected for RNA extraction. This was performed in six-well plates, 3 replicates each (sgGLI1 vs CTRL).

tag: cell line

value: Childhood T lymphoblastic lymphoma cell line CUTLL1


title: CUTLL1.Cas9_sgGLI1.B


title: SS2_17_039_E6_R1


title: M-MDSC-Ctrl-002


title: SS2_17_039_E5_R1


title: CUTLL1.Cas9_sgGLI1.A


title: CUTLL1.Cas9_Ctrl.C

value: wild type


title: SS2_17_039_E4_R1


title: SS2_17_039_E3_R1


title: M-MDSC-plus-LD-003


title: SS2_17_039_E23_R1


title: 1051C


title: SS2_17_039_E9_R1


title: SS2_17_039_E24_R1


title: MMA-10D-2

city: NEW YORK

first: John

last: Blenis

state: NY

address: 413 E 69TH ST FL 13

institute: Weill Cornell Medicine

data_processing:
The “TopHat” algorithm was used to align the reads to the hg38 genome
The alignments (37.5-51.4 M aligned pairs) in the BAM files were further analyzed using the Cufflinks suite of programs (running consecutively: Cufflinks à Cuffcompare à Cuffdiff)
Cufflinks was run using the hg38-genes as a reference data base. By doing so, the output shows the known genes with their RNA-Seq metrics (as FPKM = Fragments Per Kilobase of exon model per Million mapped fragments), but novel transcripts are not identified. The 9 (3 x 3 replicates) cufflinks outputs were compared using cuffdiff.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample (output from Cufflinks). The file "genes_10days.fpkm_tracking" includes combined values for the two conditions: VEH, MMA.

source_name: lung epithelial cells

growth_protocol: A549 cells were maintained in RPMI media supplemented with 10% FBS and penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using the PureLink RNA isolation kit (Life Technologies) and contaminant DNA was digested with DNAse I (Amplification grade, Sigma-Aldrich)
"Active Motif" processed 1 µg of total RNA (RIN values between 8.7-10.0) to obtain polyA RNA. The TruSeq RNA Sample Preparation v2 Guide protocol was followed (Illumina, Part # 15026495 Rev. F) as per the manufacturer indications. Libraries were sequenced on Illumina NextSeq 500 as paired-end 42-nt reads, to a depth of 40.2 – 54.7 M read pairs.

treatment_protocol: Cells were treated with vehicle (water) or 5 mM MMA in water for 3 days or 10 days.

tag: cell line origin

value: non-small cell lung cancer

value: 5mM MMA for 10 days


title: MMA-10D-3


title: CUTLL1.Cas9_Ctrl.B


title: MMA-10D-1


title: SS2_17_039_E22_R1


title: VEH-10D-3

value: vehicle (water) for 10 days


title: CUTLL1.Cas9_Ctrl.A


title: SS2_17_039_E21_R1


title: M-MDSC-Ctrl-001


title: SS2_17_039_E1_R1


title: SS2_17_039_E2_R1


title: SS2_17_039_E18_R1


title: VEH-10D-1


title: SS2_17_039_E16_R1


title: SS2_17_039_E15_R1


title: SS2_17_039_E14_R1


title: MMA-3D-2

description: 08_3687Cornell_A549_5mM-MMA-2_RNASeq_hs_genes.fpkm_tracking

value: 5mM MMA for 3 days


title: SS2_17_039_E20_R1


title: SS2_17_039_E12_R1


title: SS2_17_039_E13_R1


title: SS2_17_039_D9_R1


title: MMA-3D-1

description: 07_3687Cornell_A549_5mM-MMA-1_RNASeq_hs_genes.fpkm_tracking


title: VEH-3D-3

description: 03_3687Cornell_A549_Vehicle-3_RNASeq_hs_genes.fpkm_tracking

value: vehicle (water) for 3 days


title: SS2_17_039_E10_R1


title: SS2_17_039_E19_R1


title: SS2_17_039_E11_R1


title: SS2_17_039_D7_R1


title: VEH-10D-2


title: VEH-3D-2

description: 02_3687Cornell_A549_Vehicle-2_RNASeq_hs_genes.fpkm_tracking


title: SS2_17_039_D6_R1


title: SS2_17_039_E17_R1


title: MMA-3D-3

description: 09_3687Cornell_A549_5mM-MMA-3_RNASeq_hs_genes.fpkm_tracking


title: VEH-3D-1

description: 01_3687Cornell_A549_Vehicle-1_RNASeq_hs_genes.fpkm_tracking


title: SS2_17_039_D5_R1


title: SS2_17_039_D4_R1


title: SS2_17_039_D2_R1


title: SS2_17_039_D3_R1


title: 11Nov03_FF

city: St Louis

first: Winnie

middle: W

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

description: FF biological replicate 1

data_processing:
Basecalls performed using Illumina Real-Time Analysis (RTA) version 1.13.48.0 (1.13.56.0 for MiSeq) followed by demultiplexing of the index sequence using CASAVA 1.8.2.
SPIA adapter sequence aligned and trimmed from raw sequence reads using FAR 2.17 with command line parameters : --adapter CTTTGTGTTTGA --trim-end left --adaptive-overlap yes --format fastq --write-lengthdist yes --nr-threads 4 --min-overlap 7 --max-uncalled 150 --min-readlength 25
Aligned with TopHat 2.0.4, Bowtie 2.0.0-beta7 and Ensembl 67 annotation (-G param)
FPKM calculated per sample with Cufflinks 2.0.2  and Ensembl 67 annotation with -G param
Genome_build: mm9
Supplementary_files_format_and_content: FFC-FF_gene_fpkm.tsv a tab delimited file with columns for gene ID and the normalized expression values per sample name

source_name: microglia

growth_protocol: not applicable

extract_protocol:
Total RNA was isolated from snap-frozen flow sorted cell pellets using TRIzol-chloroform extraction. RNA was resuspended in 10µl Ambion Nuclease-free water (Life Technologies) and DNAse treated (Ambion TURBO DNA-free Kit)
For cDNA synthesis, we added 5µl of isolated RNA into the Ovation® RNA-Seq method.  500ng cDNA was fragmented using covaris shearing and processed for Illumina library construction with the Illumina paired-end LT indexing protocol as previously published (Mardis et al., 2009; Govindan et al., 2012). Each library was sequenced on the Illumina HiSeq, generating between 15-22Mbp per lane.
RNA-Seq (300-500bp size fractionation): cDNA samples were constructed into Illumina libraries according to the manufacturer’s protocol (Illumina Inc, San Diego, CA) with the following modifications:  1) DNA was fragmented using Covaris S2 DNA Sonicitor using the following condtions: Duty Cycle: 5, Intensity: 4, Cycles/Burst: 200, Time: 90sec (Covaris, Inc. Woburn, MA).  Fragment sizes ranged between 100 and 500bp.  2) Illumina adapter-ligated DNA was amplified in a single 50ml PCR for five cycles.  3) Solid Phase Reversible Immobilization (SPRI) bead cleanup was used to purify the PCR and select for 300-500bp fragments.   We added 0.8 volumes of the AmpureXP solution (preformulated with polyethylene glycol and sodium chloride) to size select DNA molecules greater than 300 bp.  The size-fractioned cDNA was washed three times with 750 µl of 70% ethanol, the beads were dried, and the cDNA library was eluted off the beads by adding 20µl 10 mM Tris-HCl (pH 8.0).  The size-fractioned libraries were assayed using the Agilent BioAnalyzer High Sensitivity DNA chips.

treatment_protocol: Tissue was dissociated, enriched by Percoll gradient, and cells were flow sorted.

value: optic nerve

value: 3 months

tag: gender

value: F

tag: genotype/variaton

value: Nf1 flox/flox


title: Bronchial epithelial cells, non-infected CF rep4

city: Perth

first: Kak Ming

last: Ling

state: WA

address: 15 Hospital Avenue (North Entrance)

country: Australia

institute: Telethon Kids Institute

data_processing:
RNA-Seq libraries were sequenced on the Illumina® HiSeq 2500 platform using the RAPID mode
100bp single-end reads were sequenced at a depth of >3 million reads per sample, followed by bcl2fastq conversion and de-multiplexing
Read libraries were mapped to the GRCh37 (hg19) Human genome using HISAT (0.1.6-beta)
Gene-level quantitation (counts) of HISAT alignments was performed using SummarizeOverlaps
Genome_build: hg19
Supplementary_files_format_and_content: genecounts.csv file contains a matrix of raw gene counts (unfiltered and un-normalised data)

source_name: Bronchial epithelial cells

growth_protocol: Primary cell cultures were grown as per standard airway epithelial cell culture protocols.

extract_protocol:
RNA was extracted using the Ambion Purelink® RNA mini kit (Thermo Scientific) per the manufacturer’s instructions.  KAPA Stranded mRNA-Seq kit (KAPABiosystems (Roche)) was used for mRNA capture, with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard KAPABiosystems protocols

treatment_protocol: Primary AECs exposed with RV1b for 24 hours. Cells were collected in 350 µL RLT buffer containing 1% (v/v) ß-mercaptoethanol (QIAGEN) and stored at -80°C until all participants were successfully recruited and samples obtained.

tag: individual

value: M

tag: disease state

value: CF

tag: infection

value: non-infected

value: Bronchial epithelial cells


title: SS2_17_039_D8_R1

tag: mouse strain

tag: age

value: postnatal day 28

value: ERCC


title: Bronchial epithelial cells, non-infected CF rep7


title: Bronchial epithelial cells, non-infected CF rep5


title: Bronchial epithelial cells, RV-infected CF rep4

value: RV-infected


title: Bronchial epithelial cells, RV-infected CF rep5


title: Bronchial epithelial cells, RV-infected CF rep6


title: Bronchial epithelial cells, RV-infected CF rep3


title: Bronchial epithelial cells, RV-infected CF rep7


title: Bronchial epithelial cells, non-infected CF rep6


title: Bronchial epithelial cells, non-infected CF rep3


title: SS2_17_039_D20_R1

tag: spike-in


title: SS2_17_039_D23_R1


title: SS2_17_039_D24_R1


title: SS2_17_039_D22_R1


title: SS2_17_039_D1_R1


title: SS2_17_039_D19_R1


title: Bronchial epithelial cells, RV-infected non-CF rep4

value: non-CF

tag: cell type


title: Bronchial epithelial cells, RV-infected non-CF rep5


title: Bronchial epithelial cells, non-infected non-CF rep5


title: Bronchial epithelial cells, non-infected non-CF rep4


title: SS2_17_039_D17_R1


title: SS2_17_039_D21_R1


title: Bronchial epithelial cells, RV-infected non-CF rep3


title: SS2_17_039_D15_R1


title: Bronchial epithelial cells, RV-infected non-CF rep2


title: SS2_17_039_D16_R1


title: SS2_17_039_D13_R1


title: Bronchial epithelial cells, non-infected non-CF rep2


title: ORG_CD_IE_TNF_003

city: Seoul

first: Sung Noh

last: Hong

address: 81 Irwon-Ro, Gangnam-gu

department: Gastroenterolgy

country: South Korea

institute: Samsung Medical Center

data_processing:
For cluster generation, the library is loaded into a flow cell where fragments are captured on a lawn of surface-bound oligos complementary to the library adapters. Each fragment is then amplified into distinct, clonal clusters through bridge amplification. When cluster generation is complete, the templates are ready for sequencing.
Illumina SBS technology utilizes a proprietary reversible terminator-based method that detects single bases as they are incorporated into DNA template strands. As all 4 reversible, terminator-bound dNTPs are persent during each sequencing cycle, natural competition minimizes incorporation bias and greatly reduces raw error rates compared to other technologies. The result is highly accurate base-by-base sequencing that virtually eliminates sequence-context-specific errors, even within repetitive sequence regions and homopolymers.
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file include raw read counts for samples

source_name: TNF-treated Crohn's ileal organoid

growth_protocol: The epithelium was isolated by endoscopic biopsy samples with 10 mM ethylenediaminetetraacetic acid (EDTA) and 1 mM dithiothreitol (DTT) in PBS for 30 min at 4 °C on a rocker at 50 rpm. The supernatant containing villi and debris was decanted and discarded. To release the large amounts of intestinal crypts, the mucosal surface of biopsy samples were gently scraped using glass coverslips under a dissecting microscope. The detached crypts were suspended in PBS and were broken down using pipetting with bended pipette tip. The fraction was centrifuged at 200× g for 2 min at 4 °C, and the pellet was suspended in basic medium. Isolated crypts were pelleted with three quick spins, resuspended in Matrigel, and plated in 48-well culture plates. After incubating at 37 °C for 15 min, 250 μl maintenance media (50% Wnt3a conditioned medium + 50% 2× basic medium supplemented with 50 ng/ml recombinant human epidermal growth factor (EGF), 100 ng/ml recombinant human noggin, 500 ng/ml recombinant human R-spondin 1, 10 mM nicotinamide, 10 μM p160ROCK inhibitor (Y27632), 10 μM p38 MAP kinase inhibitor (SB202190), and 10 nM PGE2) was added. GSK3 inhibitor (CHIR99021; 2.5 μM) was included in the medium for the first 2 days. The medium was changed every 2 days and organoids were passaged 1:2 at day 7 after crypt plating. For passaging, the organoids and Matrigel were mechanically disrupted using a P1000 pipette and further mechanical dissociation was achieved using a P200 pipette. The dissociated organoids were washed with 10 ml basal culture medium and centrifuged at 200× g for 30 s at 4 °C. The supernatant was discarded, the pellet was resuspended in 2 ml of cell dissociation enzyme, and then incubated for 5 min at 37 °C in a water bath. The solution was gently mixed using a P200 pipette and centrifuged at 500× g for 5 min at 4 °C. The supernatant was discarded and the cell pellet was resuspended in Matrigel using pre-chilled pipet tips. The crypt suspension (50 μl) was plated in Matrigel in each well of the pre-warmed 48-well culture plate. The plate was incubated at 37 °C in a 5% CO2 atmosphere for 20 min to allow complete polymerization of Matrigel prior to the addition of 250 μl maintenance media. The entire medium was changed every 2 days and organoids were passaged 1:2 every week. After 4–6 passages, most organoids in the maintenance medium were uniform spheroids and able to passage stably for a long time. To recapitulate the organ physiological parameters, spheroids were cultured in differentiation medium, which was the maintenance medium without Wnt3A conditional medium, SB202190, nicotinamide, and PGE2. The entire medium was changed every 2 days and enteroids were cultured for 8 days after passage. And then, total RNA was extracted from intestinal organoids using the RNeasy Mini Kit according to the manufacturer’s instructions.

extract_protocol:
For library construction, RNA is extracted from a sample. After performing quality control (QC), qualified samples
The sequencing library is prepared by random fragmentation of the DNA or cDNA sample, followed by 5' and 3' adapter ligation. Alternatively, "tagmentation" combines the fragmentation and ligation reactions into a single step that greatly increases the efficiency of the library preparation process. Adapter-ligated fragments are then PCR amplified and gel purified.

treatment_protocol: Organoids were cultured in the maintenance medium for 2 days to obtain a stable number of organoids before inducing organoid differentiation. On day 2, the maintenance medium for organoids was replaced with the TNFɑ-containing enteroid medium. Control and Crohn’s organoids—cultured for the long-term (passage ≥ 6)—were treated with 30 ng/ml TNFɑ every 24 hours until harvest.

tag: tissue

value: ileum

tag: disease

value: Crohn's disease

tag: agent

value: TNF-treated


title: SS2_17_039_C9_R1

source_name: cDNA - brain / subthalamic nucleus


title: SS2_17_039_D12_R1


title: SS2_17_039_D10_R1


title: SS2_17_039_C8_R1


title: Bronchial epithelial cells, non-infected non-CF rep1


title: SS2_17_039_C6_R1


title: Bronchial epithelial cells, RV-infected non-CF rep1


title: Bronchial epithelial cells, non-infected non-CF rep3


title: SS2_17_039_C7_R1


title: SS2_17_039_D14_R1


title: SS2_17_039_D18_R1


title: ORG_CD_IE_TNF_002


title: SS2_17_039_C4_R1


title: SS2_17_039_D11_R1


title: Bronchial epithelial cells, RV-infected CF rep2


title: SS2_17_039_C3_R1


title: SS2_17_039_C5_R1


title: Bronchial epithelial cells, non-infected CF rep2


title: ORG_NL_IE_TNF_003

source_name: TNF-treated control ileal organoid

value: control


title: ORG_CD_IE_TNF_001


title: SS2_17_039_C2_R1


title: Bronchial epithelial cells, non-infected CF rep1


title: SS2_17_039_C23_R1


title: ORG_NL_IE_TNF_002


title: ORG_CD_JE_TNF_003

source_name: TNF-treated crohn's jejunal organoid

value: Jejunum


title: Undiff MS2control miTRAP 2

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
miRNA trapping by RNA affinity purification with MS2control according to Braun et al, 2014 (PMID: 24510096)
DE_C2C12_smallRNA_MRTFA.csv

data_processing:
Sequenced reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 1.4.2) with parameters -q 10 -m 15
Trimmed reads were mapped against the mouse genome (GRCm38.77 UCSC) using Bowtie2 (v 2.0.13) with parameters -p 6 -N 1 -k 20
Mapped reads were summarized using featureCounts (v 1.4.6) with parameters -T 6  -M -t miRNA -g ID and MirBase (v 20)  annotations
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated text file including CPM, log2 fold change and false discovery rate values for each sample

source_name: C2C12 cells

extract_protocol:
miTRAP eluates were mixed with 80 µl of nuclease-free water, 80 µl ammonium acetate solution (5 M; Sigma-Aldrich) and 400 µl phenol/chloroform (5:1, pH 4.5; Sigma-Aldrich). On centrifugation at 15 000g for 10 min, 370 µl of upper phase was transferred to new tube and precipitated with 1 ml ethanol and 2 µg glycogen (Roche). RNA pellets were dissolved in 24 µl of nuclease-free water. Input RNA was phenol–chloroform extracted from 200 µl cell extract upon Proteinase K treatment (20 mg/ml; Life Technologies). Input RNA was dissolved in 30 µl of nuclease-free water. According to Braun et al, 2014 (PMID: 24510096).
RNA prepared from total miTRAP eluates and 8% input RNA (500 ng) was used in the small RNA protocol with the TruSeq™ Small RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the instructions of the manufacturer. The barcoded libraries were size restricted between 140 and 165 bp, purified and quantified using the Library Quantification Kit-Illumina/Universal (KAPA Biosystems, Woburn, MA, USA) according to the instructions of the manufacturer. A pool of up to 10 libraries was used for cluster generation per lane. Library DNA at a concentration of 10 pM was clustered using an Illumina cBot according to the SR_Amp_Lin_Block_Hybv8.0 protocol of the manufacturer. Sequencing of 50 bp was performed with an Illumina HighScan-SQ sequencer using version 3 chemistry and the version 3 flowcell according to the instructions of the manufacturer.

treatment_protocol: 7 days DMEM, 2% HS, 37°, 5% CO2

tag: differentiation

value: undifferentiated

value: myoblasts


title: ORG_CD_JE_TNF_002


title: SS2_17_039_C21_R1


title: SS2_17_039_C20_R1


title: SS2_17_039_C17_R1


title: SS2_17_039_C1_R1


title: SS2_17_039_C19_R1


title: SS2_17_039_C22_R1


title: SS2_17_039_C18_R1


title: Mesenteric Macrophages 7-days Post Injection of ID8

city: Stanford

first: Oliver

last: Dorigo

address: 300 Pasteur Dr

institute: Stanford University

data_processing:
Read quality was determined with FastQC 0.11.4. The reads were aligned to the mouse reference genome (NCBI37/mm9) using STAR 2.4.2a, with splice junctions defined by the GTF file (UCSC).
Genome_build: mm9

source_name: Mesenteric Tissue

extract_protocol:
A modified protocol of the adipose tissue dissociation kit (130-105-808, Miltenyi Biotech) was used to obtain a single cell suspension of the mouse omenta and mesentery
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 7 days post cancer (ID8) injection

value: Mesenteric Tissue


title: Undiff MS2control miTRAP 1


title: ORG_NL_IE_TNF_001


title: ORG_CD_JE_TNF_001


title: ORG_NL_JE_TNF_003

source_name: TNF-treated control jejunal organoid


title: Naïve Mesenteric Macrophages

value: Normal


title: Undiff MRTF-A miTRAP 3

description:
miRNA trapping by RNA affinity purification with MRTF-A 3'UTR according to Braun et al, 2014 (PMID: 24510096)
DE_C2C12_smallRNA_MRTFA.csv


title: Mesenteric Macrophages 24-hours Post Injection of ID8

value: 24 hour post cancer (ID8) injection


title: Undiff MS2control miTRAP 3


title: Bronchial epithelial cells, RV-infected CF rep1

value: M

value: CF


title: Omental Macrophages 7-days Post Injection of ID8

source_name: Omental Tissue

value: Omental Tissue


title: Omental Macrophages 24-hours Post Injection of ID8


title: Naïve Omental Macrophages


title: SS2_17_154_P8_R1

value: postnatal day 28

value: ERCC


title: SS2_17_154_P9_R1


title: SS2_17_154_P7_R1


title: SS2_17_154_P6_R1


title: SS2_17_154_P5_R1


title: ORG_NL_JE_TNF_002


title: ORG_CD_IE_003

source_name: Crohn's ileal organoid

value: TNF-free


title: SS2_17_154_P4_R1


title: Undiff MRTF-A miTRAP 1


title: Undiff Input 3


title: Undiff MRTF-A miTRAP 2


title: Undiff Input 2


title: in vivo activated (2w CCl4)_1

type: RNA

city: Brussels

first: Inge

last: Mannaerts

address: Laarbeeklaan 103

department: Liver Cell Biology Lab

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Hybridization for 16h at 45°C on Affymetrix GeneChip Mouse Gene 2.0 ST arrays  (Affymetrix, Santa Clara, CA)

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner

data_processing:
All image files were generated using the Affymetrix GeneChip command console (AGCC)
The *.cel files were imported into GeneSpringGX 12 (Agilent, Santa Clara, CA) for normalisation and data analysis. To create an expression matrix, the raw data were pre-processed using the multi-array average (RMA) algorithm consisting of background correction, quantile normalisation & probe summarisation.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MoGene-2_0-st
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: in vivo activated (2w CCl4)_aHSC

label_protocol: DNA is labeled by terminal deoxynucleotidyl transferase (TDT) with the Affymetrix DNA Labeling reagent that is covalently linked to biotin (GeneChip WT terminal Labeling kit, Affymetrix)

growth_protocol: Freshly isolated mouse hepatic stellate cells were isolated from BalbC mice and cultured in DMEM supplemented with 10 % FBS, 0.1% PenStrep and 0.1% Ultraglutamine

extract_protocol: RNA isolation with ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI) according to manufacturer' s protocol, preamplification using the Pico Ovation WTA V2 System was performed

treatment_protocol: 2 hours after seeding, unattached cells were washed away and valproic acid treatment was started (2.5 mM)

tag: strain background

value: BALB/c

value: primary hepatic stellate cells

tag: treatment

value: in vivo fibrosis, no seeding


title: SS2_17_154_P3_R1


title: ORG_CD_IE_001

value: ileum

value: Crohn's disease


title: in vivo activated (4w CCl4)_1

source_name: in vivo activated (4w CCl4)_aHSC


title: SS2_17_154_P2_R1


title: Undiff Input 1

value: undifferentiated


title: ORG_NL_IE_003

source_name: control ileal organoid

value: control


title: SS2_17_154_P24_R1

source_name: empty well - just lysis buffer


title: Diff MS2control miTRAP 3

value: myogenic differentiation 7d

value: myoblasts


title: SS2_17_154_P22_R1


title: Diff MS2control miTRAP 2


title: Quiescent (0h)_1

source_name: Quiescent (0h)_qHSC

value: no seeding


title: SS2_17_154_P21_R1


title: SS2_17_039_C24_R1


title: Diff MS2control miTRAP 1


title: ORG_NL_IE_002


title: in vivo activated (4w CCl4)_2


title: SS2_17_154_P1_R1


title: ORG_NL_IE_001


title: SS2_17_154_P18_R1


title: SS2_17_154_P19_R1


title: SS2_17_154_P17_R1


title: ORG_CD_JE_003

source_name: crohn's jejunal organoid

value: Jejunum


title: ORG_CD_IE_002


title: in vivo activated (2w CCl4)_2


title: vitro activated (d10)_1

source_name: vitro activated (d10)_aHSC

value: 10 days culture


title: SS2_17_154_P16_R1


title: vitro activated (d10)_2


title: Quiescent (0h)_2


title: ORG_CD_JE_002


title: Diff MRTF-A miTRAP 3


title: SS2_17_154_P15_R1


title: Diff MRTF-A miTRAP 2


title: ORG_CD_JE_001


title: SS2_17_154_P23_R1


title: Diff MRTF-A miTRAP 1


title: ORG_NL_JE_TNF_001

value: TNF-treated


title: SS2_17_154_P13_R1


title: SS2_17_154_P20_R1


title: Diff Input 3


title: SS2_17_154_P12_R1


title: SS2_17_154_P10_R1


title: SS2_17_154_P11_R1


title: Diff Input 1


title: Diff Input 2


title: SS2_17_154_O8_R1


title: SS2_17_154_O9_R1


title: ORG_NL_JE_003

source_name: control jejunal organoid


title: ORG_NL_JE_001


title: ORG_NL_JE_002


title: SS2_17_154_O6_R1


title: SS2_17_154_O4_R1


title: SS2_17_154_O5_R1


title: SS2_17_154_P14_R1


title: SS2_17_039_C16_R1


title: SS2_17_154_O3_R1


title: SS2_17_039_C15_R1


title: OX EE RNA Bio-replicate 1

city: Dublin

first: Aalap

last: Mogre

address: Moyne Institute of Preventitive Medicine

department: Department of Microbiology

country: Ireland

institute: Trinity College Dublin

description:
rRNA depleted total RNA
MB_OX_fis_dps_EE_RNA_BR1

data_processing:
Alignment: bwa + samtools
Coverage calcuation (.bw files): deeptools
Counting reads mapping to genes: Rsubread
Calculating fold changes: EdgeR
Genome_build: NC_016810, NC_017718, NC_017719, NC_017720
Supplementary_files_format_and_content: raw_counts.xlsx: raw counts of reads mapping to genes; gene_fold_changes_with_FDR.xlsx: EdgeR calculated gene expression fold changes relative to WT; .bw: BigWig files for looking at coverage in a genome browser like IGB

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: lab strain

growth_protocol: For performing growth experiments, overnight cultures were diluted to A600 of 0.003 in 25 ml LB in 250 ml conical flasks. These were incubated at 37 °C with 200 rpm orbital shaking.

extract_protocol:
At the EE or TS phases of growth, cells were harvested as described for RT-qPCR. The bacterial pellet was dissolved in TE pH 8.0 (100 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0) containing 0.5 mg/ml lysozyme. Lysis was carried out with 1% SDS and 0.1 mg/ml proteinase K while incubating at 40oC for 20 min. RNA was isolated by the addition of 0.3 M sodium acetate (pH 6.5) and 1 volume of phenol (pH 4.3):chloroform (1:1), followed by centrifugation (16000 x g, 4 °C, 10 min) in a phase lock tube (Quantbio, VWR) to separate the aqueous and organic phases. Following this, 1 volume of chloroform was added to the aqueous layer and centrifugation (16000 x g, 4 °C, 10 min) was repeated in the same phase lock tube. RNA was precipitated by the addition of 5 volumes of 100% ethanol and incubation at -20 oC for 1 h. RNA was pelleted by centrifugation (16000 x g, 4 °C, 10 min), washed once with 70% ethanol, and resuspended in 50 µl DEPC treated water. RNA was diluted to 500 ng/µl, denatured at 65oC for 5 min and treated with 10 U RNase-free DNase I (ThermoFisher Scientific, Waltham, USA) in DNase 1 buffer at 37 oC for 40 min. DNase treated RNA was cleaned up using the phenol chloroform method again.
Strand specific library preparation and sequencing of the DNase treated RNA was performed by Vertis Biotechnologie AG (Freising-Weihenstefan, Germany). Briefly, samples were analysed by capillary electrophoresis (Bioanalyzer, Agilent), and ribosomal RNA (rRNA) was depleted using the bacterial Ribo-Zero rRNA Removal Kit (Illumina). Ribodepleted RNA samples were fragmented using ultrasound (4 x 30 second pulses at 4oC). Oligonucleotide sequencing adapters were ligated to the 3’ end of each specific strand of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3’ end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/µl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis (Bioanalyzer, Agilent). For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The cDNA pool was size fractionated in the size range of 200 - 550 bp using a differential clean-up with the Agencourt AMPure kit. An aliquot of the size fractionated pool was analyzed by capillary electrophoresis . Samples were PCR amplified for Truseq according to the instructions of Illumina. The cDNA pool was paired end sequenced on an Illumina NextSeq 500 system using 2 x 75 bp read length.

treatment_protocol: Different phases of growth were harvested.

value: OX

tag: growth phase

value: Early exponential

tag: biological replicate number

tag: paired or single end

value: single


title: SS2_17_039_C14_R1

source_name: cDNA - brain / subthalamic nucleus

value: postnatal day 28

value: ERCC


title: OX EE RNA Bio-replicate 2

description:
rRNA depleted total RNA
MB_OX_fis_dps_EE_RNA_BR2


title: V2A_Cont

city: Boston

first: Daisuke

last: Ogiya

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: embedded sgRNA barcodes

data_processing:
Library strategy: Deep sequencing of embedded sgRNA barcodes
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) (https://sourceforge.net/projects/mageck/) was used to analyze data. Raw reads were quantified using "count" module and two group then compared using "test" module.
Supplementary_files_format_and_content: V2A.count.count_normalized.txt: normalized read counts
Supplementary_files_format_and_content: V2B.count.count_normalized.txt: normalized read counts
Supplementary_files_format_and_content: combined.test.sgrna_summary.txt: combined normalized read counts
Supplementary_files_format_and_content: combined.test.gene_summary.txt: gene rank based on p-value

source_name: RPMI 8226 cells

growth_protocol: RPMI 8226 cells were infected with GeCKOv2 library A and B, respectively. After 24 h incubation, cells were incubated with peuromycin for 72 h.

extract_protocol:
Genomic DNA was extracted from a sufficient number of cells to maintain a coverage of >500 using the Zymo Research Quick-gDNA MidiPrep.
sgRNA library was amplified by library PCR according to the article of Nature Protocol (Nat Protoc. 2017;12(4):828-863.).

treatment_protocol: Cells were incubated with Interleukin-6 (1 ng/ml) for 72 h.

tag: cell line

value: RPMI 8226

value: myeloma cells

tag: procedure

value: non-sorted control cells

value: CRISPR-Cas9 GeCKOv2 library A


title: V2A_Sort

description: embedded sgRNA barcodes

value: top 5% sorted cells with CD38-high expression

tag: infection


title: V2B_Cont

description: embedded sgRNA barcodes

value: CRISPR-Cas9 GeCKOv2 library B


title: B-HIVE_3 DNA Jurkat WT 31.25uM

city: Barcelona

first: Guillaume

last: Filion

address: Dr. Aiguader 88

department: GRSCC

country: Spain

institute: CRG

description:
DNA (PCR)
G247
ledgins3_integration_features.txt
ledgins3_expression.txt

library_source: genomic

data_processing:
Sequencing lane demultiplexing: Sequences were demultiplexed using bcl2fastq. In case the index was inside the sequenced amplicon, demultiplexing was carried out with custom scripts using the provided PCR indices.
Barcode extraction: Barcodes were extracted from the forward reads. The barcode sequences in the construct are flanked by the Illumina adaptor and the T7 promoter sequence (TATAGTGAGTCGTATTAAAA). The promoter sequence was identified using Seeq (github.com/ezorita/seeq) allowing up to 2 mismatches.
Barcode clustering: Barcodes were clustered by sequence similarity using starcode and allowing up to 1 mismatch (github.com/gui11aume/starcode).
Alignment: Reverse reads were aligned on GRCh37/h19 using BWA-mem with default parameters.
Filtering on alignment quality: Only SAM mapping qualities greater or equal than 20 were used in the analysis.
Filtering of recombinant molecules: A barcode was associated to a mapped locus based on their co-ocurrence in paired-end reads. Associations between a barcode and a mapped locus reported by less than 10 paired-end reads were discarded. The remaining associations were considered reliable if both the barcode and the mapped locus were found together at least 90% of the time.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: ledgins1_integration_features.txt: B-HIVE1 Integration sites
Supplementary_files_format_and_content: ledgins2_integration_expression.txt: B-HIVE2 Integration sites and expression levels
Supplementary_files_format_and_content: ledgins3_expression.txt: B-HIVE3 Expression levels
Supplementary_files_format_and_content: ledgins3_integration_features.txt: B-HIVE3 integration sites

molecule: genomic DNA

source_name: Jurkat cell line: Human T lymphocyte

growth_protocol: Jurkat and SupT1 human T cells line were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 0,1% Gentamicin (1000x) at 37℃ under a 95% air/5% CO2 atmosphere. Jurkat and SupT1 cells were passaged twice a week with 1 to 6 dilution.

extract_protocol:
Genomic DNA and total RNA from the same infected cell pool were extracted by the AllPrep DNA/RNA Mini Kit. Total RNA was further proceeded to purify mRNA by Oligotex mRNA Mini Kit.
Libraries used for mapping HIV integrations were prepared by inverse PCR. Briefly, 3 µg DNA were harvested and digested by the restriction enzyme BplI. Fragments were blunt-end self-ligated in the total volume 1 mL at 16℃ overnight. The pellet was dissolved in 84 µL distilled water for plasmid-safe DNase treatment. DNase-treated samples were cleaned up by the QIAquick PCR purification kit. Samples were eluted in 20 µL EB buffer. 8 µL eluted product were used for two rounds of nested PCR. PCR products with different indexes were pooled together in the final concentration of 4 nM for sequencing 50 bp paired end on a Illumina NextSeq sequencer. RNA and DNA libraries were prepared by RT-PCR and regular PCR, respectively, with the same primers. RNA and DNA libraries were sequenced 50 bp single read by on a Illumina NextSeq sequencer.

treatment_protocol: Cells were transduced with barcoded HIV in the presence of varying concentrations of LEDGIN CX014442: 6.25, 15.62 or 31.25 µM.

value: Jurkat

value: T lymphocyte

tag: start number of the cells

value: 10 Million

tag: pre-treatment

tag: facs sorting


title: WT TS RNA Bio-replicate 2

description:
rRNA depleted total RNA
MB_WT_fis_dps_TS_RNA_BR2

value: WT

value: Transition to stationary

value: paired


title: SS2_17_039_C13_R1

tag: mouse strain

tag: age

tag: spike-in


title: SS2_17_039_C12_R1


title: V2B_Sort

description: embedded sgRNA barcodes

tag: cell type


title: WT TS RNA Bio-replicate 1

description:
rRNA depleted total RNA
MB_WT_fis_dps_TS_RNA_BR1


title: B-HIVE_3 DNA Jurkat WT 15.62uM

description:
DNA (PCR)
G245
ledgins3_integration_features.txt
ledgins3_expression.txt


title: SS2_17_039_C11_R1


title: SS2_17_154_O7_R1


title: OX TS RNA Bio-replicate 1

description:
rRNA depleted total RNA
MB_OX_fis_dps_TS_RNA_BR1

value: OX


title: SS2_17_039_C10_R1


title: B-HIVE_3 DNA Jurkat WT 6.25uM

description:
DNA (PCR)
G243
ledgins3_integration_features.txt
ledgins3_expression.txt

value: 6.25 uM LEDGIN CX014442


title: SS2_17_039_B8_R1


title: WT EE RNA Bio-replicate 2

description:
rRNA depleted total RNA
MB_WT_fis_dps_EE_RNA_BR2

value: Early exponential


title: SS2_17_039_B7_R1

value: postnatal day 28


title: B-HIVE_3 RNA Jurkat WT 31.25uM rep2

description:
RNA (RT-PCR)
R363
ledgins3_integration_features.txt
ledgins3_expression.txt


title: SS2_17_039_B4_R1

value: ERCC


title: SS2_17_039_B5_R1


title: OX TS RNA Bio-replicate 2

description:
rRNA depleted total RNA
MB_OX_fis_dps_TS_RNA_BR2

value: single


title: SS2_17_039_B6_R1


title: B-HIVE_3 DNA Jurkat WT 0uM

description:
DNA (PCR)
G241
ledgins3_integration_features.txt
ledgins3_expression.txt


title: WT EE RNA Bio-replicate 1

description:
rRNA depleted total RNA
MB_WT_fis_dps_EE_RNA_BR1


title: B-HIVE_3 RNA Jurkat WT 31.25uM rep1

description:
RNA (RT-PCR)
R362
ledgins3_integration_features.txt
ledgins3_expression.txt


title: GX TS RNA Bio-replicate 2

description:
rRNA depleted total RNA
MB_GX_fis_dps_TS_RNA_BR2

value: GX


title: GX TS RNA Bio-replicate 1

description:
rRNA depleted total RNA
MB_GX_fis_dps_TS_RNA_BR1


title: B-HIVE_3 RNA Jurkat WT 15.62uM rep2

description:
RNA (RT-PCR)
R359
ledgins3_integration_features.txt
ledgins3_expression.txt


title: SS2_17_039_B24_R1


title: SS2_17_039_B2_R1


title: SS2_17_039_B3_R1


title: SS2_17_039_B23_R1


title: B-HIVE_3 RNA Jurkat WT 15.62uM rep1

description:
RNA (RT-PCR)
R358
ledgins3_integration_features.txt
ledgins3_expression.txt


title: SS2_17_039_B22_R1


title: SS2_17_039_B20_R1


title: B-HIVE_3 RNA Jurkat WT 6.25uM rep2

description:
RNA (RT-PCR)
R355
ledgins3_integration_features.txt
ledgins3_expression.txt


title: GX EE RNA Bio-replicate 1

description:
rRNA depleted total RNA
MB_GX_fis_dps_EE_RNA_BR1


title: SS2_17_039_B1_R1


title: B-HIVE_3 RNA Jurkat WT 6.25uM rep1

description:
RNA (RT-PCR)
R354
ledgins3_integration_features.txt
ledgins3_expression.txt


title: WT Mock

data_processing:
Alignment: bwa + samtools
Coverage calcuation (.bw files): deeptools
Peak calling: MACS2
Genome_build: NC_016810, NC_017718, NC_017719, NC_017720
Supplementary_files_format_and_content: narrow_peak_list_fdr_cutoff_annotated.xlsx: peak lists generated using MACS2 and roughly annotated using custom script; .bw: BigWig files for looking at coverage in a genome browser like IGB

growth_protocol: Overnight cultures were diluted to a starting A600 of 0.003 in 25 ml LB broth and grown to an A600 of 0.4.

extract_protocol:
Cells were harvested by centrifugation at 3,220 x g for 10 min at room temperature and resuspended in 50 ml PBS. Formaldehyde was added dropwise to a final concentration of 1% (v/v) while continuously stirring the cells. After 10 min of crosslinking the reaction was quenched with cold glycine (2M) added dropwise to a final concentration of 0.125 M. Cells were stirred further for 5 min and then harvested by centrifugation at 3220 x g for 10 min at 4 °C. The pellet was suspended in 600 μl Lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA pH 8.0, 1% (w/v) SDS, Roche protease inhibitor cocktail), incubated for 10 min on ice, prior to the addition of 1.2 ml IP Dilution Buffer (20 mM Tris-HCl pH 8.1, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% (v/v) Triton X-100, 0.01% (w/v) SDS, Roche protease inhibitor cocktail) and transferred to a sonication tube. Chromatin was sheared to an average length of 500 bp by sonicating for 30 seconds with an amplitude of 10 µm, twelve times, with a 1 min incubation on ice between bursts using a Soniprep 150. Sheared chromatin was analysed by agarose gel electrophoresis and stored at -80°C. To pre-clear chromatin for input samples, 50 µl normal rabbit IgG (Millipore, Cork, Ireland) was added and samples were incubated for 1 h on a blood tube rotator SB1 at 4oC. Antibody was removed by the addition of 100 µl homogeneous Protein G-Agarose (Roche) and a further incubation for 3 h. The Protein G-Agarose was removed by centrifugation at 3,220 x g for 2 min and 200 µl was used as input. For all ChIP experiments a mock IP and an experimental IP were set up at the same time using 1,350 µl pre-cleared chromatin and 10 µg of normal mouse IgG (Millipore) and monoclonal mouse anti-c-Myc respectively. Samples were incubated at 4oC for 16 h on a blood tube rotator SB1. 100 µl homogeneous Protein G-Agarose was added to each and the samples were incubated for a further 3 h. Protein G-Agarose beads were pelleted by centrifugation at 5,200 x g, washed 4 times with high salt IP wash buffer (50 mM HEPES pH 7.9, 500 mM NaCl, 1 mM EDTA, 0.1% (w/v) SDS, 1% (v/v) Triton X-100, 0.1% (w/v) deoxycholate), and twice with TE pH 8.0. Protein-DNA complexes were eluted from the beads twice with IP elution buffer (100 mM NaHCO3, 1% (w/v) SDS). DNA was purified and recovered by performing a standard phenol‐chloroform extraction, followed by ethanol precipitation with 5 µg of glycogen (Invitrogen, Cat. no. 10814‐010). The DNA pellets of the IP samples were re‐suspended (by heating at 37°C) in 50 µl of sterile filtered water for experimental and mock IPs, and 100 µl for the Input DNA samples.
ChIP sequencing was performed by Vertis Biotechnologie AG using Illumina NextSeq 500 technology. The DNA samples were first fragmented with ultrasound (2 pulses of 30 sec at 4°C). After end-repair, TruSeq sequencing adapters were ligated to the DNA fragments. Finally, the DNA was PCR-amplified to about 10-20 ng/µl using a high fidelity DNA polymerase. Aliquots of the PCR amplified libraries were examined by capillary electrophoresis (Bioanalyzer, Agilent). For Illumina NextSeq sequencing, the samples were pooled in approximately equimolar amounts. The DNA pool was eluted in the size range of 250 – 550 bp from a preparative agarose gel. An aliquot of the size fractionated library pool was analyzed by capillary electrophoresis (Bioanalyzer, Agilent). The adapters were designed for TruSeq sequencing according to the instructions of Illumina. The shotgun library pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

treatment_protocol: Cells harvested at early exponential phase.

tag: type

value: Mock

tag: chip antibody

value: normal mouse IgG

tag: bio-replicate number


title: WT Fis IP Bio-replicate 2

tag: strain

value: IP

value: mouse anti-c-Myc


title: B-HIVE_3 RNA Jurkat WT 0uM rep2

description:
RNA (RT-PCR)
R351
ledgins3_integration_features.txt
ledgins3_expression.txt

value: Jurkat


title: SS2_17_039_B17_R1


title: SS2_17_039_B9_R1


title: B-HIVE_3 RNA Jurkat WT 0uM rep1

description:
RNA (RT-PCR)
R350
ledgins3_integration_features.txt
ledgins3_expression.txt

value: T lymphocyte


title: SS2_17_039_B16_R1


title: SS2_17_039_B15_R1


title: B-HIVE_2 DNA Jurkat WT 31.25uM

description:
DNA (PCR)
G240
ledgins2_integration_expression.txt

value: 10 Million


title: SS2_17_039_B13_R1


title: SS2_17_039_B12_R1


title: GX EE RNA Bio-replicate 2

description:
rRNA depleted total RNA
MB_GX_fis_dps_EE_RNA_BR2

tag: growth phase


title: OX Fis IP Bio-replicate 2


title: OX Fis IP Bio-replicate 1


title: SS2_17_039_B11_R1


title: SS2_17_039_B21_R1


title: B-HIVE_2 DNA Jurkat WT 6.25uM

description:
DNA (PCR)
G238
ledgins2_integration_expression.txt


title: SS2_17_039_B10_R1


title: SS2_17_039_B19_R1


title: SS2_17_039_A9_R1


title: SS2_17_039_B18_R1


title: B-HIVE_2 DNA SupT1 WT 31.25uM

description:
DNA (PCR)
G236
ledgins2_integration_expression.txt

source_name: SupT1 cell line: Human T cell lymphoblastic Lymphoma

value: T lymphoblast


title: GX Fis IP Bio-replicate 2


title: SS2_17_039_A7_R1


title: B-HIVE_2 DNA Jurkat WT 0uM

description:
DNA (PCR)
G237
ledgins2_integration_expression.txt


title: OX Mock


title: GX Mock


title: SS2_17_039_A5_R1


title: B-HIVE_2 DNA SupT1 WT 15.62uM

description:
DNA (PCR)
G235
ledgins2_integration_expression.txt


title: SS2_17_039_A8_R1


title: SS2_17_039_A6_R1


title: SS2_17_039_B14_R1


title: B-HIVE_2 DNA Jurkat WT 15.62uM

description:
DNA (PCR)
G239
ledgins2_integration_expression.txt


title: B-HIVE_2 DNA SupT1 WT 6.25uM

description:
DNA (PCR)
G234
ledgins2_integration_expression.txt


title: MUT

city: Beijing

first: Zhi

last: Zeng

address: 7 Science Park Road, ZGC life science park

country: China

institute: National Institute of Biological Sciences, Beijing

description:
Whole Exome Sequencing
HQ461 resistant clones
processed data file: HQ461_HCT116_Whole Exome Sequencing.xlsx

data_processing:
Library strategy: WES
Fastq files were aligned to the human reference genome version GRCh38 (hg38) using Burrows-Wheeler Aligner (BWA, v0.7.17) to generate sam files, which were then transformed to bam files through samtools (v1.10).
Next, bam files were passed to the Genome Analysis Toolkit (GATK, v4.1.7) to call SNVs, deletions, and insertions.
To call variants, several tools of GATK were utilized, including BaseRecalibrator to adjust base quality scores in the bam files using known variants in dbSNP database (build 146) and 1000 Genomes database.
Mutect2 for variant calling.
GetPileupSummaries and CalculateContamination to estimate and remove cross-sample contamination.
CollectSequencingArtifactMetrics and FilterByOrientationBias to exclude sequence contextdependent artifacts.
FilterMutectCalls to filter out variants from some common sources of error.
Finally, variants generated by GATK were annotated using snpEff (v4.5) and SnpSift (v4.3t).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: HQ461_HCT116_Whole Exome Sequencing.xlsx: GATK result file; Matrix table with chromosome, position, reference, alteration, effect, impact, gene, allele depth and allele frequency for every variant.

source_name: HCT-116 cell line

growth_protocol: Parental HCT-116 were plated sparsely on 10-cm plates to allow the isolation of ten individual clones. Each of these ten clones were expanded to one confluent 15-cm plate to establish ten independent cell populations.

extract_protocol:
Cells were lysed in 10 mM Tris-HCl, pH 8.0, 100 mM EDTA, 0.5% SDS, 200 μg/ml RNase A and incubated at 37 °C for 1 hour followed by the addition of 1mg/ml of proteinase K for an overnight incubation at 50 °C. The resulting lysates were extracted three times with phenol solution equilibrated with 10 mM Tris-HCl, pH 8.0, 1 mM EDTA (Sigma P4557) mixed with chloroform (1:1 v/v) using tubes with phase lock gel (Tiangen WM5-2302831). The aqueous phase was then mixed with 0.2 volume of 10 M ammonium acetate and 1 volume of isopropanol, resulting the immediate formation of cloudy DNA precipitates. Precipitated DNA was then transferred by a pipet tip to a tube containing 75% (v/v) ethanol. This process was repeated twice to ensure complete removal of residual organic solvents. Afterwards, genomic DNA was dissolved in 1 mM Tris-HCl, pH 8.0, 0.1 mM EDTA by incubation at 50 °C for three hours.
Their genomic DNAs were then pooled in equal amounts for whole-exome sequencing at 200x average coverage (Novogene). As a control, genomic DNAs isolated from the corresponding cell populations before HQ461 selection were also pooled for whole-exome sequencing.

treatment_protocol: One million cells from each population were then plated on one 10-cm plate and treated with 20 μM HQ461 continuously for two weeks, with media change every 3 to 4 days. HQ461 resistant clones emerged from 5 out of the 10 populations. These clones were isolated, expanded, and tested for their sensitivity to HQ461 using cell viability assay. Five HQ461-resistant clones selected from independent populations were subjected to genomic DNA isolation as described in the previous session.

value: human colon cancer cell line

tag: treatment


title: GX Fis IP Bio-replicate 1


title: siCTRL_r1

type: protein

city: Poznań

first: Maciej

last: Wiznerowicz

address: Fredry 10

country: Poland

institute: Poznań University of Medical Sciences

description: Protein lysate

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and the density was quantified by Array-Pro Analyzer.

data_processing:
Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed by a script in R written by Bioinformatics. These values (given as log2 values) are defined as Supercurve Log2 (Raw) values and are provided in the raw data files.
All the data points were normalized for protein loading and transformed to linear values, designated as Normalized Linear.

label: DAB

molecule: protein

source_name: human iPSC

label_protocol: Samples were probed with primary antibodies plus biotin-conjugated secondary antibodies by CSA amplification approach. Total of 305 unique antibodies were used. Samples were visualized by DAB colorimetric reaction.

growth_protocol: iPSC were maintained in feeder-dependent culture, under hypoxic conditions (37°C, 5% CO2, 5% O2). Cells were cultured in plates coated with Matrigel (BD Biosciences) and seeded with inactivated MEF cells (Millipore) at 100% confluency, in iPSC medium: DMEM/F12 (Millipore), 20% KSR (Gibco), 1X NEAA (Merck), 1X β-mercaptoethanol (Merck), 50 U/mL penicillin and 50 µg/mL streptomycin (Sigma-Aldrich) and 10 ng/mL FGF (Gibco).

extract_protocol: Pellets of iPSC were washed with DPBS (Biowest) and lysed in 100 μL of RIPA buffer (Alfa Aestar). Cell lysates were centrifuged at 13,000 rpm, 4°C, 30 min and supernatant was collected. Protein concentration was determined by BCA reaction with Pierce™ BCA Protein Assay Kit (Thermo Fisher Scientific), according to manufacturer’s protocol. Each sample (40 μL) was mixed with 4X SDS sample buffer (40% Glycerol (AppliChem, PanReac); 8% SDS (Sigma-Aldrich); 0.25 M Tris-HCL (Roche), pH 6.8; 10% β-mercaptoethanol (Merck)) and boiled for 5 min. Samples were sent to RPPA Core Facility, MD Andersen Cancer Center, Houston, TX for RPPA analysis. Cell lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slides in 11x11 format.

treatment_protocol: iPSC were treated with siRNA targeting TRIM28 or control siRNA without any target. Cells were analyzed 14 days post siRNA treatment.

value: iPSC obtained by PHDF cells reprogramming with Stemcca-TetO LV

value: control siRNA with no target sequence


title: siCTRL_r2

description: Protein lysate

hyb_protocol: Cell lysates were two-fold-serial diluted for 5 dilutions (from undiluted to 1:16 dilution) and arrayed on nitrocellulose-coated slides in 11x11 format.


title: SS2_17_039_A4_R1

city: Uppsala

first: Åsa

last: Wallén-Mackenzie

address: Norbyvägen 18A

institute: Uppsala University

data_processing:
All reads were aligned to the mouse (mm10) genome using STAR (Dobin et al., 29, 2013)
Non-uniquely mapped reads were removed
The expression values of merged RefSeq and Ensemble gene annotations were computed as described in Rämsköld et al. (PLoS Comput. Biol., 5,2013) , using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. PLoS One, 8, 2013)
Genome_build: mm10
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

extract_protocol:
Snap frozen tissue was dissociated with lysis buffer+0.32Msucrose in 1ml dounce homogenizers. Homogenate was added over a 1.8Msucrose layer and centrifuged 2 h 20 min at 30,000 × g (Beckman J-25 centrifuge with a J13.1 rotor).  cDNA was generated from FACS sorted single nuclei using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer
Nextera XT DNA sample preparation index kit, 384 indices (Illumina)


title: siCTRL_r3

description: Protein lysate


title: WT

description:
Whole Exome Sequencing
Wild type HCT-116 cells
processed data file: HQ461_HCT116_Whole Exome Sequencing.xlsx

value: untreated


title: SS2_17_039_A3_R1


title: SS2_17_039_A2_R1


title: B-HIVE_2 DNA SupT1 WT 0uM

description:
DNA (PCR)
G233
ledgins2_integration_expression.txt


title: B-HIVE_2 RNA Jurkat WT 31.25uM rep2

description:
RNA (RT-PCR)
R349
ledgins2_integration_expression.txt


title: siTRIM28_r1

description: Protein lysate

value: siRNA targeting TRIM28


title: SS2_17_039_A24_R1

value: postnatal day 28


title: siTRIM28_r2

description: Protein lysate


title: SS2_17_039_A23_R1

value: ERCC


title: B-HIVE_2 RNA Jurkat WT 15.62uM rep1

description:
RNA (RT-PCR)
R346
ledgins2_integration_expression.txt


title: SS2_17_039_A21_R1


title: B-HIVE_2 RNA Jurkat WT 6.25uM rep2

description:
RNA (RT-PCR)
R345
ledgins2_integration_expression.txt

value: 6.25 uM LEDGIN CX014442


title: WT_r3

description: Protein lysate


title: Circulating OT-I effector T cells responding to skin vaccination

city: Amsterdam

first: Lianne

last: Kok

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Raw data were processed by Cell Ranger 3.1.0. Next, the data was filtered using the Seurat and MetaCell packages in R. Cells that could be assigned to multiple mice or to no mouse(inferred from the detection of multiple or no Hastags (HTO), cells with a transcript (UMI) count lower than 2,000 or a mitochondrial gene fraction higher than 0.075, were excluded. Additionally, cells that transcriptionally resemble non-T cells (B cells/ erythrocytes/thrombocytes) were also excluded.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: UMI_count_table: UMI counts, columns represent cells, rows represent genes. MC_log2_fold_enrichment_table: gene enrichment table (lfp values), columns represent MetaCells, rows represent genes. var_genes: list of variable genes used to generate 14 transcriptionally distinct MetaCells (see MC_log2_fold_enrichment_table), as described in the publication

source_name: Blood

extract_protocol: Blood samples were collected from 3 mice. Samples were treated with NH4Cl to lyse erythrocytes. OT-I effector T cells (CD8+CD45.2+Vb5+GFP+) were isolated by FACS. Library preparation was performed according to the manufacturers protocol of the 10X genomics Chromium Single Cell 3' kit (V3). Sequencing was performed on Next-Seq550 (Illumina)

value: OT-I

tag: time point

value: 12 days after skin vaccination

value: CD8+ T cells


title: WT_r2

description: Protein lysate


title: SS2_17_039_A20_R1


title: SS2_17_039_A1_R1


title: B-HIVE_2 RNA Jurkat WT 0uM rep2

description:
RNA (RT-PCR)
R343
ledgins2_integration_expression.txt

tag: cell line


title: B-HIVE_2 RNA Jurkat WT 0uM rep1

description:
RNA (RT-PCR)
R342
ledgins2_integration_expression.txt


title: WT_r1

description: Protein lysate


title: Lymphatic vessel patient 10

city: London

first: Sarah

middle: C

last: Johnson

state: London

address: Prince Consort Road

department: Bioengineering

country: United Kingdom

institute: Imperial College London

description: SAMPLE 10

data_processing:
The normalization and data analysis were performed according to the manufacturers instructions, using a fold change regulation and t-test between groups.
For the normalization, NormFinder and GeNorm software were used to identify the most stably expressed housekeeping genes, with subsequently the expression of SNORD 95 used for normalization
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Average 2^(-Avg.(Delta(Ct)) were calculated for each test group of n>=3. Fold change between groups were calculated and fold-regulation used to convert fold-change <1 to negative representations (-1/fold-change), eg. 0.5 = -2.0 fold-regulation
Fold Change worksheet reports test group1/test group2 (i.e., cancer-infiltrated/non-cancer-infiltrated) ratios.

label: SYBR Green

source_name: Lymphatic vessel

label_protocol: Each sample was reverse-transcribed to cDNA using a miScript II RT Kit (Qiagen), then 100 nanograms of RNA were used per sample with qPCR carried out using a miScriptSybrGreen real-time PCR kit (Qiagen) and pre-defined miScript miRNA PCR Array (Human Inflammatory Response & Autoimmunity miRNA PCR Array (MIHS-105ZA). One well was populated with a negative control sample and a RNA spike: C.elegans (miR-39) was included . The array was run using a StepOnePlus Real-Time PCR System (Applied Biosystems), according to the manufacturer’s instructions.

extract_protocol: Samples in RNAlater were individually defrosted and homogenized in 700μL of QIAzol (Qiagen, UK), using a PT 1300 D homogenisor with a 3mm dispersing aggregate head (Kinematica, Switzerland) at 20,000 RPM in a sterile 1.5 ml tube. RNA was extracted using a miRNeasy Mini Kit (Qiagen, UK) following the standard protocol and quality was verified using a NanoDropTM 2000 at A260/280nm and A260/230nm absorbance (Thermofisher, UK).

tag: tissue

value: Lymphatic vessel

tag: inflammation (high, medium, low)

value: Medium

tag: cancer cell infiltration (y/n)

value: Y

tag: stage (stage iv or <stageiv)

value: <IV

tag: relapse within 13.2 +/- 3.6 mos (y/n)

value: N


title: siTRIM28_r3

description: Protein lysate


title: B-HIVE_2 RNA Jurkat WT 31.25uM rep1

description:
RNA (RT-PCR)
R348
ledgins2_integration_expression.txt

value: Jurkat

value: T lymphocyte

tag: start number of the cells

value: 10 Million

tag: pre-treatment

tag: facs sorting


title: Lymphatic vessel patient 8

description: SAMPLE 8

value: Low


title: SS2_17_039_A19_R1

tag: mouse strain

tag: age

tag: spike-in


title: Lymphatic vessel patient 7

description: SAMPLE 7


title: B-HIVE_2 RNA Jurkat WT 15.62uM rep2

description:
RNA (RT-PCR)
R347
ledgins2_integration_expression.txt

tag: cell type


title: SS2_17_039_A18_R1


title: SS2_17_039_A22_R1


title: YM_REP3

city: Singapore

first: Han Ping

last: Loh

address: 60 Nanyang Drive

country: Singapore

institute: NTU

description: Synchronized stages of Plasmodium yoelii strain.

data_processing:
Kallisto source code was used for index building and abundance quantification (Bray et al. Nature Biotechnology, 2016).
Differential expression analysis was done according to DESeq2 source code and standard workflow using R version 3.4 (Love et al., Genome Biology 2014).
Genome_build: Plasmodium yoelii release 37 (PlasmoDB)
Supplementary_files_format_and_content: Processed data files are packaged into TAR files.
Supplementary_files_format_and_content: abundance.tsv: Kallisto abundance files; tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: abundance.h5
Supplementary_files_format_and_content: diffexpr_*.csv: DESeq2 files; comma-separated text files include differential gene expression analysis.

organism: Plasmodium yoelii

source_name: Plasmodium yoelii

growth_protocol: Parasites were injected via intraperitoneal route into mice.

extract_protocol:
RNA was extracted using Trizol Reagent, and purified with RNeasy Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were provided pyrimethamine treated water throughout the growth of the parasites.

tag: strain

value: YM

tag: genotype/variation

value: Wild type

tag: Stage

value: Trophozoite

tag: passage

value: parental


title: 1872_SC3_REP3

description:
Synchronized stages of Plasmodium yoelii strain.
processed data file: diffexpr_resSC3.csv

value: yir transfectant

value: subclone 3


title: YM_REP2


title: 1872_SC3_REP2


title: YM_REP1


title: WT Fis IP Bio-replicate 1

value: WT

tag: growth phase

value: Early exponential

tag: type

value: IP

tag: chip antibody

value: mouse anti-c-Myc

tag: bio-replicate number


title: SS2_17_039_A17_R1

value: postnatal day 28

value: ERCC


title: 1872_SC3_REP1


title: SS2_17_039_A16_R1


title: B-HIVE_2 RNA Jurkat WT 6.25uM rep1

description:
RNA (RT-PCR)
R344
ledgins2_integration_expression.txt

tag: cell line

value: 6.25 uM LEDGIN CX014442


title: Lymphatic vessel patient 6

description: SAMPLE 6

tag: tissue

value: Lymphatic vessel

tag: inflammation (high, medium, low)

tag: cancer cell infiltration (y/n)

value: N

tag: stage (stage iv or <stageiv)

value: <IV

tag: relapse within 13.2 +/- 3.6 mos (y/n)


title: Lymphatic vessel patient 5

description: SAMPLE 5

value: Low


title: Lymphatic vessel patient 9

description: SAMPLE 9

value: Medium

value: IV


title: SS2_17_039_A15_R1

tag: mouse strain

tag: age


title: B-HIVE_2 RNA SupT1 WT 15.62uM rep1

description:
RNA (RT-PCR)
R338
ledgins2_integration_expression.txt

tag: cell type

value: T lymphoblast

tag: start number of the cells

value: 10 Million

tag: pre-treatment

tag: facs sorting


title: B-HIVE_2 RNA SupT1 WT 15.62uM rep2

description:
RNA (RT-PCR)
R339
ledgins2_integration_expression.txt


title: B-HIVE_2 RNA SupT1 WT 31.25uM rep1

description:
RNA (RT-PCR)
R340
ledgins2_integration_expression.txt


title: Lymphatic vessel patient 4

description: SAMPLE 4

value: Y


title: SS2_17_039_A14_R1

tag: spike-in


title: B-HIVE_2 RNA SupT1 WT 6.25uM rep2

description:
RNA (RT-PCR)
R337
ledgins2_integration_expression.txt


title: B-HIVE_2 RNA SupT1 WT 31.25uM rep2

description:
RNA (RT-PCR)
R341
ledgins2_integration_expression.txt


title: 1872_SC1_REP1

description:
Synchronized stages of Plasmodium yoelii strain.
processed data file: diffexpr_resSC1.csv

tag: genotype/variation

value: yir transfectant

tag: Stage

value: Trophozoite

tag: passage

value: subclone 1


title: Lymphatic vessel patient 3

description: SAMPLE 3

value: High


title: 1872_SC1_REP2


title: Lymphatic vessel patient 2

description: SAMPLE 2

value: HIgh


title: B-HIVE_2 RNA SupT1 WT 6.25uM rep1

description:
RNA (RT-PCR)
R336
ledgins2_integration_expression.txt


title: SS2_17_039_A13_R1

value: postnatal day 28


title: KN3501α_Sodiumsulfate

city: Tokyo

first: Kiminori

last: Shimizu

address: Niijuku

department: Department of Biological Science and Technology

institute: Tokyo University of Science

data_processing:
Read merging, adapter trimming, and quality control were performed by cutadapt ver. 2.5
HISAT v.2.1.0 was used to map the short reads to the annotated genome sequence of C. neoformans JEC21
The transcripts for each sample were assembled and integrated using Stringtie v2.0.4 and Cuffmerge v2.2.1 respectively
The gene expression levels were measured in fragments per kilobase of transcript per million mapped reads (FPKM) using Cuffdiff v2.2.1
Genome_build: Cryptococcus neoformans var. neoformans JEC21 (2005 release, https://www.ncbi.nlm.nih.gov/assembly/GCF_000091045.1/)
Supplementary_files_format_and_content: Matrix table with abundance measurement (FPKM) for every gene and every sample generated from Cuffdiff

organism: Cryptococcus deneoformans

source_name: Yeast cells

growth_protocol: The wild-type KN3501α strain was grown in liquid B medium supplemented with four different sulfur sources, i.e., Met, Cys, homocysteine, or sodium sulfate, for 24 h at 30°C with shaking at 150 rpm. Cells were collected, frozen in liquid nitrogen, and lyophilized overnight.

extract_protocol:
Total RNAs were purified using the Fast Gene Premium Kit (Nippon-Genetics) according the protocol provided by the manufacturer. The purity of the RNA was measured on a NanoDrop 2000 instrument (Thermo Fisher). The RNA levels and integrity were determined using the RiboGreen RNA Assay Kit on a Victor X2 Fluorometer (Life Technologies, USA) and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, USA), respectively.
One library was prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina), and cDNA was sequenced on an Illumina NovaSeq 6000 instrument in a 2 ´ 150 paired-end protocol.

tag: strain

tag: genotype

value: wild-type


title: KN3501α_Methionine


title: SS2_17_039_A12_R1

value: ERCC


title: B-HIVE_2 RNA SupT1 WT 0uM rep2

description:
RNA (RT-PCR)
R335
ledgins2_integration_expression.txt

tag: cell line


title: B. subtilis PY79 + E. coli MW1255

city: Seattle

first: Anna

last: Kuchina

state: Washington

address: 185 Stevens Way, Paul Allen Center – Room AE100R

department: Electrical and Computer Engineering

institute: University of Washington

data_processing:
Library strategy: microSPLiT
The data preprocessing and alignment was performed using a modified SPLiT-seq pipeline (https://github.com/Alex-Rosenberg/split-seq-pipeline). Modifications: using STAR with the splicing isoform detection swiwwe usededt the hioutghoutest-scored multimapping re. We also keptwening a ctional count based on the number igninggood alignments, since bacterial genomes are known to contain overlapping CDSs.
Genome_build: ASM904v1.45 and ASM80076v1.37 from EnsemblBacteria
Supplementary_files_format_and_content: Cell by gene matrix (with cells above threshold 200 UMI/cell); Gene names; Cell annotations (barcode and well for heat shock data, OD for B.subtilis growth curve). For B. Subtilis growth curve, only mRNA are included in the cell-by-gene matrix.
Supplementary_files_format_and_content: For the heat-shock data, barcodes in wells 1-24 belong to heat-shocked cells and in wells 25-48 belong to control cells.

organism:
Escherichia coli
Bacillus subtilis

source_name: Bacillus Genetic Stock Center (BGSC)

growth_protocol: Liquid LB medium at 37C with shaking, starting from diluted overnight culture

extract_protocol:
Cells were fixed in cold formaldehyde overnight, permeabilized with Tween-20 and Lysozyme, then subjected to in-situ polyadenylation, reverse transcription and barcode ligation reactions. After barcoding, cells were lysed with proteinase K and barcoded cDNA was extracted on streptavidin beads
Barcoded cDNA bound to streptavidin C1 beads had a 3' adapter appended through template switching, followed by qPCR amplification and fragmentation with WGS Fragmentation Mix (Enzymatics). Adapters for Illumina sequencing were then appended by the final round of PCR.
SPLiT-seq, first barcode records sample identity

treatment_protocol: For heat shock, 47C for 8 minutes.

value: PY79 and MW1255

tag: replicate


title: Lymphatic vessel patient 1

description: SAMPLE 1

tag: tissue

value: Lymphatic vessel

tag: inflammation (high, medium, low)

tag: cancer cell infiltration (y/n)


title: B-HIVE_2 RNA SupT1 WT 0uM rep1

description:
RNA (RT-PCR)
R334
ledgins2_integration_expression.txt


title: SS2_17_039_A11_R1

tag: mouse strain


title: KN3501α_Homocysteine


title: 1872_SC1_REP3


title: SS2_17_039_A10_R1

tag: age


title: H_MO-MG17-R4-1224760

city: St Louis

first: Winnie

last: Pong

address: 660 S. Euclid Avenue

institute: Washington University School of Medicine

description: normal R4 biological replicate 3

data_processing:
Basecalls performed using Illumina Real-Time Analysis (RTA) version 1.13.48.0 (1.13.56.0 for MiSeq, 1.15.19.5 for flow cell D1CGMACXX) followed by demultiplexing of the index sequence using CASAVA 1.8.2.
SPIA adapter sequence aligned and trimmed from raw sequence reads using FAR 2.17 with command line parameters : --adapter CTTTGTGTTTGA --trim-end left --adaptive-overlap yes --format fastq --write-lengthdist yes --nr-threads 4 --min-overlap 7 --max-uncalled 150 --min-readlength 25
Aligned with TopHat 2.0.4, Bowtie 2.0.0-beta7 and Ensembl 67 annotation (-G param)
FPKM calculated per sample with Cufflinks 2.0.2  and Ensembl 67 annotation with -G param
Genome_build: hg19
Supplementary_files_format_and_content: JPA_gene_fpkm.tsv a tab delimited file with columns for gene ID and the normalized expression values per sample name

source_name: FACS population R4

extract_protocol:
Total RNA was isolated from snap-frozen flow sorted cell pellets using TRIzol-chloroform extraction. RNA was resuspended in 10µl Ambion Nuclease-free water (Life Technologies) and DNAse treated (Ambion TURBO DNA-free Kit)
For cDNA synthesis, we added 5µl of isolated RNA into the Ovation® RNA-Seq method.  500ng cDNA was fragmented using covaris shearing and processed for Illumina library construction with the Illumina paired-end LT indexing protocol as previously published (Mardis et al., 2009; Govindan et al., 2012). Each library was sequenced on the Illumina HiSeq, generating between 15-22Mbp per lane.
RNA-Seq (300-500bp size fractionation): cDNA samples were constructed into Illumina libraries according to the manufacturer’s protocol (Illumina Inc, San Diego, CA) with the following modifications:  1) DNA was fragmented using Covaris S2 DNA Sonicitor using the following condtions: Duty Cycle: 5, Intensity: 4, Cycles/Burst: 200, Time: 90sec (Covaris, Inc. Woburn, MA).  Fragment sizes ranged between 100 and 500bp.  2) Illumina adapter-ligated DNA was amplified in a single 50ml PCR for five cycles.  3) Solid Phase Reversible Immobilization (SPRI) bead cleanup was used to purify the PCR and select for 300-500bp fragments.   We added 0.8 volumes of the AmpureXP solution (preformulated with polyethylene glycol and sodium chloride) to size select DNA molecules greater than 300 bp.  The size-fractioned cDNA was washed three times with 750 µl of 70% ethanol, the beads were dried, and the cDNA library was eluted off the beads by adding 20µl 10 mM Tris-HCl (pH 8.0).  The size-fractioned libraries were assayed using the Agilent BioAnalyzer High Sensitivity DNA chips.

treatment_protocol: Tissue was dissociated and cells were flow sorted.

value: normal


title: KN3501α_Cysteine


title: 11Dec08_FFC

description: FFC biological replicate 4

data_processing:
Basecalls performed using Illumina Real-Time Analysis (RTA) version 1.13.48.0 (1.13.56.0 for MiSeq) followed by demultiplexing of the index sequence using CASAVA 1.8.2.
SPIA adapter sequence aligned and trimmed from raw sequence reads using FAR 2.17 with command line parameters : --adapter CTTTGTGTTTGA --trim-end left --adaptive-overlap yes --format fastq --write-lengthdist yes --nr-threads 4 --min-overlap 7 --max-uncalled 150 --min-readlength 25
Aligned with TopHat 2.0.4, Bowtie 2.0.0-beta7 and Ensembl 67 annotation (-G param)
FPKM calculated per sample with Cufflinks 2.0.2  and Ensembl 67 annotation with -G param
Genome_build: mm9
Supplementary_files_format_and_content: FFC-FF_gene_fpkm.tsv a tab delimited file with columns for gene ID and the normalized expression values per sample name

source_name: microglia

value: optic nerve

value: 3 months

tag: gender

value: F

tag: genotype/variaton

value: Nf1 flox/flox; GFAP-Cre


title: B. subtilis PY79 (OD0.5-OD3.2)

organism: Bacillus subtilis


title: H_MO-MG17-R3-1224759

description: normal R3 biological replicate 3

source_name: FACS population R3


title: H_MO-MG16-R4-1224758

description: normal R4 biological replicate 2


title: H_MO-MG16-R3-1224757

description: normal R3 biological replicate 2


title: Macheng2

city: Wuhan

first: Hu

last: Tao

state: Hubei

address: Shizishan street

institute: Hubei Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat2.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time.
Genome_build: ASM170441v1 ftp://ftp.ncbi.nlm.nih.gov/genomes/Capra_hircus/Assembled_chromosomes/seq/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Capra hircus

source_name: Ovarian follicle

extract_protocol:
A total amount of 5 μg RNA per sample was isolated from each individual sample using TRIzol reagent (Invitrogen, USA). Purity and quantity of total RNA were measured by using Nanodrop equipment. Ribosomal RNAs were depleted using Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Macheng black

value: ovarian follicle

tag: treated

value: Each of three Macheng black goat exhibited normal estrous cycles were treated with 1000 IU PMSG and 500 IU hCG


title: Macheng1


title: 11Nov29_FFC

description: FFC biological replicate 1


title: 11Dec02_FFC

description: FFC biological replicate 2

value: M


title: Boer2

value: Boer

value: Each of three Boer goat that exhibited normal estrous cycles were treated with 1000 IU PMSG and 500 IU hCG


title: Boer3


title: H_MO-MG11-1207681

description: JPA R4 biological replicate 3

value: tumor


title: B. subtilis PY79 (OD0.5-OD6.0)


title: 11Dec06_FF

description: FF biological replicate 4

value: Nf1 flox/flox


title: H_MO-MG15-R3-1224755

description: normal R3 biological replicate 1


title: 11Nov15_FF

description: FF biological replicate 3


title: Boer1


title: H_MO-MG11-1207680

description: JPA R3 biological replicate 3


title: 11Nov08_FF

description: FF biological replicate 2


title: Macheng3


title: 11Dec05_FFC

description: FFC biological replicate 3


title: R099-H-012

status: Public on Jul 02 2020

city: CARDIFF

first: Peter

last: Giles

address: Heath Park

institute: Cardiff University

description: Zeb1-/- HSC 4

data_processing:
Trimming to remove adapter sequencer and poor quality ends of reads was performed by Trim Galore ( a wrapper to cutadapt). Trimming was performed using default parameters in paired-end mode.
Trimmed paired-end reads were aligned to the GRCm38 reference using STAR (v2.5.1b), an ultrafast universal RNA-seq aligner, following the 2-pass method.  STAR mapping was carried out using the MultimapNMax=1 flag, whereby reads that map to more than one genomic location are treated as being unmapped so as to excluded them from downstream analysis*.
Transcript level counts were calculated using Subread featureCounts Version 1.5.1. Transcript and locations used in the analysis derive from the GENCODE GRCm38 v17 gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files containing: ensemble transcript ID, chromosome, start and end locations, strand, transcripts length and counts in STAR mapped bam file.

source_name: bone marrow

extract_protocol:
Cells were resuspended in RLT Plus buffer (Qiagen) and stored at -80 degrees. RNA extraction was carried out using a RNAeasy Plus micro kit (Qiagen) following the manufacturers instructions. Total RNA quality and quantity was assessed using Agilent 2100 Bioanalyser and a RNA Nano 6000 kit (Agilent Technologies). 30-260ng of Total RNA with a RIN value >8 was depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), (New England BioLabs, NEB)
Sequencing libraries were prepared using the NEB® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB). The steps included RNA fragmentation and priming, 1st strand cDNA synthesis, 2nd strand cDNA synthesis, adenylation of 3’ ends, adapter ligation, PCR amplification (11-cycles) and validation. The manufacturer’s instructions were followed. The libraries were validated using the Agilent 2100 Bioanalyser and a high-sensitivity kit (Agilent Technologies) to ascertain the insert size, and the Qubit® (Life Technologies) was used to perform the fluorometric quantitation. Following validation, the libraries were normalized to 10nM, pooled together and clustered on the cBot™2 following the manufacturer’s recommendations. The pool was then sequenced using a 75-base paired-end (2x75bp PE) dual index read format on the Illumina® HiSeq4000 according to the manufacturer’s instructions.

value: Zeb1 KO

value: bone marrow

tag: immunophenotype

value: LSK CD48- CD150+ (HSC)


title: R099-H-011

description: Zeb1-/- HSC 3


title: R099-H-010

description: Zeb1-/- HSC 2


title: H_MO-MG15-R4-1224756

description: normal R4 biological replicate 1


title: R099-H-004

description: Wild Type HSC 4

value: Zeb1 WT


title: R099-H-003

description: Wild Type HSC 3


title: R099-H-002

description: Wild Type HSC 2


title: R099-H-001

description: Wild Type HSC 1


title: R099-H-016

description: Zeb1-/- CLP 4

value: Lin- Sca-1 low C-kit low CD127+