title: MGH-NSCLC-L11-TR477


title: NKI-NSCLC-2685-TR2226

status: Public on Aug 05 2022

type: SRA

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

library_source: transcriptomic

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

tag: cell type

value: Thrombocytes

tag: classification group

value: Malignant

tag: patient group

value: Non-Small-Cell Lung Cancer


title: Vumc-NSCLC-66


title: Maas-GBM-M00012-TR2120

value: Glioma


title: MGH-NSCLC-L-72


title: Maas-GBM-M00015-TR2121


title: Maas-GBM-M00004-TR2113


title: Maas-GBM-M00003-TR2115


title: Radb-GBM-N14-01-TR2140


title: Radb-GBM-N15-02-TR2149


title: Vumc-GBM-550t0-TR1519


title: Vumc-GBM-506t0-TR1483


title: MGH-NSCLC-L131-TR909


title: Vumc-GBM-486-TR1366


title: Vumc-GBM-454-TR1359


title: Vumc-GBM-475-TR1362


title: Vumc-GBM-422-TR1352


title: Vienna-CRC-Vien-4-TR2951

value: nonMalignant

value: Asymptomatic Controls


title: Vienna-CRC-Vien-2-TR2949


title: Vienna-CRC-Vien-1-TR2948


title: MGH-NSCLC-L-74


title: VUMC-HC-0385-TR2640


title: VUMC-HC-0418-TR2649


title: Vienna-CRC-Vien-21-TR3006


title: VUMC-HC-0302-TR2613


title: VUMC-HC-0056-TR2638


title: Vienna-CRC-Vien-23-TR3008


title: VUMC-HC-0296-TR2612


title: VUMC-HC-0146-TR2604


title: VUMC-HC-0033-TR2591


title: RAD-ProsBlad-56059-TR2820


title: Vumc-HC-0017-TR2590


title: Vumc-HC-0171-TR2608


title: RAD-ProsBlad-56008-TR2777


title: RAD-ProsBlad-56043-TR2779


title: RAD-ProsBlad-56026-TR2778


title: RAD-ProsBlad-56076-TR2821


title: RAD-ProsBlad-55989-TR2776


title: Vumc-HC-0414-TR2648


title: Vumc-HC-0411-TR2646


title: Vumc-HC-0412-TR2647


title: Vumc-HC-0403-TR2643


title: Vumc-HC-0405-TR2644


title: Vumc-HC-0396-TR2642


title: Vumc-HC-0388-TR2641


title: Vumc-HC-0009-TR2589


title: Vumc-HC-0375-TR2639


title: RAD-HIV-HV498-1-TR1965


title: RAD-HIV-HV391-1-TR1964


title: Vumc-HC-0002-TR2588


title: RAD-HIV-HV325-1-TR1963


title: RAD-HIV-HV155-1-TR1962


title: RAD-HIV-HV014-1-TR1961


title: Vumc-HD-246-TR1916

description: Please note that the mapped and counted intron-spanning reads from both files corresponding to this sample were merged in silico to yield sufficient mapped reads for further analyses.


title: Vumc-HD-238-TR1878


title: Vumc-HD-199-TR1914


title: Vumc-HD-217-TR1915


title: Vumc-HD-280-TR1870


title: Vumc-HD-256-TR1864


title: Vumc-HD-233-TR1879


title: Vumc-HD-229-TR1882


title: Vumc-HD-224-TR1885


title: Vumc-HD-230-TR1881


title: Vumc-HC-0406-TR2645


title: Vumc-HD-244-TR1780


title: Vumc-HD-257-TR1865


title: Vumc-HD-196-TR1852


title: Vumc-HD-263-TR1877


title: Vumc-HD-189-TR1850


title: Vumc-HD-188-TR1849


title: Vumc-HD-266-TR1869


title: Vumc-HD-239-TR1781


title: VUMC-HC-0139-TR2601


title: Vumc-HD-264-TR1867


title: Vumc-HD-235-TR1761


title: Vumc-HD-195-TR1851


title: Vumc-HD-220-TR1760


title: Vumc-HD-225-TR1884


title: Vumc-HD-236-TR1782


title: Vumc-HD-228-TR1883


title: Vumc-HD-231-TR1880


title: Vumc-HD-250-TR1906


title: Vumc-HD-175-TR1913


title: Vumc-HD-283-TR1874


title: Vumc-HD-272-TR1876


title: Vumc-HD-163-TR1757


title: Vumc-HD-33-1-TR1637


title: Vumc-HD-186-TR1759


title: Vumc-HD-253-TR1861


title: Vumc-HD-198-TR1907


title: Vumc-HD-162-TR1756


title: Vumc-HD-262-TR1866


title: Vumc-HD-169-TR1758


title: Vumc-HD-265-TR1868


title: Vumc-HD-255-TR1863


title: Vumc-HD-254-TR1862


title: Vumc-HD-247-TR1859


title: Vumc-HD-1-TR1679


title: Vumc-HD-218-TR1905


title: Vumc-HD-252-TR1860


title: Vumc-HD-45-2-TR1582


title: Vumc-HD-34-1-TR1578


title: Vumc-HD-48-1-TR1666


title: Vumc-HD-13-2-TR1570


title: Vumc-HD-38-2-TR1581


title: Vumc-HD-25-2-TR1574


title: Vumc-HD-282-TR1872


title: Vumc-HD-14-1-TR1571


title: Vumc-HD-237-TR1719


title: Vumc-HD-35-2-TR1579


title: Vumc-HD-31-2-TR1577


title: Vumc-HD-226-TR1718


title: Vumc-HD-37-2-TR1580


title: Vumc-HD-6-2-TR1639


title: Vumc-HD-234-TR1717


title: Vumc-HD-10-2-TR1642


title: Vumc-HD-29-2-TR1576


title: Vumc-HD-26-2-TR1575


title: Vumc-HD-241-TR1721


title: Vumc-HD-46-2-TR1680


title: Vumc-HD-8-TR1641


title: Vumc-HD-227-TR1716


title: Vumc-HD-161-TR1522


title: Vumc-HD-173-TR1488


title: Vumc-HD-180-TR1523


title: Vumc-HD-159-TR1521


title: Vumc-HD-52-TR1489


title: Vumc-HDControl-9-TR1182


title: Vumc-HDControl-8-TR1181


title: Vumc-HDControl-6-TR1180


title: Vumc-HD-9-TR1152


title: Vumc-HD-99-TR1094


title: Vumc-HD-97-TR1089


title: Vumc-HDControl-10-TR1183


title: Vumc-HD-96-TR1088


title: Vumc-HD-95-TR1087


title: Vumc-HD-94-TR1086


title: Vumc-HD-93-TR1085


title: Vumc-HD-24-2-TR1573


title: Vumc-HD-90-TR1083


title: Vumc-HD-85-TR1084


title: Vumc-HD-242-TR1720


title: Vumc-HD-82-TR1082


title: Vumc-HD-75-TR1065


title: Vumc-HD-79-TR1081


title: Vumc-HD-78-TR1080


title: Vumc-HD-70-TR1062


title: Vumc-HD-77-TR1079


title: Vumc-HD-18-2-TR1643


title: Vumc-HD-76-TR1066


title: Vumc-HD-5-TR1151


title: Vumc-HD-71-TR1063


title: Vumc-HD-68-TR1060


title: Vumc-HD-67-TR1059


title: Vumc-HD-54-1-TR1172


title: Vumc-HD-66-TR1058


title: Vumc-HD-59-TR1093


title: Vumc-HD-69-TR1061


title: Vumc-HD-51-1-TR1170


title: Vumc-HD-50-1-TR1169


title: Vumc-HD-49-1-TR1168


title: Vumc-HD-72-TR1064


title: Vumc-HD-3-1-TR1149


title: Vumc-HD-32-2-TR1164


title: Vumc-HD-4-TR1150


title: Vumc-HD-47-1-TR1167


title: Vumc-HD-40-1-TR1159


title: Vumc-HD-39-1-TR1158


title: Vumc-HD-2-1-TR1148


title: Vumc-HD-36-TR1165


title: Vumc-HD-30-2-TR1163


title: Vumc-HD-22-1-TR1157


title: Vumc-HD-21-1-TR1161


title: Vumc-HD-20-1-TR1156


title: Vumc-HD-158-TR1138


title: Vumc-HD-16-1-TR1155


title: Vumc-HD-17-1-TR1160


title: Vumc-HD-53-1-TR1171


title: Vumc-HD-152-TR1134


title: Vumc-HD-150-TR1133


title: Vumc-HD-154-TR1136


title: Vumc-HD-141-TR1130


title: Vumc-HD-147-TR1132


title: Vumc-HD-153-TR1135


title: Vumc-HD-44-2-TR1166


title: Vumc-HD-138-TR1127


title: Vumc-HD-15-1-TR1154


title: Vumc-HD-135-TR1124


title: Vumc-HD-139-TR1128


title: Vumc-HD-146-TR1131


title: Vumc-HD-133-TR1123


title: Vumc-HD-27-2-TR1162


title: Vumc-HD-131-TR1121


title: Vumc-HD-132-TR1122


title: Vumc-HD-126-TR1118


title: Vumc-HD-125-TR1117


title: Vumc-HD-129-TR1120


title: Vumc-HD-124-TR1116


title: Vumc-HD-128-TR1119


title: Vumc-HD-120-TR1112


title: Vumc-HD-122-TR1114


title: Vumc-HD-121-TR1113


title: Vumc-HD-123-TR1115


title: Vumc-HD-157-TR1137


title: Vumc-HD-119-TR1111


title: Vumc-HD-115-TR1107


title: Vumc-HD-140-TR1129


title: Vumc-HD-114-TR1106


title: Vumc-HD-136-TR1125


title: Vumc-HD-118-TR1110


title: Vumc-HD-117-TR1109


title: Vumc-HD-113-TR1105


title: Vumc-HD-112-TR1104


title: Vumc-HD-11-1-TR1153


title: Vumc-HD-111-TR1103


title: Vumc-HD-105-TR1098


title: Vumc-HD-109-TR1101


title: Vumc-HD-106-TR1099


title: Vumc-HD-104-TR1097


title: Vumc-HD-107-TR1100


title: Vumc-HD-102-TR1096


title: AMC-HD-010-TR1147


title: AMC-HD-006-TR1144


title: AMC-HD-003-TR1141


title: AMC-HD-007-TR1145


title: AMC-HD-005-TR1143


title: Vumc-HD-116-TR1108


title: AMC-HD-004-TR1142


title: AMC-HD-001-TR1139


title: AMC-HD-002-TR1140


title: Vumc-HD-98-TR921


title: Vumc-HD-91-TR897


title: Vumc-HD-87-TR894


title: Vumc-HD-84-TR892


title: Vumc-HD-88-TR895


title: Vumc-HD-110-TR1102


title: Vumc-HD-83-TR891


title: Vumc-HD-81-TR890


title: Vumc-HD-74-TR888


title: Vumc-HD-80-TR889


title: Vumc-HD-73-TR887


title: Vumc-HD-63-TR886


title: Vumc-HD-60-TR885


title: Vumc-HD-100-TR1095


title: Vumc-HD-56-TR884


title: AMC-HD-008-TR1146


title: Vumc-HD-156-TR935


title: Vumc-HD-155-TR934


title: Vumc-HD-151-TR933


title: Vumc-HD-144-TR929


title: Vumc-HD-145-TR930


title: Vumc-HD-149-TR932


title: Vumc-HD-142-TR927


title: Vumc-HD-130-TR926


title: Vumc-HD-92-TR920


title: Vumc-HD-143-TR928


title: Vumc-HD-86-TR893


title: Vumc-HD-89-TR896


title: Vumc-HD-103-TR923


title: Vumc-HD-108-TR924


title: Vumc-HD-101-TR922


title: Vumc-EPI-013-TR1467

value: Epilepsy


title: hFOB_RNA_G34W_1

city: London

first: Adrienne

middle: M

last: Flanagan

state: Middlesex

address: Huntley Street

country: United Kingdom

institute: University College London

data_processing:
RNAseq expression count estimates were made using kallisto software together with the Ensembl GRCh38 (v99)  transcript models. RNAseq count data was then imported using tximport to the DESeq2 R package for preprocessing, normalisation and statistical analysis. Multiple hypothesis adjustments used the independent hypothesis weighting method (IHW).
Genome_build: GRCh38 (v99)

source_name: hFOB 1.19

growth_protocol: hFOB 1.19 were cultured according to ATCC guidelines (ATCC® CRL-11372™) at 34C.

extract_protocol:
Cells were lysed in Tryzol and RNA extracted using Zymo Mini Kit.
Poly(A) RNA was selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) and a first strand library prepared using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs) and sequenced on a HiSeq 2500 (Illumina).

treatment_protocol: Cells were engineered to express H3.3-G34W, H3.3-WT or EV.

tag: genotype

tag: cell line

value: hFOB 1.19


title: hFOB_RNA_G34W_2


title: hFOB_RNA_WT_1


title: hFOB_RNA_EV_2

value: Empty vector (EV)


title: hFOB_RNA_EV_1


title: MGH-Ovary-O32-TR809

value: Ovarian Cancer


title: MGH-Ovary-O2-TR838


title: MGH-Ovary-O27-TR804


title: MGH-Ovary-O33-TR810


title: MGH-Ovary-O23-TR807


title: MGH-OVARY-O24-TR678


title: MGH-Ovary-O26-TR803


title: RNAseq Trisomy21_stemcell_C06

city: Boston

first: VICTOR

last: BARRERA BURGOS

state: Massachusetts

address: Landmark 401 Park Drive 3 East

department: Biostatistics

country: USA

institute: Harvard School of Public Health

description:
counts_raw-2019-12-06.csv
counts_tpm-2019-12-06.csv

data_processing:
Sequenced reads were assessed for low-quality sequence, then mapped against the GRCh38_98 transcriptome where reads were quantified at the transcript level using Salmon
Transcript-level abundance estimates  from Salmon were collapsed to gene-leve estimates and  converted to raw count values using the R Bioconductor package tximport
Differentially expressed genes were identified using the R Bioconductor package DESeq2
Genome_build: GRCh38.90
Supplementary_files_format_and_content: comma separated file of raw count matrix where columns correspond to samples and rows correspond to genes; comma separated file of transcript per million counts where columns correspond to samples and rows correspond to genes

source_name: hPSCs

growth_protocol: All hPSCs were grown and maintained in mTeSR medium on geltrex coated plates; hPSC derived neurons were generated by transduction with Ngn2 ectopic expression constructs with the addition of SMAD inhibitors, WNT inhibitors and neurotrophins.

extract_protocol:
For RNAseq, RNA was extracted using the AllPrep DNA/RNA/miRNA universal kit (Qiagen). For eCLIP-seq, cells were UV crosslinked, lysed, sonicated and treated with RNAse I followed by IP, processing and reverse transcripion using AffinityScript. cDNAs were adaptor ligated.
For RNAseq, libraries were prepared using the Illumina TruSeq HS Stranded Total RNA kit with Ribo-Zero Gold for rRNA depletion. For eCLIP-seq, libraries were generated using Q5 PCR mix.

value: iPSCs

tag: genotype/variation

value: Trisomy21 hPSCs


title: Vumc-HD-127-TR925


title: MGH-OVARY-O17-TR660


title: MGH-OVARY-O14-TR657


title: MGH-OVARY-O13-TR656


title: MGH-OVARY-O11-TR654


title: MGH-OVARY-O21-TR674


title: MGH-OVARY-O18-TR661


title: MGH-OVARY-O20-TR675


title: MGH-OVARY-O16-TR659


title: MGH-OVARY-585-TR561


title: MGH-OVARY-O10-TR653


title: hFOB_RNA_WT_2


title: Cath-Ova-CZE-050-TR2732

source_name: Blood_Platelets_CZE 050


title: MGH-OVARY-602-TR562


title: RNAseq Trisomy21_stemcell_C04


title: MGH-OVARY-533-TR559


title: Cath-Ova-CZE-049-TR2731

source_name: Blood_Platelets_CZE 049


title: Cath-Ova-CZE-026-TR2773

source_name: Blood_Platelets_CZE 026


title: Cath-Ova-CZE-043-TR2726

source_name: Blood_Platelets_CZE 043


title: Cath-Ova-CZE-025-TR2772

source_name: Blood_Platelets_CZE 025


title: Cath-Ova-CZE-036-TR2748

source_name: Blood_Platelets_CZE 036


title: Cath-Ova-CZE-029-TR2745

source_name: Blood_Platelets_CZE 029


title: MGH-OVARY-O9-TR652


title: Cath-Ova-CZE-008-TR2276

source_name: Blood_Platelets_CZE 008


title: Cath-Ova-CZE-007-TR2275

source_name: Blood_Platelets_CZE 007


title: Cath-Ova-CZE-002-TR2271

source_name: Blood_Platelets_CZE 002


title: UMCU-nSTEM-4-1577-TR2047

value: nSTEMI


title: UMCU-nSTEM-4-1579-TR2048


title: MGH-OVARY-555-TR560


title: UMCU-nSTEMI-2-0661-TR2002


title: UMCU-nSTEMI-2-0682-TR2004


title: UMCU-nSTEMI-2-0679-TR2003


title: UMCU-nSTEMI-1-0154-TR2000


title: UMCU-nSTEM1-0139-TR1999


title: UMCU-nSTEMI-1-0137-TR1998


title: UMCU-nSTEMI-1-0104-TR1995


title: UMCU-nSTEMI-3-1100-TR2005


title: UMCU-nSTEMI-1-0105-TR1996


title: UMCU-nSTEMI-1-0085-TR1993


title: MGH-OVARY-305-TR549


title: NKI-NSCLC-4653-TR3035


title: NKI-NSCLC-4524-TR3034


title: UMCU-nSTEMI-1-0111-TR1997


title: NKI-NSCLC-4509-TR3033


title: NKI-NSCLC-4375-TR3032


title: UMCG-NCSLC-1094-TR3031


title: UMCU-nSTEMI-1-0099-TR1994


title: Cath-Ova-CZE-005-TR2273

source_name: Blood_Platelets_CZE 005


title: UMCG-NCSLC-1090-TR3030


title: UMCG-NCSLC-1076-TR3027


title: UMCG-NCSLC-1081-TR3028


title: UMCG-NCSLC-1149-TR2880


title: UMCU-nSTEMI-2-0522-TR2001


title: UMCG-NCSLC-1162-TR2886


title: UMCG-NCSLC-1116-TR2878


title: NKI-NSCLC-5021-TR2896


title: NKI-NSCLC-4916-TR2893


title: NKI-NSCLC-5207-TR2939


title: NKI-NSCLC-5135-TR2937


title: UMCG-NCSLC-1115-TR2877


title: UMCG-NCSLC-1150-TR2881


title: UMCG-NCSLC-1153-TR2883


title: UMCG-NCSLC-1154-TR2884


title: UMCG-NCSLC-1112-TR2876


title: UMCG-NCSLC-985-TR2787


title: UMCG-NCSLC-1033-TR2811


title: UMCG-NCSLC-1151-TR2882


title: UMCG-NCSLC-1159-TR2885


title: UMCG-NCSLC-1054-TR2814


title: NKI-NSCLC-4987-TR2895


title: NKI-NSCLC-4618-TR2912


title: NKI-NSCLC-4678-TR2915


title: NKI-NSCLC-5195-TR2938


title: UMCG-NCSLC-991-TR2807


title: VUMC-NSCLC-1434-TR2340


title: VUMC-NSCLC-1383-TR2316


title: UMCG-NCSLC-1096-TR2872


title: VUMC-NSCLC-1336-TR2387


title: UMCG-NCSLC-1166-TR2956


title: NKI-NSCLC-4861-TR2958


title: UMCG-NCSLC-1144-TR2879


title: NKI-NSCLC-3639-TR2935


title: NKI-NSCLC-4595-TR2911


title: UMCG-NSCLC-1140-TR2743


title: UMCG-NSCLC-1136-TR2741


title: UMCG-NSCLC-1133-TR2740


title: UMCG-NSCLC-1130-TR2738


title: UMCG-NSCLC-1141-TR2744


title: UMCG-NSCLC-1137-TR2742


title: UMCG-NSCLC-1124-TR2735


title: UMCG-NSCLC-1127-TR2736


title: UMCG-NSCLC-1120-TR2734


title: UMCG-NSCLC-1119-TR2733


title: UMCG-NSCLC-1103-TR2859


title: UMCG-NSCLC-1101-TR2858


title: UMCG-NSCLC-1098-TR2857


title: UMCG-NSCLC-1128-TR2737


title: UMCG-NSCLC-1080-TR2853


title: UMCG-NSCLC-1097-TR2856


title: UMCG-NSCLC-1073-TR2851


title: UMCG-NSCLC-1075-TR2852


title: UMCG-NSCLC-1032-TR2849


title: UMCG-NSCLC-986-TR2848


title: UMCG-NSCLC-1057-TR2850


title: UMCG-NSCLC-1047-TR2802


title: UMCG-NSCLC-1045-TR2801


title: UMCG-NSCLC-1051-TR2803


title: UMCG-NSCLC-1132-TR2739


title: UMCG-NSCLC-1038-TR2799


title: UMCG-NSCLC-1043-TR2800


title: UMCG-NSCLC-1037-TR2798


title: UMCG-NSCLC-988-TR2788


title: UMCG-NSCLC-1003-TR2793


title: UMCG-NSCLC-1004-TR2794


title: UMCG-NSCLC-1002-TR2792


title: UMCG-NSCLC-996-TR2791


title: UMCG-NSCLC-990-TR2789


title: UMCG-NSCLC-1005-TR2795


title: UMCG-NSCLC-1008-TR2796


title: UMCG-NSCLC-968-TR2783


title: UMCG-NSCLC-1160-TR2723


title: UMCG-NSCLC-1145-TR2715


title: UMCG-NSCLC-965-TR2780


title: UMCG-NSCLC-981-TR2786


title: UMCG-NSCLC-979-TR2785


title: UMCG-NSCLC-967-TR2782


title: UMCG-NSCLC-969-TR2784


title: UMCG-NSCLC-1117-TR2714


title: UMCG-NSCLC-966-TR2781


title: NKI-NSCLC-3673-TR2389


title: UMCG-NSCLC-1082-TR2710


title: UMCG-NSCLC-1077-TR2709


title: UMCG-NSCLC-1099-TR2712


title: NKI-NSCLC-3736-TR2392


title: UMCG-NSCLC-987-TR2806


title: Vumc-NSCLC-1156-TR2385


title: Vumc-NSCLC-1431-TR2338


title: UMCG-NSCLC-993-TR2790


title: Vumc-NSCLC-1421-TR2429


title: UMCG-NSCLC-1066-TR2816


title: Vumc-NSCLC-1386-TR2321


title: Vumc-NSCLC-1277-TR2322


title: Vumc-NSCLC-1448-TR2323


title: Pang-NSCLC-U6702-TR2708


title: Vumc-NSCLC-1084-TR2320


title: Pang-NSCLC-U5588-T0-TR2706


title: UMCG-NSCLC-1071-TR2819


title: Pang-NSCLC-U6414-TR2707


title: UMCG-NSCLC-1064-TR2815


title: Vumc-NSCLC-1424-TR2430


title: UMCG-NSCLC-1053-TR2813


title: UMCG-NSCLC-1104-TR2873


title: Vumc-NSCLC-1333-TR2335


title: Vumc-NSCLC-1330-TR2315


title: UMCG-NSCLC-1000-TR2808


title: UMCG-NSCLC-1015-TR2809


title: UMCG-NSCLC-1070-TR2818


title: UMCG-NSCLC-1068-TR2817


title: Vumc-NSCLC-1444-TR2383


title: UMCG-NSCLC-1035-TR2812


title: UMCG-NSCLC-1031-TR2810


title: UMCG-NSCLC-1030-TR2767


title: UMCG-NSCLC-964-TR2760


title: UMCG-NSCLC-1016-TR2761


title: UMCG-NSCLC-962-TR2759


title: Vumc-NSCLC-207-TR2336


title: Vumc-NSCLC-1308-TR2318


title: Vumc-NSCLC-986-TR2317


title: UMCG-NSCLC-1029-TR2766


title: Vumc-NSCLC-1232-TR2384


title: UMCG-NSCLC-952-TR2804


title: UMCG-NSCLC-1023-TR2764


title: UMCG-NSCLC-1022-TR2763


title: UMCG-NSCLC-951-TR2757


title: Vumc-NSCLC-1422-TR2536


title: Vumc-NSCLC-1120-TR2535


title: Vumc-NSCLC-222-TR2534


title: Vumc-NSCLC-003-TR2532


title: Vumc-NSCLC-068-TR2533


title: MGH-NSCLC-L465-TR2704


title: Vumc-NSCLC-1622-TR2539


title: Vumc-NSCLC-1507-TR2537


title: Vumc-NSCLC-1594-TR2538


title: UMCG-NSCLC-982-TR2805


title: MGH-NSCLC-L459-TR2703


title: MGH-NSCLC-L369-TR2702


title: MGH-NSCLC-L477-TR2705


title: UMCG-NSCLC-1027-TR2765


title: MGH-NSCLC-L180-TR2544


title: MGH-NSCLC-L237-TR2700


title: MGH-NSCLC-L266-TR2701


title: Vumc-NSCLC-1721-TR2540


title: Vumc-NSCLC-1375-TR2314


title: Vumc-NSCLC-1213-TR2312


title: NKI-NSCLC-4373-TR2399


title: NKI-NSCLC-4147-TR2352


title: MGH-NSCLC-L123-TR2543


title: NKI-NSCLC-4112-TR2396


title: Vumc-NSCLC-1281-TR2313


title: MGH-NSCLC-L103-TR2542


title: NKI-NSCLC-4518-TR2402


title: Vumc-NSCLC-1228-TR2319


title: NKI-NSCLC-4488-TR2400


title: NKI-NSCLC-4377-TR2401


title: NKI-NSCLC-3723-TR2393


title: NKI-NSCLC-4185-TR2397


title: NKI-NSCLC-3642-TR2344


title: NKI-NSCLC-3589-TR2388


title: NKI-NSCLC-4021-TR2395


title: MGH-NSCLC-L194-TR2500


title: NKI-NSCLC-3949-TR2431


title: NKI-NSCLC-4780-TR2523


title: NKI-NSCLC-3715-TR2348


title: NKI-NSCLC-3588-TR2390


title: NKI-NSCLC-3658-TR2347


title: NKI-NSCLC-3688-TR2349


title: MGH-NSCLC-L206-TR2497


title: NKI-NSCLC-3575-TR2311


title: NKI-NSCLC-4202-TR2520


title: NKI-NSCLC-4649-TR2522


title: NKI-NSCLC-4245-TR2521


title: MGH-NSCLC-L195-TR2496


title: NKI-NSCLC-4067-TR2519


title: NKI-NSCLC-3338-TR2341


title: MGH-NSCLC-L189-TR2494


title: NKI-NSCLC-2679-TR2492


title: NKI-NSCLC-2381-TR2514


title: NKI-NSCLC-3209-TR2517


title: NKI-NSCLC-4888-TR2493


title: NKI-NSCLC-3851-TR2391


title: NKI-NSCLC-0760-TR2490


title: NKI-NSCLC-2332-TR2513


title: NKI-NSCLC-1691-TR2491


title: NKI-NSCLC-0527-TR2489


title: NKI-NSCLC-0818-TR2512


title: NKI-NSCLC-0229-TR2488


title: NKI-NSCLC-0762-TR2511


title: MGH-NSCLC-L216-TR2498


title: NKI-NSCLC-0193-TR2486


title: NKI-NSCLC-0640-TR2509


title: NKI-NSCLC-0117-TR2484


title: NKI-NSCLC-0334-TR2506


title: NKI-NSCLC-0423-TR2507


title: MGH-NSCLC-L190-TR2495


title: Vumc-NSCLC-390-TR2479


title: Vumc-NSCLC-459-TR2480


title: Vumc-NSCLC-393-TR2478


title: Vumc-NSCLC-804-TR2502


title: Vumc-NSCLC-782-TR2501


title: Vumc-NSCLC-388-TR2477


title: NKI-NSCLC-3022-TR2259


title: NKI-NSCLC-3257-TR2266


title: NKI-NSCLC-3101-TR2257


title: Vumc-NSCLC-928-TR2504


title: NKI-NSCLC-2993-TR2234


title: NKI-NSCLC-3131-TR2236


title: NKI-NSCLC-3249-TR2264


title: NKI-NSCLC-3096-TR2235


title: NKI-NSCLC-3899-TR2217


title: NKI-NSCLC-5465-TR2524


title: NKI-NSCLC-3083-TR2262


title: NKI-NSCLC-3177-TR2260


title: NKI-NSCLC-2932-TR2231


title: NKI-NSCLC-3252-TR2269


title: NKI-NSCLC-2775-TR2232


title: NKI-NSCLC-3382-TR2268


title: Vumc-NSCLC-539-TR2482


title: Vumc-NSCLC-1193-TR2253


title: NKI-NSCLC-3178-TR2265


title: Vumc-NSCLC-1025-TR2250


title: NKI-NSCLC-3100-TR2261


title: Vumc-NSCLC-847-TR2247


title: Vumc-NSCLC-789-TR2245


title: Vumc-NSCLC-1360-TR2252


title: Vumc-NSCLC-845-TR2249


title: Vumc-NSCLC-679-TR2244


title: Vumc-NSCLC-1141-TR2248


title: NKI-NSCLC-2777-TR2233


title: Vumc-NSCLC-717-TR2243


title: Vumc-NSCLC-487-TR2239


title: NKI-NSCLC-3679-TR2222


title: Vumc-NSCLC-604-TR2241


title: Vumc-NSCLC-361-TR2237


title: Vumc-NSCLC-1064-TR2251


title: Vumc-NSCLC-1204-TR2255


title: Vumc-NSCLC-1322-TR2254


title: Vumc-NSCLC-441-TR2238


title: NKI-NSCLC-2785-TR2208


title: NKI-NSCLC-2690-TR2228


title: NKI-NSCLC-2630-TR2224


title: NKI-NSCLC-2602-TR2202


title: NKI-NSCLC-2805-TR2204


title: NKI-NSCLC-2486-TR2200


title: Vumc-NSCLC-1052-TR2196


title: NKI-NSCLC-4147-TR2216


title: NKI-NSCLC-3057-TR2213


title: Vumc-NSCLC-670-TR2242


title: NKI-NSCLC-3048-TR2212


title: NKI-NSCLC-3035-TR2210


title: NKI-NSCLC-3020-TR2211


title: NKI-NSCLC-2593-TR2201


title: Vumc-NSCLC-1339-TR2197


title: Vumc-NSCLC-821-TR2191


title: Vumc-NSCLC-749-TR2188


title: Vumc-NSCLC-611-TR2183


title: Vumc-NSCLC-560-TR2240


title: Vumc-NSCLC-734-TR2187


title: Vumc-NSCLC-551-TR2181


title: NKI-NSCLC-2530-TR2206


title: Vumc-NSCLC-546-TR2180


title: Vumc-NSCLC-483-TR2179


title: NKI-NSCLC-2586-TR2203


title: Vumc-NSCLC-374-TR2178


title: Vumc-NSCLC-1190-TR2199


title: NKI-NSCLC-3658-TR2223


title: Vumc-NSCLC-1286-TR2198


title: NKI-NSCLC-3951-TR2218


title: Vumc-NSCLC-879-TR2194


title: Vumc-NSCLC-1092-TR2195


title: Vumc-NSCLC-843-TR2193


title: NKI-NSCLC-3017-TR2209


title: Vumc-NSCLC-848-TR2192


title: Vumc-NSCLC-598-TR2185


title: NKI-NSCLC-2417-TR1857


title: Vumc-NSCLC-756-TR2189


title: NKI-NSCLC-2403-TR1844


title: NKI-NSCLC-2220-TR1807


title: NKI-NSCLC-2153-TR1839


title: NKI-NSCLC-2237-TR1853


title: NKI-NSCLC-2150-TR1847


title: NKI-NSCLC-2126-TR1843


title: Vumc-NSCLC-285-TR2177


title: NKI-NSCLC-1946-TR1898


title: NKI-NSCLC-2006-TR1842


title: NKI-NSCLC-1931-TR1840


title: Vumc-NSCLC-273-TR2176


title: NKI-NSCLC-1922-TR1841


title: NKI-NSCLC-1924-TR1892


title: NKI-NSCLC-1844-TR1890


title: NKI-NSCLC-1777-TR1788


title: NKI-NSCLC-1671-TR1912


title: NKI-NSCLC-1725-TR1896


title: Vumc-NSCLC-764-TR2190


title: NKI-NSCLC-1593-TR1845


title: NKI-NSCLC-1665-TR1894


title: NKI-NSCLC-1663-TR1808


title: NKI-NSCLC-1589-TR1895


title: NKI-NSCLC-1653-TR1893


title: NKI-NSCLC-2713-TR2205


title: Vumc-NSCLC-603-TR2184


title: NKI-NSCLC-1544-TR1891


title: NKI-NSCLC-1292-TR1806


title: NKI-NSCLC-1523-TR1846


title: NKI-NSCLC-1222-TR1837


title: NKI-NSCLC-879-TR1315


title: NKI-NSCLC-404-TR1278


title: NKI-NSCLC-1151-TR1899


title: NKI-NSCLC-1553-TR1331


title: NKI-NSCLC-1255-TR1321


title: NKI-NSCLC-1667-TR1341


title: NKI-NSCLC-352-TR1330


title: NKI-NSCLC-1016-TR1329


title: NKI-NSCLC-1041-TR1281


title: NKI-NSCLC-582-TR1279


title: NKI-NSCLC-1109-TR1284


title: NKI-NSCLC-1205-TR1320


title: NKI-NSCLC-1054-TR1324


title: NKI-NSCLC-1244-TR1280


title: NKI-NSCLC-706-TR1314


title: NKI-NSCLC-868-TR1316


title: Vumc-NSCLC-361-TR1036


title: Vumc-NSCLC-255-TR1006


title: Vumc-NSCLC-207-TR981


title: Vumc-NSCLC-169-TR961


title: Vumc-NSCLC-278-TR1048


title: Vumc-NSCLC-218-TR983


title: Vumc-NSCLC-210-TR982


title: Vumc-NSCLC-161-TR958


title: NKI-NSCLC-1485-TR1340


title: Vumc-NSCLC-166-TR960


title: Vumc-NSCLC-158-TR956


title: Vumc-NSCLC-157-TR955


title: Vumc-NSCLC-202-TR900


title: Vumc-NSCLC-168-TR694


title: Vumc-NSCLC-165-TR692


title: MGH-NSCLC-L149-TR883


title: NKI-NSCLC-1019-TR1277


title: NKI-NSCLC-1043-TR1283


title: Vumc-NSCLC-105-TR950


title: MGH-NSCLC-L133-TR910


title: MGH-NSCLC-L134-TR911


title: MGH-NSCLC-L130-TR908


title: MGH-NSCLC-L119-TR688


title: MGH-NSCLC-L116-TR685


title: MGH-NSCLC-L118-TR687


title: Vumc-NSCLC-174-TR669


title: NKI-NSCLC-107-599-TR743


title: MGH-NSCLC-L78-TR695


title: MGH-NSCLC-L127-TR718


title: MGH-NSCLC-L126-TR917


title: MGH-NSCLC-L128-TR719


title: MGH-NSCLC-L120-TR714


title: MGH-NSCLC-L126-TR717


title: Vumc-NSCLC-VU079-TR631


title: MGH-NSCLC-L125-TR716


title: Vumc-LGG-VU028-1-TR633


title: Vumc-NSCLC-VU028-TR632


title: MGH-NSCLC-L169-TR914


title: MGH-NSCLC-L178-TR918


title: MGH-NSCLC-L33-TR600


title: Vumc-NSCLC-071-TR486


title: MGH-NSCLC-L48-TR577


title: Vumc-NSCLC-052-TR460


title: Vumc-NSCLC-107-TR487


title: MGH-NSCLC-L41-TR616


title: Pang-NSCLC-B739-1-TR455


title: MGH-NSCLC-L73-TR578


title: Pang-NSCLC-B295-2-TR454


title: MGH-NSCLC-L56-TR481


title: MGH-NSCLC-L99-TR464


title: MGH-NSCLC-L44-TR504


title: MGH-NSCLC-L37-TR503


title: MGH-NSCLC-L51-TR521


title: MGH-NSCLC-L39-TR519


title: MGH-NSCLC-L20-TR500


title: MGH-NSCLC-L19-TR461


title: MGH-NSCLC-L22-TR462


title: MGH-NSCLC-L25-TR480


title: MGH-NSCLC-L36-TR502


title: MGH-NSCLC-L23-TR524


title: MGH-NSCLC-L115-TR684


title: MGH-NSCLC-L32-TR501


title: MGH-NSCLC-L18-TR479


title: MGH-NSCLC-L88-TR601


title: MGH-NSCLC-L12-TR478


title: MGH-NSCLC-L114-TR527


title: MGH-NSCLC-L100-TR526


title: Vumc-NSCLC-69


title: MGH-NSCLC-L03-TR488


title: Vumc-NSCLC-59


title: Vumc-NSCLC-57


title: Vumc-NSCLC-145


title: Vumc-NSCLC-147


title: Vumc-NSCLC-49


title: Vumc-NSCLC-137


title: Vumc-NSCLC-141


title: Vumc-NSCLC-127


title: Vumc-NSCLC-155


title: ATAC-seq_gSNF2-KO_1

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

library_source: genomic

data_processing:
Sequence data were mapped onto P. berghei genome sequence (PlasmoDB, version 3) using BOWTIE2 software in default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files.
Reads derived from duplicate fragments were removed using picard MarkDuplicates setting REMOVE_DUPLICATES=True. The resultant bam files were then converted to bed files by bedtools bamtobed.
To obtain the sites where Tn5 actually cuts, each reads were shifted using macs2 callpeak with settings -f BED -g 2e7 --nomodel --extsize 200 --shift -100 --keep-dup all -B, and bedgraph files were produced.
Assembly: PlasmoDB, version 3

molecule: genomic DNA

organism: Plasmodium berghei

source_name: Gametocyte

growth_protocol: Balb/c mice were infected with P. berghei ANKA strain. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Parasites were harvested after drug treatment for 2 days,.

extract_protocol:
The gametocyte-enriched blood was prepared as described above and uninfected red blood cells were removed by a density gradient of percoll. Purified cells were washed in  the cultre medium, and 1 106 infected erythrocytes cells were subjected to ATAC-seq
ATAC-seq was performed using ATAC-Seq kit (active motif) basically according to manufacturer’s instructions.  Genomic DNA was purified and library were prepared by PCR with primers for illumine sequencing.

treatment_protocol: Balb/c mice were infected with P. berghei ANKA strain. Sulfadiazine was added to their drinking water in order to deplete asexual blood-stage parasites. Parasites were harvested after drug treatment for 2 days.

tag: Stage

value: gametocyte

tag: strain

value: ANKA


title: Vumc-NSCLC-128


title: ATAC-seq_gam _2

value: wild type


title: Vumc-NSCLC-124


title: ATAC-seq_gSNF2-KO_2


title: ATAC-seq_gam _1


title: Vumc-NSCLC-123


title: Vumc-NSCLC-121


title: Vumc-NSCLC-120


title: Vumc-NSCLC-118


title: Vumc-NSCLC-103


title: Vumc-NSCLC-117


title: Vumc-NSCLC-129


title: Vumc-NSCLC-093


title: Vumc-NSCLC-070


title: Vumc-NSCLC-094


title: Vumc-NSCLC-068


title: PBM66

type: RNA

city: Palmerston North

first: Ankita

last: Jena

state: MANAWATU-WANGANUI

address: Massey University Manawatu (Turitea), Tennent Drive

country: New Zealand

institute: Riddet institute, Massey university

hyb_protocol: Using Nanostring manufactuers's instruction

label: NanoString

organism: Sus scrofa

source_name: Brain

extract_protocol: RNA was extracted using an RNeasy lipid tissue mini kit following the manufacturer’s instructions (Qiagen, Germany)

tag: region

value: Striatum

tag: treatment


title: PBM69

scan_protocol: Using Nanostring manufactuers's instruction


title: PBM67

data_processing: Using Nanostring manufactuers's instruction


title: PBM68

label_protocol: Using Nanostring manufactuers's instruction


title: PBM64


title: PBM65


title: PBM62


title: PBM63


title: PBM60


title: PBM59


title: PBM61


title: Vumc-NSCLC-054

value: Thrombocytes


title: MGH-NSCLC-L-96

value: Malignant


title: PBM57


title: MGH-NSCLC-L-92

value: Non-Small-Cell Lung Cancer


title: MGH-NSCLC-L-47


title: Vumc-NSCLC-027


title: MGH-NSCLC-L-42


title: PBM58


title: Vumc-BRMETA-VU687-TR2165


title: Vumc-NSCLC-088


title: Vumc-BRMETA-VU694-TR2167


title: PBM54


title: PBM56


title: Vumc-BRMETA-VU651-TR2157


title: PBM53


title: PBM52


title: Vumc-BRMETA-14-TR2159


title: Vumc-Brain-metastasis-BRMETA9-TR1710


title: PBM50


title: PBM49


title: Vumc-BRMETA-4t0-TR1544


title: Vumc-Brain-metastasis-VU589-TR1605


title: PBM55


title: Vumc-BRMETA-11-TR1449


title: Vumc-BRMETA-8t0-TR1546


title: UMCU-nonSignAth3-1079-TR2045


title: PBM46

value: Prefrontal cortex


title: PBM45


title: PBM47


title: UMCU-non-sign-athero-4-1696-TR1992

value: nonMalignant


title: UMCU-non-sign-athero-4-1691-TR1990

value: Asymptomatic Controls


title: PBM44


title: UMCU-non-sign-athero-4-1675-TR1989


title: PBM42


title: PBM43


title: PBM41


title: UMCU-non-sign-athero-4-1670-TR1988


title: PBM51


title: UMCU-non-sign-athero-2-0657-TR1986


title: UMCU-NSAth-1-0190-TR832


title: UMCU-non-sign-athero-4-1669-TR1987


title: PBM40


title: UMCU-NSAth-1-0155-TR831


title: PBM39


title: PBM48


title: PBM38


title: UMCU-NSAth-1-0147-TR829


title: UMCU-NSAth-1-0151-TR830


title: UMCU-NSAth-1-0127-TR827


title: PBM37


title: PBM36


title: Vumc-MS-069-TR2309

value: Multiple Sclerosis


title: PBM35


title: Vumc-MS-070-TR2310


title: PBM34


title: PBM33


title: PBM32


title: Vumc-MS-067-TR2307


title: PBM31


title: PBM30


title: Vumc-MS-066-TR2303


title: PBM28


title: Vumc-MS-063-TR2305


title: PBM29


title: Vumc-MS-065-TR2175


title: PBM27


title: Vumc-MS-064-TR2174


title: Vumc-MS-302-TR2173


title: PBM26


title: PBM25


title: Vumc-MS-028-TR1469


title: Vumc-MS-052-TR1533


title: Vumc-MS-061-TR1587


title: Vumc-MS-051-TR1532


title: Vumc-MS-068-TR2308


title: PBM23

value: Hippocampus


title: PBM22


title: PBM21


title: Vumc-MS-054-TR1447


title: Vumc-MS-058-TR1537


title: PBM20


title: PBM19


title: PBM17


title: Vumc-MS-059-TR1538


title: Vumc-MS-057-TR1536


title: Vumc-MS-050-TR1531


title: PBM18


title: PBM13


title: PBM14


title: PBM15


title: Vumc-MS-056-TR1535


title: PBM24


title: Vumc-MS-055-TR1586


title: Vumc-MS-062-TR1540


title: Vumc-MS-033-TR1585


title: PBM11


title: Vumc-MS-Presto-035-TR1475


title: Vumc-MS-053-TR1534


title: PBM12


title: PBM10


title: Vumc-MS-Presto-026-TR1439


title: PBM8


title: Vumc-MS-Presto-049-TR1530


title: Vumc-MS-Presto-036-TR1476


title: PBM6


title: Vumc-MS-Presto-048-TR1529


title: PBM7


title: PBM16


title: Vumc-MS-Presto-043-TR1444


title: PBM5


title: PBM4


title: Vumc-MS-Presto-045-TR1446


title: PBM3


title: Vumc-MS-Presto-041-TR1442


title: Vumc-MS-Presto-034-TR1474


title: Vumc-MS-Presto-038-TR1478


title: Vumc-MS-Presto-044-TR1445


title: Vumc-MS-Presto-031-TR1472


title: PBM9


title: Vumc-MS-Presto-029-TR1470


title: 0h-1

city: wuhan

first: Jian

last: Wu

address: donghu road

country: China

institute: wuhan university

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C(Agilent Technologies).

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis. Differentially expressed genes or lncRNAs were then identified through fold change. The threshold set for up- and down-regulated genes was a fold change>= 2.0. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs.

label: biotin

organism: Mus musculus

source_name: macrophage

label_protocol: RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Mouse RAW264.7 cells wer stimulated with 2 uM purfied recombinant Mycobacterial EST12 protein for 0 h or 3 h.

tag: time


title: 3h-2


title: 0h-2


title: 3h-1


title: Vumc-MS-Presto-024-TR1432


title: Vumc-MS-Presto-037-TR1477


title: Vumc-MS-Presto-027-TR1468


title: Human immortalized chorion trophoblast cells, term not in labor, rep3

city: Manila

first: Ryan

last: Lintao

address: 547 Pedro Gil Street

department: College of Medicine

country: Philippines

institute: University of the Philippines Manila

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
Adapter and polyA sequences were trimmed with cutadapt version 1.15
UMIs were removed from the reads and added to the read name with the extract_umi.py software provided by the Smart-3SEQ authors
Reads were aligned to the human assembly GCA_000001405.15 using STAR version 2.7.5c using the parameters recommended by the software authors for the Encode consortium
The dedup.py Smart-3SEQ software was used to mark and remove duplicated reads
FeatureCounts software was used to count reads per gene using the Gencode annotation release 35
Assembly: GCA_000001405.15
Supplementary files format and content: Tab-separated values files output containing normalized raw counts from edgeR

source_name: hFM-CTC

extract_protocol:
RNA was isolated from placental and FM tissues and cell lines using RNeasy Mini Kit (QIAGEN, Germantown, MD) according to the manufacturer’s instructions.
Using RNA extracted from placental and FM tissues (n=5 per tissue) and cells (n=3 per cell type), a cDNA library was prepared according to the Smart-3SEQ protocol

value: hFM-CTC

value: Chorion trophoblast cell

value: wild-type

value: control conditions


title: Human immortalized decidual cells, term not in labor, rep1

source_name: hFM-DEC

value: hFM-DEC

value: Decidual cell


title: Human immortalized decidual cells, term not in labor, rep2


title: Human immortalized chorion trophoblast cells, term not in labor, rep2


title: Vumc-MS-Presto-022-TR1430


title: Human immortalized chorion trophoblast cells, term not in labor, rep1


title: Vumc-MS-Presto-021-TR1429


title: Human immortalized decidual cells, term not in labor, rep3


title: Vumc-MS-Presto-020-TR1428


title: PBM1


title: PBM2


title: Human immortalized amnion mesenchymal cells, term not in labor, rep3

source_name: hFM-AMC

value: hFM-AMC

value: Amnion mesenchymal cell


title: BeWo cells, rep3

source_name: BeWo

value: BeWo

value: Choriocarcinoma


title: BeWo cells, rep1


title: Vumc-MS-Presto-040-TR1441

value: Thrombocytes


title: Vumc-MS-Presto-023-TR1431


title: Human immortalized amnion mesenchymal cells, term not in labor, rep2


title: Human immortalized amnion mesenchymal cells, term not in labor, rep1


title: Vumc-MS-Presto-042-TR1443


title: Vumc-MS-Presto-025-TR1433


title: Human immortalized amnion epithelial cells, term not in labor, rep3

source_name: hFM-AEC

value: hFM-AEC

value: Amnion epithelial cell


title: Vumc-MS-018-TR854

value: nonMalignant


title: Human immortalized amnion epithelial cells, term not in labor, rep1


title: Human fetal membrane, term not in labor, rep5

description: TNLFM

source_name: Fetal membrane

tag: tissue

value: Fetal membrane


title: Vumc-MS-016-TR852

value: Multiple Sclerosis


title: Vumc-MS-Presto-030-TR1471


title: Vumc-MS-Presto-032-TR1473


title: Vumc-MS-015-TR696


title: Human fetal membrane, term not in labor, rep4

description: FM


title: Human fetal membrane, term not in labor, rep2


title: Human fetal membrane, term not in labor, rep3


title: BeWo cells, rep2


title: Vumc-MS-012-TR850


title: Human fetal membrane, term not in labor, rep1


title: Vumc-MS-Presto-039-TR1440


title: Vumc-MS-014-TR673


title: Vumc-MS-013-TR672


title: Vumc-MS-011-TR645


title: Human placenta, term not in labor, rep5

description: PLA

source_name: Placenta

value: Placenta


title: Human placenta, term not in labor, rep2


title: Human placenta, term not in labor, rep3


title: Human placenta, term not in labor, rep4


title: Vumc-MS-009-TR643


title: Vumc-MS-019-TR855


title: Human placenta, term not in labor, rep1


title: Human immortalized amnion epithelial cells, term not in labor, rep2


title: Vumc-MS-008-TR642


title: Vumc-MS-007-TR641


title: Vumc-MS-017-TR853


title: PBMCs_3 with ConA

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

institute: Yamaguchi university

data_processing:
BCL files produced by Illimina NextSeq 500 were converted to FASTQ files using bcl2fastq tool. Created FASTQ files were imported to CLC Genomics Workbench software (ver.20.0.4).
Reads with more than 2 ambiguous nucleotides and reads with quality scores less  than 20 as calculated by the Phred program were removed using CLC Genomics Workbench software (ver.20.0.4). Long reads with more than 1000 nucleotides and short reads with fewer than 20 nucleotides were also discarded.
The trimmed reads were mapped to the human reference genome CanFam3.1 release-98 using CLC Genomics Workbench software (ver.20.0.4) with default setting.
Reads Per Kilobase of exon per Million mapped reads (RPKM) and Transcripts Per Million (TPM) were calculated using CLC Genomics Workbench software (ver.20.0.4).
Assembly: CanFam3.1
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample.

organism: Canis lupus familiaris

source_name: peripheral blood mononuclear cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy specific pathogen-free male beagles (maintained as blood donors in our veterinary teaching hospital). PBMCs were isolated by density gradient centrifugation with Lymphoprep (Axis-Shield, Olso, Norway) and cultured in the RPMI1640-based complete medium (RPMI1640 (FUJIFILM Wako Pure Chemical Corporation), 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, and 55 μM 2-mercaptoethanol).

extract_protocol:
Total RNA was isolated from the PBMCs using the Maxwell RSC simplyRNA cells kit (Promega). Polyadenylated  mRNA was purified with oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs, NEB). Complementary DNA (cDNA) libraries for Illumina sequencing were generated with NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos for Illumina (NEB).
Extracted mRNA was incubated with NEBNext Random Primers in NEBNext First Strand Synthesis Reaction Buffer at 94°C for 15 min, and reverse transcription was performed with NEBNext Strand Synthesis Enzyme Mix. After reverse transcription, index sequences were inserted to cDNA fragments with PCR amplification using primers included in NEBNext Multiplex Oligos for Illumina. Following purification with AMPureXP beads (Beckman Coulter), the quality and the concentration of the libraries was evaluated using a Bioanalyzer. The confirmed libraries were mixed to equal molecular amounts against the clustering and sequencing on an Illumina NextSeq 500 DNA sequencer with 75 bp paired-end sequencing kit (Illumina).

treatment_protocol: PBMCs were treated with ConA (0.5 μg/ml) alone or ALA (1.0 mM) alone or both reagents for 24 hours before being harvested.

value: peripheral blood mononuclear cells

value: treated with ConA


title: PBMCs_3 with ALA

value: treated with ALA


title: Vumc-MM-SMM6-TR2471

value: Malignant

value: Multiple Myeloma


title: Vumc-MS-003-TR638


title: PBMCs_3 without ALA and ConA

value: untreated


title: Vumc-MM-MM9-TR2453


title: PBMCs_2 with ConA


title: Vumc-MS-010-TR644


title: Vumc-MS-001-TR636


title: Vumc-Brain-metastasis-BRMETA2t0-TR1542

value: Melanoma


title: Vumc-BRMETA-VU659-TR2164


title: Vumc-MS-004-TR639


title: Vumc-BRMETA-10-TR1448


title: PBMCs_1 without ALA and ConA


title: Vumc-Brain-metastasis-BRMETA1t0-TR1541


title: Vumc-BRMETA-5-t0-TR1545


title: PBMCs_2 with ALA


title: Vumc-MS-002-TR637


title: PBMCs_1 with ALA


title: Vumc-LGG-VU680-TR2155

value: Glioma


title: PBMCs_1 with ConA


title: PBMCs_3 with ConA and ALA

value: treated with ConA and ALA


title: Vumc-LGG-VU656-TR2154


title: PBMCs_1 with ConA and ALA


title: Vumc-MS-005-TR640


title: PBMCs_2 without ALA and ConA


title: RPE/choroid/slera complexes, cnvd7, 3

city: Shanghai

first: Yu

last: Liang

address: 83 Fenyang Road

institute: Eye & ENT Hospital, Fudan University

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality are examined by FastQC and trimmed reads are aligned allowing for 1 mismatch only to the mature tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software. The remaining reads are aligned allowing for 1 mismatch only to miRNA reference sequences with miRDeep2.
The expression profiling of tRF and tiRNA can be calculated based on counts of reads mapped.
The differentially expressed tRFs and tiRNAs are screened based on the count value with R package edgeR.
Assembly: mm10
Supplementary files format and content: xlsx, CPM value for each sample

source_name: RPE-Choroid-slera complex

growth_protocol: mice are fed in air-conditioned room with 12-hour light-dark cycle.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
Total RNA samples were first pretreated as following to remove some RNA modifications that interfere with small RNA-seq library construction: 3'-aminoacyl (charged) deacylation to 3'-OH for 3'-adaptor ligation, 3'-cP (2',3'-cyclic phosphate) removal to 3'-OH for 3'-adaptor ligation, 5'-OH (hydroxyl group) phosphorylation to 5'-P for 5'-adaptor ligation, m1A and m3C demethylation for efficient reverse transcription. Then, total RNA was sequentially ligated to 3’ and 5’ small RNA adapters. cDNA was synthesized and amplified using Illumina’s proprietary RT primers and amplification primers. Subsequently, ~134-160 bp PCR amplified fragments were extracted and purified from the PAGE gel. And finally, the completed libraries were quantified by Agilent 2100 Bioanalyzer.

treatment_protocol: Laser photocoagulation was performed to make laser burns in each eye of 6-8 weeks old C57BL/6 mice. The mice were anesthetized by intraperitoneal injection of 1.25% avertin. The pupil was dilated by tropicamide. A 532 nm laser (VITRA, Quantel medical, France, CS 40015) with the power of 110 mW and duration of 100ms was used to induced laser spots. Every spot was 2-3 papillary diameters away from optic disc, and the clear bubble formation indicated the disruption of Bruch’s membrane. At different time point, mice were sacrificed by cervical dislocation and the RPE-choroid-sclera complexes were obtained.

value: RPE-Choroid-slera complex


title: RPE/choroid/slera complexes, cnvd7, 2


title: RPE/choroid/slera complexes, cnvd3, 3


title: RPE/choroid/slera complexes, cnvd7, 1


title: Vumc-LGG-VU653-TR2152

value: Thrombocytes


title: Vumc-LGG-VU634-TR2151


title: RPE/choroid/slera complexes, cnvd3, 2


title: Vumc-LGG-VU633-TR2150


title: Vumc-LGG-VU545-TR1902


title: RPE/choroid/slera complexes, cnvd3, 1


title: RPE/choroid/slera complexes, control, 3

value: control


title: RPE/choroid/slera complexes, control, 2


title: Vumc-LGG-VU625-TR1723


title: RPE/choroid/slera complexes, control, 1


title: Vumc-LGG-VU600-TR1665


title: Exp3 10x Genomics Gene Expression

city: New York

first: Dalia

last: Barkley

state: NY

address: 435 E 30th st

department: Institute for Computational Medicine

institute: NYU Langone Health

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop scRNA-Seq method were processed using a custom-built pipeline, available online (https:__github.com_flo-compbio_singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the 10x Genomics Visium method were processed using the SpaceRanger pipeline.
Raw sequencing data obtained from the 10x Gene Expression method were processed using the CellRanger pipeline.
Assembly: hg38, mm10
Supplementary files format and content: for inDrop single-cell RNA-Seq data: genes as rows and cells as columns. For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline, including gene expression and spatial contents. For 10x Genomics single-cell RNA-Seq: output of CellRanger pipeline, including gene expression, features and barcodes.

source_name: Single-cell RNA-Seq of mouse pancreatic adenocarcinoma in peritoneum and liver

growth_protocol: For mouse pancreatic adenocarcinoma, Rag1-_- and WT C57BL_6 mice were obtained from Jackson Laboratories (Bar Harbor, ME). The KrasG12D;Tp53R172H;Pdx1Cre (KPC) derived cell line FC1242 was utilized for orthotopic injection of 100,000 cells into the tail of pancreata of 8-12 week old C57BL_6 or Rag mice. To model liver and peritoneal metastases, mice received FC1242 via splenic (1,000,000 cells) and intraperitoneal (100,000 cells) injection, respectively. Tumors were harvested 2-3 weeks after injection.

extract_protocol:
For inDrop single-cell RNA-Seq of patient tumor samples, cell suspension was generated from minced tumor tissue using human tumor dissociation kit (Miltenyi) prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For 10x Genomics spatial transcriptomics of patient tumor samples, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation for 12 minutes. For 10x Genomics single-cell RNA-Seq of mouse tumors, cell suspension was generated from minced tumor tissue using the mouse tumor dissociation kit (Miltenyi) enzymes D and R prior to droplet encapsulation and individual barcoding of cells using the 10x Genomics platform.
For inDrop single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England BiolaBS). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For 10x Genomics spatial transcriptomic and single-cell RNA-Seq library construction, we followed the manufacturer's instructions.

tag: cancer type

value: Pancreatic adenocarcinoma

tag: organ

tag: method

value: 10x Genomics Gene Expression


title: Vumc-LGG-VU566-TR1608


title: Vumc-LGG-VU532-TR1591


title: Exp1 10x Genomics Gene Expression

source_name: Single-cell RNA-Seq of mouse pancreatic adenocarcinoma in WT and Rag-_- mice

value: Pancreas


title: Vumc-LGG-VU599-TR1613


title: PBMCs_2 with ConA and ALA


title: Vumc-LGG-VU526-TR1590


title: Vumc-LGG-VU572-TR1609


title: pDC sup-LPS-4

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

data_processing:
fastp -q 15 -n 10 -l 20 –detect_adapter_for_pe  -i target_R1.fastq -I target_R2.fastq (fastp v0.19.10)
STAR --readFilesIn target_R1.fastq target_R2.fastq --outSAMtype BAM Unsorted --outFilterMultimapNmax 4 --outFilterType BySJout --outSAMmultNmax 1 --outFilterMismatchNoverReadLmax 0.1 --outSAMstrandField intronMotif --sjdbGTFfile gencode_v33.gtf --outReadsUnmapped Fastx (STAR v2.7.3a)
samtools sort -n target_STAR.Aligned.out.bam | samtools fixmate -rm - - | samtools sort - | samtools markdup -l 800 -rs – target_STAR.Aligned.sortedByCoord.out.bam (samtools v1.9)
featureCounts -p -a gencode_v33.gtf -s 2 -o reverse_stranded.txt target_STAR.Aligned.sortedByCoord.out.bam (featureCounts v2.0.1)
Genome_build: hg38
Supplementary_files_format_and_content: TSV file containing sample by gene matrix

molecule: polyA RNA

source_name: human blood primary monocytes

growth_protocol: cells were cultured in 20 ng/ml hM-CSF

extract_protocol:
cell were harvested and total RNA were extreacted using Rneasy Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were treated with  30ng/ml IFNα or the supernatant of SARS-CoV-2 activated pDCs  for 24 h and followed by 2 ng/ml LPS for 3 h

tag: cells

value: monocytes

tag: agent

value: pDC sup-LPS


title: pDC sup-LPS-2


title: Vumc-LGG-VU575-TR1610

tag: cell type


title: IFNα-LPS-4

value: IFNalpha-LPS


title: IFNα-LPS-3


title: Vumc-LGG-VU588-TR1612

tag: classification group


title: IFNα-LPS-2


title: LPS-4

value: LPS


title: pDC sup-LPS-1


title: Retina Ythdf2 rep2

city: Shenzhen

first: Fugui

last: Niu

state: Guangdong

address: 1088 Xueyuan Avenue

department: Biology

institute: Southern University of Science and Technology

data_processing:
The filtered reads were mapped to the mouse reference genome (GRCm38) using STAR v2.5.
The resulting bam files were fed to HTSeq tool to count the number of RNA-seq reads.
The number of RNA-seq reads was further normalized to calculate FPKM.
The FPKM from RIP elute to input and any fold change greater than 2 was considered enriched.
Assembly: GRCm38
Supplementary files format and content: raw counts and FPKM

source_name: Retina

extract_protocol:
Mouse cortices and retinas were removed and dissociated, then neurons were treated following the manual of the EZ-Magna RIPTM RNA-Binding Protein Immunoprecipitation Kit (Millipore) with minor modifications.
100 ng RNA of input and elutes after RIP were used to generate the library using the TruSeq Stranded RNA Sample Preparation Kit (Illumina).

value: Retina

tag: age

value: post natal day 0

value: wild type

tag: rip antibody


title: Vumc-LGG-VU576-TR1611

value: Malignant

tag: patient group


title: Vumc-LGG-VU536-TR1592


title: Retina Ythdf2 rep1

tag: genotype


title: LPS-3


title: Vumc-LGG-VU612-TR1614


title: IFNα-LPS-1


title: Exp2 10x Genomics Gene Expression

source_name: Single-cell RNA-Seq of mouse pancreatic adenocarcinoma in pancreas and peritoneum


title: Retina Input rep2

value: none (input)


title: Retina Ythdf1 rep1


title: Vumc-LGG-VU479-1-TR554

value: Glioma


title: Vumc-LGG-VU619-TR1615


title: Retina Input rep1


title: pDC sup-LPS-3


title: Cortex Ythdf2 rep2

source_name: Cortex

value: Cortex

value: Embryonic day 12.5


title: LPS-1


title: Retina Ythdf1 rep2


title: Vumc-LGG-VU621-TR1722

value: Thrombocytes


title: Cortex Ythdf2 rep1


title: Vumc-LGG-VU441-1-TR583


title: Cortex Ythdf1 rep2


title: pDC sup-3

value: pDC sup


title: pDC sup-4


title: Cortex Input rep2


title: Cortex Ythdf1 rep1


title: Vumc-LGG-449-1-TR585


title: Cortex Input rep1


title: Vumc-LGG-446-1-TR584


title: pDC sup-1


title: MGH-LGG-VU525-TR610


title: Input chromatin used for H3K27ac ChIP-seq

city: Lille

first: Jérôme

last: Eeckhoute

address: Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc

country: France

institute: CNRS

data_processing:
Reads were mapped to the human genome (hg38) using Bowtie 2
Input DNA was used as control, duplicate tags and those mapping to ENCODE blacklisted regions v2
Signal tracks corresponding to enrichment over input were obtained using MACS2 bdgcmp (Poisson pvalue)
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files for BNC2 ChIP-seq enrichment over input, H3K27ac ChIP-seq enrichment over input and CoP-seq enrichment over input. Bed file provides BNC2 peaks.

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 5% fetal bovine serum (FCS, Deutscher).

extract_protocol:
ChIP was performed using BNC2 (Sigma, HPA018525) or H3K27ac antibody (Active Motif ref 39685).
TruSeq ChIP Sample Preparation Kit (BNC2) or DNBseq involving Probe-Anchor Synthesis (cPAS), linear isothermal Rolling-Circle Replication  and DNA Nanoballs (DNBTM) technology, followed by high-resolution digital imaging.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 10min at room temperature. Samples for ChIP were processed as in Dubois V. et al Mol Syst Biol 2020 while samples for CoP were processed as in Zhang et al Epigenetics & Chromatin 2020.

tag: antibody


title: CoP-seq for LX2 cells

description: CoP-seq LX2 cells


title: Input chromatin used for CoP-seq

description: Input chromatin used for CoP-seq


title: pDC sup-2


title: Vumc-LGG-VU487-1-TR555


title: LPS-2


title: Vumc-LGG-VU490-TR512


title: H3K27ac ChIP-seq for LX2 cells

description: H3K27ac ChIP-seq LX2 cells

value: H3K27ac from Active Motif ref 39685


title: IFNα-3

value: IFNalpha


title: Vumc-LGG-VU507-TR513


title: IFNα-4


title: Vumc-LGG-VU464-TR509


title: IFNα-2


title: Vienna-CRC-Vien-11-TR2975

value: nonMalignant

value: Bowel Disease


title: IFNα-1

value: monocytes


title: Vienna-CRC-Vien-10-TR2974


title: Resting-4

value: Resting


title: Vienna-CRC-Vien-19-TR3004


title: Resting-3


title: Vienna-CRC-Vien-17-TR2995


title: Vienna-CRC-Vien-15-TR2993


title: Resting-2


title: Resting-1


title: Vienna-CRC-Vien-14-TR2992


title: ThMix_73_2

city: Bonn

first: Kevin

last: Thurley

address: Venusberg 1

department: Institute of Experimental Oncology

country: Germany

institute: University Hospital Bonn

description: replicate 2

hyb_protocol: 1,5 ug of cRNA were hybridized for 17 hr at 58°C on Illumina Mouse Sentrix 6 array

scan_protocol: Standard Illumina scanning protocol

data_processing: data were quantile-normalized and background corrected. Outliers were removed. Processing was performed using R software.

source_name: ThMix cell 73 hours

label_protocol: The Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion) is used to generate biotin labeled cRNA from input amounts of 500ng total RNA

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain

value: Balb/c

tag: activation

value: Anti-CD3, anti-CD28

tag: time point

value: 73 hours

value: 5-8 weeks

value: Spleen + lymph node

tag: condition

value: IL12, IL4


title: Vumc-HL-65-TR2420

value: Malignant

value: Hodgkin Lymphoma


title: Tnaiv_0_2

description: replicate 2

source_name: Tnaiv cell 0 hours

value: 0 hours

tag: tissue


title: ThMix_24_2

description: replicate 2

source_name: ThMix cell 24 hours

value: 24 hours


title: ThMix_48_2

description: replicate 2

source_name: ThMix cell 48 hours

value: 48 hours


title: ThMix_120_2

description: replicate 2

source_name: ThMix cell 120 hours

value: 120 hours


title: ThMix_96_2

description: replicate 2

source_name: ThMix cell 96 hours

value: 96 hours


title: ThMix_35_2

description: replicate 2

source_name: ThMix cell 35 hours

value: 35 hours


title: ThMix_73_1

description: replicate 1


title: ThMix_96_1

description: replicate 1


title: Tnaiv_0_1

description: replicate 1


title: ThMix_3_2

description: replicate 2

source_name: ThMix cell 3 hours

value: 3 hours


title: ThMix_12_2

description: replicate 2

source_name: ThMix cell 12 hours

value: 12 hours


title: ThMix_6_2

description: replicate 2

source_name: ThMix cell 6 hours

value: 6 hours


title: Vumc-HL-64-TR2419

value: Thrombocytes


title: ThMix_48_1

description: replicate 1

value: Balb/c

value: Anti-CD3, anti-CD28


title: ThMix_120_1

description: replicate 1

value: 5-8 weeks


title: ThMix_12_1

description: replicate 1

value: Spleen + lymph node


title: ThMix_35_1

description: replicate 1

value: IL12, IL4


title: ThMix_24_1

description: replicate 1


title: EMS404 siBNC2 #4

description: Transcriptomic EMS404 siBNC2

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene2.0st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

scan_protocol: Affymetrix GeneChip Scanner 7G and Affymetrix GeneChip Command Console software (AGCC).

data_processing: Normalization was performed using the apt-probeset-summarize tool of Affymetrix Power Tools (https://www.affymetrix.com/support/developer/powertools/changelog/index.html) using “gc correction+scale intensity+rma”. Normalization level was set to “Core genes”. The data obtained are log2-transformed.

source_name: EMS404 cells transfected with siBNC2

label_protocol: RNA were processed using Affymetrix GeneChip® WT PLUS Reagent Kit.

extract_protocol: RNA was extracted using Trizol and reverse transcribed using the High Capacity cDNA Reverse Transcription kit (Applied Biosystems, USA). Total RNA was checked for quantity and quality using the Agilent 2100 Bioanalyzer (Agilent Biotechnologies).

treatment_protocol: Cells were transfected using lipofectamine with 20 nM siRNA targeting BNC2 (siBNC2, Thermo Fisher Scientific, Cat# (Cat# 4390771 s109765) or a non-targeting control siRNA (siCTRL, Thermo Fisher Scientific Cat# 4390844)

tag: cell line

tag: treatment


title: Vumc-HL-56-TR2418

value: Malignant


title: EMS404 siBNC2 #3

description: Transcriptomic EMS404 siBNC2


title: Vumc-HL-49-TR2417

value: Hodgkin Lymphoma


title: ThMix_6_1

description: replicate 1


title: Vumc-HL-47-TR2416


title: Vumc-HL-38-TR2413


title: Vumc-HL-37-TR2412


title: Vumc-HL-33-TR2411


title: Th2_73_2

description: replicate 2

source_name: Th2 cell 73 hours

value: 73 hours

value: IL4, anti IL12, anti IFNg


title: Th2_120_2

description: replicate 2

source_name: Th2 cell 120 hours


title: Th2_96_2

description: replicate 2

source_name: Th2 cell 96 hours


title: ThMix_3_1

description: replicate 1


title: EMS404 siBNC2 #2

description: Transcriptomic EMS404 siBNC2


title: Th2_35_2

description: replicate 2

source_name: Th2 cell 35 hours


title: Th2_12_2

description: replicate 2

source_name: Th2 cell 12 hours


title: EMS404 siBNC2 #1

description: Transcriptomic EMS404 siBNC2


title: Vumc-HL-30-TR2409


title: EMS404 siCTRL #2

description: Transcriptomic EMS404 siCTRL

source_name: EMS404 cells transfected with siCTRL

value: siCTRL


title: Th2_96_1

description: replicate 1


title: Th2_12_1

description: replicate 1


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #9

description: Transcriptomic liver Bnc2 heterozygous mouse

hyb_protocol: Affymetrix GeneChip Hybridization Oven 640 for 16h at 45°C and 60 rpm on MoGene-2_0-st Chip. GeneChips were washed and stained in the Affymetrix Fluidics.

source_name: C57BL/6 x CBA adult male mouse

growth_protocol: Mice were housed in a temperature-controlled room (22–24°C) with a 12h dark-light cycle. Animal studies were performed in compliance with European Community specifications regarding the use of laboratory animals and approved by the Nord-Pas de Calais Ethical Committee for animal use (APAFIS#15539-2018053011323354).

treatment_protocol: Mice were fed with a CDAA-HFSC for 7.5 weeks

value: Bnc2 heterozygous


title: Th2_48_1

description: replicate 1

source_name: Th2 cell 48 hours

value: 48 hours


title: EMS404 siCTRL #3

description: Transcriptomic EMS404 siCTRL


title: Th2_6_2

description: replicate 2

source_name: Th2 cell 6 hours


title: EMS404 siCTRL #4

description: Transcriptomic EMS404 siCTRL


title: Vumc-HL-32-TR2410


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #10


title: Vumc-HL-27-TR2407


title: Th2_24_1

description: replicate 1

source_name: Th2 cell 24 hours

value: 24 hours


title: Th2_24_2

description: replicate 2


title: Th2_3_2

description: replicate 2

source_name: Th2 cell 3 hours

value: 3 hours


title: Th2_120_1

description: replicate 1

value: 120 hours


title: EMS404 siCTRL #1

description: Transcriptomic EMS404 siCTRL


title: Th2_73_1

description: replicate 1


title: Th2_48_2

description: replicate 2


title: Th2_35_1

description: replicate 1

value: 35 hours


title: Th2_6_1

description: replicate 1

value: 6 hours


title: Vumc-HL-24-TR2405

value: Thrombocytes


title: Vumc-Hodg-HL15-TR580


title: Vumc-HNSCC-HN-642-TR1944

value: Head and Neck Cancer


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #7


title: Vumc-HNSCC-HN-632-TR1983


title: Th1_120_2

description: replicate 2

source_name: Th1 cell 120 hours

value: Balb/c

value: Anti-CD3, anti-CD28

value: 5-8 weeks

value: IL-12, anti IL4


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #8


title: Th2_3_1

description: replicate 1

value: Spleen + lymph node


title: Th1_96_2

description: replicate 2

source_name: Th1 cell 96 hours

value: 96 hours


title: Vumc-HNSCC-HN-629-TR1981

value: Malignant


title: Vumc-HNSCC-HN-630-TR1982


title: Th1_73_2

description: replicate 2

source_name: Th1 cell 73 hours

value: 73 hours


title: Th1_48_2

description: replicate 2

source_name: Th1 cell 48 hours


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #5

value: Bnc2 heterozygous


title: Th1_35_2

description: replicate 2

source_name: Th1 cell 35 hours


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #6


title: Th1_12_2

description: replicate 2

source_name: Th1 cell 12 hours

value: 12 hours


title: Th1_6_2

description: replicate 2

source_name: Th1 cell 6 hours


title: Vumc-Hodg-HL13-TR579

value: Hodgkin Lymphoma


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #4


title: Th1_24_2

description: replicate 2

source_name: Th1 cell 24 hours

value: 24 hours


title: Th1_120_1

description: replicate 1

value: 120 hours


title: Th1_3_2

description: replicate 2

source_name: Th1 cell 3 hours

value: 3 hours


title: Th1_73_1

description: replicate 1


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #1


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #2


title: Th1_35_1

description: replicate 1

value: 35 hours


title: Vumc-HNSCC-HN-619-TR1976

value: Thrombocytes


title: Th1_24_1

description: replicate 1


title: Th1_96_1

description: replicate 1


title: Th1_48_1

description: replicate 1

value: 48 hours


title: Liver of Bnc2 heterozygous mouse under CDAA-HSFC diet #3


title: Liver of WT mouse under CDAA-HSFC diet #10

description: Transcriptomic liver WT mouse

value: WT


title: Vumc-HNSCC-HN-617-TR1974

value: Head and Neck Cancer


title: Vumc-HNSCC-HN-616-TR1952


title: Vumc-headNeck-611-TR1092


title: Vumc-headNeck-610-TR1075


title: Vumc-headNeck-608-TR1074


title: Th1_6_1

description: replicate 1

value: Balb/c

value: Anti-CD3, anti-CD28

value: 6 hours

value: 5-8 weeks


title: Liver of WT mouse under CDAA-HSFC diet #9

description: Transcriptomic liver WT mouse


title: Vumc-headNeck-604-TR1072

value: Malignant


title: Liver of WT mouse under CDAA-HSFC diet #5

description: Transcriptomic liver WT mouse


title: Th1_12_1

description: replicate 1

value: Spleen + lymph node

value: IL-12, anti IL4


title: Liver of WT mouse under CDAA-HSFC diet #6

description: Transcriptomic liver WT mouse


title: Vumc-headNeck-594-TR1056


title: Th0_24_2

description: replicate 2

source_name: Th0 cell 24 hours

value: anti IFNg,anti IL4, anti IL12


title: Th0_120_2

description: replicate 2

source_name: Th0 cell 120 hours


title: Liver of WT mouse under CDAA-HSFC diet #8

description: Transcriptomic liver WT mouse


title: Th0_6_2

description: replicate 2

source_name: Th0 cell 6 hours


title: Vumc-headNeck-589-TR1052


title: Th0_73_2

description: replicate 2

source_name: Th0 cell 73 hours

value: 73 hours


title: Th0_35_2

description: replicate 2

source_name: Th0 cell 35 hours


title: Th0_48_2

description: replicate 2

source_name: Th0 cell 48 hours


title: Th0_96_2

description: replicate 2

source_name: Th0 cell 96 hours

value: 96 hours


title: Liver of WT mouse under CDAA-HSFC diet #3

description: Transcriptomic liver WT mouse

source_name: C57BL/6 x CBA adult male mouse


title: Liver of WT mouse under CDAA-HSFC diet #7

description: Transcriptomic liver WT mouse


title: Th0_73_1

description: replicate 1


title: Th0_120_1

description: replicate 1

value: 120 hours


title: Th0_3_2

description: replicate 2

source_name: Th0 cell 3 hours

value: 3 hours


title: Th0_48_1

description: replicate 1


title: Th0_96_1

description: replicate 1


title: Liver of WT mouse under CDAA-HSFC diet #4

description: Transcriptomic liver WT mouse


title: Liver of WT mouse under CDAA-HSFC diet #2

description: Transcriptomic liver WT mouse


title: Th0_12_2

description: replicate 2

source_name: Th0 cell 12 hours

value: 12 hours


title: Th0_35_1

description: replicate 1

value: 35 hours


title: Vumc-headNeck-587-TR1050

value: Thrombocytes


title: Maas-GBM-NICT-035G-TR2170

value: Glioma


title: Maas-GBM-M00009-TR2117


title: Maas-GBM-M00007-TR2116


title: B16 sgCTRL  - Dox - Biorep 3

city: Durham

first: Shane

last: Killarney

state: NC

address: 4 SCOTTISH LANE

institute: Duke University School of Medicine

data_processing:
Raw fastq files were trimmed using TrimGalore followed by quality control analysis with FastQC. Reads were mapped to the mouse genome (GRCm38) using the HISAT2 alignment tool. Reads were filtered to include only those mapping to a single genomic locus, and read counts were compiled with FeatureCounts. Normalization and differential expression analyses were conducted with the DESeq2 package in the R programming environment.
Assembly: NOT PROVIDED
Supplementary files format and content: RNAseq Counts.txt

extract_protocol:
RNA was isolated from whole cells with RNEasy Mini kit (QIAGEN)
Kapa Stranded mRNA-seq library prep kit

value: Melanoma

value: WT

value: .5 μM of Doxorubicin - 48hrs


title: B16 sgCasp3/7 - Dox - Biorep 1

value: Casp3/7 knockout


title: B16 sgCasp3/7 - Dox - Biorep 3


title: B16 sgCasp3/7 - Dox - Biorep 2


title: B16 sgCTRL  - Dox - Biorep 1


title: B16 sgCTRL  - Dox - Biorep 2


title: Maas-GBM-M00002-TR2114


title: Th0_24_1

description: replicate 1

value: Balb/c

value: Anti-CD3, anti-CD28

value: 24 hours

value: 5-8 weeks


title: Maas-GBM-M00001-TR2112

value: Malignant


title: Th0_6_1

description: replicate 1

value: 6 hours

value: Spleen + lymph node

value: anti IFNg,anti IL4, anti IL12


title: overexpression-CBX4+TNF-α group3 [OE_TNF-3]

city: Guangzhou

first: Yang

middle: yang

last: Zhang

address: 107 Yanjiang West Road

institute: Sun Yat Sen Memorial Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to RGSC 6.0/rn6 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: rn6
Supplementary files format and content: FPKM values for each Sample

organism: Rattus norvegicus

source_name: Primary nucleus pulposus cells

growth_protocol: Primary nucleus pulposus cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)  in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
To overexpress CBX4, rat NP cells were transfected with an adenovirus carrying a recombinant CBX4 plasmids and free plasmids constructed by Hanbio Biotechnology (Shanghai, China).
TNF- α was added after cbx4 overexpression.

value: Primary nucleus pulposus cells

tag: strain background

value: Sprague dawley

tag: time

value: 48 hours


title: overexpression-CBX4+TNF-α group2 [OE_TNF-2]


title: overexpression-CBX4+TNF-α group1 [OE_TNF-1]


title: Maas-GBM-NICT-040G-TR2172

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the Rdata-file were processed according to the described protocol (after filtering for low-abundent RNAs).

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations and submitted for 100 bp Single Read sequencing on the Hiseq 2500 or 4000 platform (Illumina).

value: Thrombocytes


title: overexpression-CBX4 group3 [OE_3]


title: Liver of WT mouse under CDAA-HSFC diet #1

description: Transcriptomic liver WT mouse


title: Th0_12_1

description: replicate 1

value: 12 hours


title: Th0_3_1

description: replicate 1

value: 3 hours


title: SP P 5 41-1_(SNOWBALLs520824F)

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

source_name: porcine myoblasts

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol:
The isolation of satellite cells from the M. rhomboideus of ten female five- and twenty days old piglets and the establishment and validation of two muscle cell pools (pool 5 (P5) or pool 20 (P20))
For proliferation experiments cells from both pools stored in liquid nitrogen were defrosted and permanently cultured at 35°, 37° (control), 39° or 41°C over a period of 72 h in growth medium

value: myoblasts

tag: pool

value: P 5

tag: temperature

value: 41 degrees C


title: SP P 5 41-2_(SNOWBALLs520824F)

tag: cell type


title: SP P 5 41-3_(SNOWBALLs520824F)


title: SP P 5 39-3_(SNOWBALLs520824F)

value: 39 degrees C


title: SP P 5 39-2_(SNOWBALLs520824F)


title: overexpression-CBX4 group1 [OE_1]


title: SP P 5 39-1_(SNOWBALLs520824F)


title: overexpression-NC+TNF-α group3 [NC_TNF-3]

value: overexpression-NC+TNF-alpha


title: overexpression-NC+TNF-α group2 [NC_TNF-2]


title: Maas-GBM-NICT-027G-TR2169

first: Myron

last: Best

institute: VU University Medical Center

tag: classification group

value: Glioma


title: overexpression-NC+TNF-α group1 [NC_TNF-1]


title: Maas-GBM-NICT-037G-TR2171


title: overexpression-NC group3 [NC_3]

value: overexpression-NC


title: Maas-GBM-NICT-004G-TR2168

value: Malignant


title: overexpression-NC group2 [NC_2]


title: overexpression-NC group1 [NC_1]


title: Gametocyte gSNF2 KO-3

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Assembly: PlasmoDB, version 3
Supplementary files format and content: BAM

source_name: Gametocyte

extract_protocol:
Gametocytes enriched blood were subjected to erythrocyte lysis in 0.84% NH4Cl. Residual cells were lysed in and total RNA was extracted by Isogen 2 (Nippon gene) according to manufacturer protocols.
Libraries were prepared using the RNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with an Illumina NEXTseq sequencer.

tag: Stage

value: gametocyte

value: ANKA

value: gSNF2 knockout


title: overexpression-CBX4 group2 [OE_2]

value: Primary nucleus pulposus cells


title: SP P 5 37-3_(SNOWBALLs520824F)

value: 37 degrees C


title: Gametocyte gSNF2 KO-2


title: Radb-GBM-N14-03-TR2142

tag: patient group


title: Gametocyte gSNF2 KO-1

tag: genotype


title: Gametocyte WT3

value: wild type


title: Gametocyte WT2


title: SP P 5 37-2_(SNOWBALLs520824F)


title: Gametocyte WT1


title: SP P 5 37-1_(SNOWBALLs520824F)


title: ChIP-seq_gSNF2-2-INPUT

data_processing:
Sequence data were mapped onto P. berghei genome sequence (PlasmoDB, version 3) using BOWTIE2 software in default settings. Mapping data were analyzed using MACS2 peak-calling algorithm using approximately 0.3 × 107 reads or 0.5 × 107 reads. Conditions for peak calling were FDR < 0.01
Assembly: PlasmoDB, version 3

extract_protocol:
Blood was filtered with Plasmodipur to remove lymphocytes and fixed with 1% formaldehyde for 60 min at 30C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were subjected to ChIP-seq. Cells were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power in the cell lysis solution containing 1% sodium dodecyl sulfate. The supernatant was subjected to immunoprecipitation with anti-GFP antibodies using Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

value: parasites expressing GFP-fused gSNF2


title: Vumc-GBM-504t0-TR1516

value: Thrombocytes


title: Th1_3_1

description: replicate 1

value: Balb/c

value: Anti-CD3, anti-CD28

value: 3 hours

tag: age

value: 5-8 weeks

value: Spleen + lymph node

value: IL-12, anti IL4


title: ChIP-seq_gSNF2-2-IP

tag: strain


title: Maas-GBM-M00010-TR2118

value: Glioma


title: Vumc-GBM-488t0-TR1514


title: ChIP-seq_gSNF2-1-INPUT


title: SP P 5 35-2_(SNOWBALLs520824F)

value: myoblasts

value: P 5

value: 35 degrees C


title: Vumc-GBM-517t0-TR1518

value: Malignant


title: Vumc-GBM-508t0-TR1517


title: INPUT_1

data_processing:
Reads were mapped on the P. berghei genome using Bowtie 2.0 with default settings. The reads mapped onto multiple sites were removed using grep command. The SAM files were sorted using samtools to produce BAM files. The mapping data were analyzed with the MACS2 peak-calling algorithm.
Genome_build: PlasmoDB, version 3
Supplementary_files_format_and_content: Peak-calling, text.

growth_protocol: Balb/c mice were infected with P. berghei expressing GFP-fused AP2-Z.

extract_protocol:
Cultures were filtered with Plasmodipur to remove lymphocytes and fixed with 1% formaldehyde for 60 min at 30 °C with shaking. After erythrocyte lysis in 0.85% NH4Cl, residual cells were subjected to ChIP-seq. Cells were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power in the cell lysis solution containing 1% sodium dodecyl sulfate. The supernatant was subjected to immunoprecipitation with anti-GFP antibodies using Dynabeads protein A.
Libraries were constructed using KAPA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

treatment_protocol: Infected mice were treated with sulfadiazine for 2 days. Parasites were then subjected to ookinete cultures and harvested at 6 hpoc

value: zygote at 6 hpoc

value: ANKA

value: GFP-fused AP2-Z expressing


title: Radb-GBM-N14-10-TR2146


title: INPUT_2


title: SP P 20 41-2_(SNOWBALLs520824F)

value: 41 degrees C


title: Vumc-GBM-500tO-TR1582


title: IP(anti-GFP)_2


title: SP P 5 35-3_(SNOWBALLs520824F)


title: IP(anti-GFP)_1


title: ap2-z_KO_6hpoc_RNA-seq_3

data_processing:
Sequence data were mapped onto the P. berghei genome sequence (PlasmoDB, version 3) by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” which was set to 1000. The SAM files were then sorted using samtools to produce BAM files.
Using the BAM files, number of reads mapped on each gene was counted by featureCounts.
Genome_build: PlasmoDB, version 3

source_name: Zygote

growth_protocol: Balb/c mice were infected with P. berghei ANKA strain.

extract_protocol:
Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s protocols.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

treatment_protocol: Infected mice were treated with sulfadiazine in their drinking water for 2 days in order to deplete asexual blood-stage parasites. Parasites were then subjected to ookinete cultures and harvested at 6 hpoc.


title: SP P 20 39-3_(SNOWBALLs520824F)

value: 39 degrees C


title: WT_6hpoc_RNA-seq_2

value: wild type


title: ap2-z_KO_6hpoc_RNA-seq_2


title: SP P 20 41-1_(SNOWBALLs520824F)


title: Vumc-GBM-540t0-TR1485

value: Thrombocytes


title: WT_6hpoc_RNA-seq_3


title: ap2-z_KO_6hpoc_RNA-seq_1


title: Vumc-GBM-542t0-TR1486


title: WT_6hpoc_RNA-seq_1


title: SP P 5 35-1_(SNOWBALLs520824F)


title: ChIP-seq_gSNF2-1-IP

value: gametocyte

value: parasites expressing GFP-fused gSNF2


title: Vumc-GBM-518t0-TR1584


title: Vumc-GBM-497t0-TR1481


title: Vumc-GBM-489-t0-TR1479


title: Vumc-GBM-505-TR1389


title: Vumc-GBM-499-TR1388


title: SP P 20 39-1_(SNOWBALLs520824F)


title: Vumc-GBM-485-TR1365


title: SP P 20 41-3_(SNOWBALLs520824F)


title: SP P 20 39-2_(SNOWBALLs520824F)


title: Adjacent tissue 2_adrenal 2

city: Paris

first: Maria-Christina

last: Zennaro

address: 56 rue Leblanc

institute: Inserm

description: nuclear RNA

data_processing:
Cellranger-4.0.0
cellranger count --id=sample_id --transcriptome=/path/to/10X/reference --fastqs=/path/to/fastqs --sample=sample_id-1,sample_id-2,sample_id-3,sample_id-4 –localcores=20
Assembly: GRCh38 (GENCODE v32/Ensembl 98)
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx files

source_name: adrenal gland

extract_protocol: not provided

value: adrenal gland

value: adrenal cortex cells adjacent to aldosterone-producing adenoma


title: Vumc-GBM-484-TR1387

city: Amsterdam

address: De Boelelaan 1117

description: Please note that the mapped and counted intron-spanning reads from the file corresponding to this sample were merged in silico twice with the counts from Vumc-GBM-484-TR1387-seq2_AGTTCC_L004_R1_001.fastq.gz to yield sufficient mapped reads for further analyses.


title: Adjacent tissue 1_adrenal 2

description: nuclear RNA


title: SP P 20 37-3_(SNOWBALLs520824F)

value: 37 degrees C


title: SP P 20 37-1_(SNOWBALLs520824F)


title: SP P 20 37-2_(SNOWBALLs520824F)


title: Vumc-GBM-480-TR1364

value: Glioma


title: SP P 20 35-2_(SNOWBALLs520824F)

value: myoblasts


title: Vumc-GBM-476-TR1363


title: Vumc-GBM-471-TR1361


title: Adjacent tissue 3_adrenal 2

description: nuclear RNA


title: Adjacent tissue 2_adrenal 1

description: nuclear RNA


title: SP P 20 35-3_(SNOWBALLs520824F)


title: Vumc-GBM-468-TR1360


title: Adjacent tissue 1_adrenal 1

description: nuclear RNA


title: AML1172 [scTCR-seq]

first: Yan

last: Tang

address: 20 Shattuck street

institute: Brigham and Women's Hospital

data_processing:
library strategy: scTCR-seq
Raw sequencing data was aligned to GRCh38 reference genome using Cell Ranger (v 3.0.0) pipeline (10x Genomics) to generate gene counts matrix by cell barcodes.
Assembly: GRCh38
Supplementary files format and content: csv files, gene-cell matrix

source_name: AML tumor

extract_protocol: Standard 10x genomics library construction protocol

value: AML tumor

tag: molecule/exp type

value: TCR sequence


title: Vumc-GBM-456-TR1386

description: Please note that the mapped and counted intron-spanning reads from the file corresponding to this sample were merged in silico twice with the counts from Vumc-GBM-456-TR1386-seq2_GTCCGC_L001_R1_001.fastq.gz to yield sufficient mapped reads for further analyses.

value: Malignant


title: AML tumor [SpatialTranscriptomics]

data_processing:
library strategy: Spatial Transcriptomics
Raw sequencing data was aligned to GRCh38 reference genome using Cell Ranger (v 3.0.0) pipeline (10x Genomics) to generate gene counts matrix by cell barcodes.
Assembly: GRCh38
Supplementary files format and content: csv files, gene-cell matrix

value: Spatial transcriptomics


title: AML1171 [scTCR-seq]


title: SP P 20 35-1_(SNOWBALLs520824F)

value: 35 degrees C


title: Vumc-GBM-445-TR1358


title: AML1167-2 [scTCR-seq]


title: Vumc-GBM-443-TR1357


title: AML1167-1 [scTCR-seq]


title: Vumc-GBM-440-TR1356


title: AML1166 [scTCR-seq]


title: ID986390.SecondDraw.204221250105_R08C01

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Blood species=Human

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium HumanMethylation850 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Noob normalization as implemented in the minfi R package M. Aryee et al 2014. PMID: 24478339

label: Cy3 and Cy5

source_name: Blood

label_protocol: Bisulfite conversion was performed on 500 ng of DNA using the llumina Infinium Methylation Assay protocol in the EZ DNA Methylation kit (Zymo Research). Next the samples were loaded onto the Infinium Human MethylationEPIC BeadChip

extract_protocol: Genomic DNA of whole blood samples

treatment_protocol: Standard Illumina Protocol

tag: Sex

value: Female

value: Blood

value: SecondDraw

tag: weight

tag: sampleID


title: ID731697.SecondDraw.204221250105_R06C01

value: Male

tag: tissue


title: ID268761.BaselineDraw.204221250015_R03C01

value: BaselineDraw


title: ID772378.BaselineDraw.204221250075_R03C01


title: ID986390.BaselineDraw.204221250105_R04C01


title: ID743150.SecondDraw.204221250112_R07C01


title: ID743150.BaselineDraw.204221250112_R03C01


title: ID731697.BaselineDraw.204221250105_R02C01


title: ID568174.BaselineDraw.204221250075_R04C01


title: ID781761.SecondDraw.204221250075_R05C01


title: ID654859.SecondDraw.204221250075_R06C01


title: ID363200.SecondDraw.204221250112_R05C01


title: ID363200.BaselineDraw.204221250112_R01C01


title: ID200485.SecondDraw.204221250015_R05C01


title: ID268761.SecondDraw.204221250015_R07C01


title: ID772378.SecondDraw.204221250075_R07C01


title: ID180959.SecondDraw.204221250105_R07C01


title: NYU_UCEC3  inDrop

data_processing:
Illumina RTA v2 software was used for basecalling and quality determination.
Raw sequencing data obtained from the inDrop scRNA-Seq method were processed using a custom-built pipeline, available online (https:__github.com_flo-compbio_singlecell). Briefly, the “W1” adapter sequence of the inDrop RT primer was located in the barcode read (the second read of each fragment), by comparing the 22-mer sequences starting at positions 9-12 of the read with the known W1 sequence (“GAGTGATTGCTTGTGACGCCTT”), allowing at most two mismatches. Reads for which the W1 sequence could not be located in this way were discarded. The start position of the W1 sequence was then used to infer the length of the first part of the inDrop cell barcode in each read, which can range from 8-11 bp, as well as the start position of the second part of the inDrop cell barcode, which always consists of 8 bp. Cell barcode sequences were mapped to the known list of 384 barcode sequences for each read, allowing at most one mismatch. The resulting barcode combination was used to identify the cell from which the fragment originated. Finally, the UMI sequence was extracted, and reads with low-confidence base calls for the six bases comprising the UMI sequence (minimum PHRED score less than 20) were discarded. The reads containing the mRNA sequence (the first read of each fragment) were mapped by STAR 2.5.1 with parameter “—outSAMmultNmax 1” and default settings otherwise36. Mapped reads were split according to their cell barcode and assigned to genes by testing for overlap with exons of protein-coding genes.
Raw sequencing data obtained from the 10x Genomics Visium method were processed using the SpaceRanger pipeline.
Raw sequencing data obtained from the 10x Gene Expression method were processed using the CellRanger pipeline.
Assembly: hg38, mm10
Supplementary files format and content: for inDrop single-cell RNA-Seq data: genes as rows and cells as columns. For 10x Genomics spatial transcriptomic data: output of SpaceRanger pipeline, including gene expression and spatial contents. For 10x Genomics single-cell RNA-Seq: output of CellRanger pipeline, including gene expression, features and barcodes.

source_name: Single-cell RNA-Seq of patient primary endometrial carcinoma

extract_protocol:
For inDrop single-cell RNA-Seq of patient tumor samples, cell suspension was generated from minced tumor tissue using human tumor dissociation kit (Miltenyi) prior to droplet encapsulation and individual barcoding of cells using the inDrop platform. Cell lysis was performed in droplets to release RNA, and reverse transcription and barcoding took place in droplets at 50C for 2h. For 10x Genomics spatial transcriptomics of patient tumor samples, 10 µm cryosections were mounted onto spatially barcoded arrays where reverse transcription of cellular transcripts took place in situ after tissue permeabilisation for 12 minutes. For 10x Genomics single-cell RNA-Seq of mouse tumors, cell suspension was generated from minced tumor tissue using the mouse tumor dissociation kit (Miltenyi) enzymes D and R prior to droplet encapsulation and individual barcoding of cells using the 10x Genomics platform.
For inDrop single-cell RNA-seq library construction, we followed the inDrop library construction protocol detailed by Klein et al,  Cell 2015, with minor changes. Briefly, RNA was reverse transcribed (RT) with SuperScript III (Invitrogen) in droplets. Droplet emulsions were broken, and post-RT material underwent second strand syntehsis and in vitro transcription using the T7 High Yield Enzyme mix (New England BiolaBS). RNA was fragmented for 105 seconds with 1X fragmentation reagent (1CellBio) prior to RT with random hexamers, eliminating the need for an adaptor ligation step. Cycles required for final library amplification was assessed by quantitative PCR (qPCR) with KAPA HiFi Hot Start PCR Mix (KAPA Biosystems) and EvaGreen dye (Biotium). Final libraries were amplified with KAPA HiFi Hot Start PCR mix for 9 to 13 cycles. inDrop library size assessed on a DNA BioAnalyzer chip following the manufacturer's instructions (Agilent).   For 10x Genomics spatial transcriptomic and single-cell RNA-Seq library construction, we followed the manufacturer's instructions.

tag: cancer type

value: Endometrial carcinoma

tag: organ

value: Endometrium

tag: method

value: inDrop


title: Vumc-GBM-438-TR1354

description: Please note that the mapped and counted intron-spanning reads from the file corresponding to this sample were merged in silico twice with the counts from Vumc-GBM-438-TR1354-seq2_CAGATC_L006_R1_001.fastq.gz to yield sufficient mapped reads for further analyses.

value: Thrombocytes


title: ID781761.BaselineDraw.204221250075_R01C01

tag: time


title: Vumc-GBM-436-TR1353

description: Please note that the mapped and counted intron-spanning reads from the file corresponding to this sample were merged in silico twice with the counts from Vumc-GBM-436-TR1353-seq2_GCCAAT_L005_R1_001.fastq.gz to yield sufficient mapped reads for further analyses.


title: ID180959.BaselineDraw.204221250105_R03C01


title: NYU_UCEC2  inDrop


title: Vumc-GBM-408-TR1350


title: Vumc-GBM-406-TR1349


title: NYU_UCEC1  inDrop


title: ID219298.BaselineDraw.204221240113_R02C01


title: ID219298.SecondDraw.204221240113_R04C01


title: ID568174.SecondDraw.204221250075_R08C01


title: ID289960.BaselineDraw.204221250015_R02C01


title: ID289960.SecondDraw.204221250015_R06C01


title: ID200485.BaselineDraw.204221250015_R01C01


title: ID654859.BaselineDraw.204221250075_R02C01


title: NYU_PRAD1  inDrop

source_name: Single-cell RNA-Seq of patient primary prostate adenocarcinoma

value: Prostate adenocarcinoma

value: Prostate


title: Vumc-GBM-439-TR1355

value: Glioma


title: NYU_PDAC1_Vis 10x Genomics Visium

source_name: Spatial transcriptomics of patient primary pancreatic ductal adenocarcinoma

value: Ovarian carcinoma

value: Ovary

value: 10x Genomics Visium


title: Vumc-GBM-402-TR1348

value: Malignant


title: Vumc-GBM-378-TR1347


title: Vumc-GBM-417-TR1351


title: NYU_OVCA3  inDrop

source_name: Single-cell RNA-Seq of patient primary ovarian carcinoma


title: Vumc-GBM-306-TR1346


title: NYU_OVCA3_Vis 10x Genomics Visium

source_name: Spatial transcriptomics of patient primary ovarian carcinoma


title: NYU_UCEC3_Vis 10x Genomics Visium

source_name: Spatial transcriptomics of patient primary endometrial carcinoma


title: ID182040.BaselineDraw.204221250045_R01C01


title: ID182040.SecondDraw.204221250045_R02C01


title: NYU_OVCA2  inDrop


title: NYU_OVCA1_Vis 10x Genomics Visium


title: UMCG-esoph-P102t0-TR2698

value: Esophageal Cancer


title: UMCG-esoph-P103t0-TR2699


title: UMCG-esoph-P101t0-TR2697


title: ID156595.SecondDraw.204221250112_R06C01

value: Female


title: NYU_LIHC1_Vis 10x Genomics Visium

source_name: Spatial transcriptomics of patient primary liver hepatocellular carcinoma

value: Liver hepatocellular carcinoma

value: Liver


title: Sample46.Eudragit.205844020021_R04C02

description: genomic DNA methylation from tissue=Liver species=Mouse

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

source_name: Liver

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted

tag: agemonths

tag: treatment

value: Eudragit

tag: platenumber

value: Plate 01

tag: welladdress


title: NYU_LIHC1  inDrop

source_name: Single-cell RNA-Seq of patient primary liver hepatocellular carcinoma


title: NYU_OVCA1  inDrop


title: UMCG-esoph-P100t0-TR2696

tag: cell type

tag: classification group

tag: patient group


title: UMCG-esoph-P99t0-TR2695


title: Sample48.Eudragit.205844020021_R06C02

tag: age


title: Sample40.Eudragit.205844020021_R04C01

value: Male


title: Sample41.Eudragit.205844020021_R05C01


title: Sample43.eRapa.205844020021_R01C02

value: eRapa


title: ID156595.BaselineDraw.204221250112_R02C01

value: Blood

value: BaselineDraw