title: Sample 475_Cdh1725_P18_R15

description: BSSE_QGF_141037_HLLWMDRXX_2_Cdh1725_P18_CCACCGGAGT_GCCTGCCATG_S165_L002


title: Sample 451_Cdh1624_P15_R6

status: Public on Nov 18 2021

type: SRA

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

description: BSSE_QGF_141013_HLLWMDRXX_2_Cdh1624_P15_CTCGAATATA_GAGATGTCGA_S141_L002

library_source: transcriptomic

data_processing:
Paired-end reads were aligned to the mouse genome (UCSC version mm10 analysis set) with STAR with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
The output was sorted and indexed with samtools. Read and alignment quality was evaluated using the qQCReport function of the Bioconductor package QuasR.
The featureCounts function from Bioconductor package subread was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (with used gene model provided by ensembl v96).
Processing of the read count matrix for genes was done according to the steps illustrated in Bioconductor Single Cell Analysis workflow (Amezquita et al., 2020).
Genome_build: mm10
Supplementary_files_format_and_content: TXT file (with tab separated values) with raw counts for Ensembl Genes, 1.column is Ensembl Gene ID, 2. and remaining columns contain raw counts

molecule: total RNA

organism: Mus musculus

source_name: Murine mammary tumor cell lines derived from tumors of lineage-traced MMTV-PyMT transgenic mice

growth_protocol: Cells were directly sorted from tumors of mice

extract_protocol:
FACS-sorted cells were collected as 5-cell pools in 2.5µl of 0.2% TX-100 and 2U/μl RNase inhibitor (TakaraBio, 2313B) in PBS into 96-well plates (Thermo Fisher Scientific, 4346906) and kept in -80°C prior to use. RNAseq libraries were prepared according to the Smart-seq2 method (Picelli, 2014).
5-cell RNA-seq: RNA/cDNA preamplification and Nextera XT library preparation reactions were set up with a Mosquito HV system (SPT Labtech). After reverse transcription and amplification, the concentration of cDNA generated from each sample was measured using PicoGreen (Thermo Fisher Scientific). cDNA was normalized to 0.1-0.15ng/µl and 0.75 µl were used for library preparation with the Nextera XT DNA library preparation kit (Illumina). Multiplexed library pools were then pooled and PE 2x51 sequenced with an Illumina NovaSeq 6000 system, v1 reagents.

treatment_protocol: Each mouse was treated with 2mg of Tamoxifen twice per week starting at 9 weeks of age and continuing until sacrifice (around 13 to 14 weeks of age)

tag: system

value: Cdh

tag: mouse

tag: population

tag: egfp

value: high

tag: mcherry

value: neg

tag: epcam

tag: passedqc

value: TRUE


title: Sample 449_Cdh1725_P18_R10

description: BSSE_QGF_141011_HLLWMDRXX_2_Cdh1725_P18_CCTCCGGTTG_CATAACACCA_S139_L002


title: Sample 450_Cdh1725_P05_R10

description: BSSE_QGF_141012_HLLWMDRXX_2_Cdh1725_P5_ATTGTTCGTC_TCTCTAGATT_S140_L002


title: Sample 447_Cdh1654_P18_R10

description: BSSE_QGF_141009_HLLWMDRXX_2_Cdh1654_P18_GCACCACCAA_TGGTACTGAT_S137_L002


title: Sample 444_Cdh1725_P18_R9

description: BSSE_QGF_141006_HLLWMDRXX_2_Cdh1725_P18_CGTGTACCAG_AGGATAAGTT_S134_L002


title: Sample 443_Cdh1624_P18_R9

description: BSSE_QGF_141005_HLLWMDRXX_2_Cdh1624_P18_ACTTGTTATC_CGCGCCTAGA_S133_L002

value: FALSE


title: Sample 442_Cdh1654_P18_R9

description: BSSE_QGF_141004_HLLWMDRXX_2_Cdh1654_P18_TTAACGGTGT_TCCTGACCGT_S132_L002


title: Sample 439_Cdh1725_P18_R8

description: BSSE_QGF_141001_HLLWMDRXX_2_Cdh1725_P18_GCAATATTCA_GGCGCCAATT_S129_L002


title: Sample 437_Cdh1654_P18_R8

description: BSSE_QGF_140999_HLLWMDRXX_2_Cdh1654_P18_GTTCGGAGTT_CGCCTTCTGA_S127_L002


title: Sample 441_Cdh1624_P15_R4

description: BSSE_QGF_141003_HLLWMDRXX_2_Cdh1624_P15_AATTCCATCT_CTTCAGTTAC_S131_L002


title: Sample 438_Cdh1624_P18_R8

description: BSSE_QGF_141000_HLLWMDRXX_2_Cdh1624_P18_ATAGCGGAAT_GCGCAGAGTA_S128_L002


title: Sample 482_Cdh1739_P15_R5

description: BSSE_QGF_141044_HLLWMDRXX_2_Cdh1739_P15_CGCCATATCT_GACCGGAGAT_S172_L002


title: Sample 440_Cdh1725_P05_R8

description: BSSE_QGF_141002_HLLWMDRXX_2_Cdh1725_P5_CGATGCGGTT_CCTGCTTGGT_S130_L002


title: Sample 432_Cdh1654_P18_R7

description: BSSE_QGF_140994_HLLWMDRXX_2_Cdh1654_P18_CGCAGCAATT_ATTCCGCTAT_S122_L002


title: Sample 434_Cdh1725_P18_R7

description: BSSE_QGF_140996_HLLWMDRXX_2_Cdh1725_P18_CCGCGTATAG_TAGGAACCGG_S124_L002


title: Sample 433_Cdh1624_P18_R7

description: BSSE_QGF_140995_HLLWMDRXX_2_Cdh1624_P18_ACGTTCCTTA_GACCGCTGTG_S123_L002


title: Sample 430_Cdh1725_P05_R6

description: BSSE_QGF_140992_HLLWMDRXX_2_Cdh1725_P5_ACAACTACTG_AGTTATCACA_S120_L002


title: Sample 425_Cdh1725_P05_R5

description: BSSE_QGF_140987_HLLWMDRXX_2_Cdh1725_P5_TGGTGTTATG_TCCAATTCTA_S115_L002


title: Sample 428_Cdh1624_P18_R6

description: BSSE_QGF_140990_HLLWMDRXX_2_Cdh1624_P18_GAATACCTAT_ACAATAGAGT_S118_L002


title: Sample 426_Cdh1624_P15_R1

description: BSSE_QGF_140988_HLLWMDRXX_2_Cdh1624_P15_CCGGTTCCTA_TATATTCGAG_S116_L002


title: Sample 427_Cdh1654_P18_R6

description: BSSE_QGF_140989_HLLWMDRXX_2_Cdh1654_P18_GGCCAATATT_CGGTCCGATA_S117_L002


title: Sample 448_Cdh1624_P18_R10

description: BSSE_QGF_141010_HLLWMDRXX_2_Cdh1624_P18_AGGCGTTCGC_TTCATCCAAC_S138_L002


title: Sample 445_Cdh1725_P05_R9

description: BSSE_QGF_141007_HLLWMDRXX_2_Cdh1725_P5_CATATGCGAT_CCTTGAACGG_S135_L002


title: Sample 446_Cdh1624_P15_R5

description: BSSE_QGF_141008_HLLWMDRXX_2_Cdh1624_P15_ATGTTGTTGG_CAATCTATGA_S136_L002


title: Sample 424_Cdh1725_P18_R5

description: BSSE_QGF_140986_HLLWMDRXX_2_Cdh1725_P18_ATGTAACGTT_ACGATTGCTG_S114_L002


title: Sample 423_Cdh1624_P18_R5

description: BSSE_QGF_140985_HLLWMDRXX_2_Cdh1624_P18_TTCGGTGTGA_GAACAAGTAT_S113_L002


title: Sample 420_Cdh1725_P18_R4

description: BSSE_QGF_140982_HLLWMDRXX_2_Cdh1725_P18_CTGCGTTACC_TATGGCTCGA_S110_L002


title: Sample 418_Cdh1654_P18_R4

description: BSSE_QGF_140980_HLLWMDRXX_2_Cdh1654_P18_GATATTGTGT_ACCACACGGT_S108_L002


title: Sample 421_Cdh1725_P05_R4

description: BSSE_QGF_140983_HLLWMDRXX_2_Cdh1725_P5_AGGAGGTATC_CCAGTTGGCA_S111_L002


title: Sample 435_Cdh1725_P05_R7

description: BSSE_QGF_140997_HLLWMDRXX_2_Cdh1725_P5_TAGAGAATAC_TATAGATTCG_S125_L002


title: Sample 419_Cdh1624_P18_R4

description: BSSE_QGF_140981_HLLWMDRXX_2_Cdh1624_P18_CGTACAGGAA_TAGGTTCTCT_S109_L002


title: Sample 422_Cdh1654_P18_R5

description: BSSE_QGF_140984_HLLWMDRXX_2_Cdh1654_P18_ATAGCCAAGA_AGTGCCACTG_S112_L002


title: Sample 415_CTRL_R12

description: BSSE_QGF_140977_HLLWMDRXX_2_negative_no_template_control__TCCGCCAATT_CTCCGTGCTG_S105_L002

source_name: Empty well

value: CTRL


title: Sample 431_Cdh1624_P15_R2

description: BSSE_QGF_140993_HLLWMDRXX_2_Cdh1624_P15_TATGATGGCC_GATTGTCATA_S121_L002


title: Sample 413_Cdh1725_P15_R3

description: BSSE_QGF_140975_HLLWMDRXX_2_Cdh1725_P15_CCGTGACCGA_CCGAACGTTG_S103_L002


title: Sample 417_CTRL_R14

description: BSSE_QGF_140979_HLLWMDRXX_2_negative_no_template_control__AGAGAACCTA_GGTTATGCTA_S107_L002


title: Sample 414_Cdh1725_P05_R3

description: BSSE_QGF_140976_HLLWMDRXX_2_Cdh1725_P5_ATACTTGTTC_TAACCGCCGA_S104_L002


title: Sample 412_Cdh1725_P18_R3

description: BSSE_QGF_140974_HLLWMDRXX_2_Cdh1725_P18_ATCGGCGAAG_TCCAAGAATT_S102_L002


title: Sample 411_Cdh1624_P18_R3

description: BSSE_QGF_140973_HLLWMDRXX_2_Cdh1624_P18_AGGCAGCTCT_CGGCTAACGT_S101_L002


title: Sample 436_Cdh1624_P15_R3

description: BSSE_QGF_140998_HLLWMDRXX_2_Cdh1624_P15_CCACGCTGAA_TATTCCTCAG_S126_L002


title: Sample 408_Cdh1725_P05_R2

description: BSSE_QGF_140970_HLLWMDRXX_2_Cdh1725_P5_TAATTAGCGT_TGGTTAAGAA_S98_L002


title: Sample 407_Cdh1725_P15_R2

description: BSSE_QGF_140969_HLLWMDRXX_2_Cdh1725_P15_GGTAGAATTA_GTAGCCATCA_S97_L002


title: Sample 405_Cdh1624_P18_R2

description: BSSE_QGF_140967_HLLWMDRXX_2_Cdh1624_P18_GAACGCAATA_ATCTTACTGT_S95_L002


title: Sample 406_Cdh1725_P18_R2

description: BSSE_QGF_140968_HLLWMDRXX_2_Cdh1725_P18_AGTACTCATG_ATGTCGTGGT_S96_L002


title: Sample 410_Cdh1654_P18_R3

description: BSSE_QGF_140972_HLLWMDRXX_2_Cdh1654_P18_TAGAATTGGA_GTTAATCTGA_S100_L002


title: Sample 429_Cdh1725_P18_R6

description: BSSE_QGF_140991_HLLWMDRXX_2_Cdh1725_P18_TACGTGAAGG_CGGTTATTAG_S119_L002


title: Sample 403_Cdh1654_P15_R2

description: BSSE_QGF_140965_HLLWMDRXX_2_Cdh1654_P15_CAGCAATCGT_TGTGATGTAT_S93_L002


title: Sample 400_Cdh1725_P05_R1

description: BSSE_QGF_140962_HLLWMDRXX_2_Cdh1725_P5_ATGGCGCCTG_TCCACGGCCT_S90_L002


title: Sample 404_Cdh1654_P18_R2

description: BSSE_QGF_140966_HLLWMDRXX_2_Cdh1654_P18_TTCTGTAGAA_GAGCGCAATA_S94_L002


title: Sample 401_CTRL_R10

description: BSSE_QGF_140963_HLLWMDRXX_2_negative_no_template_control__TCCGTTATGT_TTGTAGTGTA_S91_L002


title: Sample 402_CTRL_R11

description: BSSE_QGF_140964_HLLWMDRXX_2_negative_no_template_control__GGTCTATTAA_CCACGACACG_S92_L002


title: Sample 399_Cdh1725_P15_R1

description: BSSE_QGF_140961_HLLWMDRXX_2_Cdh1725_P15_ATATGCATGT_TGGTGCCTGG_S89_L002


title: Sample 398_Cdh1725_P18_R1

description: BSSE_QGF_140960_HLLWMDRXX_2_Cdh1725_P18_TCAATGGAGA_GCACTACAAC_S88_L002


title: Sample 393_TENA2524_P09_R12

description: BSSE_QGF_140955_HLLWMDRXX_2_TENA2524_P9_GTATTCCACC_ATGTAGACAA_S83_L002

value: TENA

value: med


title: Sample 394_TENA2524_P22_R12

description: BSSE_QGF_140956_HLLWMDRXX_2_TENA2524_P22_CCTCCGTCCA_CACATCGGTG_S84_L002


title: Sample 392_TENA2524_P17_R12

description: BSSE_QGF_140954_HLLWMDRXX_2_TENA2524_P17_TCAGAAGGCG_GGCCATCATA_S82_L002


title: Sample 396_Cdh1654_P18_R1

description: BSSE_QGF_140958_HLLWMDRXX_2_Cdh1654_P18_CACTCAATTC_TTAAGTTGTG_S86_L002


title: Sample 395_Cdh1654_P15_R1

description: BSSE_QGF_140957_HLLWMDRXX_2_Cdh1654_P15_TGCCGGTCAG_CCTGATACAA_S85_L002


title: Sample 391_TENA2524_P18_R12

description: BSSE_QGF_140953_HLLWMDRXX_2_TENA2524_P18_ACTTCAAGCG_GAACCATGAA_S81_L002


title: Sample 390_TENA2524_P05_R12

description: BSSE_QGF_140952_HLLWMDRXX_2_TENA2524_P5_GTCCGTAAGC_CGTGTATCTT_S80_L002


title: Sample 409_Cdh1654_P15_R3

description: BSSE_QGF_140971_HLLWMDRXX_2_Cdh1654_P15_GAATTACAAG_ACCGGCTCAG_S99_L002


title: Sample 389_TENA2524_P22_R11

description: BSSE_QGF_140951_HLLWMDRXX_2_TENA2524_P22_GGAGCGTGTA_ATCCGTAAGT_S79_L002


title: Sample 386_TENA2524_P18_R11

description: BSSE_QGF_140948_HLLWMDRXX_2_TENA2524_P18_ACCGTTACAA_CTCATAGCGA_S76_L002


title: Sample 388_TENA2524_P09_R11

description: BSSE_QGF_140950_HLLWMDRXX_2_TENA2524_P9_CCTCTACATG_GATACCTCCT_S78_L002


title: Sample 387_TENA2524_P17_R11

description: BSSE_QGF_140949_HLLWMDRXX_2_TENA2524_P17_TATGCCTTAC_AGACACATTA_S77_L002


title: Sample 381_TENA2524_P18_R10

description: BSSE_QGF_140943_HLLWMDRXX_2_TENA2524_P18_TTCATAAGGT_TGTTAGAAGG_S71_L002


title: Sample 382_TENA2524_P17_R10

description: BSSE_QGF_140944_HLLWMDRXX_2_TENA2524_P17_CTCTGCAGCG_GATGGATGTA_S72_L002


title: Sample 383_TENA2524_P09_R10

description: BSSE_QGF_140945_HLLWMDRXX_2_TENA2524_P9_ACGGTCAGGA_CGGCCTCGTT_S73_L002


title: Sample 385_TENA2524_P05_R11

description: BSSE_QGF_140947_HLLWMDRXX_2_TENA2524_P5_TGTCGCTGGT_TCGTCTGACT_S75_L002


title: Sample 380_TENA2524_P05_R10

description: BSSE_QGF_140942_HLLWMDRXX_2_TENA2524_P5_CCTGCGGAAC_ATCATAGGCT_S70_L002


title: Sample 384_TENA2524_P22_R10

description: BSSE_QGF_140946_HLLWMDRXX_2_TENA2524_P22_GGCAAGCCAG_CAAGCATCCG_S74_L002


title: Sample 379_TENA2524_P22_R9

description: BSSE_QGF_140941_HLLWMDRXX_2_TENA2524_P22_ACACAGGTGG_TGAGCGTTGT_S69_L002


title: Sample 378_TENA2524_P09_R9

description: BSSE_QGF_140940_HLLWMDRXX_2_TENA2524_P9_CTTGTACACC_AAGCGCGCTT_S68_L002


title: Sample 377_TENA2524_P17_R9

description: BSSE_QGF_140939_HLLWMDRXX_2_TENA2524_P17_AGGATGTGCT_TTACAATTCC_S67_L002


title: Sample 375_TENA2524_P05_R9

description: BSSE_QGF_140937_HLLWMDRXX_2_TENA2524_P5_TAATGTGTCT_GTAAGGCATA_S65_L002


title: Sample 397_Cdh1624_P18_R1

description: BSSE_QGF_140959_HLLWMDRXX_2_Cdh1624_P18_TCTCACACGC_CGGACAGTGA_S87_L002


title: Sample 374_TENA2524_P22_R8

description: BSSE_QGF_140936_HLLWMDRXX_2_TENA2524_P22_TGGCGCGAAC_AACTGATACT_S64_L002


title: Sample 372_CTRL_R9

description: BSSE_QGF_140934_HLLWMDRXX_2_negative_no_template_control__AACACTGTTA_GCAAGTCTCA_S62_L002


title: Sample 373_TENA2524_P09_R8

description: BSSE_QGF_140935_HLLWMDRXX_2_TENA2524_P9_ATTGCGCGGT_TTGGCTCCGC_S63_L002


title: OR024

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Genome_build: Mouse: GRCm38
Supplementary_files_format_and_content: estimated counts for each transcript
Supplementary_files_format_and_content: transcripts per million (tpm) values for each transcript

source_name: total RNA extracted from mice lung

growth_protocol: Female CD-1 mice weighing 27-32 g were obtained from Charles River Laboratories Ltd. U.K. Prior to exposure, animals were habituated for 5 days. All mice were housed in filter-top cages in an enviromentally controled room and maintained at 21°C and 55% humidity. Lighting was set to mimic a 12/12 h dawn to dusk cycle. Animals had acess to food and water ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Mice were anesthetized by an interperitoneal injection of ketamine (1.9 mg/mouse) and xylazine (0.19 mg/mouse), and were intranasally (50 µl/nostril) intoxicated with crude ricin  (1.7 µg/kg  or 10 µg/kg  ) or intranasally infected with SARS-CoV-2 ( 5 x 106 PFU).

tag: treatment

value: 96 hr post  5x10^6 PFU per mouse SARS-Cov-2

tag: strain

tag: tissue

value: lung


title: Sample 370_CTRL_R7

description: BSSE_QGF_140932_HLLWMDRXX_2_negative_no_template_control__TTACCTGGAA_ACAGTTCCAG_S60_L002


title: Sample 368_TENA2524_P18_R8

description: BSSE_QGF_140930_HLLWMDRXX_2_TENA2524_P18_CTCGCTTCGG_TACTAGTCAA_S58_L002


title: Sample 371_CTRL_R8

description: BSSE_QGF_140933_HLLWMDRXX_2_negative_no_template_control__TGGCTAATCA_AGGCATGTAG_S61_L002


title: Sample 369_TENA2524_P17_R8

description: BSSE_QGF_140931_HLLWMDRXX_2_TENA2524_P17_CTGTTGGTCC_ATAGACCGTT_S59_L002


title: Sample 367_TENA2524_P05_R8

description: BSSE_QGF_140929_HLLWMDRXX_2_TENA2524_P5_TCTATCCTAA_CGTCGACTGG_S57_L002


title: Sample 366_TENA2524_P22_R7

description: BSSE_QGF_140928_HLLWMDRXX_2_TENA2524_P22_AACGCACGAG_GCCTCGGATA_S56_L002


title: Sample 365_TENA2524_P09_R7

description: BSSE_QGF_140927_HLLWMDRXX_2_TENA2524_P9_CTGAGGAATA_CTTAACCACT_S55_L002


title: Sample 364_TENA2524_P16_R7

description: BSSE_QGF_140926_HLLWMDRXX_2_TENA2524_P16_GCATAAGCTT_TTCCGTCGCA_S54_L002


title: Sample 363_TENA2524_P10_R7

description: BSSE_QGF_140925_HLLWMDRXX_2_TENA2524_P10_GGAATTGTAA_AGCACATCCT_S53_L002

value: low


title: Sample 362_TENA2524_P15_R7

description: BSSE_QGF_140924_HLLWMDRXX_2_TENA2524_P15_TGATGTAAGA_GTGCGTCCTT_S52_L002


title: CTL_1_M63

city: San Diego

first: Oscar

middle: E

last: Echeagaray

state: CA

address: 5500 Campanile Drive

department: Biology

country: USA

institute: San Diego State University

data_processing:
The raw data was processed on the SpaceRanger pipeline (10X Genomics; version 1.2.2). Sequencing reads were aligned to the 10x mouse genome mm10-2020-A.
Preparations derived from slide preparation yielded 4933 barcoded spots for analysis, from which 1315 corresponded to Control (842 male, 473 female), and 3618 corresponded to 0% vape group (1565 male, 2053 female). Final removal of unwanted sources of variation and batch effect corrections was performed using Seurat R Package (v4.0.3).
Sequencing reads were aligned to the 10x mouse genome mm10-2020-A. Spots maintained comparable UMI and gene count detection throughout the tissue section
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are cells with cell barcode

molecule: polyA RNA

source_name: Non-Vaped Male

extract_protocol:
Freshly obtained cryosections were placed in Visium gene expression slides (10X Genomics, Cat# 2000233) for processing. Tissue staining with hematoxylin and eosin and image collections were done as suggested by  10X Genomics Visium protocol.
Spatial transcriptomic libraries were prepared using Visium Spatial Gene Expression Slide & Reagent Kit following manufacturer’s protocol (10X Genomics, PN-1000184). Lung permabilization time was optimized Visium Spatial Tissue Optimization Slide & Reagent Kit (10X Genomics, PN-1000193). Samples were processed together to avoid introduction of technical batch effects. Sequencing libraries were submitted to the UCSD IGM Genomics Core for sequencing (NovaSeq 6000), aiming for > 50K reads per spot.

tag: sample group

value: Non-Vaped (NV)

tag: Sex

value: male

value: upper pulmonary brances


title: Sample 361_TENA2524_P17_R7

description: BSSE_QGF_140923_HLLWMDRXX_2_TENA2524_P17_CCTGTCTGTC_ACTGTTGTGA_S51_L002


title: Sample 360_TENA2524_P18_R7

description: BSSE_QGF_140922_HLLWMDRXX_2_TENA2524_P18_GACACCATGT_TCAACGTGTA_S50_L002


title: Sample 357_TENA2524_P09_R6

description: BSSE_QGF_140919_HLLWMDRXX_2_TENA2524_P9_GTCCTGGATA_CGGTGGCGAA_S47_L002


title: Sample 359_TENA2524_P05_R7

description: BSSE_QGF_140921_HLLWMDRXX_2_TENA2524_P5_AGTGTTGCAC_CTGGTACACG_S49_L002


title: Sample 358_TENA2524_P22_R6

description: BSSE_QGF_140920_HLLWMDRXX_2_TENA2524_P22_CAGTGGCACT_TAACAATAGG_S48_L002


title: Sample 356_TENA2524_P16_R6

description: BSSE_QGF_140918_HLLWMDRXX_2_TENA2524_P16_AGATCCATTA_ATCTCTACCA_S46_L002


title: Sample 354_TENA2524_P15_R6

description: BSSE_QGF_140916_HLLWMDRXX_2_TENA2524_P15_CTGCGAGCCA_AATCCGGCCA_S44_L002


title: Sample 353_TENA2524_P17_R6

description: BSSE_QGF_140915_HLLWMDRXX_2_TENA2524_P17_CCATCTCGCC_TTCTATGGTT_S43_L002


title: Sample 352_TENA2524_P18_R6

description: BSSE_QGF_140914_HLLWMDRXX_2_TENA2524_P18_GTCTAATGGC_AGTGGTCAGG_S42_L002


title: Sample 355_TENA2524_P10_R6

description: BSSE_QGF_140917_HLLWMDRXX_2_TENA2524_P10_CGTTATTCTA_CCATAAGGTT_S45_L002


title: Sample 351_TENA2524_P05_R6

description: BSSE_QGF_140913_HLLWMDRXX_2_TENA2524_P5_ACTCGGCAAT_GACAACTGAA_S41_L002


title: Sample 350_TENA2524_P22_R5

description: BSSE_QGF_140912_HLLWMDRXX_2_TENA2524_P22_TATGTAGTCA_CGCACTAATG_S40_L002


title: Sample 348_TENA2524_P16_R5

description: BSSE_QGF_140910_HLLWMDRXX_2_TENA2524_P16_GTGCAGACAG_TACCATCCGT_S38_L002


title: Sample 347_TENA2524_P10_R5

description: BSSE_QGF_140909_HLLWMDRXX_2_TENA2524_P10_TGTAATCGAC_GATCACCGCG_S37_L002


title: Sample 349_TENA2524_P09_R5

description: BSSE_QGF_140911_HLLWMDRXX_2_TENA2524_P9_CAATCGGCTG_GCTGTAGGAA_S39_L002


title: Sample 345_TENA2524_P17_R5

description: BSSE_QGF_140907_HLLWMDRXX_2_TENA2524_P17_GGTAACTCGC_AAGTTGGTGA_S35_L002


title: Sample 346_TENA2524_P15_R5

description: BSSE_QGF_140908_HLLWMDRXX_2_TENA2524_P15_ACCGGCCGTA_TGGCAATATT_S36_L002


title: Sample 341_TENA2524_P09_R4

description: BSSE_QGF_140903_HLLWMDRXX_2_TENA2524_P9_GTGACACGCA_GCTTACGGAC_S31_L002


title: Sample 343_TENA2524_P05_R5

description: BSSE_QGF_140905_HLLWMDRXX_2_TENA2524_P5_TGATTATACG_GTCGATTACA_S33_L002


title: Sample 340_TENA2524_P16_R4

description: BSSE_QGF_140902_HLLWMDRXX_2_TENA2524_P16_CCACCAGGCA_CTTATGGAAT_S30_L002


title: Sample 342_TENA2524_P22_R4

description: BSSE_QGF_140904_HLLWMDRXX_2_TENA2524_P22_ACAGTGTATG_GAACATACGG_S32_L002


title: Sample 339_TENA2524_P10_R4

description: BSSE_QGF_140901_HLLWMDRXX_2_TENA2524_P10_GCCGCACTCT_TCCGACCTCG_S29_L002


title: Sample 338_TENA2524_P15_R4

description: BSSE_QGF_140900_HLLWMDRXX_2_TENA2524_P15_ACCACGACAT_TCGTATGCGG_S28_L002


title: Sample 334_TENA2524_P22_R3

description: BSSE_QGF_140896_HLLWMDRXX_2_TENA2524_P22_TTCTACATAC_CTAACTGTAA_S24_L002


title: Sample 337_TENA2524_P17_R4

description: BSSE_QGF_140899_HLLWMDRXX_2_TENA2524_P17_TAAGCATCCA_TCAATCCATT_S27_L002


title: Sample 335_TENA2524_P05_R4

description: BSSE_QGF_140897_HLLWMDRXX_2_TENA2524_P5_AACCATAGAA_GGCGAGATGG_S25_L002


title: Sample 333_TENA2524_P09_R3

description: BSSE_QGF_140895_HLLWMDRXX_2_TENA2524_P9_ACGCCTTGTT_TAAGGAACGT_S23_L002


title: Sample 332_TENA2524_P16_R3

description: BSSE_QGF_140894_HLLWMDRXX_2_TENA2524_P16_TATTGCGCTC_CTGTGTTAGG_S22_L002


title: Sample 331_TENA2524_P10_R3

description: BSSE_QGF_140893_HLLWMDRXX_2_TENA2524_P10_ATGGTTGACT_GGCCTGTCCT_S21_L002


title: Sample 330_TENA2524_P15_R3

description: BSSE_QGF_140892_HLLWMDRXX_2_TENA2524_P15_GATAGGCCGA_CGCACATGGC_S20_L002


title: Sample 329_TENA2524_P17_R3

description: BSSE_QGF_140891_HLLWMDRXX_2_TENA2524_P17_CCATCATTAG_GGTTGCCTCT_S19_L002


title: Sample 328_TENA2524_P18_R3

description: BSSE_QGF_140890_HLLWMDRXX_2_TENA2524_P18_AGAGGCAACC_CTAATGATGG_S18_L002


title: Sample 323_TENA2524_P10_R2

description: BSSE_QGF_140885_HLLWMDRXX_2_TENA2524_P10_CTTGCCATTA_ATCACGAAGG_S13_L002


title: Sample 325_TENA2524_P09_R2

description: BSSE_QGF_140887_HLLWMDRXX_2_TENA2524_P9_TCCATTGCCG_GAATGCACGA_S15_L002


title: Sample 322_TENA2524_P15_R2

description: BSSE_QGF_140884_HLLWMDRXX_2_TENA2524_P15_GAGTCATAGG_GTGTGGCGCT_S12_L002


title: Sample 321_TENA2524_P17_R2

description: BSSE_QGF_140883_HLLWMDRXX_2_TENA2524_P17_CCGTATGTTC_CATACACTGT_S11_L002


title: Sample 344_TENA2524_P18_R5

description: BSSE_QGF_140906_HLLWMDRXX_2_TENA2524_P18_CAGCCGCGTA_ACTAGCCGTG_S34_L002


title: Sample 317_TENA2524_P09_R1

description: BSSE_QGF_140879_HLLWMDRXX_2_TENA2524_P9_CTAGTGCTCT_TGGAACAGTA_S7_L002


title: Sample 319_TENA2524_P05_R2

description: BSSE_QGF_140881_HLLWMDRXX_2_TENA2524_P5_GACTGAGTAG_GTTGATAGTG_S9_L002


title: Sample 316_TENA2524_P16_R1

description: BSSE_QGF_140878_HLLWMDRXX_2_TENA2524_P16_AACATCGCGC_GTCCACTTGT_S6_L002


title: Sample 336_TENA2524_P18_R4

description: BSSE_QGF_140898_HLLWMDRXX_2_TENA2524_P18_GGTTGCGAGG_AATAGAGCAA_S26_L002


title: Sample 318_TENA2524_P22_R1

description: BSSE_QGF_140880_HLLWMDRXX_2_TENA2524_P22_GATCAAGGCA_CCTTGTTAAT_S8_L002


title: Sample 314_TENA2524_P15_R1

description: BSSE_QGF_140876_HLLWMDRXX_2_TENA2524_P15_ATTCCATAAG_TGCCTGGTGG_S4_L002


title: Sample 312_TENA2524_P18_R1

description: BSSE_QGF_140874_HLLWMDRXX_2_TENA2524_P18_AGGTCAGATA_CTACAAGATA_S2_L002


title: Sample 311_TENA2524_P05_R1

description: BSSE_QGF_140873_HLLWMDRXX_2_TENA2524_P5_I2_I151_GAACTGAGCG_TCGTGGAGCG_S1_L002


title: Sample 313_TENA2524_P17_R1

description: BSSE_QGF_140875_HLLWMDRXX_2_TENA2524_P17_CGTCTCATAT_TATAGTAGCT_S3_L002


title: Sample 308_TENA2483_P16_R12

description: BSSE_QGF_140674_HLLWMDRXX_1_TENA2483_P16_TGGTTCTCAT_CTCAAGGCCG_S308_L001


title: Sample 310_TENA2483_P22_R12

description: BSSE_QGF_140676_HLLWMDRXX_1_TENA2483_P22_TATGAACTTG_AATCCTTAGG_S310_L001


title: Sample 309_TENA2483_P09_R12

description: BSSE_QGF_140675_HLLWMDRXX_1_TENA2483_P9_TCAACCACGA_CAAGTTCATA_S309_L001


title: Sample 327_TENA2524_P05_R3

description: BSSE_QGF_140889_HLLWMDRXX_2_TENA2524_P5_GAGAATGGTT_TCGGCAGCAA_S17_L002


title: Sample 324_TENA2524_P16_R2

description: BSSE_QGF_140886_HLLWMDRXX_2_TENA2524_P16_GAAGCGGCAC_CGGCTCTACT_S14_L002


title: Sample 307_TENA2483_P18_R12

description: BSSE_QGF_140673_HLLWMDRXX_1_TENA2483_P18_CCGCGGTTCT_GGAGTAGATT_S307_L001


title: Sample 303_TENA2483_P16_R11

description: BSSE_QGF_140669_HLLWMDRXX_1_TENA2483_P16_GTTGCGTTCA_GTTGCAGTTG_S303_L001


title: Sample 304_TENA2483_P09_R11

description: BSSE_QGF_140670_HLLWMDRXX_1_TENA2483_P9_CTTCAACCAC_TTATGCGCCT_S304_L001


title: Sample 305_TENA2483_P22_R11

description: BSSE_QGF_140671_HLLWMDRXX_1_TENA2483_P22_TCTATTCAGT_TCTCAGTACA_S305_L001


title: Sample 326_TENA2524_P22_R2

description: BSSE_QGF_140888_HLLWMDRXX_2_TENA2524_P22_CGGTTACGGC_AAGACTATAG_S16_L002


title: Sample 320_TENA2524_P18_R2

description: BSSE_QGF_140882_HLLWMDRXX_2_TENA2524_P18_AGTCAGACGA_ACCAGCGACA_S10_L002


title: Sample 315_TENA2524_P10_R1

description: BSSE_QGF_140877_HLLWMDRXX_2_TENA2524_P10_GACGAGATTA_ACATTATCCT_S5_L002


title: Sample 298_TENA2483_P16_R10

description: BSSE_QGF_140664_HLLWMDRXX_1_TENA2483_P16_GGTGAGTAAT_AACATCTAGT_S298_L001


title: Sample 300_TENA2483_P22_R10

description: BSSE_QGF_140666_HLLWMDRXX_1_TENA2483_P22_AGGTATGGCG_GTGGCGAGAC_S300_L001


title: Sample 299_TENA2483_P09_R10

description: BSSE_QGF_140665_HLLWMDRXX_1_TENA2483_P9_TACTCTGCGC_CCTTACTATG_S299_L001


title: Sample 297_TENA2483_P18_R10

description: BSSE_QGF_140663_HLLWMDRXX_1_TENA2483_P18_ACCTGGCCAA_TCACAGATCG_S297_L001


title: Sample 296_TENA2483_P05_R10

description: BSSE_QGF_140662_HLLWMDRXX_1_TENA2483_P5_GTGTACCTTC_CTGTGAGCTA_S296_L001


title: Sample 301_TENA2483_P05_R11

description: BSSE_QGF_140667_HLLWMDRXX_1_TENA2483_P5_GCCATATAAC_ACACAATATC_S301_L001


title: Sample 295_TENA2483_P22_R9

description: BSSE_QGF_140661_HLLWMDRXX_1_TENA2483_P22_TCGTTGCTGC_GTCTCGTGAA_S295_L001


title: Sample 291_TENA2483_P05_R9

description: BSSE_QGF_140657_HLLWMDRXX_1_TENA2483_P5_GATATCACAC_GACTATATGT_S291_L001


title: Sample 306_TENA2483_P05_R12

description: BSSE_QGF_140672_HLLWMDRXX_1_TENA2483_P5_TGAGTACAAC_ACGCTTGGAC_S306_L001


title: Sample 292_TENA2483_P18_R9

description: BSSE_QGF_140658_HLLWMDRXX_1_TENA2483_P18_AGCGCTGTGT_CGTTCGGAAC_S292_L001


title: Sample 293_TENA2483_P16_R9

description: BSSE_QGF_140659_HLLWMDRXX_1_TENA2483_P16_CCTGGACGCA_TGGTATACCA_S293_L001


title: Sample 290_TENA2483_P22_R8

description: BSSE_QGF_140656_HLLWMDRXX_1_TENA2483_P22_ACTTACTTCA_TCTGGAATTA_S290_L001


title: Sample 286_TENA2483_P05_R8

description: BSSE_QGF_140652_HLLWMDRXX_1_TENA2483_P5_CTGAATTAGT_AATTCGATCG_S286_L001


title: Sample 284_TENA2483_P09_R7

description: BSSE_QGF_140650_HLLWMDRXX_1_TENA2483_P9_CGAACGCACC_ATGACAGAAC_S284_L001


title: Sample 285_TENA2483_P22_R7

description: BSSE_QGF_140651_HLLWMDRXX_1_TENA2483_P22_TCTTACGCCG_ATTCATTGCA_S285_L001


title: Sample 288_TENA2483_P16_R8

description: BSSE_QGF_140654_HLLWMDRXX_1_TENA2483_P16_CTTAAGTCGA_CAGTAGTTGT_S288_L001


title: Sample 302_TENA2483_P18_R11

description: BSSE_QGF_140668_HLLWMDRXX_1_TENA2483_P18_AGTGCGAGTG_TGGAGGTAAT_S302_L001


title: Sample 283_TENA2483_P16_R7

description: BSSE_QGF_140649_HLLWMDRXX_1_TENA2483_P16_GAGCGACGAT_CGTATAATCA_S283_L001


title: Sample 280_TENA2483_P05_R7

description: BSSE_QGF_140646_HLLWMDRXX_1_TENA2483_P5_TGTAAGGTGG_AAGGCCTTGG_S280_L001


title: Sample 281_TENA2483_P18_R7

description: BSSE_QGF_140647_HLLWMDRXX_1_TENA2483_P18_CAACTGCAAC_TGAACGCAAC_S281_L001


title: Sample 279_CTRL_R6

description: BSSE_QGF_140645_HLLWMDRXX_1_negative_no_template_control__TTAGGCTCAA_TCGAATGGAA_S279_L001


title: Sample 278_TENA2483_P22_R6

description: BSSE_QGF_140644_HLLWMDRXX_1_TENA2483_P22_ATGATTCCGG_CTCTGACGTG_S278_L001


title: Sample 277_TENA2483_P09_R6

description: BSSE_QGF_140643_HLLWMDRXX_1_TENA2483_P9_AATGACTGGT_TCTCACGCGT_S277_L001


title: Sample 276_TENA2483_P16_R6

description: BSSE_QGF_140642_HLLWMDRXX_1_TENA2483_P16_CGTCACCTTG_CAGCCGATTG_S276_L001


title: Sample 294_TENA2483_P09_R9

description: BSSE_QGF_140660_HLLWMDRXX_1_TENA2483_P9_TTACGCACCT_GCTCTCGTTG_S294_L001


title: Sample 274_TENA2483_P15_R6

description: BSSE_QGF_140640_HLLWMDRXX_1_TENA2483_P15_CAATCCTTGT_CGAAGACGCA_S274_L001


title: Sample 275_TENA2483_P10_R6

description: BSSE_QGF_140641_HLLWMDRXX_1_TENA2483_P10_CACCTGTTGC_ATTGACACAT_S275_L001


title: Sample 272_TENA2483_P05_R6

description: BSSE_QGF_140638_HLLWMDRXX_1_TENA2483_P5_GAGCTTGCCG_AGGTTGCAGG_S272_L001


title: Sample 273_TENA2483_P18_R6

description: BSSE_QGF_140639_HLLWMDRXX_1_TENA2483_P18_AGCTAGCTTC_TAATACGGAG_S273_L001


title: Sample 270_TENA2483_P22_R5

description: BSSE_QGF_140636_HLLWMDRXX_1_TENA2483_P22_TTGAATCCAA_GTCACGGTGT_S270_L001


title: Sample 271_CTRL_R5

description: BSSE_QGF_140637_HLLWMDRXX_1_negative_no_template_control__CACGGCTAGT_GGTGTACAAG_S271_L001


title: Sample 287_TENA2483_P18_R8

description: BSSE_QGF_140653_HLLWMDRXX_1_TENA2483_P18_TAAGGAGGAA_TTCCGACATT_S287_L001


title: Sample 289_TENA2483_P09_R8

description: BSSE_QGF_140655_HLLWMDRXX_1_TENA2483_P9_GCCTAACGTG_AGCTCTCAAG_S289_L001


title: Sample 269_TENA2483_P09_R5

description: BSSE_QGF_140635_HLLWMDRXX_1_TENA2483_P9_TGGATCTGGC_CAATGCTGAA_S269_L001


title: Sample 267_TENA2483_P10_R5

description: BSSE_QGF_140633_HLLWMDRXX_1_TENA2483_P10_CCAAGAGGTG_AACGAGCCAG_S267_L001


title: Sample 266_TENA2483_P15_R5

description: BSSE_QGF_140632_HLLWMDRXX_1_TENA2483_P15_AAGTTCTAGT_GGTAAGATAA_S266_L001


title: Sample 265_TENA2483_P18_R5

description: BSSE_QGF_140631_HLLWMDRXX_1_TENA2483_P18_CTCGTAGGCA_TCATCCTCTT_S265_L001


title: Sample 264_TENA2483_P05_R5

description: BSSE_QGF_140630_HLLWMDRXX_1_TENA2483_P5_TCGACGCTAG_CCTCTTCGAA_S264_L001


title: Sample 268_TENA2483_P16_R5

description: BSSE_QGF_140634_HLLWMDRXX_1_TENA2483_P16_ATATCTGCTT_TAGACAATCT_S268_L001


title: Sample 282_TENA2483_P10_R7

description: BSSE_QGF_140648_HLLWMDRXX_1_TENA2483_P10_GCAACCAGTC_CACCGAGGAA_S282_L001


title: Sample 262_TENA2483_P22_R4

description: BSSE_QGF_140628_HLLWMDRXX_1_TENA2483_P22_CAACGACCTA_GCGACTCGAT_S262_L001


title: Sample 263_CTRL_R4

description: BSSE_QGF_140629_HLLWMDRXX_1_negative_no_template_control__CGGTCGGCAT_CTAGGCAAGG_S263_L001


title: Sample 261_TENA2483_P09_R4

description: BSSE_QGF_140627_HLLWMDRXX_1_TENA2483_P9_TGTGTTAGTA_TACTCTGTTA_S261_L001


title: Sample 255_CTRL_R3

description: BSSE_QGF_140621_HLLWMDRXX_1_negative_no_template_control__GCTAGGAAGT_TCTCGGACGA_S255_L001


title: Sample 257_TENA2483_P18_R4

description: BSSE_QGF_140623_HLLWMDRXX_1_TENA2483_P18_CATTCACGCT_GTTGTACTCA_S257_L001


title: Sample 258_TENA2483_P15_R4

description: BSSE_QGF_140624_HLLWMDRXX_1_TENA2483_P15_GGCACTAAGG_TCAGGTCAAC_S258_L001


title: Sample 256_TENA2483_P05_R4

description: BSSE_QGF_140622_HLLWMDRXX_1_TENA2483_P5_TTAATAGCAC_ACCACGTCTG_S256_L001


title: Sample 254_TENA2483_P22_R3

description: BSSE_QGF_140620_HLLWMDRXX_1_TENA2483_P22_TTCTCGTGCA_ATACACAGAG_S254_L001


title: Sample 250_TENA2483_P15_R3

description: BSSE_QGF_140616_HLLWMDRXX_1_TENA2483_P15_CACCTAGCAC_TGCTGGACAT_S250_L001


title: Sample 248_TENA2483_P05_R3

description: BSSE_QGF_140614_HLLWMDRXX_1_TENA2483_P5_ATACATCACA_TCTCCATTGA_S248_L001


title: Sample 253_TENA2483_P09_R3

description: BSSE_QGF_140619_HLLWMDRXX_1_TENA2483_P9_CACCTCTCTT_CTCGACTCCT_S253_L001


title: Sample 249_TENA2483_P18_R3

description: BSSE_QGF_140615_HLLWMDRXX_1_TENA2483_P18_TAGGTATGTT_CGAGACCAAG_S249_L001


title: Sample 251_TENA2483_P10_R3

description: BSSE_QGF_140617_HLLWMDRXX_1_TENA2483_P10_TTCAAGTATG_GATGGTATCG_S251_L001


title: Sample 252_TENA2483_P16_R3

description: BSSE_QGF_140618_HLLWMDRXX_1_TENA2483_P16_TTAAGACAAG_GGCTTAATTG_S252_L001


title: Sample 247_CTRL_R2

description: BSSE_QGF_140613_HLLWMDRXX_1_negative_no_template_control__CCGCTCCGTT_TACGGCGAAG_S247_L001


title: Sample 244_TENA2483_P16_R2

description: BSSE_QGF_140610_HLLWMDRXX_1_TENA2483_P16_CAACGAGAGC_GAATTGAGTG_S244_L001


title: Sample 416_CTRL_R13

description: BSSE_QGF_140978_HLLWMDRXX_2_negative_no_template_control__AGGACAGGCC_CATTCCAGCT_S106_L002


title: Sample 246_TENA2483_P22_R2

description: BSSE_QGF_140612_HLLWMDRXX_1_TENA2483_P22_GGAGAGACTC_TTGAAGCAGA_S246_L001


title: Sample 245_TENA2483_P09_R2

description: BSSE_QGF_140611_HLLWMDRXX_1_TENA2483_P9_ATTGAGGTCC_CGGATTATAT_S245_L001


title: Sample 260_TENA2483_P16_R4

description: BSSE_QGF_140626_HLLWMDRXX_1_TENA2483_P16_ACTAATCTCC_CACTTAATCT_S260_L001


title: Sample 241_TENA2483_P18_R2

description: BSSE_QGF_140607_HLLWMDRXX_1_TENA2483_P18_AGGAGTCGAG_TTAGGCTTAC_S241_L001


title: Sample 243_TENA2483_P10_R2

description: BSSE_QGF_140609_HLLWMDRXX_1_TENA2483_P10_GGTCCGCTTC_CTCACACAAG_S243_L001


title: Sample 242_TENA2483_P15_R2

description: BSSE_QGF_140608_HLLWMDRXX_1_TENA2483_P15_TTCACTCACT_TATCATGAGA_S242_L001


title: Sample 239_CTRL_R1

description: BSSE_QGF_140605_HLLWMDRXX_1_negative_no_template_control__CTATGAAGGA_CTTATACCTG_S239_L001


title: Sample 240_TENA2483_P05_R2

description: BSSE_QGF_140606_HLLWMDRXX_1_TENA2483_P5_GAAGACTAGA_ACTAGAACTT_S240_L001


title: Sample 238_TENA2483_P22_R1

description: BSSE_QGF_140604_HLLWMDRXX_1_TENA2483_P22_TGCAATGAAT_CCAGAAGTAA_S238_L001


title: Sample 259_TENA2483_P10_R4

description: BSSE_QGF_140625_HLLWMDRXX_1_TENA2483_P10_ATTCGGTACA_AGTCCGAGGA_S259_L001


title: Sample 237_TENA2483_P09_R1

description: BSSE_QGF_140603_HLLWMDRXX_1_TENA2483_P9_AAGATACACG_TGTGCTAACA_S237_L001


title: Ctnnb1 gain-of-function (GOF)  LSECs, replicate 4

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression data from Ctnnb1OE-EC LSECs

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: C57BL/6J LSECs

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

growth_protocol: RNA was extracted from primary murine LSECs immediately after isolation

extract_protocol: RNA was extracted from primary endothelial cells using using InnuPrep RNA Mini Kit (Analytik Jena, Jena,Thuringia, Germany).

treatment_protocol: Murine LSECs from different groups were isolated and purified using CD146 (LSEC) MicroBeads. Purity was assessed using FACS. Two mice per genotype were pooled per biological replicate in Microarray analyis.

tag: genotype

tag: cell type

value: liver sinusoidal endothelial cells

value: female

tag: age

value: 2 months


title: Sample 235_TENA2483_P10_R1

description: BSSE_QGF_140601_HLLWMDRXX_1_TENA2483_P10_AATATTGCCA_CGGTGACACC_S235_L001


title: Sample 233_TENA2483_P18_R1

description: BSSE_QGF_140599_HLLWMDRXX_1_TENA2483_P18_TGTGGTCCGG_AGAGCACTAG_S233_L001


title: Sample 236_TENA2483_P16_R1

description: BSSE_QGF_140602_HLLWMDRXX_1_TENA2483_P16_TCGTGCATTC_GCGTTGGTAT_S236_L001


title: Sample 232_TENA2483_P05_R1

description: BSSE_QGF_140598_HLLWMDRXX_1_TENA2483_P5_GAACAATTCC_TAGAGTTGGA_S232_L001


title: Ctnnb1 gain-of-function (GOF)  LSECs, replicate 2


title: Ctnnb1 gain-of-function (GOF)  LSECs, replicate 3


title: Sample 234_TENA2483_P15_R1

description: BSSE_QGF_140600_HLLWMDRXX_1_TENA2483_P15_CTTCTAAGTC_ACTCTACAGG_S234_L001


title: Ctnnb1 gain-of-function (GOF)  LSECs, replicate 1


title: Control LSECs, replicate 2

description: Gene expression data from Wildtype LSECs

value: Ctrl


title: C57BL/6 SD0

city: Baltimore

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

description: Gene expression data from  keratinocytes extracted from wild-type or Rnasel KO mice

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform. RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
Clariom_S_Mouse.r1.pgf
Clariom_S_Mouse.na36.mm10.transcript.csv

label: biotin

source_name: Wild-type skin tissue

label_protocol: Biotinylated cRNAs were prepared with the Affymetrix GeneChip 3' IVT Plus Kit per manufacturer's instructions.

growth_protocol: Tissues from re-epithelialized wounds were surgically removed.

extract_protocol: Total RNA was isolated from cells using the Direct-zol RNA Miniprep kit (Zymo) according to manufacturer's instructions.

treatment_protocol: Other than wounding, no additional treatment was administered.

value: Wild-type

value: skin

value: keratinocyte


title: Control LSECs, replicate 3


title: Rnasel-/- SD0

source_name: Knock-out skin tissue

value: Rnasel KO


title: Control LSECs, replicate 1


title: Sample 230_TENA2462_P09_R12

description: BSSE_QGF_140596_HLLWMDRXX_1_TENA2462_P9_CATAGTAAGG_ACCAAGTTAC_S230_L001

value: high

value: neg

value: TRUE


title: Sample 231_TENA2462_P22_R12

description: BSSE_QGF_140597_HLLWMDRXX_1_TENA2462_P22_ATTGGCTTCT_TGGCTCGCAG_S231_L001

value: TENA


title: Sample 229_TENA2462_P16_R12

description: BSSE_QGF_140595_HLLWMDRXX_1_TENA2462_P16_TGATAACGAG_GTTCCGCAGG_S229_L001

value: med


title: Sample 228_TENA2462_P10_R12

description: BSSE_QGF_140594_HLLWMDRXX_1_TENA2462_P10_AGCTGGAATG_ACGGAATGCG_S228_L001

value: low


title: 218N_Low Protein_DBA/2J_F

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

data_processing:
To remove any genes that exhibited no or a very low number of mapped reads, only genes that had more than 1 count per million in at least 6 samples across all treatments were retained for further analysis. This resulted in a total of 17575  unique genes. Raw counts were normalized using the trimmed mean of M values (TMM normalization) (Robinson and Oshlack 2010). Differential gene expression was modeled using the edgeR package (Robinson, McCarthy et al. 2010) in R (version 3.4.3) and pairwise comparisons were conducted between Control and medium or low protein in each strain/sex group. To control for type I errors, the Benjamini Hochberg adjusted p-value was used (5% FDR). We tested for over-representation of gene ontology (GO) terms or KEGG pathways in each comparison, using the limma package (Ritchie, Phipson et al. 2015).
Supplementary_files_format_and_content: Comparison table.csv (Benjamini Hochberg Adjusted P-Values, unadjusted P values)
Supplementary_files_format_and_content: rsem_GENE.csv

source_name: Liver, Fasted

growth_protocol: Diet started at 10 weeks of age

extract_protocol:
Liver tissues were harvested and snap frozen in liquid nitrogen. Transcriptional profiling: RNA was extracted from liver as previously described (Cummings et al., 2018). Concentration and purity of RNA was initially determined using a Nanodrop 2000c, and then submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center & DNA Sequencing Facility. RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
Sample libraries were combined and striped across two lanes, the data from each lane was merged into a single sample file prior to expression estimation

treatment_protocol: Mice were placed on either a control, medium or low protein diet

value: 23 weeks

tag: diet

value: Low Protein

value: F

value: liver


title: 206R_Low Protein_DBA/2J_F


title: 215N_Low Protein_DBA/2J_F


title: 212R_Low Protein_DBA/2J_F


title: Sample 226_TENA2462_P18_R12

description: BSSE_QGF_140592_HLLWMDRXX_1_TENA2462_P18_AGAATTCGCC_CGGCAAGCTC_S226_L001


title: 216N_Medium Protein_DBA/2J_F

value: Medium Protein


title: Control LSECs, replicate 4

value: liver sinusoidal endothelial cells

value: female

value: 2 months


title: Sample 225_TENA2462_P05_R12

description: BSSE_QGF_140591_HLLWMDRXX_1_TENA2462_P5_TATCACTCTG_AACGTTACAT_S225_L001


title: 209R_Low Protein_DBA/2J_F


title: Sample 222_TENA2462_P16_R11

description: BSSE_QGF_140588_HLLWMDRXX_1_TENA2462_P16_CGATCTGTGA_TAGGAAGACT_S222_L001


title: Sample 223_TENA2462_P09_R11

description: BSSE_QGF_140589_HLLWMDRXX_1_TENA2462_P9_GTGGACAAGT_CCGTGGCCTT_S223_L001


title: Sample 224_TENA2462_P22_R11

description: BSSE_QGF_140590_HLLWMDRXX_1_TENA2462_P22_AACAAGTACA_GGATATATCC_S224_L001


title: 214N_Medium Protein_DBA/2J_F


title: 211R_Medium Protein_DBA/2J_F


title: 208R_Medium Protein_DBA/2J_F


title: Sample 221_TENA2462_P10_R11

description: BSSE_QGF_140587_HLLWMDRXX_1_TENA2462_P10_CTTCCTAGGA_CCTAGAGTAT_S221_L001


title: Sample 219_TENA2462_P18_R11

description: BSSE_QGF_140585_HLLWMDRXX_1_TENA2462_P18_GAGGCCTATT_CTAGTCCGGA_S219_L001


title: 217R_Control_DBA/2J_F

value: Control


title: Sample 218_TENA2462_P05_R11

description: BSSE_QGF_140584_HLLWMDRXX_1_TENA2462_P5_CCAATGATAC_GAGTGTGCCG_S218_L001

value: FALSE


title: 205R_Control_DBA/2J_F


title: 204R_Medium Protein_DBA/2J_F


title: Sample 227_TENA2462_P17_R12

description: BSSE_QGF_140593_HLLWMDRXX_1_TENA2462_P17_CCTGACCACT_TCTTGGCTAT_S227_L001


title: Sample 216_TENA2462_P09_R10

description: BSSE_QGF_140582_HLLWMDRXX_1_TENA2462_P9_AACTTATCCT_GTACTGGCGT_S216_L001


title: Sample 220_TENA2462_P17_R11

description: BSSE_QGF_140586_HLLWMDRXX_1_TENA2462_P17_AGCTAAGCGG_ATTAATACGC_S220_L001


title: 213N_Control_DBA/2J_F


title: Sample 217_TENA2462_P22_R10

description: BSSE_QGF_140583_HLLWMDRXX_1_TENA2462_P22_ATTATGTCTC_AGTTAAGAGC_S217_L001


title: Sample 215_TENA2462_P16_R10

description: BSSE_QGF_140581_HLLWMDRXX_1_TENA2462_P16_GTAGGCGAGC_TAGGAGCGCA_S215_L001


title: 203N_Low Protein_DBA/2J_F


title: 210R_Control_DBA/2J_F


title: Sample 214_TENA2462_P10_R10

description: BSSE_QGF_140580_HLLWMDRXX_1_TENA2462_P10_AAGAGAGTCT_TACGAATCTT_S214_L001


title: 201N_Control_DBA/2J_F


title: 3N_Low Protein_DBA/2J_M

value: M


title: 207R_Control_DBA/2J_F


title: 2N_Low Protein_DBA/2J_M


title: Sample 213_TENA2462_P17_R10

description: BSSE_QGF_140579_HLLWMDRXX_1_TENA2462_P17_TAACCGGCGA_GCTACATTAG_S213_L001

value: high


title: 202N_Medium Protein_DBA/2J_F


title: Sample 212_TENA2462_P18_R10

description: BSSE_QGF_140578_HLLWMDRXX_1_TENA2462_P18_CTGTTATATC_GTATAGCTGT_S212_L001

value: neg


title: 16R_Low Protein_DBA/2J_M


title: 8R_Low Protein_DBA/2J_M


title: Sample 208_TENA2462_P16_R9

description: BSSE_QGF_140574_HLLWMDRXX_1_TENA2462_P16_AGCGAATTAG_AGCCGGAACA_S208_L001

value: TRUE


title: 15R_Low Protein_DBA/2J_M


title: 5N_Low Protein_DBA/2J_M


title: 6R_Medium Protein_DBA/2J_M


title: Sample 209_TENA2462_P09_R9

description: BSSE_QGF_140575_HLLWMDRXX_1_TENA2462_P9_TTAGACCATG_TCCTAGGAAG_S209_L001

value: TENA


title: Sample 207_TENA2462_P10_R9

description: BSSE_QGF_140573_HLLWMDRXX_1_TENA2462_P10_GGCGCCATTG_ACCGCGCAAT_S207_L001


title: 9R_Medium Protein_DBA/2J_M


title: Sample 210_TENA2462_P22_R9

description: BSSE_QGF_140576_HLLWMDRXX_1_TENA2462_P22_CACACAGTAT_TTGAGCCTAA_S210_L001


title: 10N_Medium Protein_DBA/2J_M


title: Sample 205_TENA2462_P18_R9

description: BSSE_QGF_140571_HLLWMDRXX_1_TENA2462_P18_CAGCGGTAGA_GCAACAGGTG_S205_L001


title: Sample 204_TENA2462_P05_R9

description: BSSE_QGF_140570_HLLWMDRXX_1_TENA2462_P5_GTAACAATCT_CTCTGTATAC_S204_L001


title: Sample 203_TENA2462_P22_R8

description: BSSE_QGF_140569_HLLWMDRXX_1_TENA2462_P22_TCAGTCTCGT_CACGGATTAT_S203_L001


title: 13N_Medium Protein_DBA/2J_M


title: 11N_Control_DBA/2J_M


title: 12R_Medium Protein_DBA/2J_M


title: Sample 201_TENA2462_P16_R8

description: BSSE_QGF_140567_HLLWMDRXX_1_TENA2462_P16_TCTCAATACC_GACGTTCGCG_S201_L001

value: med


title: 7R_Control_DBA/2J_M


title: 1N_Control_DBA/2J_M


title: 17N_Control_DBA/2J_M


title: Sample 200_TENA2462_P10_R8

description: BSSE_QGF_140566_HLLWMDRXX_1_TENA2462_P10_GTTGTGACTA_ACATAACGGA_S200_L001

value: low


title: Sample 199_TENA2462_P17_R8

description: BSSE_QGF_140565_HLLWMDRXX_1_TENA2462_P17_GCGTATTAAT_TGCGGTGTTG_S199_L001


title: Sample 211_TENA2462_P05_R10

description: BSSE_QGF_140577_HLLWMDRXX_1_TENA2462_P5_TACCGCCTCG_CCTCGCAACC_S211_L001


title: Sample 198_TENA2462_P18_R8

description: BSSE_QGF_140564_HLLWMDRXX_1_TENA2462_P18_CAACGTTCGG_GGATCCGCAT_S198_L001


title: Sample 206_TENA2462_P17_R9

description: BSSE_QGF_140572_HLLWMDRXX_1_TENA2462_P17_TCATACCGTT_GGTAACGCAG_S206_L001


title: 14N_Medium Protein_DBA/2J_M

value: 23 weeks


title: 4R_Control_DBA/2J_M


title: 5R_Low Protein_C57BL/6J_F

value: Low Protein


title: Sample 195_TENA2462_P09_R7

description: BSSE_QGF_140561_HLLWMDRXX_1_TENA2462_P9_ATTATCCACT_TACGCACGTA_S195_L001


title: Sample 202_TENA2462_P09_R8

description: BSSE_QGF_140568_HLLWMDRXX_1_TENA2462_P9_AAGCATCTTG_CATTCAACAA_S202_L001


title: 16N_Low Protein_C57BL/6J_F

value: F


title: 8R_Low Protein_C57BL/6J_F

value: liver


title: Sample 194_TENA2462_P16_R7

description: BSSE_QGF_140560_HLLWMDRXX_1_TENA2462_P16_CACTAGACCA_ACTGCCTTAT_S194_L001


title: 15OM

city: East Lansing

first: David

middle: Rodrigo

last: Salcedo-Tacuma

state: Mi

address: 567 Wilson road

department: Physiology

institute: Michigan State University

data_processing:
Fastq files were obatined from BGI and FastQC was performed on the files to check quality.
Sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, then mapped to hg19  whole genome using HISAT v2.1.0
After genome mapping, featureCounts v.  was used to count the number of reads to perform differential expression analysis
DESEQ v2.0 was used to detect differentially expressed genes in pairwise comparisons
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Adipose Tissue

extract_protocol:
Adipose Tissue  samples from the SC and OM depots were collected during C-Section in patients.  The SC samples were harvested from the incision area using surgical scalpel. OM samples, were collected from the surgical area using scissors and ligature at the omentum majus level. Both Adipose tissue samples were flash frozen and store in liquid nitrogen until processing. Total RNA was extracted using Trizol and the Quick RNA MiniPrep kit R1054. At least 1 ug of each sample was used for NGS.
RNA libraries were prepared for sequencing using standard DNBSEQ protocols from BGI

value: Omental adipose tissue

tag: time point


title: 14OM


title: 2R_Low Protein_C57BL/6J_F


title: 5N_Low Protein_C57BL/6J_F


title: Sample 192_TENA2462_P17_R7

description: BSSE_QGF_140558_HLLWMDRXX_1_TENA2462_P17_TTCATGGTTC_GACATTGTCA_S192_L001

tag: system


title: 3R_Low Protein_C57BL/6J_F


title: 13N_Medium Protein_C57BL/6J_F

value: Medium Protein


title: 11OM

value: Gestational diabetes


title: Sample 191_TENA2462_P18_R7

description: BSSE_QGF_140557_HLLWMDRXX_1_TENA2462_P18_CCTGCAACCT_GTAGAGTCAG_S191_L001

tag: mouse


title: 14R_Medium Protein_C57BL/6J_F


title: 10R_Medium Protein_C57BL/6J_F


title: 6N_Medium Protein_C57BL/6J_F


title: Sample 190_TENA2462_P05_R7

description: BSSE_QGF_140556_HLLWMDRXX_1_TENA2462_P5_TGAACGCGGA_CTTCGAAGGA_S190_L001

tag: population


title: 10OM


title: 11R_Control_DBA/2J_M


title: 9N_Medium Protein_C57BL/6J_F


title: 9OM


title: Sample 197_TENA2462_P05_R8

description: BSSE_QGF_140563_HLLWMDRXX_1_TENA2462_P5_ATGTCCAGCA_CAGCGGACAA_S197_L001

tag: egfp


title: Sample 196_TENA2462_P22_R7

description: BSSE_QGF_140562_HLLWMDRXX_1_TENA2462_P22_ATGGCGTGCC_CGCTTGAAGT_S196_L001

tag: mcherry


title: 12R_Medium Protein_C57BL/6J_F


title: 8OM


title: 18R_Control_C57BL/6J_F


title: 17R_Control_C57BL/6J_F


title: 7OM


title: Sample 188_TENA2462_P09_R6

description: BSSE_QGF_140554_HLLWMDRXX_1_TENA2462_P9_TTCTTAACCA_TCTACATACC_S188_L001

tag: epcam


title: Sample 193_TENA2462_P10_R7

description: BSSE_QGF_140559_HLLWMDRXX_1_TENA2462_P10_ATCCTCTCAA_TCCGCAAGGC_S193_L001

tag: passedqc


title: Sample 189_TENA2462_P22_R6

description: BSSE_QGF_140555_HLLWMDRXX_1_TENA2462_P22_AAGGAAGAGT_CACGTTAGGC_S189_L001


title: 7N_Control_C57BL/6J_F


title: Sample 187_TENA2462_P16_R6

description: BSSE_QGF_140553_HLLWMDRXX_1_TENA2462_P16_ATAGGTCTTA_GTCACCACAG_S187_L001


title: 18N_Control_C57BL/6J_F


title: Sample 376_TENA2524_P18_R9

description: BSSE_QGF_140938_HLLWMDRXX_2_TENA2524_P18_ATACCAACGC_AATTGCTGCG_S66_L002


title: 4OM


title: Sample 186_TENA2462_P10_R6

description: BSSE_QGF_140552_HLLWMDRXX_1_TENA2462_P10_ATAGTTAGCA_CTCTAAGTAG_S186_L001


title: 9R_Low Protein_C57BL/6J_M


title: 1N_Control_C57BL/6J_F


title: 3N_Low Protein_C57BL/6J_M


title: Sample 184_TENA2462_P18_R6

description: BSSE_QGF_140550_HLLWMDRXX_1_TENA2462_P18_CTGTGGTGAC_GACAGACAGG_S184_L001


title: 15SC

value: Subcutaneous adipose tissue


title: 3OM


title: 12R_Low Protein_C57BL/6J_M


title: 2OM

value: Control


title: 5N_Low Protein_C57BL/6J_M


title: Sample 183_TENA2462_P05_R6

description: BSSE_QGF_140549_HLLWMDRXX_1_TENA2462_P5_TACAAGACTT_CAGGTGTTCA_S183_L001


title: 9N_Low Protein_C57BL/6J_M


title: 7N_Medium Protein_C57BL/6J_M


title: 14SC


title: 11N_Control_C57BL/6J_F


title: 4R_Medium Protein_C57BL/6J_M


title: 8R_Medium Protein_C57BL/6J_M


title: Sample 182_TENA2462_P22_R5

description: BSSE_QGF_140548_HLLWMDRXX_1_TENA2462_P22_TGACGGCCGT_AGTCAACCAT_S182_L001


title: 11SC


title: Sample 181_TENA2462_P09_R5

description: BSSE_QGF_140547_HLLWMDRXX_1_TENA2462_P9_GTGGTATCTG_GCTACTATCT_S181_L001


title: 10N_Medium Protein_C57BL/6J_M


title: 10SC


title: 9SC


title: 6R_Control_C57BL/6J_M


title: Sample 185_TENA2462_P17_R6

description: BSSE_QGF_140551_HLLWMDRXX_1_TENA2462_P17_CTCCACTAAT_TGTACTTGTT_S185_L001

value: FALSE


title: 10R_Medium Protein_C57BL/6J_M

value: M


title: Sample 180_TENA2462_P16_R5

description: BSSE_QGF_140546_HLLWMDRXX_1_TENA2462_P16_GCTCTTAACT_CACGTCCACC_S180_L001

value: high


title: Sample 179_TENA2462_P10_R5

description: BSSE_QGF_140545_HLLWMDRXX_1_TENA2462_P10_ACTAGCGCTA_TTACTTCCTC_S179_L001

value: neg


title: 2R_Control_C57BL/6J_M


title: N1380: BL6 thymus CD4+ NKT1, 105000 cells

city: Hannover

first: Hristo

last: Georgiev

address: Carl Neuberg Str. 1

department: Institute of Immunology

institute: Hannover Medical School

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (version 1.5dev). Sequenced reads were trimmed for adaptor sequence (Trim Galore! 0.4.4 dev), the reads were aligned (STAR2.5.3a_modified) and RNA reads were assigned and counted (featureCounts1.6.1). MultiQC report was generated with MultiQCv1.5.
Normalization and differential expression analysis was performed with DESeq2 (Galaxy Tool Version 2.11.40.2) with default settings except for “Output normalized counts table” which was set to “Yes”.
Genome_build: The genome reference and annotation data were taken from GENCODE.org (Mus musculus; GRCm38.p6; release M17).
Supplementary_files_format_and_content: DESeq2 was used to generate normalized read counts for all twenty samples. Statistics were generated by testing three contained Thymus samples against all other samples.

source_name: Thymus

extract_protocol:
CD4i+iNKT1 cells were lysed immediately following flow cytometry sorts, RNA was prepared using RNeasy Plus Mini Kit (QIAGEN)
1-5ng of total RNA were used for library preparation with the ‘SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian’ (#634413; Takara/Clontech) according to conditions recommended in user manual #063017. Generated libraries were barcoded by dual indexing approach and were finally amplified by 11 cycles of pcr. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).  Equal molar amounts of twelve to thirteen individually barcoded libraries were pooled for one sequencing run. Accordingly, each analyzed library constitutes 8.3% (7.7%) of overall flowcell capacity. The library pool was denatured with NaOH and was finally diluted to 1.5pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3 ml of denatured pool was loaded on an Illumina NextSeq 550 sequencer using a High Output Flowcell for 75bp single reads (#FC-404-2005; Illumina).


title: 15N_Medium Protein_C57BL/6J_M


title: 11N_Low Protein_C57BL/6J_M


title: Sample 178_TENA2462_P17_R5

description: BSSE_QGF_140544_HLLWMDRXX_1_TENA2462_P17_GCTTCATATT_CGTTCAGCCT_S178_L001


title: 1N_Control_C57BL/6J_M


title: N1376: BL6 thymus CD4+ NKT1, 83300 cells


title: 8SC


title: 7SC


title: Sample 177_TENA2462_P18_R5

description: BSSE_QGF_140543_HLLWMDRXX_1_TENA2462_P18_CGCCATATCT_GACCGGAGAT_S177_L001

value: TRUE


title: 17N_Control_C57BL/6J_M


title: N0967: BL6 Thymus NKT1 CD4+ 121.000 cells


title: 4SC


title: N1383: BL6 liver on ice CD4+ NKT1, 87300 cells

source_name: Liver


title: Sample 176_TENA2462_P05_R5

description: BSSE_QGF_140542_HLLWMDRXX_1_TENA2462_P5_TAGTGGAAGC_AGTACCTATA_S176_L001

value: TENA


title: N1382: BL6 blood CD4+ NKT1, 10700 cells

source_name: Blood


title: Sample 175_TENA2462_P22_R4

description: BSSE_QGF_140541_HLLWMDRXX_1_TENA2462_P22_TAGCATAACC_GCTATGCGCA_S175_L001


title: 13R_Control_C57BL/6J_M


title: 3SC


title: 2SC


title: N1381: BL6 spleen CD4+ NKT1, 169000 cells

source_name: Spleen


title: Sample 174_TENA2462_P09_R4

description: BSSE_QGF_140540_HLLWMDRXX_1_TENA2462_P9_CTATTACTAC_GAGTCTCTCC_S174_L001

value: med


title: 1R_Control_C57BL/6J_M


title: Surf4 OE_2

city: Shanghai

first: Li

last: Wu

state: Yangpu District

address: No. 1239, Siping Road

department: School of Life and Science

country: China

institute: Tongji University

data_processing:
All of the RNA-Seq sequencing reads were processed using BBDuk (version 38.34) to remove adapters and low-quality reads
The filted reads were mapped to the mouse reference genome using STAR (version 0.6.0) with the default parameters excepting using the ‘‘–quantMode GeneCounts’’ parameter
Gene expression for each sample was quantified to FPKM using Stringtie (version 1.3.3b)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.
Supplementary_files_format_and_content: Bigwiggle files are generated through MASC14 with parameters(macs14 -t Sample.bam -c input.bam -g mm -n name -B -S).

source_name: fibroblasts

growth_protocol: The reprogrammable MEFs were cultured in DMEM supplemented with 10% fetal bovine serum and Glutamine. The reprogramming cells were induced with doxycycline (Dox) (1ug/ml) for 3 days in ES medium consisted of DMEM supplemented with 15% fetal bovine serum, nonessential amino acids, Glutamine, Nucleosides, 2-mercaptoethanol and LIF.

extract_protocol:
The cells were lysed using RLT buffer supplemented with β-mercaptoethanol and processed using the RNeasy mini kit (Cat. 74104).
KAPA Stranded mRNA-Seq Kit (KK8420)

treatment_protocol: The reprogrammable MEFs or reprogramming cells (3 days post-Dox induction with or without Surf4’s overexpression) were digested to single cell and harvested to performed RNA-seq.

tag: reprogramming stage

tag: dox-induced genes


title: N1379: BL6 liver on ice CD4+ NKT1, 69300 cells

tag: strain


title: Surf4 OE_1


title: Sample 172_TENA2462_P10_R4

description: BSSE_QGF_140538_HLLWMDRXX_1_TENA2462_P10_CTAAGTACGC_AACATACCTA_S172_L001

value: low


title: ast10

city: St Louis

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

description: ast10.GCTAACGGCA-GCAACTCCTG.GCTAACGGCA-GCAACTCCTG_S10

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were aligned to the Ensembl release 99 primary assembly with STAR version 2.6.1d
The raw gene count matrix was imported into Partek Flow software, version 9.0. Normalization size factors were calculated for all genes counts by median ratio.
Gene-specific analysis was then performed using DESeq2 to analyze for differential expression between the two groups of samples
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing normalized gene counts for each sample

source_name: FMC-OVA Spleen CD3+ T cells

growth_protocol: Mouse spleens were homogenized into single cell suspensions by digesting in PBS containing 0.1% BSA and 0.6% Na-citrate, washed, and incubated with 120 Kunitz units of DNase I for 15 min following red blood cell lysis (eBioscience, 00433357)10. Cells were then filtered through a 30-µM cell strainer to generate a single cell suspension. CD4+ and CD8+ T cells were isolated using CD8a (Miltenyi Biotec, 130-104-075) and CD4 (Miltenyi Biotec, 130-117-043)

extract_protocol:
Spleen CD3+ T cells were isolated, flash frozen on dry ice, and RNA was harvested using NucleoSpin® RNA Plus kit (Takara- 740984.205) . Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq

treatment_protocol: Ovalbumin (OVA)-induced asthma model, mice were intraperitoneally injected with 0.5 mL of chicken-egg ovalbumin (16 μg/mL) in aluminum hydroxide (2 mg/mL) weekly for two weeks (days -14 and -7)

tag: mouse model

value: Ovalbumin (OVA)-induced asthma model

tag: treatment

value: chicken-egg ovalbumin for 2 wks

value: Spleen CD3+ T cells


title: N1378: BL6 blood CD4+ NKT1, 10700 cells


title: Sample 173_TENA2462_P16_R4

description: BSSE_QGF_140539_HLLWMDRXX_1_TENA2462_P16_TAGTTCGGTA_CCATGTGTAG_S173_L001


title: Control_2

value: OSKM+Vector


title: Control_1


title: ast8

description: ast8.CGCTGTTGAC-ACGTCTACGA.CGCTGTTGAC-ACGTCTACGA_S8


title: ast7

description: ast7.GTGAAGACAC-CTTAGGCAAC.GTGAAGACAC-CTTAGGCAAC_S7


title: N1227: BALBc liver on ice 208200 cells

value: BALB/c


title: Sample 171_TENA2462_P17_R4

description: BSSE_QGF_140537_HLLWMDRXX_1_TENA2462_P17_TTACAGTTAG_ACATGCATAT_S171_L001


title: N1377: BL6 spleen CD4+ NKT1, 133000 cells


title: N1229: BALBc liver digested 25500


title: MEF_1


title: Sample 170_TENA2462_P18_R4

description: BSSE_QGF_140536_HLLWMDRXX_1_TENA2462_P18_TTGCTCTATT_GTGACCTTGA_S170_L001


title: MEF_2


title: ast6

description: ast6.AATGCGATGG-GCACACAGCA.AATGCGATGG-GCACACAGCA_S6


title: Sample 169_TENA2462_P05_R4

description: BSSE_QGF_140535_HLLWMDRXX_1_TENA2462_P5_CACTATCAAC_TCAGTTAATG_S169_L001


title: N1226: BL6 spleen 120000 cells


title: ast4

description: ast4.AACGCACGAG-ATAACCACAC.AACGCACGAG-ATAACCACAC_S4

source_name: FMC-PBS Spleen CD3+ T cells

value: PBS


title: N1225: BL6 liver digested 33500 cells


title: ast5

description: ast5.TCGGAGACCT-AGTAGCTAGT.TCGGAGACCT-AGTAGCTAGT_S5


title: Sample 168_TENA2462_P22_R3

description: BSSE_QGF_140534_HLLWMDRXX_1_TENA2462_P22_CGCTTAGAAT_CAGAGTGATA_S168_L001


title: ast9

description: ast9.CGGACAGCTA-GCCTTCCTCT.CGGACAGCTA-GCCTTCCTCT_S9


title: ast3

description: ast3.CACCGAATCA-CTTAGTCCAA.CACCGAATCA-CTTAGTCCAA_S3


title: Sample 167_TENA2462_P09_R3

description: BSSE_QGF_140533_HLLWMDRXX_1_TENA2462_P9_TTATACGCGA_GCCGTCTGTT_S167_L001


title: N1224: BL6 liver on ice 209900 cells


title: Sample 166_TENA2462_P16_R3

description: BSSE_QGF_140532_HLLWMDRXX_1_TENA2462_P16_TTAGGATATC_TATACCATGG_S166_L001


title: N0972: BALBc Liver digested  NKT1 CD4+ 23.000 cells


title: ast2

description: ast2.CCTCTATCTC-CTCATTCTGC.CCTCTATCTC-CTCATTCTGC_S2


title: N0971: BALBc Liver digested  NKT1 CD4+ 14.000 cells


title: Shank3_4_rep3

first: Lisa

middle: Nicole

last: Learman

address: 725 N. Wolfe St., PCTB 917

department: Neuroscience

institute: Johns Hopkins University School of Medicine

description: Ribosome-bound (RiboTag) RNA

data_processing:
Trimmomatic 0.39 (http://www.usadellab.org/cms/?page=trimmomatic) was used to trim adapters and low-quality reads from the raw paired-end fastq files, using default parameters.
FastQC analysis (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to determine the quality of each file.
Reads were aligned to mouse reference genome mm10 using the HISAT2 (2.2.0) (https://daehwankimlab.github.io/hisat2/) splice-mapping algorithm with default parameters.
Read coverage tables for each gene were created using StringTie (2.1.3) (https://ccb.jhu.edu/software/stringtie/).
Read coverage tables for each transcript were created using Salmon (1.4) (https://salmon.readthedocs.io/en/latest/salmon.html).
To determine normalized gene counts and differential gene or transcript expression, DESeq2 was used (1.12.3) (https://www.rdocumentation.org/packages/DESeq2/versions/1.12.3).
Genome_build: mm10
Supplementary_files_format_and_content: raw counts for each each Ensembl ID, 1 file per sample

source_name: Pyramidal Neurons

growth_protocol: For transriptomic studies of excitatory neurons, Shank3(ΔC/+) mice were crossed with homozygous HA-Rpl22(f/f);Camk2a-Cre mice on C57BL6JL stain background to receive hemizygous mice with mutated Shank3 allele, Shank3(ΔC/+); HA-Rpl22(f/+);Camk2a-Cre(+/-). The controls were littermates from the above breeding that lacked mutated Shank3, Shank3(+/+);HA-Rpl22(f/+);Camk2a-Cre(+/-), referred to as WT controls.

extract_protocol:
Immunoprecipitation and purification of ribosome-associated RNA from pyramidal neurons was performed on Shank3(dC);HA-Rpl22(f/f);Camk2a-Cre(+/-) and Shank3(+/+);HA-Rpl22(f/f);Camk2a-Cre(+/-) mouse brains as described(23) with minor modifications. Briefly, mouse corti were homogenized in lysis buffer (50 mM Tris, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 100 μg/ml cycloheximide, 10 mM Ribonucleoside Vanadyl Complex, 1 mM DTT, plus RNAsin and CompleteTM EDTA-free protease inhibitor mixture, pH 7.4) on ice.  Homogenates were spun at 10, 000 g for 10 min to remove debris. After collecting the supernatants, ribosomes and associated RNA were immunoprecipitated with an anti-HA antibody. Ribosome-associated RNA was purified by RNeasy mini kit (Qiagen),
RNA-seq libraries were prepared using Illumina TruSeq stranded mRNA library preparation kit (Illumina). Library quality was validated by high sensitivity DNA analysis kit using Agilent Bioanalyzer 2100, and the concentration of RNA-seq libraries was quantified by qPCR using the KAPA library quantification kit (Kapabiosystems). Sequencing of RNA-Seq libraries was performed on a HiSeq 2500 instrument (Illumina) with 100 bp (x2) reads according to manufacturer’s instructions. 36 libraries with distinct barcodes were sequenced in 6 lanes (3 flow cells). The depth of RNA-seq was 15 million reads per sample.

treatment_protocol: For swim stress studies, behaviorally naïve mice were placed in a container (40 cm x 20 cm in diameter) half-filled with water at 25oC. The forced swim stress procedure lasted 6 min, and then mice were returned to their home cages. Stress-naïve mice were left in home cages undisturbed. After a one- or four-hour delay, separate cohorts of mice were used in behavioral studies or sacrificed for brain and blood samples collection.

tag: tissue

value: cortex (brain)

value: pyramidal neurons

tag: genotype

value: 4 hours post 5 min swim stress

tag: cohort

tag: ip antibody

value: anti-HA


title: Shank3_4_rep4

description: Ribosome-bound (RiboTag) RNA

tag: cell type


title: Shank3_4_rep5

description: Ribosome-bound (RiboTag) RNA


title: Shank3_4_rep6

description: Ribosome-bound (RiboTag) RNA


title: Sample 165_TENA2462_P10_R3

description: BSSE_QGF_140531_HLLWMDRXX_1_TENA2462_P10_CTTACCGCAC_TAAGACCTAT_S165_L001

source_name: Murine mammary tumor cell lines derived from tumors of lineage-traced MMTV-PyMT transgenic mice

tag: system

value: FALSE


title: Sample 164_TENA2462_P17_R3

description: BSSE_QGF_140530_HLLWMDRXX_1_TENA2462_P17_CCACCGGAGT_GCCTGCCATG_S164_L001

tag: mouse

value: high


title: N0970: BALBc Liver on ice  NKT1 CD4+ 75.000 cells


title: Sample 163_TENA2462_P18_R3

description: BSSE_QGF_140529_HLLWMDRXX_1_TENA2462_P18_AGCTACTATA_GTTATATGGC_S163_L001

tag: population

value: neg


title: PANC-1_ASC siRNA (2)_rep3

city: Toon

first: Mitsuhito

last: Koizumi

state: Ehime

address: Shitsukawa

country: Japan

institute: Ehime University Graduate School

data_processing:
Sequencing of paired-end reads (75 bp) was performed with the MiSeq Reagent kit V3 150 cycle on a MiSeq system (Illumina).
Mapping to human genome data hg19 was performed using Tophat, and the expression analysis tool Cufflinks was used to normalize each sample before determining the differences in expression between Control siRNA (n = 3) and ASC siRNA (1) (n = 3) and ASC siRNA (2) (n = 3) by tmm using R.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include trimmed mean of M values for each Sample.

source_name: PANC-1_ASC siRNA (2)_siRNA

growth_protocol: PANC-1 cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% fetal bovine serum and 1% penicillin.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Thermo Fisher Scientific). The integrity of isolated RNA was verified using an Agilent 2100 Bioanalyzer. RNA samples with an RNA integrity number (RIN) greater than eight were normalized to 100 ng/μl before further analyses. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit setA according to the manufacturer's instructions and subsequently validated for an average size of about 330-340 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit setA according to the manufacturer's instructions and subsequently validated for an average size of about 330-340 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit.

treatment_protocol: Cell lines were transfected with 25 pM siRNA using Lipofectamine 2000. Three days after transferring siRNA, mRNA and protein were extracted and analyzed.

value: pancreas/duct

value: epithelial

tag: cell line

tag: knockdown

value: ASC siRNA (2)


title: PANC-1_ASC siRNA (2)_rep2


title: Shank3_4_rep1

description: Ribosome-bound (RiboTag) RNA


title: N0969: BL6 Liver digested NKT1 CD4+ 38.000 cells


title: WT_4_rep5

description: Ribosome-bound (RiboTag) RNA


title: PANC-1_ASC siRNA (2)_rep1


title: N0963: BL6 WT Liver digested CD4+ NKT1, 167.000 cells


title: Sample 161_TENA2462_P22_R2

description: BSSE_QGF_140527_HLLWMDRXX_1_TENA2462_P22_GAATATGCGG_ACGAGACTGA_S161_L001

value: TENA

tag: egfp

tag: mcherry

tag: epcam

value: TRUE


title: PANC-1_ASC siRNA (1)_rep3

source_name: PANC-1_ASC siRNA (1)_siRNA

value: ASC siRNA (1)


title: N0962: BL6 WT Blood CD4+ NKT1, 126.000 cells


title: WT_4_rep4

description: Ribosome-bound (RiboTag) RNA


title: WT_4_rep3

description: Ribosome-bound (RiboTag) RNA


title: ast1

description: ast1 .CCTCCAGGTA-ATTCACGTGA.CCTCCAGGTA-ATTCACGTGA_S1

value: Ovalbumin (OVA)-induced asthma model

value: Spleen CD3+ T cells


title: Sample 160_TENA2462_P09_R2

description: BSSE_QGF_140526_HLLWMDRXX_1_TENA2462_P9_CTGGAACTGT_CGTAATTAAC_S160_L001

value: med

tag: passedqc


title: Sample 159_TENA2462_P16_R2

description: BSSE_QGF_140525_HLLWMDRXX_1_TENA2462_P16_TCCTCGGACT_AACGCCAGAG_S159_L001


title: WT_4_rep2

description: Ribosome-bound (RiboTag) RNA

tag: strain


title: Sample 158_TENA2462_P10_R2

description: BSSE_QGF_140524_HLLWMDRXX_1_TENA2462_P10_GTAACTGAAG_GGAGTCGCGA_S158_L001

value: low


title: Shank3_4_rep2

description: Ribosome-bound (RiboTag) RNA

value: cortex (brain)


title: PANC-1_ASC siRNA (1)_rep1


title: PANC-1_Control siRNA_rep2

value: Control siRNA


title: Shank3_1_rep5

description: Ribosome-bound (RiboTag) RNA

value: pyramidal neurons

value: 1 hour post 5 min swim stress


title: PANC-1_ASC siRNA (1)_rep2


title: Sample 157_TENA2462_P17_R2

description: BSSE_QGF_140523_HLLWMDRXX_1_TENA2462_P17_AGTATGCTAC_TTAATAGACC_S157_L001

value: FALSE


title: Sample 162_TENA2462_P05_R3

description: BSSE_QGF_140528_HLLWMDRXX_1_TENA2462_P5_GCTAGACTAT_AATACGACAT_S162_L001

value: high


title: Shank3_1_rep4

description: Ribosome-bound (RiboTag) RNA

value: anti-HA


title: Sample 156_TENA2462_P18_R2

description: BSSE_QGF_140522_HLLWMDRXX_1_TENA2462_P18_TGTGATAACT_CAGGCGCCAT_S156_L001

value: neg


title: Sample 154_TENA2462_P22_R1

description: BSSE_QGF_140520_HLLWMDRXX_1_TENA2462_P22_CGCACGACTG_GGACCAACAG_S154_L001


title: Shank3_1_rep2

description: Ribosome-bound (RiboTag) RNA


title: Shank3_1_rep1

description: Ribosome-bound (RiboTag) RNA


title: Sample 152_TENA2462_P16_R1

description: BSSE_QGF_140518_HLLWMDRXX_1_TENA2462_P16_TCCTGGTTGT_CTGACCGGCA_S152_L001


title: Shank3_1_rep3

description: Ribosome-bound (RiboTag) RNA


title: PANC-1_Control siRNA_rep3

value: pancreas/duct

value: epithelial


title: X187_SM-sensitive

city: Ulm

first: Hans

middle: A

last: Kestler

address: Albert-Einstein-Allee 11

department: Research Group Bioinformatics and Systems Biology

institute: University of Ulm

hyb_protocol: Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450DX.

scan_protocol: GeneChips were scanned using the Scan GCS3000Dx.

data_processing: The data were normalized using RMA algorithm in R software [www.r-ptoject.org], BioConductor package [www.bioconductor.org]

source_name: human white blood cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: xenograft

extract_protocol: Lysis of the mononuclear cells followed by lysate homonogenization using a biopolymer shredding system in a microcentrifuge spin-column format followed by total RNA purification using selective binding columns

treatment_protocol: White blood cells were isolated through Ficoll-Hypaque density gradient centrifugation

tag: disease state

value: pediatric BCP-ALL

value: white blood cells

tag: sm response

value: SM-sensitive


title: WT_4_rep1

description: Ribosome-bound (RiboTag) RNA

tag: tissue

tag: treatment

value: 4 hours post 5 min swim stress


title: X112_SM-sensitive


title: X093_SM-sensitive


title: X134_SM-sensitive


title: WT_1_rep6

description: Ribosome-bound (RiboTag) RNA

tag: genotype

tag: cohort


title: WT_1_rep5

description: Ribosome-bound (RiboTag) RNA

tag: cell type

tag: ip antibody


title: PANC-1_Control siRNA_rep1


title: Sample 150_TENA2462_P17_R1

description: BSSE_QGF_140516_HLLWMDRXX_1_TENA2462_P17_TTCACGAGAC_AGATTGTTAC_S150_L001

tag: system

value: TENA

tag: mouse


title: WT_1_rep4

description: Ribosome-bound (RiboTag) RNA


title: Sample 155_TENA2462_P05_R2

description: BSSE_QGF_140521_HLLWMDRXX_1_TENA2462_P5_AACCGAGTTC_GATCTCTGGA_S155_L001

tag: population


title: Sample 153_TENA2462_P09_R1

description: BSSE_QGF_140519_HLLWMDRXX_1_TENA2462_P9_TAATTCTGCT_TCTCATCAAT_S153_L001

value: med

value: TRUE


title: Sample 151_TENA2462_P10_R1

description: BSSE_QGF_140517_HLLWMDRXX_1_TENA2462_P10_GCGTGGATGG_TTGACCAATG_S151_L001

value: low


title: X139_SM-sensitive


title: WT_1_rep3

description: Ribosome-bound (RiboTag) RNA

value: cortex (brain)


title: X172_SM-sensitive


title: Sample 149_TENA2462_P18_R1

description: BSSE_QGF_140515_HLLWMDRXX_1_TENA2462_P18_CGAGGCCAAG_GTGTTACCGG_S149_L001


title: X074_SM-sensitive


title: Sample 148_TENA2462_P05_R1

description: BSSE_QGF_140514_HLLWMDRXX_1_TENA2462_P5_TCTCATGATA_AACACGTGGA_S148_L001


title: WT_1_rep2

description: Ribosome-bound (RiboTag) RNA

value: pyramidal neurons


title: X142_SM-insensitive

value: SM-insensitive


title: X068_SM-sensitive


title: X116_SM-insensitive


title: Sample 147_TENA2560_P05_R12

description: BSSE_QGF_140513_HLLWMDRXX_1_TENA2560_P5_AGCGCCACAC_CTAATGTCTT_S147_L001


title: Sample 146_TENA2560_P17_R12

description: BSSE_QGF_140512_HLLWMDRXX_1_TENA2560_P17_GTAACTTGGT_CGCCATACCT_S146_L001

value: FALSE


title: WT_1_rep1

description: Ribosome-bound (RiboTag) RNA

value: 1 hour post 5 min swim stress


title: D-HEp3 rep1

city: Bronx

first: Julio

last: Aguirre-Ghiso

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Quality control was performed using FastQC (v0.11.8).
Trim Galore! (version 0.6.5) was used to trim the adapter sequences with a quality threshold of 20. The human genome reference used was GRCh38.p13 and GENCODE release 36.
Alignment was performed using STAR aligner (v2.7.5b)
Gene level read counts were obtained by using Salmon (v1.2.1) for all libraries. All samples passed the quality control requirements with > 60% of reads uniquely mapping (>20M uniquely mapped reads for each library) using STAR.
Genome_build: Differential expression analysis was performed using the gene level read counts and the DESeq2 (v1.28.1) R package
Supplementary_files_format_and_content: GRCh38.p13
Supplementary_files_format_and_content: CSV file of normalized gene counts from all replicates or differential gene expression
Supplementary_files_format_and_content: normalized gene counts
Supplementary_files_format_and_content: Differentuial gene expression

source_name: D-HEp3 rep1

growth_protocol: T-HEp3 tumor grown on chicken CAM were extracted and dissociated with collagenase. Single cell suspension of T-HEp3 were grown on dish for three days and RNA extracted. D-HEp3 cells were grown on dish and RNA extracted from passage >P130 cells.

extract_protocol:
RNA was extracted using Trizol reagent and total RNA was selected for polyA+ RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: human neck and squamous cell carcinoma cell


title: Sample 145_TENA2560_P18_R12

description: BSSE_QGF_140511_HLLWMDRXX_1_TENA2560_P18_ACGGTCCAAC_TCTTACATCA_S145_L001

tag: egfp

value: neg

value: high


title: Sample 144_TENA2560_P05_R11

description: BSSE_QGF_140510_HLLWMDRXX_1_TENA2560_P5_TATCCGAGGC_GGCCAATAAG_S144_L001

tag: mcherry


title: Shank3_Naive_rep5

description: Ribosome-bound (RiboTag) RNA

value: Naïve

value: anti-HA


title: Shank3_Naive_rep6

description: Ribosome-bound (RiboTag) RNA


title: Shank3_Naive_rep7

description: Ribosome-bound (RiboTag) RNA


title: T-HEp3 rep2

source_name: T-HEp3 rep2


title: Sample 143_TENA2560_P17_R11

description: BSSE_QGF_140509_HLLWMDRXX_1_TENA2560_P17_GATCGTCGCG_CTGGATATGT_S143_L001

tag: epcam


title: T-HEp3 rep1

source_name: T-HEp3 rep1


title: Sample 142_TENA2560_P18_R11

description: BSSE_QGF_140508_HLLWMDRXX_1_TENA2560_P18_CTCGAATATA_GAGATGTCGA_S142_L001

tag: passedqc


title: CB6_MKM-018

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

description:
The SW 1353 cell line was initiated by A. Leibovitz at the Scott and White Clinic, Temple, Texas in 1977 from a primary grade II chondrosarcoma of the right humerus obtained from a 72 year old female Caucasian.
Mut_2

data_processing:
Illumina reads were mapped to human genome release GRCh38 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: GRCh38
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: Chondrosarcoma

growth_protocol: Human chondrosarcoma cells were grown in DMEM-F12 (Gibco) supplemented with 10% FBS (Invitrogen) and 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco), and maintained in 5% CO2 at 37°C.

extract_protocol:
Cells were scraped in TRIzol reagent total RNA was isolated using phenol-chloroform extraction using Invitrogen PureLink RNA Mini Kit (#12183018A)
RNA sequencing libraries were prepared using the TruSeq Stranded Total RNA with Ribo-Zero Gold kit (Illumina). This protocol provides strand specific data while
simultaneously removing both cytoplasmic and mitochondrial rRNA. Libraries were sequenced on the HiSeq 2500 instruments and 50 million 50 base pair single end
reads were produced per sample. Data was extracted, de-convoluted based on dual index reads and analyzed using CLC Genomics Workbench software (Qiagen).

treatment_protocol: Chondrosarcoma cells, were infected with lentivirus shRNAs targeting JAB1 or a scrambled control shRNA (Sigma) at MOI = 5. After 48 hours after infection, cells were cultured in puromycin (Sigma) containing media at 2µg/mL for 72 hours.

value: SW1353 (ATCC HTB-94)

value: Chondrosarcoma cells

value: shRNA JAB1-KD


title: Sample 141_TENA2560_P05_R10

description: BSSE_QGF_140507_HLLWMDRXX_1_TENA2560_P5_AGGCGTTCGC_TTCATCCAAC_S141_L001

value: TENA


title: CB5_MKM-017

description:
The SW 1353 cell line was initiated by A. Leibovitz at the Scott and White Clinic, Temple, Texas in 1977 from a primary grade II chondrosarcoma of the right humerus obtained from a 72 year old female Caucasian.
Mut_1


title: D-HEp3 rep2

source_name: D-HEp3 rep2


title: Sample 140_TENA2560_P17_R10

description: BSSE_QGF_140506_HLLWMDRXX_1_TENA2560_P17_GCACCACCAA_TGGTACTGAT_S140_L001


title: Shank3_Naive_rep4

description: Ribosome-bound (RiboTag) RNA

tag: strain


title: Shank3_Naive_rep3

description: Ribosome-bound (RiboTag) RNA


title: Shank3_Naive_rep2

description: Ribosome-bound (RiboTag) RNA


title: X036_SM-insensitive

tag: disease state

value: pediatric BCP-ALL

value: white blood cells


title: CB4_MKM-016

description:
The SW 1353 cell line was initiated by A. Leibovitz at the Scott and White Clinic, Temple, Texas in 1977 from a primary grade II chondrosarcoma of the right humerus obtained from a 72 year old female Caucasian.
Mut_0


title: X024_SM-insensitive

tag: sm response


title: Shank3_Naive_rep1

description: Ribosome-bound (RiboTag) RNA

tag: tissue


title: WT_Naive_rep7

description: Ribosome-bound (RiboTag) RNA

tag: treatment


title: Sample 139_TENA2560_P18_R10

description: BSSE_QGF_140505_HLLWMDRXX_1_TENA2560_P18_ATGTTGTTGG_CAATCTATGA_S139_L001

value: TRUE


title: X018_SM-insensitive


title: X015_SM-insensitive


title: Sample 138_TENA2560_P05_R9

description: BSSE_QGF_140504_HLLWMDRXX_1_TENA2560_P5_ACTTGTTATC_CGCGCCTAGA_S138_L001


title: Sample 136_TENA2560_P18_R9

description: BSSE_QGF_140502_HLLWMDRXX_1_TENA2560_P18_AATTCCATCT_CTTCAGTTAC_S136_L001


title: WT_Naive_rep6

description: Ribosome-bound (RiboTag) RNA

value: cortex (brain)

tag: genotype


title: WT_Naive_rep5

description: Ribosome-bound (RiboTag) RNA

value: pyramidal neurons

tag: cohort


title: Sample 137_TENA2560_P17_R9

description: BSSE_QGF_140503_HLLWMDRXX_1_TENA2560_P17_TTAACGGTGT_TCCTGACCGT_S137_L001


title: CB2_MKM-014

description:
The SW 1353 cell line was initiated by A. Leibovitz at the Scott and White Clinic, Temple, Texas in 1977 from a primary grade II chondrosarcoma of the right humerus obtained from a 72 year old female Caucasian.
WT_1

tag: cell type

value: scrambled control shRNA


title: CB1_MKM-013

description:
The SW 1353 cell line was initiated by A. Leibovitz at the Scott and White Clinic, Temple, Texas in 1977 from a primary grade II chondrosarcoma of the right humerus obtained from a 72 year old female Caucasian.
WT_0


title: Sample 135_TENA2560_P22_R8

description: BSSE_QGF_140501_HLLWMDRXX_1_TENA2560_P22_GTGACGGAGC_TGGCGGTCCA_S135_L001


title: WT_Naive_rep3

description: Ribosome-bound (RiboTag) RNA

tag: ip antibody


title: WT_Naive_rep2

description: Ribosome-bound (RiboTag) RNA


title: si-NC-2

first: Qiang

last: Ji

address: 180 Fenglin Rd.

institute: Zhongshan Hospital Fudan University

data_processing:
The gene expression profile was acquired by RNA sequencing. The differentially expressed RNAs were statistically significant with a change of >2.0 or <2.0-fold with P<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: si.LIN02015.vs.NC.Seq.all *.xls includes all the identified expressed genes

source_name: Vascular smooth muscle cells

growth_protocol: Human aortic VSMCs (HAVSMCs) were cultured with Ham’s F-12K medium (Gibco, NY, USA) containing 10% fetal bovine serum (Gibco, Australia). Cells were cultured in a humidified 37°C incubator with 5% CO2.

extract_protocol:
Cells were washed with PBS and incubated in lysis buffer. Total RNA was extracted from cells using Trizol Reagent (Invitrogen, Carlsbad, USA). RNA concentration was measured by NanoDrop ND-1000.
RNA samples were reversely transcribed to cDNA library using the SuperScript III Reverse Transcriptase kit (Invitrogen).

treatment_protocol: The cells were plated in 6-well plates and treated with different agents when they became 70%–80% confluent.To knockdown LINC02015, three short hairpin RNAs (shRNAs) and a negative control shRNA were transfected into VSMCs with Lipofectamine 3000 (Invitrogen, USA). Transfection medium was replaced after 6 hours. All transfected VSMCs were collected after 48 hours.

value: Human aortic vascular smooth muscle cells

value: si-NC


title: si-LINC02015-2


title: Sample 134_TENA2560_P05_R8

description: BSSE_QGF_140500_HLLWMDRXX_1_TENA2560_P5_ATAGCGGAAT_GCGCAGAGTA_S134_L001

tag: system


title: CB3_MKM-015

description:
The SW 1353 cell line was initiated by A. Leibovitz at the Scott and White Clinic, Temple, Texas in 1977 from a primary grade II chondrosarcoma of the right humerus obtained from a 72 year old female Caucasian.
WT_2


title: si-LINC02015-1


title: Sample 132_TENA2560_P18_R8

description: BSSE_QGF_140498_HLLWMDRXX_1_TENA2560_P18_CCACGCTGAA_TATTCCTCAG_S132_L001

tag: mouse


title: si-NC-1


title: WT_Naive_rep4

description: Ribosome-bound (RiboTag) RNA


title: Sample 133_TENA2560_P17_R8

description: BSSE_QGF_140499_HLLWMDRXX_1_TENA2560_P17_GTTCGGAGTT_CGCCTTCTGA_S133_L001

tag: population


title: Sample 131_TENA2560_P22_R7

description: BSSE_QGF_140497_HLLWMDRXX_1_TENA2560_P22_CACAGCGGTC_ATTCCTATTG_S131_L001


title: HSB282_8_DG

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

institute: Yale University

description:
nuclear RNA
Human_cell_meta.txt.gz
Human_counts.mtx.gz
Human_genes.txt.gz

data_processing:
Cell Raner (v3.0.2) were used for reads alignment, filtering, UMI and barcode counting
Seurat (v3) was used for quality control, batch correction, dimension reduction and cell clustering
Please refer STAR methods for more details
Genome_build: hg38; Mmul10; susScr11
Supplementary_files_format_and_content: tab-delimited text files including meta annotation for each cell; tab-delimited text files including UMI counts; tab-delimited text files for gene symbols

source_name: Human HIP-EC

extract_protocol:
The brain cell nuclei were isolated according to our previous protocol (Li et al., 2018; Zhu et al., 2018) with some modifications. Hippocampal regions (DG, CA1, CA2-4, Sub) and adjacent entorhinal cortex were dissected from three frozen adult human brains (Table S1). In order to avoid experimental bias and evenly dissociate the tissue for cell nuclei isolation, whole tissue was finely pulverized to powder in liquid nitrogen with mortar and pestle (Coorstek #60316, #60317). All buffers were ice cold and all reagents used for consequent nuclear isolation were molecular biology grade unless stated otherwise. 5 - 10 mg of pulverized tissue was added into 5 ml of ice-cold lysis buffer consisting of 320 mM sucrose (Sigma #S0389), 5 mM CaCl2 (Sigma #21115), 3 mM Mg(Ace)2 (Sigma #63052), 10mM Tris-HCl (pH 8) (AmericanBio #AB14043), protease inhibitors w/o EDTA (Roche #11836170001), 0.1 mM EDTA (AmericanBio #AB00502), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186), and  0.1% TX-100 (v/v) (Sigma#T8787). DTT, RNAse Protector, protease inhibitors, and TX-100 were added immediately before use. The suspension was transferred to Dounce tissue grinder (15ml volume, Wheaton #357544; autoclaved, RNAse free, ice-cold) and homogenized with loose and tight pestles, 30 cycles each, with constant pressure and without introduction of air. The homogenate was strained through 40 um tube top cell strainer (Corning #352340) which was pre-wetted with 1ml wash buffer: (250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)). Additional 4 ml of wash buffer was added to wash the strainer. Final 10 ml of solution was mixed with 10 ml of 50% Optiprep (Axis-Shield# 1114542) solution (50% iodixanol (v/v), 250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)) by inverting the tube 10x and carefully pipetted into 2 centrifuge tubes (Corning #430791). The tubes were centrifuged at 1000g, for 30 min at 4 ˚C on centrifuge (Eppendorf #5804R) and rotor (Eppendorf #S-4-72). Upon end of centrifugation, the supernatant was carefully and completely removed and total of 5 ml of resuspension buffer (250 mM sucrose (Sigma #S0389), 25 mM KCl (Sigma #60142), 5mM MgCl2 (Sigma #M1028), 20mM Tris-HCl (pH 7.5) (AmericanBio #AB14043; Sigma #T2413), protease inhibitors w/o EDTA (Roche #11836170001), RNAse inhibitor (80U/ml) (Roche #03335402001), 1mM DTT (Sigma #43186)) was added carefully on the pellets in tubes and centrifuged at 1000g, for 10 min at 4 ˚C on the same centrifuge and rotor. Supernatants were then carefully and completely removed, pellets were gently dissolved by adding 100 ul of resuspension buffer (see above) and pipetting 30x with 1ml pipette tip, pooled and filtered through 35 um tube top cell strainer (Corning #352340). Finally, nuclei were counted on hemocytometer and diluted to 1 million/ml with sample-run buffer: 0.1% BSA (Gemini Bio-Products #700-106P), RNAse inhibitor (80U/ml) (Roche#03335402001), 1mM DTT (Sigma #43186) in DPBS (Gibco #14190).
10X Chromium Single Cell 3ʹ v3

value: Dentate gyrus

tag: age

tag: Sex

value: Male


title: HSB282_7_DG


title: HA+ Lung BRM 2

city: Melbourne

first: Hyon Xhi

last: Tan

state: Victoria

address: 792 Elizabeth St

department: Department of Microbiology and Immunology

country: Australia

institute: The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity

data_processing:
RNAseq analysis was performed using the web-based Galaxy platform maintained by Melbourne Bioinformatics.
Reads were mapped to the Mus musculus reference genome (mm10) using HISAT2 and reads were quantified using HTSeq.
Count matrices were generated and inputted into Degust (http://degust.erc.monash.edu) for final data analysis and visualization. The Degust Voom/Limma method was selected for data processing.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized abundance measurements - Degust output
Supplementary_files_format_and_content: Raw counts -- HTseq

source_name: Murine lungs

extract_protocol:
RNA was isolated from sorted cells using a QIAGEN RNeasy Plus Micro Kit, as per manufacturer's protocol.
Illumina Truseq Stranded mRNA kit was use for library construction. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissues

value: Lungs

value: B220+ IgD- CD38hi GL7- HA+ CD45.2IV-

value: Post-intranasal influenza virus infection


title: HA+ Lung BRM 1


title: Total Lung GC 2

value: B220+ IgD- CD38lo GL7+


title: Total MLN GC 2

source_name: Murine mediastinal lymph node

value: Mediastinal lymph node


title: Total Lung GC 1


title: Sample 128_TENA2560_P18_R7

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

institute: University of Basel

description: BSSE_QGF_140494_HLLWMDRXX_1_TENA2560_P18_TATGATGGCC_GATTGTCATA_S128_L001

data_processing:
Paired-end reads were aligned to the mouse genome (UCSC version mm10 analysis set) with STAR with default parameters except for allowing up 10 hits to genome (outFilterMultimapNmax 10), reporting only one location for hits with equal score (outSAMmultNmax 1), and for filtering reads without evidence in spliced junction table (outFilterType "BySJout").
The output was sorted and indexed with samtools. Read and alignment quality was evaluated using the qQCReport function of the Bioconductor package QuasR.
The featureCounts function from Bioconductor package subread was used to count the number of read (5'ends) overlapping with the exons of each gene assuming an exon union model (with used gene model provided by ensembl v96).
Processing of the read count matrix for genes was done according to the steps illustrated in Bioconductor Single Cell Analysis workflow (Amezquita et al., 2020).
Genome_build: mm10
Supplementary_files_format_and_content: TXT file (with tab separated values) with raw counts for Ensembl Genes, 1.column is Ensembl Gene ID, 2. and remaining columns contain raw counts

extract_protocol:
FACS-sorted cells were collected as 5-cell pools in 2.5µl of 0.2% TX-100 and 2U/μl RNase inhibitor (TakaraBio, 2313B) in PBS into 96-well plates (Thermo Fisher Scientific, 4346906) and kept in -80°C prior to use. RNAseq libraries were prepared according to the Smart-seq2 method (Picelli, 2014).
5-cell RNA-seq: RNA/cDNA preamplification and Nextera XT library preparation reactions were set up with a Mosquito HV system (SPT Labtech). After reverse transcription and amplification, the concentration of cDNA generated from each sample was measured using PicoGreen (Thermo Fisher Scientific). cDNA was normalized to 0.1-0.15ng/µl and 0.75 µl were used for library preparation with the Nextera XT DNA library preparation kit (Illumina). Multiplexed library pools were then pooled and PE 2x51 sequenced with an Illumina NovaSeq 6000 system, v1 reagents.

tag: egfp

value: neg

tag: mcherry

value: high

tag: epcam


title: HSB282_5_DG


title: HSB282_6_DG


title: HSB282_3_DG


title: HSB282_2_DG


title: Total Spleen GC 3

source_name: Murine spleen

value: Spleen


title: Sample 126_TENA2560_P05_R6

description: BSSE_QGF_140492_HLLWMDRXX_1_TENA2560_P5_GAATACCTAT_ACAATAGAGT_S126_L001

value: TENA

tag: passedqc


title: Sample 127_TENA2560_P22_R6

description: BSSE_QGF_140493_HLLWMDRXX_1_TENA2560_P22_AATCCAATTG_CATGTAGAGG_S127_L001

value: TRUE


title: Sample 125_TENA2560_P17_R6

description: BSSE_QGF_140491_HLLWMDRXX_1_TENA2560_P17_GGCCAATATT_CGGTCCGATA_S125_L001

value: FALSE


title: Total Spleen GC 2


title: HSB282_1_DG


title: Total MLN GC 1


title: Sample 124_TENA2560_P18_R6

description: BSSE_QGF_140490_HLLWMDRXX_1_TENA2560_P18_CCGGTTCCTA_TATATTCGAG_S124_L001


title: HSB282_4_DG


title: Sample 123_TENA2560_P22_R5

description: BSSE_QGF_140489_HLLWMDRXX_1_TENA2560_P22_CCAGGCACCA_ACGCTAATTA_S123_L001


title: HSB181_7_DG


title: Total Lung BRM 2

value: B220+ IgD- CD38hi GL7- CD45.2IV-


title: day9, differentiated adipocyte (Tmem120a+Tmem120b knock-down), rep2

city: Edinburgh

first: Jose

middle: Ignacio

last: de las Heras

address: Max Born Crescent

department: Wellcome Trust Centre

country: United Kingdom

institute: University of Edinburgh

description: replicate 2

scan_protocol: Standard Protocols (Clinical Research Facility Edinburgh), Scanner: HiScan H166

data_processing: Data were log2 transformed and quantile normalised using the BioConductor package Limma.

source_name: 3T3L1 preadipocyte cell line

label_protocol: Ambion Illumina TotalPrep kit

growth_protocol: 3T3-L1 cells were maintained in high glucose DMEM (SIGMA) supplemented with 10% fetal bovine serum (FBS), MEM non-essential amino acids, 1 mM Sodium Pyruvate, 100 µg/µl penicillin and 100 µg/µl streptomycin sulfate. Cells were plated at ~10% confluency and always split by 60% confluency to maintain differentiation capacity.

extract_protocol: total RNA extraction was performed using Trizol reagent (Invitrogen) according to the manufacturer's instructions

treatment_protocol:
Adipogenesis was induced two days post-confluency by replacing growth medium with induction medium containing 0.5 μM insulin, 1 µM dexamethasone, 0.5 mM 3-isobutyl-1-methylxanthine (IBMX), and 1 μM rosiglitazone. Induction medium was replaced after two days with maintenance medium containing growth medium supplemented with insulin and rosiglitazone only, which was replaced every 48h, up to day 9 post-induction.
Control and Tmem120a/b knock-downs were generated by transduction of non-target (control) or Tmem120a/b-specific shRNA-encoding lentiviruses as described in Batrakou et al. (2015) PLoS ONE 10(05): e0127712.

tag: time

value: day 9

value: differentiation

tag: genotype/variation

value: Tmem120a/Tmem120b knock-down


title: HSB181_6_DG

tag: tissue

value: Dentate gyrus


title: Total Spleen GC 1

tag: treatment


title: Total Lung Bmem IV+ 2

value: B220+ IgD- CD38hi GL7- CD45.2IV+


title: day9, differentiated adipocyte (Tmem120b knock-down), rep2

description: replicate 2

hyb_protocol: Standard Protocols (Clinical Research Facility Edinburgh)

value: Tmem120b knock-down


title: WT_Naive_rep1

description: Ribosome-bound (RiboTag) RNA

tag: strain

value: cortex (brain)

value: pyramidal neurons

tag: genotype

value: Naïve

tag: cohort

value: anti-HA


title: Total Lung BRM 1

value: Lungs

tag: cell type

value: Post-intranasal influenza virus infection


title: Sample 120_TENA2560_P17_R5

city: Basel

description: BSSE_QGF_140486_HLLWMDRXX_1_TENA2560_P17_ATAGCCAAGA_AGTGCCACTG_S120_L001

tag: system

tag: mouse

value: neg

value: high


title: HSB181_5_DG

tag: age

value: Male


title: Sample 121_TENA2560_P05_R5

description: BSSE_QGF_140487_HLLWMDRXX_1_TENA2560_P5_TTCGGTGTGA_GAACAAGTAT_S121_L001

value: TENA

tag: population

value: FALSE


title: HSB181_2_DG

tag: Sex


title: HSB181_3_DG


title: Total Blood Bmem 3

source_name: Murine blood

tag: tissues

value: Blood


title: Sample 122_TENA2560_P09_R5

description: BSSE_QGF_140488_HLLWMDRXX_1_TENA2560_P9_TGGCCTCTGT_TGAGACAGCG_S122_L001

tag: egfp

tag: mcherry

value: med

value: TRUE


title: UCSF EWSR1-BEND2 glioma #4

type: genomic

city: Stanford

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description: EWSR1-BEND2 glioma

hyb_protocol: bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium EPIC 850k Human DNA Methylation Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan instrument following standard recommended Illumina scanner setting

data_processing: Methylation data were preprocessed using the minfi package (v.1.30.0) in R. The detection p-value for each sample was computed. Functional normalization with NOOB background correction and dye-bias normalization was performed.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: glioma tumor tissue

label_protocol: standard Illumina protocol

growth_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients.  No ex vivo culture or xenografting was performed.

extract_protocol: Tumor tissue was selectively punched from formalin-fixed, paraffin-embedded tissue blocks using using 2.0 mm disposable biopsy punches (Integra Miltex Instruments, cat# 33-31-P/25) or selectively scraped from unstained sections cut from formalin-fixed, paraffin-embedded tissue blocks.  Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Primary human tumor tissue was used as the source of genomic DNA for all patients in the absence of any radiation or chemotherapy administration.  No ex vivo culture or xenografting was performed.

tag: patient sex

value: Female

tag: patient age at dx (yrs)

tag: fusion type

value: EWSR1-BEND2 fusion


title: day9, differentiated adipocyte (Tmem120a knock-down), rep1

description: replicate 1

tag: time

value: day 9

value: differentiation

tag: genotype/variation

value: Tmem120a knock-down


title: HSB181_4_DG

tag: tissue

value: Dentate gyrus


title: Sample 118_TENA2560_P22_R4

description: BSSE_QGF_140484_HLLWMDRXX_1_TENA2560_P22_CTAATAACCG_AACCGCATCG_S118_L001

source_name: Murine mammary tumor cell lines derived from tumors of lineage-traced MMTV-PyMT transgenic mice

tag: epcam

tag: passedqc


title: day9, differentiated adipocyte (Tmem120b knock-down), rep1

description: replicate 1

tag: treatment

value: Tmem120b knock-down


title: UCSF EWSR1-BEND2 glioma #2

description: EWSR1-BEND2 glioma


title: UCSF EWSR1-BEND2 glioma #1

description: EWSR1-BEND2 glioma


title: Total Blood Bmem 2

tag: cell type

value: B220+ IgD- CD38hi GL7- CD45.2IV+


title: day9, differentiated adipocyte, rep3

description: replicate 3

value: non-target shRNA control


title: day9, differentiated adipocyte (Tmem120a knock-down), rep2

description: replicate 2


title: HSB181_1_DG


title: Sample 117_TENA2560_P09_R4

description: BSSE_QGF_140483_HLLWMDRXX_1_TENA2560_P9_GCTGACGTTG_TGTTCGCATT_S117_L001

tag: system

tag: mouse

value: neg


title: day9, differentiated adipocyte (Tmem120a+Tmem120b knock-down), rep1

description: replicate 1

value: Tmem120a/Tmem120b knock-down


title: HSB179_7_DG

tag: age

value: Male


title: Total MLN Bmem 3

value: Mediastinal lymph node

value: B220+ IgD- CD38hi GL7-

value: Post-intranasal influenza virus infection


title: Sample 116_TENA2560_P15_R4

description: BSSE_QGF_140482_HLLWMDRXX_1_TENA2560_P15_CTGCGTTACC_TATGGCTCGA_S116_L001

value: TENA

tag: population

value: high

value: FALSE


title: Total MLN Bmem 2

tag: tissues


title: HSB179_6_DG

tag: Sex