title: S207_dog_KO3_CD4_p1_SC


title: S206_dog_KO3_CD4_p1_SC

status: Public on Jun 14 2018

type: SRA

city: Boston

first: Asaf

last: Madi

state: MA

address: 60 Fenwood Road, BTM 10016F

department: Neurology

country: USA

institute: BWH

description:
Single cell RNAseq
R1_rsem.genes.counts.matrix.TMM_normalized.FPKM

library_source: transcriptomic

data_processing:
paired reads were mapped to mouse annotation mm10 using Bowtie (allowing a maximum of one mismatch in seed alignment, and suppressing reads that had more than 10 valid alignments).
TPMs were computed using RSEM, and log2(TPM+1) values were used for subsequent analyses.
filtered out low quality cells and cell doublets, maintaining for subsequent analysis the cells that had (1) 1,000-4,000 detected genes (defined by at least one mapped read), (2) at least 200,000 reads mapped to the transcriptome, and (3) at least 50% of the reads mapped to the transcriptome, ending with a total of 707 CD4+ and 825 CD8+ WT TILs and 376 CD4+ and 394 CD8+ IL27ra KO TILs.
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: Tumor B16F10 melanoma

extract_protocol:
5 µl lysis buffer comprised of Buffer TCL (Qiagen) plus 1% 2-mercaptoethanol.
Plates were then spun down for one minute at 3000rpm and immediately frozen at -80°C. Cells were thawed and RNA was isolated with 2.2x RNAClean SPRI beads (Beckman Coulter Genomics) without final elution. The beads were then air-dried and processed immediately for cDNA synthesis. Samples were then processed using the Smart-seq2 protocol. This was followed by making a 25µl reaction mix for each PCR and performing 21 cycles for cDNA amplification. Then 0.25 ng cDNA from each cell and ¼ of the standard Illumina NexteraXT reaction volume were used in both the tagmentation and final PCR amplification steps

treatment_protocol: Tumor infiltrating CD8+ T cells were isolated from WT and IL27ra KO B16F10 melanoma bearing mice.

tag: strain

tag: tissue

value: Tumor

tag: genotype/variation


title: S205_dog_KO3_CD4_p1_SC


title: S225_dog_KO3_CD4_p1_SC


title: S204_dog_KO3_CD4_p1_SC


title: S201_dog_KO3_CD4_p1_SC


title: S203_dog_KO3_CD4_p1_SC


title: S202_dog_KO3_CD4_p1_SC


title: S221_dog_KO3_CD4_p1_SC


title: S196_dog_KO3_CD4_p1_SC


title: S197_dog_KO3_CD4_p1_SC


title: S193_dog_KO3_CD4_p1_SC


title: S199_dog_KO3_CD4_p1_SC


title: S194_dog_KO3_CD4_p1_SC


title: S192_cat_KO3_CD8_p2_SC


title: S195_dog_KO3_CD4_p1_SC


title: S190_cat_KO3_CD8_p2_SC


title: S191_cat_KO3_CD8_p2_SC


title: S217_dog_KO3_CD4_p1_SC


title: S215_dog_KO3_CD4_p1_SC


title: S188_cat_KO3_CD8_p2_SC


title: S187_cat_KO3_CD8_p2_SC


title: S186_cat_KO3_CD8_p2_SC


title: S184_cat_KO3_CD8_p2_SC


title: S181_cat_KO3_CD8_p2_Population


title: S183_cat_KO3_CD8_p2_SC


title: S198_dog_KO3_CD4_p1_SC


title: S200_dog_KO3_CD4_p1_SC


title: S178_cat_KO3_CD8_p2_SC


title: S179_cat_KO3_CD8_p2_SC


title: S229_dog_KO3_CD4_p1_SC


title: S180_cat_KO3_CD8_p2_SC


title: S174_cat_KO3_CD8_p2_SC


title: S189_cat_KO3_CD8_p2_SC


title: S175_cat_KO3_CD8_p2_SC


title: S176_cat_KO3_CD8_p2_SC


title: S177_cat_KO3_CD8_p2_SC


title: S166_cat_KO3_CD8_p2_SC


title: S163_cat_KO3_CD8_p2_SC


title: S168_cat_KO3_CD8_p2_SC


title: S173_cat_KO3_CD8_p2_SC


title: S167_cat_KO3_CD8_p2_SC


title: S172_cat_KO3_CD8_p2_SC


title: S170_cat_KO3_CD8_p2_SC


title: S169_cat_KO3_CD8_p2_SC


title: S165_cat_KO3_CD8_p2_SC


title: S162_cat_KO3_CD8_p2_SC


title: S185_cat_KO3_CD8_p2_SC


title: S159_cat_KO3_CD8_p2_SC


title: S160_cat_KO3_CD8_p2_SC


title: S157_cat_KO3_CD8_p2_SC


title: S155_cat_KO3_CD8_p2_SC


title: S154_cat_KO3_CD8_p2_SC


title: S158_cat_KO3_CD8_p2_SC


title: S156_cat_KO3_CD8_p2_SC


title: S152_cat_KO3_CD8_p2_SC


title: S150_cat_KO3_CD8_p2_SC


title: S153_cat_KO3_CD8_p2_SC


title: S171_cat_KO3_CD8_p2_SC


title: S146_cat_KO3_CD8_p2_SC


title: S164_cat_KO3_CD8_p2_SC


title: S151_cat_KO3_CD8_p2_SC


title: S148_cat_KO3_CD8_p2_SC


title: S142_cat_KO3_CD8_p2_SC


title: S147_cat_KO3_CD8_p2_SC


title: S137_cat_KO3_CD8_p2_SC


title: S144_cat_KO3_CD8_p2_SC


title: S136_cat_KO3_CD8_p2_SC


title: S141_cat_KO3_CD8_p2_SC


title: S145_cat_KO3_CD8_p2_SC


title: S161_cat_KO3_CD8_p2_SC


title: S138_cat_KO3_CD8_p2_SC


title: S143_cat_KO3_CD8_p2_SC


title: S134_cat_KO3_CD8_p2_SC


title: S135_cat_KO3_CD8_p2_SC


title: S133_cat_KO3_CD8_p2_SC


title: S132_cat_KO3_CD8_p2_SC


title: S131_cat_KO3_CD8_p2_SC


title: S130_cat_KO3_CD8_p2_SC


title: S129_cat_KO3_CD8_p2_SC


title: S149_cat_KO3_CD8_p2_SC


title: S127_cat_KO3_CD8_p2_SC


title: S126_cat_KO3_CD8_p2_SC


title: S124_cat_KO3_CD8_p2_SC


title: S125_cat_KO3_CD8_p2_SC


title: S123_cat_KO3_CD8_p2_SC


title: S122_cat_KO3_CD8_p2_SC


title: S121_cat_KO3_CD8_p2_SC


title: S139_cat_KO3_CD8_p2_SC


title: S120_cat_KO3_CD8_p2_SC


title: S140_cat_KO3_CD8_p2_SC


title: S119_cat_KO3_CD8_p2_SC


title: S118_cat_KO3_CD8_p2_SC


title: S116_cat_KO3_CD8_p2_SC


title: S112_cat_KO3_CD8_p2_SC


title: S113_cat_KO3_CD8_p2_SC


title: S114_cat_KO3_CD8_p2_SC


title: S111_cat_KO3_CD8_p2_SC


title: S128_cat_KO3_CD8_p2_SC


title: S109_cat_KO3_CD8_p2_SC


title: S110_cat_KO3_CD8_p2_SC


title: S108_cat_KO3_CD8_p2_SC


title: S107_cat_KO3_CD8_p2_SC


title: S105_cat_KO3_CD8_p2_SC


title: S106_cat_KO3_CD8_p2_SC


title: S117_cat_KO3_CD8_p2_SC


title: S103_cat_KO3_CD8_p2_SC


title: S102_cat_KO3_CD8_p2_SC


title: S115_cat_KO3_CD8_p2_SC


title: S101_cat_KO3_CD8_p2_SC


title: S104_cat_KO3_CD8_p2_SC


title: S100_cat_KO3_CD8_p2_SC


title: S99_cat_KO3_CD8_p2_SC


title: S98_cat_KO3_CD8_p2_SC


title: SE_31 Sun-exposed normal skin

type: RNA

city: London

first: Ai

last: Nagano

state: --- Select a state ---

address: John Vane Science Centre, Charterhouse Square

department: Centre for Molecular Oncology

country: United Kingdom

institute: Barts Cancer Institute

description: Laser capture microdissection from Sun-exposed normal skin

hyb_protocol: Samples were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned according to the standard Affymetrix protocol

data_processing: Data were analysed in O-miner transcriptomics analysis platform using R/Bioconductor RMA (robust multi-array average) approach

label: Biotin

organism: Homo sapiens

source_name: Sun exposed normal skin

label_protocol: 10 ng of RNA was amplified using the NuGen WT-ovation Pico RNA Amplification System and labelled with the FL-ovation Biotin Kit (NuGen).

extract_protocol: RNA was extracted from fresh frozen tissue specimens by laser capture microdissection.

treatment_protocol: Biopsies of tissue were snap frozen with liquid nitrogen upon excision during surgery and stored at -80 oC until use.

value: Sun-exposed normal skin


title: SE_55 Sun-exposed normal skin


title: S96_bird_WT3_CD4_p1_SC


title: SE_34 Sun-exposed normal skin


title: SE_56 Sun-exposed normal skin


title: SE_28 Sun-exposed normal skin


title: SE_33 Sun-exposed normal skin


title: SE_23 Sun-exposed normal skin


title: SE_35 Sun-exposed normal skin


title: SE_21 Sun-exposed normal skin


title: SE_20 Sun-exposed normal skin


title: S95_bird_WT3_CD4_p1_SC

value: wild type


title: S94_bird_WT3_CD4_p1_SC


title: SE_46 Sun-exposed normal skin


title: SE_30 Sun-exposed normal skin


title: SE_27 Sun-exposed normal skin


title: S93_bird_WT3_CD4_p1_SC


title: SE_32 Sun-exposed normal skin


title: S92_bird_WT3_CD4_p1_SC


title: SE_24 Sun-exposed normal skin


title: S97_cat_KO3_CD8_p2_SC


title: S91_bird_WT3_CD4_p1_SC


title: SE_29 Sun-exposed normal skin


title: SE_07 Sun-exposed normal skin


title: NSE55 Non-sun-exposed normal skin

description: Laser capture microdissection from Non-sun-exposed normal skin

source_name: Normal skin without sun exposure

value: Non-sun-exposed normal skin


title: SE_11 Sun-exposed normal skin


title: S89_bird_WT3_CD4_p1_SC


title: S88_bird_WT3_CD4_p1_SC


title: SE_12 Sun-exposed normal skin


title: SE_13 Sun-exposed normal skin


title: S87_bird_WT3_CD4_p1_SC


title: S83_bird_WT3_CD4_p1_SC


title: S85_bird_WT3_CD4_p1_Population


title: S82_bird_WT3_CD4_p1_SC


title: S84_bird_WT3_CD4_p1_SC


title: S80_bird_WT3_CD4_p1_SC


title: NSE35 Non-sun-exposed normal skin


title: S90_bird_WT3_CD4_p1_SC


title: S81_bird_WT3_CD4_p1_SC


title: S79_bird_WT3_CD4_p1_SC


title: NSE34 Non-sun-exposed normal skin


title: S78_bird_WT3_CD4_p1_SC


title: NSE33 Non-sun-exposed normal skin


title: S76_bird_WT3_CD4_p1_SC


title: S77_bird_WT3_CD4_p1_SC


title: NSE21 Non-sun-exposed normal skin


title: NSE24 Non-sun-exposed normal skin


title: S75_bird_WT3_CD4_p1_SC


title: NSE30 Non-sun-exposed normal skin


title: NSE13 Non-sun-exposed normal skin


title: S74_bird_WT3_CD4_p1_SC


title: S73_bird_WT3_CD4_p1_SC


title: NSE27 Non-sun-exposed normal skin


title: S72_bird_WT3_CD4_p1_SC


title: S71_bird_WT3_CD4_p1_SC


title: NSE20 Non-sun-exposed normal skin


title: S70_bird_WT3_CD4_p1_SC


title: NSE28 Non-sun-exposed normal skin


title: NSE07 Non-sun-exposed normal skin


title: NSE31 Non-sun-exposed normal skin


title: NSE23 Non-sun-exposed normal skin


title: S69_bird_WT3_CD4_p1_SC


title: NSE11 Non-sun-exposed normal skin


title: AK_55 Actinic Keratosis

description: Laser capture microdissection from Actinic Keratosis

source_name: Actinic Keratosis

value: Actinic Keratosis


title: AK_56 Actinic Keratosis


title: S66_bird_WT3_CD4_p1_SC


title: S62_bird_WT3_CD4_p1_SC


title: S63_bird_WT3_CD4_p1_SC


title: AK_34 Actinic Keratosis


title: AK_35 Actinic Keratosis


title: S65_bird_WT3_CD4_p1_SC


title: S67_bird_WT3_CD4_p1_SC


title: S68_bird_WT3_CD4_p1_SC


title: S64_bird_WT3_CD4_p1_SC


title: AK_33 Actinic Keratosis


title: AK_30 Actinic Keratosis


title: AK_23 Actinic Keratosis


title: NSE12 Non-sun-exposed normal skin


title: AK_24 Actinic Keratosis


title: S60_bird_WT3_CD4_p1_SC


title: AK_32 Actinic Keratosis


title: AK_46 Actinic Keratosis


title: S61_bird_WT3_CD4_p1_SC


title: AK_22 Actinic Keratosis


title: AK_31 Actinic Keratosis


title: S59_bird_WT3_CD4_p1_SC


title: S58_bird_WT3_CD4_p1_SC


title: AK_21 Actinic Keratosis


title: S56_bird_WT3_CD4_p1_SC


title: S55_bird_WT3_CD4_p1_SC


title: S57_bird_WT3_CD4_p1_SC


title: TNL_1

city: Columbus

first: William

middle: Edward

last: Ackerman IV

state: Ohio

address: N521 Doan Hall, 410 West 10th Avenue

department: Obstetrics and Gynecology

institute: The Ohio State University

data_processing:
Adapter sequences from the small-RNA-Seq libraries were removed using Cutadapt version 1.4.1.
Trimmed reads were mapped to the miRBase 21 database and tabulated using miRExpress version 2.0 to yield raw (non-normalized) expression data.
Genome_build: miRBase 21
Supplementary_files_format_and_content: Tab-delimted text file of raw (non-normalized) mapped reads.

source_name: Pregnant Myometrium, term non-labor

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life Technologies) according to the instructions of the manufacturer, followed by purification using the RNA Clean-Up and Concentration Kit (Norgen Biotek).
Small RNA-Seq libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs), according to the manufacturer's protocols. In brief, 300 ng total RNA (as determined by the Qubit RNA assay, Life Technologies) with an RNA Quality Score > 7 (as determined by the LabChip GX Microfluidics Electrophoresis system, PerkinElmer) was used to prepare sequencing libraries. The small RNAs were targeted with modified Illumina-compatible 3’ and 5' adaptors and a reverse transcription primer. Next, first strand synthesis was achieved using Protoscript II Reverse Transcriptase (New England Biolabs), followed by 15 cycles of PCR amplification. The small RNA-Seq libraries were then assessed for relative amounts of miRNAs and piwi-interacting RNAs (piRNAs) migrating between 140 to 160 bp using the LabChip GX DNA assay (PerkinElmer). DNA concentrations were assessed using the Qubit fluorometer. Information from the LabChip and Qubit assays allowed pooling of samples prior to size selection using the Pippin Prep system (Sage Science). The profile of the combined size-selected libraries was ascertained using the LabChip GX DNA assay. Each pooled library was then sequenced together with other samples tagged with compatible barcodes within a single channel of an Illumina single-read 50 bp flow cell, using the Illumina HiSeq 2500 platform.

tag: gestational age at delivery (wks)

tag: birthweight (g)

tag: maternal age (y)

tag: maternal race/ethnicity

value: White Non-Hispanic

tag: disease

value: Term non-labor

tag: cervical dilation (cm)

tag: membranes status before cesarean

value: Intact

tag: cesarean indication

value: History of shoulder dystocia

value: myometrium


title: S54_bird_WT3_CD4_p1_SC


title: TNL_3

value: Asian

value: Breech presentation


title: TL_4

source_name: Pregnant Myometrium, term labor of spontaneous onset

value: Term labor

value: Ruptured in labor

value: Failure to progress


title: TNL_2


title: TNL_5


title: TL_5

value: African American

value: Failure to descend


title: TL_2

value: White Hispanic


title: S53_bird_WT3_CD4_p1_SC

value: Tumor


title: TL_1


title: AK_20 Actinic Keratosis


title: PTB-NL_5

source_name: Pregnant Myometrium, preterm birth non-labor

value: Preterm severe preeclampsia

value: Eclampsia, emergent CS


title: PTB-NL_4

value: Severe preeclampsia, transverse lie


title: S48_bird_WT3_CD4_p1_SC

value: wild type


title: S49_bird_WT3_CD4_p1_SC


title: S50_bird_WT3_CD4_p1_SC


title: S52_bird_WT3_CD4_p1_SC


title: TL_3


title: AK_07 Actinic Keratosis

value: Actinic Keratosis


title: AK_28 Actinic Keratosis


title: AK_11 Actinic Keratosis


title: TNL_4

value: White Non-Hispanic

value: Term non-labor

value: Intact

value: Fetal macrosomia


title: AK_12 Actinic Keratosis


title: S46_bird_WT3_CD4_p1_SC


title: PTB-NL_2

value: Severe preeclampsia, active genital HSV infection

value: myometrium


title: PTB-NL_1

value: Severe preeclampsia, non-reassuring fetal status


title: S45_bird_WT3_CD4_p1_SC


title: S51_bird_WT3_CD4_p1_SC


title: PTB-HCA_5

source_name: Pregnant Myometrium, spontaneous preterm birth in the setting of chorioamnionitis

value: Preterm premature rupture of the membranes + histologic chorioamnionitis

value: Ruptured, managed expectantly

value: Non-reassuring fetal status


title: S43_bird_WT3_CD4_p1_SC


title: PTB-HCA_2

value: African American

value: Preterm labor + histologic chorioamnionitis

value: Acute clinical chorioamnionitis, +IAI, non-reassuring fetal status


title: S44_bird_WT3_CD4_p1_SC

value: Tumor


title: PTB-HCA_1

value: Acute clinical chorioamnionitis, +IAI


title: S42_bird_WT3_CD4_p1_SC

value: wild type


title: PTB-HCA_4

value: Acute chorioamnionitis


title: S38_bird_WT3_CD4_p1_SC


title: S39_bird_WT3_CD4_p1_SC


title: S40_bird_WT3_CD4_p1_SC


title: PTB-HCA_3

value: White Hispanic

value: Acute clinical chorioamnionitis, +IAI, breech presentation


title: S41_bird_WT3_CD4_p1_SC


title: PTB-NL_3

value: White Non-Hispanic

value: Preterm severe preeclampsia

value: Intact

value: Severe preeclampsia, breech presentation


title: S37_bird_WT3_CD4_p1_SC


title: S34_bird_WT3_CD4_p1_SC


title: S33_bird_WT3_CD4_p1_SC


title: S36_bird_WT3_CD4_p1_SC


title: S35_bird_WT3_CD4_p1_SC


title: S31_bird_WT3_CD4_p1_SC


title: S32_bird_WT3_CD4_p1_SC


title: S30_bird_WT3_CD4_p1_SC


title: S47_bird_WT3_CD4_p1_SC


title: S27_bird_WT3_CD4_p1_SC


title: S29_bird_WT3_CD4_p1_SC


title: S28_bird_WT3_CD4_p1_SC


title: S26_bird_WT3_CD4_p1_SC


title: S25_bird_WT3_CD4_p1_SC


title: S24_bird_WT3_CD4_p1_SC


title: S21_bird_WT3_CD4_p1_SC


title: S22_bird_WT3_CD4_p1_SC


title: S19_bird_WT3_CD4_p1_SC


title: S16_bird_WT3_CD4_p1_SC


title: S20_bird_WT3_CD4_p1_SC


title: S23_bird_WT3_CD4_p1_SC


title: S17_bird_WT3_CD4_p1_SC


title: S15_bird_WT3_CD4_p1_SC


title: S8_bird_WT3_CD4_p1_SC


title: S10_bird_WT3_CD4_p1_SC


title: S12_bird_WT3_CD4_p1_SC


title: S13_bird_WT3_CD4_p1_SC


title: S11_bird_WT3_CD4_p1_SC


title: S14_bird_WT3_CD4_p1_SC


title: S9_bird_WT3_CD4_p1_SC


title: S7_bird_WT3_CD4_p1_SC


title: S5_bird_WT3_CD4_p1_SC


title: S6_bird_WT3_CD4_p1_SC


title: S4_bird_WT3_CD4_p1_SC


title: cMaf_Prdm1_DKO_3

data_processing:
RNA-seq reads were aligned using Tophat and RSEM-based quantification using known transcripts,
followed by further processing using the Bioconductor package DESeq in R.
Genome_build: mm9
Supplementary_files_format_and_content: The data was normalized using TMM normalization. The TMM method estimates scale factors between samples that can be incorporated into currently used statistical methods for DE analysis. Post-processing and statistical analysis was carried out in R. Differentially expressed genes were defined using the differential expression pipeline on the raw counts with a single call to the function DESeq (adjusted p value<0.1).

extract_protocol:
5uL of lysate from bulk CD8+ T cells as the input for each sample during RNA cleanup via SPRI beads (~2,000 cells lysed on average in RLT).
Tumor infiltrating CD8+ T cells were processed using an adaptation of the SMART-Seq 2 protocol.

treatment_protocol: Tumor infiltrating CD8+ T cells were isolated from WT, Prdm1 cKO, c-Maf cKO, and Prdm1/c-Maf cDKO B16F10 melanoma bearing mice.

value: Prdm1/c-Maf cDKO


title: S1_bird_WT3_CD4_p1_SC


title: cMaf_KO_3

value: c-Maf cKO


title: S3_bird_WT3_CD4_p1_SC


title: WT_16


title: cMaf_KO_2


title: WT_15


title: cMaf_KO_1


title: S18_bird_WT3_CD4_p1_SC


title: WT_13


title: WT_12


title: WT_6


title: WT_10


title: WT_11


title: WT_5


title: WT_2


title: WT_4


title: S2_bird_WT3_CD4_p1_SC


title: Prdm1_KO_2

value: Prdm1 cKO


title: Prdm1_KO_3


title: cMaf_Prdm1_DKO_1


title: WT_7


title: WT_1


title: WT_14


title: Prdm1_KO_1


title: IL27ra KO rep 1

description: WT_IL27rKO_CD8_TILs_rsem.genes.counts.matrix.TMM_normalized.FPKM

data_processing:
RNA-seq reads were aligned using Tophat and RSEM-based quantification using known transcripts, followed by further processing using the Bioconductor package DESeq in R.
Genome_build: mm9
Supplementary_files_format_and_content: The data was normalized using TMM normalization. The TMM method estimates scale factors between samples that can be incorporated into currently used statistical methods for DE analysis. Post-processing and statistical analysis was carried out in R.

tag: genotype

value: IL27ra KO


title: IL27ra KO rep 4


title: WT rep5


title: WT rep4


title: D. simulans miR-983KO replicate 1

city: Cold Spring Harbor

first: Yixin

last: Zhao

state: NEW YORK

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Gene expression in testes

data_processing:
For transcriptome analyses, raw data from RNA-seq were mapped to the D. melanogaster or D. simulans genome, and normalized using Tophat (Trapnell, et al. 2009) and SeqMonk version 1.36.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). The expression level of each gene was calculated in Reads Per Kilobase per Million (RPKM) and log2 transformed.
For small RNA seq, sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and collapsed to the fasta format. The expression of mature miRNA was then measured using the Mapper and Quantifier modules of miRDeep2 version 2.0.0.7 (Friedlander, et al. 2012) with default parameters, normalized by the total reads matching all the miRNAs annotated by miRBase (Release 21) per library, and scaled as Reads Per Million (RPM).
Genome_build: FlyBase D. melanogaster: r6.04
Genome_build: FlyBase D. simulans: r2.01
Genome_build: FlyBase D. sechellia: r1.3
Genome_build: FlyBase D. erecta: r1.04
Supplementary_files_format_and_content: gene expression, miRNA expression and fasta files include clean reads and raw read count

organism: Drosophila simulans

source_name: testes

growth_protocol: Fruit flies were cultured under 25℃.

extract_protocol:
Tissues were dissected on dry ice, and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions.For small RNA seq, RNA segment of different size was seperated on PAGE gel, 18-30nt stripe was selected.

tag: age

value: 3-5d adult

value: testes

value: miR-983 mutant


title: D. simulans miR-983KO replicate 2

description: Gene expression in testes


title: IL27ra KO rep 3

value: Tumor


title: cMaf_Prdm1_DKO_2


title: D. simulans control replicate 1

description: Gene expression in testes

value: control


title: D. simulans control replicate 2

description: Gene expression in testes


title: WT_3

value: wild type


title: WT_9


title: IL27ra KO rep 2


title: WT_8


title: WT rep1


title: D. melanogaster miR-983KO replicate 2

description: Gene expression in testes

organism: Drosophila melanogaster


title: D. melanogaster miR-983KO replicate 1

description: Gene expression in testes


title: Dgcr8 KO transfected with siMbnl1/2_rep1

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

country: China

institute: Peking University

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
Mbnl-si1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.0
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.2.1
Genome_build: mm10 from Ensemble
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

molecule: polyA RNA

source_name: Dgcr8 KO transfected with siMbnl1/2

growth_protocol: Embryonic stem cell medium was composed of DMEM supplemented with 15% FBS, glutamate, nonessential amino acids, 2-mercaptoethanol (all from Gibco/Life Science Technologies) and LIF . Cells were grown on gelatin-coated plates or irradiated mouse embryonic fibroblast feeder cells (MEFs) .

extract_protocol:
Total RNA was prepared using Trizol (Invitrogen) and quantified on a BiodropsisBD2000 (OSTC)
RNA-seq libraries are prepared using Illumina dUTP protocols

treatment_protocol: 50 nM miRNA mimics (Dharmacon, Thermo Fisher)or siRNAs (GenePharma) were transfected into cells in each well of a six-well plate with DharmaFECT1 (Dharmacon, Thermo Fisher) 16 hr after plating.

tag: cell line

tag: cell type

value: mouse embryonic stem cells

value: Dgcr8 KO

tag: treatment

value: transfected with siMbnl1/2

tag: replicate


title: Dgcr8 KO transfected with miR-294_rep1

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
294-1

source_name: Dgcr8 KO transfected with miR-294

tag: strain

value: transfected with miR-294


title: D. melanogaster control replicate 2

description: Gene expression in testes

tag: tissue


title: Dgcr8 KO transfected with siMbnl1/2_rep2

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
Mbnl-si2

tag: genotype/variation


title: Dgcr8 KO transfected with miR-294_rep2

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
294-2


title: Dgcr8 KO control_rep2

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
ES1-mock2

source_name: Dgcr8 KO control


title: WT control_rep2

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
V65-mock2

source_name: WT control

value: WT


title: WT control_rep1

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
V65-mock1


title: scRNA-Seq by Drop-Seq, replicate 3

city: BEIJING

first: Xiannian

last: Zhang

state: BEIJING

address: YIHEYUAN ROAD NO.5

data_processing:
Pair-End 1 reads are processed to get the Cell Barcode and UMI sequences for each read. These infos are attached to Read2 headers.
Cell Barcodes are corrected, aggragated and the valid cell barcodes are filtered by requiring enough reads (40000 reads for each Cell barcode).
The Pair-End2(R2) with valid barcodes are splitted to different files accoding to cell barcode prefix. The headers contains information of cell barcodes and UMIs. R1 is not used for alignment.
The reads are mapped to GRCh38 with STAR aligner
The aligned bam file is processed to tag the mapped reads to the gene names
The UMIs counts and read counts for each gene of each cell barcode is calculated and form a expression matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include UMI counts  for each gene and each cell barcode (GeneExp.UMIs.XX.txt)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts  for each gene and each cell barcode (GeneExp.ReadCounts.XX.txt)

source_name: lymphoblastoid cell line GM12891

growth_protocol: GM12891 cell line were grown in RPMI-1640 medium with L-glutamine containing 10% FBS and 1% penicillin, streptomycin.

extract_protocol:
cell lysis were followed inDrop, Drop-seq and 10X cell lysis standard protocol respectively.
library constructions were followed inDrop, Drop-seq and 10X standart protocol respectively.

treatment_protocol: All cells were incubated at 37°C in 5% CO2 in culture bottle. Before experiment, cells were spun down in 150 g for 5 min and cell number was estimated by hemocytometer.

value: lymphoblastoid cell

tag: cell barcode base location

value: base 1-12 of R1

tag: umi base location

value: base 13-20 of R1


title: scRNA-Seq by Drop-Seq, replicate 2


title: scRNA-Seq by 10X, replicate 1

value: base 1-16 of R1

value: base 17-26 of R1


title: scRNA-Seq by inDrop, replicate 1


title: 5B

city: Providence

first: Stephanie

last: Post

state: Rhode Island

address: 84 Olive St room 502

department: EEB

institute: Brown University

data_processing:
Illumina software was used for base-calling
Bowtie was used to assemble sequence reads to dm3 using parameters -p 8 -i 30 -I 20000 --segment-length 25
In R, raw counts and RPKM values were computed by the ‘easyRNASeq’ package and differential expression calculated by the ‘edgeR’ package.
Genome_build: dm3
Supplementary_files_format_and_content: CSV file is a matrix of raw counts for all 9 samples

source_name: S2 cells

growth_protocol: S2 cells were grown to a density of ~1E6 cells and serum-depleted overnight (~16 hours)

extract_protocol:
Cells were lysed with lysis buffer from NE BioLabs magnetic mRNA isolation kit #S1550S
mRNA was purified and fragmented (Ambion #AM8740), then reverse transcribed to cDNA (Invitrogen SuperScript III # 18080051). DNA was purified by Agencourt Ampure XP beads and quantified by Qubit. DNA was repaired by End-It DNA Repair Kit (Epicentre, #ER0720) then supplemented with Klenow fragment (NE BioLabs #M0212s). Adapters were ligated using the T4 DNA Ligase Quick Ligase Kit (Enzymatics L603-HC-L) and PCR enriched using Phusion DNA polymerase (NE BioLabs #F-531). Libraries were gel purified, selecting DNA from 200-500bp, and gel extracted (Qiagen Qiaquick #28704).

treatment_protocol: 100nM DILP treatment or solvent (mock) for one hour


title: WT rep3


title: 5A


title: scRNA-Seq by 10X, replicate 2


title: D. melanogaster control replicate 1

description: Gene expression in testes


title: scRNA-Seq by inDrop, replicate 2


title: WT rep2


title: 2C


title: scRNA-Seq by Drop-Seq, replicate 1


title: 2B


title: Dgcr8 KO control_rep1

description:
WT_Dgcr8--_miR-294_siMbnl_FPKM.txt
ES1-mock1


title: DA

value: Mock


title: DB


title: True naive CD8 cells timestamped at day 28, rep 2

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description:
TgTrueNaive_28dayTimestampB
True naive cells made (Td-Tomato stamped) at 28 days.
gene_exp.diff: 28dTN
genes.read_group_tracking.txt: 28dTN_1

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 50 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the mouse mm10 reference genome+transcriptome (UCSC).
cuffquant (--library-type fr-firststrand) was used to quantify transcripts based on the mouse mm10 reference genome+transcriptome (UCSC).
cuffdiff v2.2.1 was used to call differentially expressed genes based on the mouse mm10 reference genome+transcriptome (UCSC).
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: Tab-delimited text files are standard cuffdiff2 output files for gene-level analysis, including counts, FPKM values, and q-values for differential expression testing (corrected for multiple hypothesis testing). The 'gene_exp.diff' file contains average FPKM values for each pair of replicates, as well as results for statistical testing for differential expression. The 'genes.read_group_tracking' file contains raw mapped read counts and FPKM values for individual samples.

source_name: CD4-CD8+CD44lo TdTomato+ sorted cells

growth_protocol: CD4cre-ERT2 mice were crossed to Ai9 mice bearing a floxed-stop TdTomato element such that when F1 offspring are exposed to tamoxifen, all cells bearing CD4 will begin expressing TdTomato for the duration of tamoxifen exposure.

extract_protocol:
CD8+ cells were magnetically enriched with CD8 microbeads and sorted to > 95% purity with a FACS Aria III on CD4- CD8+ TdTomato+ CD44 hi (virtual memory) or lo (true naïve) populations. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Directional RNA-seq libraries were prepared from total RNA isolated from 10,000 cells (~10-20ng) using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: To mark cell with TdTomato at specific times during development, mice were given tamoxifen at 1 day (through lactation, by administering tamoxifen orally to the Dam) or at 28 days of age (by direct oral administration to the mouse). The mice were then aged to allow for the same amount of post-thymic maturation (4 weeks).

tag: strain/background

tag: transgenic insertions

value: gBT-I, Ai9, CD4cre-ERT2

tag: timestamp age

value: 28 days

tag: age at collection

value: 8 weeks

value: spleen

value: CD4-CD8+CD44lo TdTomato+ sorted cells


title: VM CD8+ cells timestamped at day 1, moved to congenic recipients at 4 wks, collected 5 dpi (Listeria), rep 1

description:
TgVirtualMemory5dpi_1dayTimestampA
Virtual memory CD8 cells timestamped at day 1, transferred to congenic recipients at 4 wks who were infected with Listeria and timestamped CD8+ T cells collected 5 days post-infection, rep 1.
gene_exp.diff: 1dMP5
genes.read_group_tracking.txt: 1dMP5_0

source_name: CD4-CD8+CD44hi TdTomato+ sorted cells

growth_protocol: CD4cre-ERT2 mice were crossed to Ai9 mice bearing a floxed-stop TdTomato (RFP) element such that when F1 offspring are exposed to tamoxifen, all cells bearing CD4 will begin expressing TdTomato for the duration of tamoxifen exposure.

extract_protocol:
CD8+ cells were magnetically enriched with CD8 microbeads and sorted to > 95% purity with a FACS Aria III on CD4- CD8+TdTomato+. Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation.
Directional RNA-seq libraries were prepared from 25 ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: To mark cell with TdTomato at specific times during development, mice were given tamoxifen at 1 day (through lactation, by administering tamoxifen orally to the Dam) or at 28 days of age (by direct oral administration to the mouse). The mice were then allowed to age such that both populations had the same amount of post-thymic maturation (4 wks). Adoptive transfers of stamped, CD44+ CD8+ T cells were performed to transfer equivalent numbers of antigen-specific CD8+ T cells in to congenically marked recipients. These recipients were infected with Listeria bearing the antigen the timestamped CD8+ T cells respond to (gB). 5 days later, timestamped cells were recovered for sequencing.

value: 1 day

tag: age at congenic transfer

value: 4 weeks

tag: collection time post-infection

value: 5 days

value: CD4-CD8+CD44hi TdTomato+


title: VM CD8+ cells timestamped at day 28, moved to congenic recipients at 8 wks, collected 5 dpi (Listeria), rep 2

description:
TgVirtualMemory5dpi_28dayTimestampB
Virtual memory CD8 cells timestamped at day 28, transferred to congenic recipients at 8 wks who were infected with Listeria and timestamped CD8+ T cells collected 5 days post-infection, rep 2.
gene_exp.diff: 28dMP5
genes.read_group_tracking.txt: 28dMP5_1


title: 5C


title: VM CD8+ cells timestamped at day 28, moved to congenic recipients at 8 wks, collected 5 dpi (Listeria), rep 1

description:
TgVirtualMemory5dpi_28dayTimestampA
Virtual memory CD8 cells timestamped at day 28, transferred to congenic recipients at 8 wks who were infected with Listeria and timestamped CD8+ T cells collected 5 days post-infection, rep 1.
gene_exp.diff: 28dMP5
genes.read_group_tracking.txt: 28dMP5_0


title: VM CD8+ cells timestamped at day 1, moved to congenic recipients at 4 wks, collected 5 dpi (Listeria), rep 2

description:
TgVirtualMemory5dpi_1dayTimestampB
Virtual memory CD8 cells timestamped at day 1, transferred to congenic recipients at 4 wks who were infected with Listeria and timestamped CD8+ T cells collected 5 days post-infection, rep 2.
gene_exp.diff: 1dMP5
genes.read_group_tracking.txt: 1dMP5_1


title: Virtual memory CD8 cells timestamped at day 1, rep 1

description:
TgVirtualMemory_1dayTimestampA
Virtual memory cells made (Td-Tomato stamped) at 1 day.
gene_exp.diff: 1dMP
genes.read_group_tracking.txt: 1dMP_0

value: CD4-CD8+CD44hi TdTomato+ sorted cells


title: Virtual memory CD8 cells timestamped at day 28, rep 2

description:
TgVirtualMemory_28dayTimestampB
Virtual memory cells made (Td-Tomato stamped) at 28 days.
gene_exp.diff: 28dMP
genes.read_group_tracking.txt: 28dMP_1


title: Virtual memory CD8 cells timestamped at day 1, rep 2

description:
TgVirtualMemory_1dayTimestampB
Virtual memory cells made (Td-Tomato stamped) at 1 day.
gene_exp.diff: 1dMP
genes.read_group_tracking.txt: 1dMP_1


title: Virtual memory CD8 cells timestamped at day 28, rep 1

description:
TgVirtualMemory_28dayTimestampA
Virtual memory cells made (Td-Tomato stamped) at 28 days.
gene_exp.diff: 28dMP
genes.read_group_tracking.txt: 28dMP_0


title: 2A


title: SPR_LP_Rep3

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

description: Small RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie2 v2.3.4.1 with parameters --sensitive-local -p 4 -q
Exon, piRNA, miRNA, precursor, GtRNA and ncRNA GTF files were acquired from UCSC genome browser. Raw reads were generated from R package GenomicAlignment and GenomicFeatures.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw reads for each Sample

source_name: mature sperm cells

extract_protocol:
Mammary gland and sperm samples were removed.  Frozen crushed tissue were used for RNA extraction according with the manufacturer's instructions. The total RNA was performed using miRNeasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Males were fed etiher a control or low-protein (LP) diet from 3 to 10 weeks of age.Mature sperm was collected from fathers and Mammary tissue from their female offspring.

tag: gender

value: male

value: mature sperm cells


title: SPR_LP_Rep2

description: Small RNA


title: SPR_LP_Rep1

description: Small RNA


title: SPR_CO_Rep3

description: Small RNA


title: SPR_LP_Rep4

description: Small RNA


title: SPR_CO_Rep1

description: Small RNA


title: MG_LP_Rep4

description: Small RNA

source_name: mammary gland tissue

value: female

value: mammary gland tissue


title: DC


title: SPR_CO_Rep2

description: Small RNA


title: Rec10 in Clr4Δ at 3.5h post-meiosis

type: genomic

city: Seattle

first: Gerald

middle: R

last: Smith

state: Washington

address: 1100 Fairview Ave. N.

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Research Center

description: Rec10_Clr4Δ_3.5h GFP-IP Dyes swapped

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed.

scan_protocol: Slides were imaged on an Agilent G2565AA Microarray Scanner and quantified using Agilent Feature Extraction Software (v 10.1.1.1 or 10.5.1.1).

data_processing: Output ratios were corrected for dye swapping and then normalized to the genome median. The 0h data was subtracted from 3.5h to reduce the background noise.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Whole-cell input for Rec10 protein in Clr4Δ cells at 3.5 hours in meiosis

label_protocol: Immunoprecipitated material was PCR amplified to increase signal and incorporate Cy3/Cy5-labeled dUTPs.

growth_protocol: S. pombe cells were grown in minimal media without nitrogen for ~18 hours to synchronize the cells. Nitrogen was added and the temperature shifted to 34°C, marking the start of meiosis (t=0).

extract_protocol: 200 ml culture was removed and formaldehyde was added to a final concentration of 1%. Chromatin was sonicated to ~1000 bp and the protein of interest was immunoprecipitated.

tag: time since meiosis started

value: 3.5 hours

tag: chip antibody

source_name: IP Rec10 protein at 3.5 hours in clr4Δ cells in meiosis

value: anti-GFP from mouse (clones 7.1 & 13.1)

tag: antibody vendor (catalog #)


title: Rec10 in WT at 3.5h post-meiosis

description: Rec10_WT_3.5h GFP-IP Dyes swapped

source_name: Whole-cell input for Rec10 protein in WT cells at 3.5 hours in meiosis

value: WT

source_name: IP Rec10 protein at 3.5 hours in WT cells in meiosis


title: Rec10 in WT at 0h

description: Rec10_WT_0h GFP-IP Dyes swapped

source_name: Whole-cell input for Rec10 protein in WT cells at 0 hour in meiosis

value: 0 hour

source_name: IP Rec10 protein at 0 hour in WT cells in meiosis


title: MG_LP_Rep2

description: Small RNA


title: True naive CD8 cells timestamped at day 28, rep 1

description:
TgTrueNaive_28dayTimestampA
True naive cells made (Td-Tomato stamped) at 28 days.
gene_exp.diff: 28dTN
genes.read_group_tracking.txt: 28dTN_0

value: gBT-I, Ai9, CD4cre-ERT2

value: 28 days

tag: cell type


title: MG_CO_Rep4

description: Small RNA


title: MG_LP_Rep1

description: Small RNA


title: MG_CO_Rep2

description: Small RNA


title: Vinh1: scramble siRNA

city: Singapore

first: Ying

last: Li

address: 14 Medical Dr, Singapore

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Sequenced reads were mapped to mm10 whole genome using STAR_2.4.0i with default parameters
gene exprisson was called by featureCounts v1.5.0-p1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: E14 cells with sramble siRNA

growth_protocol: E14 mouse ESCs were maintained in GMEM supplemented with 15%FBS, 2mM L-glutamine, 100 mM non-essential amino acids, 0.1mM b-mercaptoethanol, 1mM sodium pyruvate (Invitrogen) and 1,000U/ml LIF (Millipore) on gelatin-coated plates.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: E14 cells were then transfected with scramble or Mettl8 siRNA with the aid of Lipofectamine RNAiMAX in Opti-MEM l reduced serum medium (Invitrogen). Seventy-two hours later cells were harvested for RNA extraction.

value: mouse ES cells

tag: passages


title: SPR_CO_Rep4

description: Small RNA

tag: strain


title: MG_CO_Rep3

description: Small RNA

tag: tissue


title: Vinh2: Mettl8 siRNA

source_name: E14 cells with Mettl8 siRNA


title: MG_LP_Rep3

description: Small RNA


title: shKdm5b_Input_TSC_diff_d3

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

institute: Wayne State University

description: Direct sequencing following sonication of x-linked chromatin

library_source: genomic

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

growth_protocol: shLuc and Kdm5b TS cells were cultured in the presence of FGF4 to maintain self-renewal, and in the absence of FGF4 to induce differentiation at 37oC with 5% CO2. TS cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: genotype/variation

value: differentiated TS cell

tag: differentiation day

value: day 3


title: shLuc_Input_TSC_diff_d4

value: shLuc

value: day 4


title: shKdm5b_Input_TSC_diff_d2

value: day 2


title: shLuc_Input_TSC_diff_d3


title: shKdm5b_H3K4me3_TSC_diff_d4

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: shLuc_H3K4me3_TSC_diff_d4

description: Chromatin IP against H3K4me3


title: shKdm5b_H3K4me3_TSC_diff_d3

description: Chromatin IP against H3K4me3


title: MG_CO_Rep1

description: Small RNA


title: shKdm5b_Input_TSC_diff_d4


title: shKdm5b_H3K4me3_TSC_diff_d2

description: Chromatin IP against H3K4me3


title: shLuc_H3K4me3_TSC_diff_d3

description: Chromatin IP against H3K4me3


title: Medulloblastoma_CNMC843

first: Samuel

last: Rivero-Hinojosa

state: District of Columbia

address: 111 Michigan Ave NW

department: Children’s Research Institute, Center for Cancer and Immunology Research

institute: Children’s National Health System

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip  Human Gene 2.0 ST Array (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned using the GeneChip® System 3000Dx v.2 (Affymetrix, Santa Clara, CA)

data_processing: The data were analyzed in the R environment (v3.4.1) (https://www.r-project.org) with the oligo package (v1.36.1) usimng the RMA olgorithm

source_name: pediatric medulloblastoma

label_protocol: Biotynilated cRNA were prepared accoriding to the GeneChip WT Plus kit (Affymetrix, Santa Clara, CA)  from total of 250ng of total RNA

growth_protocol: all samples are frozen primary tissues

extract_protocol: specimens were homogenized in Trizol followed by phase separation of nucleic acids with chloroform. RNA was extracted using Picopure RNA isolation kit (Arcturus Bioscience, Mountain View, CA). DNA was removed by treating columns with RNase Free DNase (Qiagen, Valencia, CA)

treatment_protocol: all samples are untreated primary tissue

tag: age

tag: subgroup

value: WNT

value: M

tag: metastasis stauts

tag: tissue type

value: pediatric medulloblastoma


title: shLuc_H3K4me3_TSC_diff_d2

description: Chromatin IP against H3K4me3


title: Medulloblastoma_MDT3612

value: SHH

value: F


title: Medulloblastoma_MDT2955


title: Medulloblastoma_CNMC58

value: M+


title: shLuc_Input_TSC_diff_d2


title: Rec10 in Clr4Δ at 0h

description: Rec10_Clr4Δ_0h GFP-IP Dyes swapped

source_name: Whole-cell input for Rec10 protein in Clr4Δ cells at 0 hour in meiosis

tag: strain/background

source_name: IP Rec10 protein at 0 hour in clr4Δ cells in meiosis

value: anti-GFP from mouse (clones 7.1 & 13.1)


title: Medulloblastoma_CNMC763


title: Medulloblastoma_MDT1380


title: Medulloblastoma_MDT2381


title: Medulloblastoma_MDT1367

value: Group 4


title: Medulloblastoma_CNMC336


title: Medulloblastoma_CNMC789


title: Medulloblastoma_CNMC605


title: Medulloblastoma_CNMC59


title: Medulloblastoma_CNMC732

value: Group 3


title: Medulloblastoma_CNMC498


title: Medulloblastoma_CNMC673


title: Medulloblastoma_CNMC698


title: Medulloblastoma_MDT1219


title: Cerebellum_860

source_name: normal cerebellum

value: Cerebellum

value: normal cerebellum


title: Cerebellum_865


title: Medulloblastoma_CNMC56


title: Cerebellum_859


title: Cerebellum_855


title: TMX-treated rep2

city: Tehran

first: Milad

last: Rouhimoghadam

address: 3rd Floor., NO.3., 12th Alley., Shahid Ghandi St., Sohrevardi Shomali St., Tehran., Iran

country: Iran

institute: University of Tehran

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Gene expression data are reported in Excel files.
In All genes.xlsx, sample_1 (CR) = control, sample_2 (TR) = TMX.

source_name: mammary gland, breast; derived from metastatic site

growth_protocol: Human breast cancer cell line, MCF7 cells (ATCC® HTB-22™), were purchased from Iranian Biological Resource Center (Tehran, Iran). Cells were cultured in RPMI-1640 medium (Sigma, USA) containing 100 μg/ml penicillin, 100 μg/ml streptomycin, 2 mM glutamine, 10% heat-inactivated fetal bovine serum (FBS) (Invitrogen, USA), and incubated at 37 °C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from the cells using TriPure Isolation Reagent (Roche Diagnostics GmbH, Germany) according to the kit’s protocol. To avoid genomic DNA contamination, the RNA samples were treated with DNase for one hour.
Following RNA isolation, creation of an RNA-seq library is the next step in transcriptome sequencing. The preparation of intended cDNA libraries and paired-end sequencing were performed by the Beijing Genome Institute (BGI), China. In total, four cDNA paired-end libraries were generated for transcriptome sequencing on Illumina HiSeq 2000 platform. Briefly, rRNA depletion methods were used for library construction. Based on the protocol, after rRNA depletion all other RNAs with or without the polyA sequence were subjected to adaptor ligation. The adapter-ligated templates were purified by the Agencourt AMPure SPRI beads and fragments with insert size about 200 bp were excised and used to synthesize the first strand cDNA.

treatment_protocol: According to MTT assay, the LC50 of tamoxifen after 48 h was determined as 250 µM. Tamoxifen was dissolved in DMSO and then added to culture medium to the final desired concentration based on the determined LC50 and filtered. Cells (at 80% confluency) were incubated with freshly prepared drugs for 48h in a humidified incubator before being trypsinized and washed with phosphate-buffered saline 3 times and stored at −70°C.

tag: cell line

tag: agent

value: TMX


title: Untreated rep2

value: untreated control


title: Untreated rep1


title: TMX-treated rep1


title: Cerebellum_849

tag: gender


title: OVCAR3-Sensitive

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

country: Spain

institute: Hospital La Paz Institute for Health Research

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin OVCAR3 ovarian cancer cell line

data_processing:
The mapping was carried out using GEM 1.242 to a converted reference sequence (Homo sapiens, GRCh37). The reference file contains two copies of the hsapiens GRCh37 reference, one with all C's changes to T's and one with all G's changed to A's. In addition the file also contains two copies of the NCBI viral genome dataset (rel 53, http://www.ncbi.nlm.nih.gov/genomes/GenomesHome.cgi?taxid=10239), modified in the same way as for the human genome. Before mapping, the original sequence data was then modified so that any C's in the first read of a pair were converted to T's, and any G's on the second read of a pair were converted to A's. The mapping was then performed, and the original sequence was replaced in the output mapping.
Read Filtering: Read pairs were selected where a single paired mapping existed with the correct read pair orientation and with a fragment size within the central 95% of the read size distribution.
Calling of methylation levels and genotypes was performed by the program bscall using the default settings.
Filtering of homozygous CpG sites and homozygous cytosines was performed using a maximum coverage cutoff of 250 reads per position.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file include methylation probability estimation for each CpG

source_name: Sensitive cisplatin OVCAR3 ovarian cancer cell line

growth_protocol: Following the culture recommendations from ATCC and ECACC

extract_protocol:
DNA was extracted using conventional techniques of digestion with proteinase K followed by phenol/chloroform extraction.
Genomic DNA (2 μg) was spiked with unmethylated λ DNA (Promega) at a concentration of 5 ng of λ DNA per 1 μg of genomic DNA. The short-insert paired-end library was prepared using the TruSeq™DNA Sample Preparation Kit v2 (Illumina Inc.) following manufacturer’s guidelines with minor modifications. In brief: The DNA was sheared with a Covaris E220 (Covaris) to 50–500 bp and size-selected to 150-300 bp fragments using AMPure XP beads (Agencourt Bioscience Corp.). DNA fragments were end-repaired, adenylated and ligated to Illumina specific indexed paired-end adaptors. After adaptor ligation, the DNA was treated with sodium bisulfite using the EpiTect Bisulfite kit (Qiagen) following the manufacturer's instructions for formalin-fixed and paraffin-embedded (FFPE) tissue samples with two rounds of conversions. After bisulfite conversion the adaptor-ligated DNA was amplified with 7 cycles of PCR using the PfuTurboCx Hotstart DNA polymerase (Stratagene). The library was quality controlled using BioAnalyzer 7500 assay (Agilent).

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatin.

value: Ovarian

tag: chemoterapy drug

value: cisplatin

tag: phenotype

value: Sensitive


title: H460-Sensitive

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin H460 lung cancer cell line

source_name: Sensitive cisplatin H460 lung cancer cell line

value: Lung


title: H460-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin H460 lung cancer cell line

source_name: Resistant cisplatin H460 lung cancer cell line

value: Resistant


title: OVCAR3-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin OVCAR3 ovarian cancer cell line

source_name: Resistant cisplatin OVCAR3 ovarian cancer cell line


title: H23-Sensitive

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin H23 lung cancer cell line

source_name: Sensitive cisplatin H23 lung cancer cell line


title: Medulloblastoma_CNMC57

value: M


title: H23-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin H23 lung cancer cell line

source_name: Resistant cisplatin H23 lung cancer cell line


title: Cerebellum_cer865 [methylation]

hyb_protocol: DNA was prepared for methylation analysis via bisulphate conversion using EZ DNA Methylation-Gold kit (Zymo Research, Irvine, CA). Bisulphite-converted DNA was denatured and neutralized. After amplification via PCR, DNA was fragmented and hybridized onto the Infinium Methylation EPIC BeadChip (Illumina, San Diego, CA) using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan system

data_processing:
Data was processed in the R statistical environment (v3.3.1) (https://www.r-project.org) using minfi (v 1.22.1) and ChAMP (v2.4.1) packages.
The Methylation_Matrix_signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from 33 tumor and 5 control cerebellum tissue lysates using the Gentra Puregene DNA extraction kit (Quiagen, Valencia, CA)


title: Cerebellum_cer859 [methylation]


title: Cerebellum_cer849 [methylation]


title: Tumor_CNMC698 [methylation]

value: pediatric medulloblastoma


title: Tumor_CNMC732 [methylation]


title: Tumor_CNMC673 [methylation]


title: A2780-Sensitive

description: DNA methylation profiling data by bisulfite conversion from sensitive cisplatin A2780 ovarian cancer cell line

source_name: Sensitive cisplatin A2780 ovarian cancer cell line


title: Cerebellum_cer855 [methylation]


title: Cerebellum_cer860 [methylation]


title: Tumor_MDT1219 [methylation]


title: Tumor_MDT1365 [methylation]


title: Tumor_CNMC605 [methylation]


title: A2780-Resistant

description: DNA methylation profiling data by bisulfite conversion from resistant cisplatin A2780 ovarian cancer cell line

source_name: Resistant cisplatin A2780 ovarian cancer cell line


title: Tumor_CNMC59 [methylation]


title: Tumor_MB18 [methylation]


title: Tumor_MDT3612 [methylation]

value: SHH


title: Tumor_MB95 [methylation]


title: Tumor_MDT530 [methylation]


title: Tumor_MDT1166 [methylation]

value: F


title: Tumor_MDT1361 [methylation]

value: M+


title: Tumor_CNMC57 [methylation]


title: Tumor_MB90 [methylation]


title: Tumor_MDT1367 [methylation]


title: Tumor_MB51 [methylation]


title: OVCAR3-Resistant-Rep2

description: LncRNA and mRNA expression profiling data from resistant cisplatin OVCAR3 ovarian cancer cell line

hyb_protocol: The labeled cRNAs were hybridized onto the Human LncRNA Array v3.0 (8 x 60K, Arraystar).

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner (G2505C). Data was extracted using Agilent Feature Extraction software (version 11.0.1.1).

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 1 out of 16 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA from S and R cells was extracted by the guanidine thiocyanate method using TRIzol reagent (Invitrogen) and followed by a DNAse treatment (Qiagen). RNA integrity and concentration were assessed by Nanodrop ND-1000 and 2100 Bioanalyzer (Agilent Technologies). mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatine. There are two independent biological replicates per cell line.

tag: replicate


title: OVCAR3-Sensitive-Rep1

description: LncRNA and mRNA expression profiling data from sensitive cisplatin OVCAR3 ovarian cancer cell line


title: OVCAR3-Sensitive-Rep2


title: Tumor_MDT223 [methylation]


title: Tumor_CNMC498 [methylation]


title: H460-Sensitive-Rep2

description: LncRNA and mRNA expression profiling data from sensitive cisplatin H460 lung cancer cell line


title: OVCAR3-Resistant-Rep1


title: H460-Sensitive-Rep1


title: Tumor_CNMC541 [methylation]


title: Tumor_MDT2063 [methylation]


title: Tumor_MB91 [methylation]


title: H460-Resistant-Rep2

description: LncRNA and mRNA expression profiling data from resistant cisplatin H460 lung cancer cell line


title: Tumor_MDT161 [methylation]


title: D. erecta testes

description: Small RNAs expression

organism: Drosophila erecta

source_name: testes

value: 3-5d adult

value: testes

tag: genotype

value: wild type


title: H23-Sensitive-Rep2

description: LncRNA and mRNA expression profiling data from sensitive cisplatin H23 lung cancer cell line


title: SPR_LP_Rep2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to custom miRNA reference sequence derived from mm10 whole genome using bismark v0.18.1_dev and bowtie2 v2.3.4.1 with parameters -q --parallel 2 -N 1 --score-min L,0,-0.2 --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500
Coverage results and beta value were calculted from R package GenomicAlignment and GenomicFeatures.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include abundance and beta value for each sample

source_name: Mature sperm cells

extract_protocol:
Genomic DNA was isolated from paternal sperm and offspring’s mammary tissue (n=3/group). Methylated DNA was eluted by the MethylMiner Methylated DNA Enrichment Kit (Invitrogen).  Briefly, one microgram of genomic DNA was sheared by sonication and captured by MBD proteins. The methylated DNA was eluted and used to generate Methyl-CpG binding domain-based capture (MDBCap) libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Males were fed etiher a control or low-protein (LP) diet from 3 to 10 weeks of age. Mature sperm was collected from fathers and Mammary tissue from their female offspring.

value: male

value: Mature sperm cells


title: A2780-Sensitive-Rep2

description: LncRNA and mRNA expression profiling data from sensitive cisplatin A2780 ovarian cancer cell line


title: SPR_CO_Rep3


title: SPR_LP_Rep1


title: H23-Resistant-Rep2

description: LncRNA and mRNA expression profiling data from resistant cisplatin H23 lung cancer cell line


title: SPR_CO_Rep2


title: A2780-Resistant-Rep2

description: LncRNA and mRNA expression profiling data from resistant cisplatin A2780 ovarian cancer cell line


title: H23-Resistant-Rep1


title: H23-Sensitive-Rep1


title: A2780-Sensitive-Rep1


title: SPR_CO_Rep1


title: Tumor_MDT2381 [methylation]


title: MG_LP_Rep3

source_name: Mammary gland tissue

value: female

value: Mammary gland tissue


title: A2780-Resistant-Rep1

value: Ovarian


title: MG_LP_Rep1


title: MG_CO_Rep3


title: MG_CO_Rep2


title: MG_CO_Rep1


title: 399-CD4

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

hyb_protocol: Standard Illumina hybridization protocol for cRNA target (carried out by UCLA Neuroscience Genomics Core). Illumina Human HT-12 BeadArray.

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1. All available probe values are provided, with no additional filtering. Normalized data omit genes that were missing values due to random variations in Illumina microarray probe synthesis (i.e., missing data were not imputed).

label: biotin

source_name: CD3+/CD4+ leukocytes

label_protocol: Ambion TotalPrep target synthesis for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

extract_protocol: Total RNA was extracted from MACS-isolated (Miltenyi Biotec) CD14+ and CD3+/CD4+ primary peripheral blood mononuclear cell samples using the manufacturer's standard protocol & reagents.

tag: cell type

value: Helper T Cell

tag: low ses

value: Male

tag: bmi

tag: race

tag: asthma severity

tag: ics

tag: saba


title: 379-CD4

tag: age


title: 401-CD4

value: Female


title: 362-CD4


title: 367-CD4


title: 396-CD4


title: 382-CD4


title: 355-CD4


title: 361-CD4


title: 363-CD4


title: 394-CD4


title: 393-CD4


title: 372-CD4


title: 400-CD4


title: 350-CD4


title: Tumor_CNMC336 [methylation]

source_name: pediatric medulloblastoma

tag: subgroup

tag: metastasis stauts

tag: tissue type


title: 356-CD4


title: 348-CD4


title: 397-CD4


title: Tumor_MB37 [methylation]


title: Tumor_CNMC789 [methylation]


title: 347-CD4


title: Tumor_CNMC843 [methylation]

value: WNT


title: 316-CD4


title: Tumor_MDT2955 [methylation]


title: 332-CD4


title: 319-CD4


title: 330-CD4


title: 327-CD4


title: 290-CD4


title: 267-CD4


title: 269-CD4


title: 323-CD4


title: 287-CD4


title: 312-CD4


title: 262-CD4


title: MG_LP_Rep2

tag: strain

tag: tissue


title: 320-CD4

tag: gender


title: 275-CD4


title: 302-CD4


title: 259-CD4


title: 291-CD4


title: 273-CD4


title: 255-CD4


title: 249-CD4


title: Tumor_CNMC58 [methylation]


title: Tumor_MB88 [methylation]

value: M


title: Tumor_MDT1380 [methylation]

value: pediatric medulloblastoma


title: Tumor_CNMC763 [methylation]


title: H460-Resistant-Rep1

tag: cell line

value: Lung

tag: chemoterapy drug

value: cisplatin

tag: phenotype

value: Resistant


title: 245-CD4

tag: cell type


title: 247-CD4

tag: low ses


title: 243-CD4

tag: bmi


title: 345-CD4

tag: race


title: 241-CD4

tag: asthma severity


title: 234-CD4

tag: ics


title: 227-CD4

tag: saba


title: 222-CD4

tag: age


title: 308-CD4


title: 200-CD4


title: 223-CD4


title: 228-CD4


title: 203-CD4


title: 211-CD4


title: 205-CD4


title: 204-CD4


title: 188-CD4


title: 185-CD4


title: 201-CD4


title: 217-CD4


title: 180-CD4


title: 187-CD4


title: 199-CD4


title: 191-CD4


title: 230-CD4


title: 192-CD4


title: 202-CD4


title: 178-CD4


title: 167-CD4


title: 171-CD4


title: 177-CD4


title: 195-CD4


title: 165-CD4


title: 166-CD4


title: 158-CD4


title: 160-CD4


title: 155-CD4


title: 153-CD4


title: 137-CD4


title: 145-CD4


title: 154-CD4


title: 131-CD4


title: 117-CD4


title: 113-CD4


title: 135-CD4


title: 124-CD4


title: 129-CD4


title: 400-CD14

source_name: CD14+ leukocytes

value: Monocyte


title: 399-CD14


title: 121-CD4


title: 401-CD14


title: 120-CD4


title: 106-CD4


title: 107-CD4


title: 110-CD4


title: 396-CD14


title: 115-CD4


title: 109-CD4


title: 112-CD4


title: 394-CD14


title: 367-CD14


title: 372-CD14


title: 363-CD14


title: 356-CD14


title: D. sechellia testes

description: Small RNAs expression

organism: Drosophila sechellia

extract_protocol:
Tissues were dissected on dry ice, and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions.For small RNA seq, RNA segment of different size was seperated on PAGE gel, 18-30nt stripe was selected.

value: 3-5d adult

value: testes

tag: genotype


title: 142-CD4


title: 133-CD4


title: 397-CD14


title: 101-CD4


title: 355-CD14


title: 393-CD14


title: 362-CD14


title: 382-CD14


title: 350-CD14


title: 348-CD14


title: Huh-7.5 cells treated with mock (0.1% ethanol) 2

city: Frankfurt am Main

first: Christian

middle: M

last: Lange

address: Theodor-Stern-Kai 7

department: Department of Medicine 1

country: Germany

institute: Goethe University Hospital Frankfurt

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
Unsupported Human Gene 1.0 ST Array CDF Files
HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Huh-7.5 cells were grown in complete DMEM at a confluency of 70% prior to treatment.

extract_protocol: RNA were extracted with the RNeasy Micro Kit from Qiagen. RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 40ng total RNA.

treatment_protocol: Cells were treated with mock (0.1% ethanol), 10 nM calcitriol or calcipotriol for 12 hours.

value: hepatoma


title: Huh-7.5 cells treated with calcipotriol (10 nM) 2


title: 345-CD14


title: 379-CD14


title: 361-CD14


title: 347-CD14


title: Huh-7.5 cells treated with calcipotriol (10 nM) 1


title: 327-CD14


title: 320-CD14


title: Huh-7.5 cells treated with calcitriol (10 nM) 1


title: 332-CD14


title: AM_03175_LCMV

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4966

hyb_protocol: Following fragmentation and labeling, 2.6ug of cDNA were hybridized for 16 hr at 45°C on GeneChip Mouse Gene ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Average signal intensities for each probe set within arrays were calculated by and exported from Affymetrix’s Expression Console (Version 1.1) software using the RMA method which incorporates convolution background correction, summarization based on a multi-array model fit robustly using the median polish algorithm, and sketch-quantile normalization.  For this experiment, two pairwise comparisons were used to statistically resolve gene expression differences between Strain groups using the R/maanova analysis package.  Specifically, differentially expressed genes will be detected by using F1, the classical F-statistic that only uses data from individual genes. Statistical significance levels of the pairwise comparisons will be calculated by permutation analysis (1000 permutations) and adjusted for multiple testing using the false discovery rate (FDR), q-value, method. Differentially expressed genes are declared at an FDR q-value threshold of 0.05.

source_name: NOD.LCMV thymus, 2hs post-injection gp33 peptide

label_protocol: Fragmented biotinylated cDNA were produced from 250ng total RNA according to the standard protocol for the Applied Biosystems WT Expression Kit for Gene 1.0 ST Arrays.

growth_protocol: Three to five 5-week-old, NOD.LCMV and NOD.Ln82-LCMV female mice.

extract_protocol: Trizol extraction of total RNA from whole thymus was performed using Ambion's PureLink RNA Mini Kit according to the manufacturer's instructions..

treatment_protocol: Mice were i.v. injected with 0.5μg of gp33 (KAVYNFATM) or Db binding control peptide (ASNENMETM). Two hours post-injection, mice were euthanized and whole thymus tissue was dissected.

value: 5 weeks old

tag: treatment

value: injection of gp33 peptide

value: Thymus


title: Huh-7.5 cells treated with calcitriol (10 nM) 2


title: 330-CD14


title: AM_03170_LCMV

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4965

value: female


title: 323-CD14


title: LCMV_4

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4961

source_name: NOD.Ln82-LCMV thymus, 2hs post-injection gp33 peptide


title: AM_03178_Db

description:
Gene expression data from Thymus 2hs post injection with Db control peptide
GES11_4964

source_name: NOD.LCMV thymus, 2hs post-injection Db peptide

value: injection of Db peptide


title: 308-CD14


title: LCMV_3

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4960


title: AM_03177_Db

description:
Gene expression data from Thymus 2hs post injection with Db control peptide
GES11_4963


title: AM_03179_Db

description:
Gene expression data from Thymus 2hs post injection with Db control peptide
GES11_4962


title: AM_03176_LCMV

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4967


title: Db_4

description:
Gene expression data from Thymus 2hs post injection with Db control peptide
GES11_4956

source_name: NOD.Ln82-LCMV thymus, 2hs post-injection Db peptide


title: Db_1

description:
Gene expression data from Thymus 2hs post injection with Db control peptide
GES11_4953


title: 312-CD14

value: Male


title: LCMV_1

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4958


title: Huh-7.5 cells treated with mock (0.1% ethanol) 1


title: 316-CD14


title: LCMV_2

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4959


title: 319-CD14

value: Female


title: Db_3

description:
Gene expression data from Thymus 2hs post injection with Db control peptide
GES11_4955


title: Db_2

description:
Gene expression data from Thymus 2hs post injection with Db control peptide
GES11_4954


title: LCMV_5

description:
Gene expression data from Thymus 2hs post injection with gp33 peptide. Induced negative selection
GES11_4957


title: 291-CD14


title: NHKBr17_3

first: Ai

last: Nagano

address: John Vane Science Centre, Charterhouse Square

description: primary normal human keratinocytes

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised with LUMI in R

source_name: normal human keratinocyte cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen). Quantification and quality control of RNA was performed on a Nanodrop spectrophotometer (Thermo) and Agilent Bioanalyser (Agilent

tag: metastat

value: Keratinocytes

tag: immune

value: Normal

tag: replicate


title: NHKAbd16_3

description: primary normal human keratinocytes

scan_protocol: Standard Illumina hybridization protocol


title: NHKAbd15_3

description: primary normal human keratinocytes


title: 287-CD14

tag: gender


title: 290-CD14


title: NHKAbd16_2

description: primary normal human keratinocytes


title: NHKBr17_2

description: primary normal human keratinocytes


title: IC19_3

description: primary lesion

source_name: human cutaneous squamous cell carcinoma (cSCC) cell line

value: Primary

value: Immunocompetent


title: 275-CD14


title: 269-CD14


title: NHKAbd16_1

description: primary normal human keratinocytes


title: NHKBr17_1

description: primary normal human keratinocytes


title: 262-CD14


title: IC19_2

description: primary lesion


title: IC12_3

description: primary lesion


title: IC18_1

description: primary lesion


title: NHKAbd15_2

description: primary normal human keratinocytes


title: IC12_2

description: primary lesion


title: 273-CD14


title: IC19_1

description: primary lesion


title: T8_3

description: primary lesion

value: Treated with immunosuppressive drugs


title: IC12_1

description: primary lesion


title: IC18_3

description: primary lesion


title: NHKAbd15_1

description: primary normal human keratinocytes


title: IC18_2

description: primary lesion


title: 267-CD14


title: T8_2

description: primary lesion


title: T8_1

description: primary lesion


title: 259-CD14


title: 255-CD14


title: T2_1

description: primary lesion


title: 249-CD14


title: 102-CD4

value: Helper T Cell


title: T2_3

description: primary lesion


title: T11_3

description: primary lesion


title: 245-CD14

value: Monocyte


title: T11_2

description: primary lesion


title: T11_1

description: primary lesion


title: T2_2

description: primary lesion


title: T1_1

description: primary lesion


title: 243-CD14


title: 247-CD14


title: T1_3

description: primary lesion


title: PM1_1

description: Pre-malignant scalp of MET1

value: Pre-malignant scalp


title: 234-CD14


title: T1_2

description: primary lesion


title: T10_3

description: primary lesion


title: T10_2

description: primary lesion


title: 230-CD14


title: PM1_3

description: Pre-malignant scalp of MET1


title: PM1_2

description: Pre-malignant scalp of MET1


title: 228-CD14


title: MET4_3

description: MET4 from a lymph node metastasis of MET1

value: Metastat


title: 227-CD14


title: 223-CD14


title: MET4_2


title: 222-CD14


title: MET4_1


title: MET2_2

description: MET2 from a recurrence of MET1


title: MET2_3

description: MET2 from a recurrence of MET1


title: MET2_1

description: MET2 from a recurrence of MET1


title: IC8_3

description: primary lesion

value: Immuno-competent


title: T10_1

description: primary lesion


title: MET1_2

description: primary lesion


title: 217-CD14


title: MET1_3

description: primary lesion


title: MET1_1

description: primary lesion


title: 205-CD14


title: 204-CD14


title: IC8_1

description: primary lesion


title: Tg_rep3

city: Ann Arbor

first: Tomonori

last: Hosoya

address: 109 Zina Pitcher Place

department: CDB

institute: University of Michigan

description:
Sample_55171
sample name in processed data: 720VA_2

data_processing:
TopHat 2
Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: DN3a stage thymocytes

extract_protocol:
QIAGEN RNeasy Micro Kit with in-column DNase treatment
Ribo-Zero Gold rRNA Removal Kit (Illumina) followed by library preparation

tag: strain

value: thymocytes

tag: developmental stage

tag: sample id


title: 203-CD14

tag: cell type


title: 200-CD14

tag: low ses


title: IC8_2

city: London

institute: Barts Cancer Institute

description: primary lesion


title: 211-CD14

tag: bmi


title: IC1SCC_2

description: primary lesion


title: 201-CD14

tag: race


title: IC1SCC_1

description: primary lesion


title: 199-CD14

tag: asthma severity


title: 195-CD14

tag: ics


title: IC1MET_3

description: IC1MET from a lymph node metastasis of IC1SCC


title: IC1SCC_3

description: primary lesion


title: 302-CD14

tag: saba


title: 202-CD14

tag: age


title: IC1MET_2


title: Tg_rep2

description:
Sample_55170
sample name in processed data: 720VA_1

tag: genotype


title: IC1MET_1


title: wildtype_rep3

description:
Sample_55167
sample name in processed data: Ctrl_2

value: wild type


title: Tg_rep1

description:
Sample_55169
sample name in processed data: 720VA_0


title: green_rep3

data_processing:
TopHat 2
Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample. Excel file includes differential expression analysis from Cuffdiff.

source_name: GFP-positive DN4 stage thymocytes

extract_protocol:
QIAGEN RNeasy Micro Kit with in-column DNase treatment
NEBNext rRNA depletion Kit (New England BioLabs) followed by library preparation

tag: gfp status

value: GFP-positive


title: 187-CD14


title: pituitary_adenoma_nonfunctioning [5_13]

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular Oncology Department

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

hyb_protocol: Not provided.

scan_protocol: Not provided.

data_processing: DNA methylation data was analyzed using ChAMP (Morris TJ, 2014) package from Bioconductor repository. Data quality was assessed and probe filtering was done using default parameters. Intensity values were normalized with a BMIQ method. Differentially methylated probes and differentially methylated regions were identified. Gene context and CpG island location of differentially methylated probes was assessed.

source_name: nonfunctioning pituitary adenoma

label_protocol: Not provided.

extract_protocol: QIAamp DNA Mini Kit [Qiagen]

tag: tissue

value: nonfunctioning pituitary adenoma

tag: invasiveness

value: Invasive

tag: tumor type

value: Gonadotroph


title: 191-CD14

tag: gender

value: Female


title: green_rep2

tag: strain


title: 185-CD14

value: Male


title: 188-CD14


title: 180-CD14


title: 192-CD14


title: 178-CD14


title: pituitary_adenoma_nonfunctioning [57_14]


title: green_rep1

tag: developmental stage


title: 241-CD14


title: white_rep3

source_name: GFP-negative DN4 stage thymocytes

value: GFP-negative


title: pituitary_adenoma_nonfunctioning [55_14]

value: Noninvasive


title: pituitary_adenoma_nonfunctioning [9_13]


title: pituitary_adenoma_nonfunctioning [59_11]


title: pituitary_adenoma_nonfunctioning [52_12]


title: pituitary_adenoma_nonfunctioning [51_12]


title: 177-CD14


title: pituitary_adenoma_nonfunctioning [46_12]


title: pituitary_adenoma_nonfunctioning [44_14]


title: 167-CD14


title: Gata3(g/g)_rep2

description:
Sample_22344
sample name in processed data file: DN3gg_1

data_processing:
tophat-2.0.8b
bowtie2-2.1.0
cuffdiff-2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample (fpm.txt) and abundance comparison (exp.diff.txt).

source_name: DN3 stage thymocytes

extract_protocol:
QIAGEN RNeasy Mini Kit with in-column DNase treatment
NuGEN Encore Complete RNA-Seq Library Systems

value: Gata3(g/g) hypomorph

tag: sequenceid


title: pituitary_adenoma_nonfunctioning [44_12]


title: WT_rep2

description:
Sample_22343
sample name in processed data file: DN3wt_1

tag: cell type


title: white_rep2


title: 171-CD14

tag: low ses


title: pituitary_adenoma_nonfunctioning [40_14]


title: pituitary_healthy [37_15]

source_name: healthy pituitary

value: healthy pituitary


title: Gata3(g/g)_rep1

description:
Sample_9963
sample name in processed data file: DN3gg_0


title: WT_rep1

description:
Sample_9962
sample name in processed data file: DN3wt_0


title: pituitary_adenoma_nonfunctioning [4_14]


title: 165-CD14

tag: bmi


title: pituitary_adenoma_nonfunctioning [37_12]


title: 166-CD14

tag: race


title: pituitary_healthy [38_15]


title: RNA-seq_mTS_shLuc_diff_d14

description: RNA-Seq

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph and text file with RPKM.  Column headers for RPKM files are: refseqID, rpkm, gene length, counts, geneID

source_name: mouse TS cells

growth_protocol: shLuc and Kdm5b TS cells were cultured in the presence of FGF4 to maintain self-renewal, and in the absence of FGF4 to induce differentiation at 37oC with 5% CO2. For RNA-Seq experiments, TS cells were passed by washing with PBS, and dissociating with trypsin.

extract_protocol:
RNA was harvest using RNeasy and miRNeasy Qiagen kits.
Double-stranded cDNA was sonicated and end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: genotype/variation

value: shLuc

value: differentiated TS cell

tag: differentiation day

value: day 14


title: pituitary_healthy [39_15]


title: RNA-seq_mTS_shKdm5b_rep2

description: RNA-Seq

value: TS cell


title: pituitary_adenoma_nonfunctioning [37_14]


title: pituitary_adenoma_nonfunctioning [43_11]


title: wildtype_rep2

description:
Sample_55166
sample name in processed data: Ctrl_1

tag: sample id


title: 158-CD14

value: Monocyte

tag: age

tag: asthma severity

tag: ics

tag: saba


title: 160-CD14


title: RNA-seq_mTS_shKdm5b_rep1

description: RNA-Seq


title: white_rep1

value: thymocytes

tag: genotype

tag: gfp status


title: wildtype_rep1

description:
Sample_55165
sample name in processed data: Ctrl_0

value: wild type


title: pituitary_adenoma_nonfunctioning [37_10]

tag: tissue

tag: invasiveness

tag: tumor type

tag: gender


title: 155-CD14

tag: cell type


title: 154-CD14

tag: low ses


title: 153-CD14

tag: bmi


title: RNA-seq_mTS_shLuc_rep2

description: RNA-Seq


title: shKdm5b_Input_TSC_diff_d14

description: Direct sequencing following sonication of x-linked chromatin

extract_protocol:
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: chip antibody


title: shLuc_Input_TSC_diff_d14

tag: genotype/variation


title: shKdm5b_Input_TSC

tag: differentiation day


title: 145-CD14

tag: race


title: RNA-seq_mTS_shLuc_rep1

description: RNA-Seq


title: shKdm5b_H3K4me2_TSC_diff_d14

description: Chromatin IP against H3K4me3

value: Anti-H3K4me3 antibody (Millipore; 17-614)


title: shLuc_Input_TSC


title: pituitary_adenoma_nonfunctioning [35_11]

value: nonfunctioning pituitary adenoma

tag: age


title: pituitary_healthy [32_15]


title: 124-CD14

tag: asthma severity


title: 135-CD14

tag: ics


title: 142-CD14

tag: saba


title: shLuc_H3K4me2_TSC_diff_d14

description: Chromatin IP against H3K4me3


title: pituitary_adenoma_nonfunctioning [35_12]

value: Invasive


title: pituitary_adenoma_nonfunctioning [36_12]

value: Gonadotroph


title: pituitary_adenoma_nonfunctioning [26_10]

value: Multihormonal


title: 129-CD14

value: Male


title: 133-CD14


title: 137-CD14

value: Female


title: pituitary_healthy [31_15]


title: 131-CD14


title: pituitary_adenoma_nonfunctioning [26_14]

value: Noninvasive


title: shLuc_H3K4me3_TSC_diff_d14

description: Chromatin IP against H3K4me3


title: shKdm5b_H3K4me3_TSC_diff_d14

description: Chromatin IP against H3K4me3


title: 121-CD14


title: shKdm5b_H3K4me2_TSC

description: Chromatin IP against H3K4me3


title: 117-CD14


title: shLuc_H3K4me2_TSC

description: Chromatin IP against H3K4me3


title: shLuc_H3K4me3_TSC

description: Chromatin IP against H3K4me3


title: 113-CD14


title: pituitary_adenoma_nonfunctioning [16_14]


title: 115-CD14


title: pituitary_healthy [36_15]


title: pituitary_adenoma_nonfunctioning [18_08]


title: brpL mutant Rep4 2

city: Richmond

first: Ping

last: Xu

state: VA

address: 521 North 11th street

department: Philips Institute for Oral Health Research

institute: Virginia Commonwealth Univ. School of Dentistry

description: replicate 4

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intesity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using EDGE-pro.
Differential genes analysis was executed by DESeq2.
Genome_build: Streptococcus sanguinis reference genome
Supplementary_files_format_and_content: tab-delimited text file includes gene name and ID, fold change of expression, p-value

organism: Streptococcus sanguinis

growth_protocol: Cells were incubated at 37°C under anaerobic conditions in brain-heart infusion media and harvested at late-log phase. The brpL mutant was supplemented with kanamycin (500 µg/ml) for selection of the antibiotic resistance cassette.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacterer's protocol. Illlumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligs for Illumina - Index Primers 2, 11, 12, 13, 15, 16, 18, 20, 21, 22). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

tag: strain

value: parent strain:SK36

tag: growth phase

value: late-log

tag: genotype

value: brpL mutant


title: 110-CD14


title: pituitary_adenoma_nonfunctioning [17_13]

tag: tissue

tag: invasiveness


title: brpL mutant Rep4

description: replicate 4


title: 109-CD14

tag: gender


title: shKdm5b_H3K4me3_TSC

description: Chromatin IP against H3K4me3

data_processing:
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

tag: cell type


title: 106-CD14

tag: low ses


title: brpL mutant Rep3 2

description: replicate 3


title: obese 38

city: Xi’an

first: Yuesheng

last: Liu

state: Shaanxi

address: 157 Xiwu Road

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

description: lncRNA and mRNA expression data from abdomen subcutaneous adipose tissue of obese children.

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: GeneChips were scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

label: fluorescent

source_name: adipose tissue of obese child

label_protocol: Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Immediately after skin incision and subcutaneous tissue exposure during the operation, adipose tissue were separated bluntly, washed in cold PBS, and stored at liquid nitrogen for further use

value: Abdomen subcutaneous adipose tissue

value: 11 years

tag: Sex


title: pituitary_adenoma_nonfunctioning [19_08]

tag: tumor type


title: pituitary_adenoma_nonfunctioning [10_14]


title: pituitary_adenoma_nonfunctioning [17_12]

value: Null cell adenoma


title: 105-CD14

value: Monocyte

tag: bmi


title: CD8 No2 IL27RKO IL27

city: Boston

first: Asaf

last: Madi

address: 60 Fenwood Road, BTM 10016F

institute: BWH

description: Naïve T cells stimulated with IL-27

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Individual .CEL files were RMA normalized and merged to an expression matrix using the ExpressionFileCreator of GenePattern with default parameters.

source_name: primary CD8 T cells

label_protocol: standard Affymetrix protocol

growth_protocol: Naïve CD4+ and CD8+ T cells were isolated from WT or IL27ra KO mice, and differentiated in vitro with or without IL-27. Cells were collected at 72 hours for CD8+ and 96 hours for CD4+.

extract_protocol: standard Affymetrix protocol

treatment_protocol: Affymetrix GeneChip Mouse Genome 430 2.0 Arrays were used to measure the resulting mRNA levels.

tag: genotype/variation

value: IL27ra KO


title: brpL mutant Rep2

description: replicate 2


title: 107-CD14

tag: race


title: pituitary_adenoma_nonfunctioning [24_14]

tag: age


title: obese 32

value: 9 years


title: brpL mutant Rep1 2

description: replicate 1


title: pituitary_adenoma_nonfunctioning [1_14]


title: 102-CD14

tag: asthma severity


title: 101-CD14

tag: ics


title: CD8 No2 Tc0

description: Naïve T cells stimulated with IL-27

value: wild type


title: pituitary_adenoma_nonfunctioning [10_13]

value: nonfunctioning pituitary adenoma


title: pituitary_adenoma_nonfunctioning [15_13]


title: L1601435-EcN_coincubated_with_stx-phages_for_16_h_Rep_3

city: Würzburg

first: Richa

last: Bharti

state: Bavaria

address: Josef-Schneider-Straße 2 / Bau D15

department: IMIB,Core Unit Systemmedizin

institute: University of Wuerzburg

data_processing:
Demultiplexing
Quality control Fastq quality trimming using FastX version 0.0.13 and a cut-off value of phred score 20
Size filtering: discarding reads shorter than 15 nt (READemption 0.4.2, Förstner et al., 2014)
Mapping: Reads were mapped to reference genome sequences using segemehl version 0.2.0-418 (READemption 0.4.2, Förstner et al., 2014)
Coverage calculation, normalization (READemption 0.4.2, Förstner et al., 2014) and differential gene expression profiling (DESeq2 version 1.16.1,  Love et al., 2014)
Supplementary_files_format_and_content: abundance measurements: text format, coverage files: wiggle format

organism: Escherichia coli Nissle 1917

source_name: Escherichia coli with stx phages

growth_protocol: The OD600 of bacterial overnight cultures (ONC) was determined and the cells were collected by centrifugation at 9,400 x g for 5 min at RT. The bacterial pellet was resuspended in LB medium to obtain ~1e8 CFUs/ml.

extract_protocol: Total EcN bacterial RNA was isolated from 3 ml cultures after 16 h of a static incubation period with or without phages. RNA was isolated with the RNase Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: 100 µl of the EcN culture (1e8 CFUs/ml) and 100 µl of a phage extract (~1e7 pfus/ml) were added to final volume of 1 ml LB medium in a 24 well plate. The plates were incubated in a static manner for 16 h of time at 37 °C.

value: Escherichia coli with stx phages

value: Nissle 1917


title: pituitary_adenoma_nonfunctioning [13_14]

value: Multihormonal


title: CD4 No2 IL27RKO Tr1

department: Neurology

description: Naïve T cells stimulated with IL-27

source_name: primary CD4 T cells


title: brpL mutant Rep3

description: replicate 3


title: CD4 No2 Tr1

description: Naïve T cells stimulated with IL-27


title: non-obese 22

description: lncRNA and mRNA expression data from abdomen subcutaneous adipose tissue of non-obese children.

source_name: adipose tissue of non-obese child

value: 7 years

value: Male


title: non-obese 26

value: 6 years


title: Wild-type SK36 Rep4 2

description: replicate 4

source_name: Wild-type SK36


title: CD4 No2 Th0

description: Naïve T cells stimulated with IL-27


title: Wild-type SK36 Rep4

description: replicate 4


title: L1601433-EcN_coincubated_with_stx-phages_for_16_h_Rep_1


title: non-obese 21


title: L1601434-EcN_coincubated_with_stx-phages_for_16_h_Rep_2


title: brpL mutant Rep1

description: replicate 1

value: parent strain:SK36


title: non-obese 27


title: pituitary_adenoma_nonfunctioning [1_13]

value: Noninvasive

value: Gonadotroph


title: Wild-type SK36 Rep3 2

description: replicate 3

value: late-log


title: L1601432-EcN_coincubated_with_LB_medium_for_16_h_Rep_3

source_name: Escherichia coli without stx phages

value: Escherichia coli without stx phages


title: CD8 No1 IL27RKO IL27

description: Naïve T cells stimulated with IL-27


title: CD8 No1 IL27

description: Naïve T cells stimulated with IL-27


title: L1601431-EcN_coincubated_with_LB_medium_for_16_h_Rep_2


title: CD8 No1 Tc0

description: Naïve T cells stimulated with IL-27


title: Wild-type SK36 Rep3

description: replicate 3


title: L1601430-EcN_coincubated_with_LB_medium_for_16_h_Rep_1


title: CD4 No1 IL27RKO Tr1

description: Naïve T cells stimulated with IL-27


title: Wild-type SK36 Rep2 2

description: replicate 2


title: Wild-type SK36 Rep1 2

description: replicate 1


title: Wild-type SK36 Rep2

description: replicate 2


title: CD4 No1 Tr1

description: Naïve T cells stimulated with IL-27


title: CD4 No1 Th0

description: Naïve T cells stimulated with IL-27


title: Wild-type SK36 Rep1

description: replicate 1


title: 120-CD14

source_name: CD14+ leukocytes

value: Female

tag: saba


title: Injected with SAV plasmid, fish 3

status: Public on Jun 13 2018

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

source_name: skeletal muscle_SAV plasmid

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was kept at 10°C in 300 L tanks supplied with fresh water and fed with commercial dry food

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

value: skeletal muscle


title: uaf-1(n4588)-rep3

city: Changsha

first: Chuanman

last: Zhou

state: Hunan

address: Xiangya road 110

department: School of Life Sciences

institute: Central South University, Changsha, Hunan, China

data_processing:
Raw data was processed with Perl scripts to ensure the quality of data used in further analysis, clean data was obtained by removing reads Vontaining adapter.
Bowtie2 was used for building the genome index, and Clean Data was mapped to the WBcel235 alignments using TopHat v2.0.12.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, Vonsidering the effect of sequencing depth and gene length for the reads count.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/985/GCF_000002985.6_WBcel235/
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

organism: Caenorhabditis elegans

source_name: egg

growth_protocol: 20 degree constant temperature culture.

extract_protocol:
Total RNA was prepared using Trizol (Invitrogen), treated with RNase-Free DNase I (New England Biolabs) and incubated at 75 °C for 10 min to inactivate DNase I.
RNA libraries were prepareed for seqeuncing using standard illumina protocols

treatment_protocol: Synchronized adult animals were bleached to obtain enough eggs, which were washed three times with H2O.

tag: developmental stage

value: embryo

tag: strain

value: egg


title: uaf-1(n4588); rbm-5(n5119)-rep1


title: uaf-1(n4588); rbm-5(n5119)-rep2


title: uaf-1(n4588); rbm-5(n5132)-rep2


title: uaf-1(n4588)-rep2


title: uaf-1(n4588)-rep1


title: uaf-1(n4588); rbm-5(n5132)-rep3


title: uaf-1(n4588); rbm-5(n5132)-rep1


title: uaf-1(n4588); rbm-5(n5119)-rep3


title: Injected with SAV plasmid, fish 1


title: Injected with PBS, fish 1, replicate

source_name: skeletal muscle_PBS


title: Injected with SAV plasmid, fish 2


title: brpL mutant Rep2 2

description: replicate 2

tag: growth phase

tag: genotype

value: brpL mutant


title: Injected with pcDNA3.3, fish 2

source_name: skeletal muscle_pcDNA3.3

tag: tissue


title: Injected with SAV plasmid, fish 4


title: Injected with pcDNA3.3, fish 3


title: Injected with PBS, fish 1


title: Injected with PBS, fish 3


title: Injected with pcDNA3.3, fish 4


title: Injected with pcDNA3.3, fish 1


title: Injected with PBS, fish 4


title: Injected with PBS, fish 2


title: Injected with SAV plasmid, fish 5


title: Injected with PBS, fish 2, replicate


title: Injected with pcDNA3.3, fish 1, replicate


title: obese 35

value: Abdomen subcutaneous adipose tissue

value: 11 years


title: pituitary_adenoma_nonfunctioning [1_12]

source_name: nonfunctioning pituitary adenoma

value: nonfunctioning pituitary adenoma

tag: invasiveness

value: Invasive

tag: gender


title: rbm-5(n5132)-rep3


title: rbm-5(n5119)-rep3


title: rbm-5(n5119)-rep1


title: rbm-5(n5132)-rep1


title: rbm-5(n5119)-rep2


title: rbm-5(n5132)-rep2


title: WT-rep2


title: WT-rep1


title: WT-rep3