title: adipose_wt2

city: Wuerzburg

first: Marietta

last: Herrmann

address: Roentgenring 11

department: IZKF Group Tissue Regeneration in Musculoskeletal Diseases

country: Germany

institute: University Hospital Wuerzburg

description: This sample failed quality control and was excluded from the analysis.

hyb_protocol: Biotin-labeled cRNA samples were fragmented randomly to 35-200 bp at 94°C for 35 min in fragmentation buffer (P/N 900371; Affymetrix) and  hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0002

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data processing was performed using Bioconductor under R.  ArrayQualityMetrics package  was used for quality assessment. Background adjustment and normalization awere applied using the RMA algorithm within the Affy package.

source_name: adipose tissue wildtype mouse  44 days

label_protocol: Each 5 µg total RNA samples were reverse-transcribed into doublestranded cDNA with the One-Cycle cDNA synthesis kit (P/N 900431; Affymetrix, Santa Clara, CA). The doublestranded cDNA was purified using a Sample Cleanup Module (P/N 900371; Affymetrix). The purified doublestranded cDNAs were in vitro-transcribed in the presence of biotin-labeled nucleotides using a IVT labeling kit (P/N 900449; Affymetrix). The biotinylated c RNA was purified by using a Sample Cleanup Module (P/N 900371; Affymetrix), and its quality and quantity were determined with a NanoDrop ND 1000 and Bioanalyzer 2100.

growth_protocol: Mice were maintained in a temperature-controlled room on a 12-hour light/dark cycle. Standard diet and water were given ad libitum.

extract_protocol: Tissue samples were homogenized and stored in peqGOLD RNAPure reagent (PEQLAB Biotechnologie GMBH). RNA extraction was performed using RNeasy Lipid Tissue Mini Kit (Qiagen)

value: brown adipose

tag: genotype

value: wt

tag: gender

value: female


title: adipose_wt6

status: Public on Dec 05 2019

type: RNA

label: biotin

molecule: total RNA

organism: Mus musculus

tag: tissue

value: male


title: 00iCTR_A

type: SRA

city: Los Angeles

first: Samuel

middle: A

last: Sances

state: CA

address: 8500 Beverly Blvd

department: Regenerative Medicine Institute

country: USA

institute: Cedars Sinai

library_source: transcriptomic

data_processing:
RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0) (Dobin A et al., 2013) / RSEM (version 1.2.25) (Li B and Dewey CN, 2011) with default parameters, using a custom human GRCh38 (or mouse CRCm38)
Expression counts for each gene (TPM: transcripts per million) in all samples were normalized

organism: Homo sapiens

extract_protocol: Illumina TruSeq Stranded mRNA library preparation kit

tag: cell type

value: iPSC-mDA Neurons

tag: disease state

value: Control

tag: cell line


title: 00iCTR_B


title: hela_overexpression_1.5ug

city: Philadelphia

first: Gideon

last: Dreyfuss

state: PA

address: 415 curie blvd

institute: University of Pennsylvania

description: nascent polyA mRNA

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were trimmed of adapter sequences using TrimGalore, and thenwere aligned to the reference genome (UCSC, hg38) using STAR by default parameters.
Reads with multiple alignments were filtered for downstream analysis.
FPKMs for RNA-seq were generated using GFold with default parameters.
3'UTR shortening was calculated using the new LECDS method where 3’UTR signals were compared to that from the last exon’s coding sequence. The significance of this read change was detected using a Fisher’s Exact test followed by Benjamini–Hochberg multiple testing with an adjusted P-value ≤ 0.01
Genome_build: hg38
Supplementary_files_format_and_content: Alignment data for the RNA-seq are given in bigwig format.

molecule: polyA RNA

source_name: Human Carcinoma Cells

growth_protocol: Cells grown in DMEM supplemented with 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA extracted using trizol, total mRNA extracted using Oligotext poly(dT) beads from Qiagen, nascent RNA linked to Biotin and etracted on magnetic streptavidin beads
Libraries were prepared according to instructions accompanying the Ovation RNA-Seq System V2 and the Encore NGS Library System, both from NuGEN.

treatment_protocol: Cells transfected with antisense morpholino to control or U1 or U1 snRNA containing plasmid using Neon system for 8 hours or 24 hours.

value: HeLa

tag: strain

value: PV

tag: genotype/variation

value: U1 overexpression


title: helaoverexpression_1ug

description: nascent polyA mRNA


title: hela_overexpression_control

description: nascent polyA mRNA

value: control


title: CTCF_ChIA-PET_ZnSO4 Treatment

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

description: CTCF_ChIA-PET_ZnSO4 Treatment

library_source: genomic

data_processing:
Library strategy: ChIA-PET
Filtering linker sequence using in-house script
Mapping to reference genome using BWA MEM
Deduplicating reads using Picard (MarkDuplicates)
Peak-calling using MACS (v1.4)
2D contact map using Juicer tool
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt format for peak (bed), loop (bedpe), binary data format for Juicebox (hic)

molecule: genomic DNA

growth_protocol: Both U937-PR9 and NB4 cells were cultured in RPMI 1640 (ThermoFisher, A10491), supplemented with 10% fetal bovine serum (ThermoFisher, 10082147). These cells were cultured at 37 ℃ , 5% CO2, and ambient oxygen levels.

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 ×150bp) was used for ChIA-PET libraries  with Illumina Hiseq 2500 or Illumina Nextseq 500.

treatment_protocol: The U937-PR9 cells were treated with 100 μM ZnSO4 (Sigma, Z0251) for 4 hours for ChIA-PET and ChIP-Seq experiment. The U937-PR9 cells were treated with 100 μM ZnSO4  and then collected these cells at 4, 6, 12, 24 hours for RNA-Seq experiment. These cells was preincubated with 100 μM ZnSO4 for 4 hours and then treated with ATRA (Sigma, R2625) for 24 and 48 hours used for RNA-Seq experiment. NB4 cells were treated with ATRA for 24 and 48 hours used for RNA-Seq experiment.

tag: method

value: ChIA-PET

tag: factor

value: CTCF (Abcam, catalog# ab70303)

tag: molecule subtype

value: nuclear chromatin


title: adipose_wt5


title: adipose_ko4

source_name: adipose tissue Ahsg -/- mouse  44 days

value: Ahsg ko


title: RARA_ChIA-PET_Control

value: RARA (Santa Cruz, catalog# sc-551X)


title: input DNA

city: HANGZHOU

first: XIUWEN

last: TANG

address: YUHANGTONG ROAD

department: BIOCHEMISTRY AND GENETICS

country: China

institute: ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE

description: ChIP-IgG

data_processing:
ChIP-seq reads were aligned to the human (hg19) genome using bowtie
Peak calling was performed by using Homer
Homer peak files were converted to WIG files using Homer
Genome_build: hg19
Supplementary_files_format_and_content: WIG files

source_name: A549 NSCLC cells

growth_protocol: A549 NSCLC cells were maintained in a growth medium containing Dulbecco's MEM with Glutamax supplemented with 10% fetal bovine serum (FBS) and antibiotics

extract_protocol:
Cells were seeded in 100-mm dishes at 2 × 106 cells/dish then cross-linked with 1% formaldehyde and immunoprecipitation was performed overnight with Nrf2-specific antibody (Santa Cruz Biotechnology) and IgG as control following the instructions with the immunoprecipitation kit (Upperstate, Shanghai, China)
The sequencing and generation of short DNA reads of immunoprecipitated samples were carried out at Genenergy Inc. (Shanghai, China) using an Illumina Hiseq 2000.

value: lung epithelial adenocarcinoma cell line

tag: passages

tag: chip antibody

value: IgG antibody


title: kidney_ko3

data_processing: Data processing was performed using Bioconductor under R.  ArrayQualityMetrics package  was used for quality assessment.Background adjustment, normalization and summarization were applied using the RMA algorithm within the Affy package.

source_name: kidney Ahsg -/- mouse  38 days

extract_protocol: Tissue samples were homogenized and stored in peqGOLD RNAPure reagent (PEQLAB Biotechnologie GMBH). RNA extraction was performed using a standard phenol-chloroform extraction procedure.

value: kidney


title: adipose_ko1

value: brown adipose


title: kidney_ko4

value: female


title: adipose_ko2

value: male


title: NRF2_ChIPSeq

description: IP of NRF2 bound DNA

value: Nrf2-specific antibody (Santa Cruz Biotechnology)


title: kidney_ko2


title: adipose_wt1

value: wt


title: kidney_wt2

source_name: kidney WT mouse  36 days


title: adipose_wt7


title: adipose_ko5


title: adipose_ko6


title: kidney_ko6


title: kidney_ko5


title: kidney_wt3


title: kidney_wt4


title: kidney_wt1


title: kidney_ko1


title: adipose_wt4


title: T-divSLAM cell 304 [062316_Cell95-G12]

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: run1646_lane1_read1_indexN706-S507=062316_Cell95-G12

data_processing:
RNA reads were aligned to the reference mm9 mouse genome using Bowtie2.
Single-cell and matched bulk sorted RNA-Seq were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using a FDR adjusted empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values

source_name: T-divSLAM cell

extract_protocol:
Cells were harvested from bone marrow. Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS, then enriched using CD117 MicroBeads on a Automacs Pro separator (Miltenyi, San Diego, CA). CD117+ cells were stained with CD16/32-PerCp-ef710 (clone 93), CD3-biotin (clone 145-2C11), CD4-biotin (clone RM4-5), CD8-biotin (clone 53-6.7), CD11b-biotin (clone M1/70), CD19-biotin (clone 6D5), Gr1-biotin (clone RB6-8C5), Ter119-biotin (clone Ter-119) CD45R-biotin (clone RA3-6B2), CD117-APC (clone 2B8), Sca-1-Pe-Cy7 (clone D7), CD34-BV421 (clone RAM34), CD115-BV605 (clone TR15-12F1 2.2), CD135-PE (A2F10.1), CCR3-FITC (clone 83101), SiglecF (clone E50-2440) and Gr1-FITC (clone RB6-8C5). Cell sorting was performed on MoFloXDP (Beckman Coulter, Brea, CA) or BD FACSAria II with a 100μm nozzleand subjected to flow cytrometric sorting of bone marrow lineage-negative Sca1+ CD117+ cells (LSK).
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system

value: Bone Marrow

value: LSK-SLAM Stem cells

tag: cell phenotype

tag: cdna synthesis protocol

value: Fluidigm C1 protocol

tag: library prep

value: Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA)


title: T-divSLAM cell 303 [062316_Cell94-E12]

description: run1646_lane1_read1_indexN705-S506=062316_Cell94-E12


title: adipose_ko3


title: T-divSLAM cell 302 [062316_Cell93-D12]

description: run1646_lane1_read1_indexN704-S505=062316_Cell93-D12


title: T-divSLAM cell 305 [062316_Cell96-H12]

description: run1646_lane1_read1_indexN707-S508=062316_Cell96-H12


title: T-divSLAM cell 301 [062316_Cell92-C12]

description: run1646_lane1_read1_indexN703-S504=062316_Cell92-C12


title: 3D9_13 7d ITIH5 Mouse wt

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

hyb_protocol: Hybridization cocktails containing 5.5 Ig of fragmented, end-labelled cDNA were prepared and applied to GeneChip Mouse Gene 2.0 ST arrays. Hybridization was performed in 45°C hybridization oven at 60 rpm for 16 hours. Using the GeneChip® Fluidics Station 450 the hybridized GeneChip® Mouse Gene 2.0 ST Arrays were washed and stained (Fluidics Protocol FS450_0001).

scan_protocol: Arrays were scanned using Affymetrix GeneChip® Scanner 3000 7G controlled by GeneChip®Operating Software (GCOS) version 1.4 to produce CEL intensity files.

data_processing:
Data analysis from the exon arrays were processed using GeneSpring GX 14.9 software (Agilent Technologies).
Expression values of each probe set were determined using the GeneSpring GX 13.1.1 software (Agilent Technologies). Normalization method: Quantile.

source_name: fibroblasts and keratinocytes

label_protocol: 300µg total RNA from each model were processed using the WT Expression Kit (Ambion)  to generate amplified sense-strand cDNA. Fragmentation and labeling was done using the Affymetrix® GeneChip® WT Terminal Labeling Kit Assay (Affymetrix, Inc., Santa Clara, CA, USA).

growth_protocol: Epidermal keratinocytes and dermal fibroblasts were obtained from adult mouse skin. Mouse skin was removed from sacrificed adult Itih5 wild‐type and knockout mice, respectively. For fibroblast culture, dermal part of the skin was digested in Collagenase 100 U/ml (Sigma‐Aldrich, München, Germany), at 37°C in a humidified atmosphere for 3 h. For keratinocyte isolation, skin of either Itih5 wild‐type or knockout mice was sterilized in 70% ethanol and washed three times in sterile phosphate‐buffered saline (PBS) without calcium and magnesium (Life Technologies, Paisley, UK) containing 100 U/ml penicillin, 100 mg/ml streptomycin (Life Technologies) and 0.05 mg/ml amphotericin B (Biochrom, Berlin, Germany). Skin was cut into small pieces, which were placed in dispase solution (2 U/ml; Gibco, Paisley, UK) overnight at 4°C and subsequently incubated at 37°C for 30 min. After a washing step with PBS, cells were digested with trypsin/EDTA (Lifeline Cell Technology, Frederick, MD, USA) for 15 min at 37°C and completed by adding equal amount of trypsin neutralization solution (Lifeline Cell Technology). After the cell suspension was filtered and centrifuged, cells were plated onto coated collagen type I dishes. For cultivation, keratinocytes were grown in Derma Life K (Life Technologies) and fibroblasts in DMEM high glucose medium (Life Technologies), supplemented with 20% fetal calf serum (FCS; Biochrom, Berlin, Germany). Cells were cultured at 37°C under a humidified atmosphere with 5% CO2. All primary cultures were serially passaged and the resulting colonies cultivated continuously. After approximately nine population doublings, cells became independent of collagen support without apparent signs of proliferative crisis.

extract_protocol: Total RNA was isolated using the Nucleo Spin II RNA Mini Kit, (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions, including on-column digestion of DNA with RNase-free DNase I.

treatment_protocol: All mice were untreated.

value: skin

value: wildtype


title: T-divSLAM cell 299 [062316_Cell90-H11]

description: run1646_lane1_read1_indexN701-S502=062316_Cell90-H11


title: T-divSLAM cell 298 [062316_Cell89-G11]

description: run1646_lane1_read1_indexN712-S517=062316_Cell89-G11


title: T-divSLAM cell 300 [062316_Cell91-A12]

description: run1646_lane1_read1_indexN702-S503=062316_Cell91-A12


title: 3D9_13 7d ITIH5 Mouse ko

value: Itih5 knockout


title: T-divSLAM cell 297 [062316_Cell88-F11]

description: run1646_lane1_read1_indexN706-S508=062316_Cell88-F11


title: T-divSLAM cell 296 [062316_Cell87-E11]

description: run1646_lane1_read1_indexN705-S507=062316_Cell87-E11


title: T-divSLAM cell 293 [062316_Cell84-H10]

description: run1646_lane1_read1_indexN702-S504=062316_Cell84-H10


title: T-divSLAM cell 289 [062316_Cell80-C10]

description: run1646_lane1_read1_indexN705-S508=062316_Cell80-C10


title: T-divSLAM cell 291 [062316_Cell82-E10]

description: run1646_lane1_read1_indexN712-S502=062316_Cell82-E10


title: T-divSLAM cell 292 [062316_Cell83-G10]

description: run1646_lane1_read1_indexN701-S503=062316_Cell83-G10


title: T-divSLAM cell 288 [062316_Cell79-A10]

description: run1646_lane1_read1_indexN704-S507=062316_Cell79-A10


title: T-divSLAM cell 287 [062316_Cell78-H9]

description: run1646_lane1_read1_indexN703-S506=062316_Cell78-H9


title: T-divSLAM cell 285 [062316_Cell76-F9]

description: run1646_lane1_read1_indexN701-S504=062316_Cell76-F9


title: T-divSLAM cell 283 [062316_Cell74-B9]

description: run1646_lane1_read1_indexN711-S502=062316_Cell74-B9


title: T-divSLAM cell 280 [062316_Cell71-G8]

description: run1646_lane1_read1_indexN703-S507=062316_Cell71-G8


title: T-divSLAM cell 286 [062316_Cell77-G9]

description: run1646_lane1_read1_indexN702-S505=062316_Cell77-G9


title: T-divSLAM cell 281 [062316_Cell72-H8]

description: run1646_lane1_read1_indexN704-S508=062316_Cell72-H8


title: T-divSLAM cell 282 [062316_Cell73-A9]

description: run1646_lane1_read1_indexN710-S517=062316_Cell73-A9


title: T-divSLAM cell 279 [062316_Cell70-B8]

description: run1646_lane1_read1_indexN702-S506=062316_Cell70-B8


title: T-divSLAM cell 278 [062316_Cell69-H7]

description: run1646_lane1_read1_indexN701-S505=062316_Cell69-H7


title: T-divSLAM cell 276 [062316_Cell67-E7]

description: run1646_lane1_read1_indexN711-S503=062316_Cell67-E7


title: T-divSLAM cell 275 [062316_Cell66-D7]

description: run1646_lane1_read1_indexN710-S502=062316_Cell66-D7


title: T-divSLAM cell 277 [062316_Cell68-G7]

description: run1646_lane1_read1_indexN712-S504=062316_Cell68-G7


title: T-divSLAM cell 284 [062316_Cell75-C9]

description: run1646_lane1_read1_indexN712-S503=062316_Cell75-C9


title: T-divSLAM cell 274 [062316_Cell65-B7]

description: run1646_lane1_read1_indexN709-S517=062316_Cell65-B7


title: T-divSLAM cell 273 [062316_Cell64-H6]

description: run1646_lane1_read1_indexN703-S508=062316_Cell64-H6


title: T-divSLAM cell 269 [062316_Cell60-B6]

description: run1646_lane1_read1_indexN711-S504=062316_Cell60-B6


title: T-divSLAM cell 294 [062316_Cell85-A11]

description: run1646_lane1_read1_indexN703-S505=062316_Cell85-A11


title: T-divSLAM cell 270 [062316_Cell61-D6]

description: run1646_lane1_read1_indexN712-S505=062316_Cell61-D6


title: T-divSLAM cell 268 [062316_Cell59-A6]

description: run1646_lane1_read1_indexN710-S503=062316_Cell59-A6


title: T-divSLAM cell 290 [062316_Cell81-D10]

description: run1646_lane1_read1_indexN711-S517=062316_Cell81-D10


title: T-divSLAM cell 267 [062316_Cell58-H5]

description: run1646_lane1_read1_indexN709-S502=062316_Cell58-H5


title: T-divSLAM cell 266 [062316_Cell57-G5]

description: run1646_lane1_read1_indexN708-S517=062316_Cell57-G5


title: T-divSLAM cell 263 [062316_Cell54-B5]

description: run1646_lane1_read1_indexN712-S506=062316_Cell54-B5


title: T-divSLAM cell 262 [062316_Cell53-H4]

description: run1646_lane1_read1_indexN711-S505=062316_Cell53-H4


title: T-divSLAM cell 261 [062316_Cell52-G4]

description: run1646_lane1_read1_indexN710-S504=062316_Cell52-G4


title: T-divSLAM cell 258 [062316_Cell49-H3]

description: run1646_lane1_read1_indexN707-S517=062316_Cell49-H3


title: T-divSLAM cell 260 [062316_Cell51-E4]

description: run1646_lane1_read1_indexN709-S503=062316_Cell51-E4


title: T-divSLAM cell 256 [062316_Cell47-F3]

description: run1646_lane1_read1_indexN712-S507=062316_Cell47-F3


title: T-divSLAM cell 255 [062316_Cell46-C3]

description: run1646_lane1_read1_indexN711-S506=062316_Cell46-C3


title: T-divSLAM cell 257 [062316_Cell48-G3]

description: run1646_lane1_read1_indexN701-S508=062316_Cell48-G3


title: T-divSLAM cell 254 [062316_Cell45-B3]

description: run1646_lane1_read1_indexN710-S505=062316_Cell45-B3


title: T-divSLAM cell 253 [062316_Cell44-H2]

description: run1646_lane1_read1_indexN709-S504=062316_Cell44-H2


title: T-divSLAM cell 252 [062316_Cell43-G2]

description: run1646_lane1_read1_indexN708-S503=062316_Cell43-G2


title: T-divSLAM cell 272 [062316_Cell63-G6]

description: run1646_lane1_read1_indexN702-S507=062316_Cell63-G6


title: T-divSLAM cell 248 [062316_Cell39-H1]

description: run1646_lane1_read1_indexN711-S507=062316_Cell39-H1


title: T-divSLAM cell 251 [062316_Cell42-E2]

description: run1646_lane1_read1_indexN707-S502=062316_Cell42-E2


title: T-divSLAM cell 246 [062316_Cell37-F1]

description: run1646_lane1_read1_indexN709-S505=062316_Cell37-F1


title: T-divSLAM cell 250 [062316_Cell41-C2]

description: run1646_lane1_read1_indexN706-S517=062316_Cell41-C2


title: T-divSLAM cell 271 [062316_Cell62-F6]

description: run1646_lane1_read1_indexN701-S506=062316_Cell62-F6


title: T-divSLAM cell 247 [062316_Cell38-G1]

description: run1646_lane1_read1_indexN710-S506=062316_Cell38-G1


title: T-divSLAM cell 249 [062316_Cell40-A2]

description: run1646_lane1_read1_indexN712-S508=062316_Cell40-A2


title: T-divSLAM cell 243 [062316_Cell34-C1]

description: run1646_lane1_read1_indexN706-S502=062316_Cell34-C1


title: T-divSLAM cell 245 [062316_Cell36-E1]

description: run1646_lane1_read1_indexN708-S504=062316_Cell36-E1


title: T-divSLAM cell 242 [062316_Cell33-A1]

description: run1646_lane1_read1_indexN705-S517=062316_Cell33-A1


title: T-divSLAM cell 244 [062316_Cell35-D1]

description: run1646_lane1_read1_indexN707-S503=062316_Cell35-D1


title: T-aSLAM cell 241 [062216_Cell9-F5]

description: run1646_lane1_read1_indexN702-S517=062216_Cell9-F5

source_name: T-aSLAM cell


title: T-divSLAM cell 264 [062316_Cell55-D5]

description: run1646_lane1_read1_indexN701-S507=062316_Cell55-D5


title: T-divSLAM cell 265 [062316_Cell56-E5]

description: run1646_lane1_read1_indexN702-S508=062316_Cell56-E5


title: T-aSLAM cell 238 [062216_Cell6-H3]

description: run1646_lane1_read1_indexN706-S506=062216_Cell6-H3


title: T-aSLAM cell 240 [062216_Cell8-A5]

description: run1646_lane1_read1_indexN708-S508=062216_Cell8-A5


title: T-aSLAM cell 239 [062216_Cell7-H4]

description: run1646_lane1_read1_indexN707-S507=062216_Cell7-H4


title: T-divSLAM cell 259 [062316_Cell50-B4]

description: run1646_lane1_read1_indexN708-S502=062316_Cell50-B4


title: T-aSLAM cell 237 [062216_Cell5-A3]

description: run1646_lane1_read1_indexN705-S505=062216_Cell5-A3


title: T-aSLAM cell 234 [062216_Cell31-E12]

description: run1646_lane1_read1_indexN710-S507=062216_Cell31-E12


title: T-aSLAM cell 236 [062216_Cell4-D2]

description: run1646_lane1_read1_indexN704-S504=062216_Cell4-D2


title: T-aSLAM cell 235 [062216_Cell32-G12]

description: run1646_lane1_read1_indexN711-S508=062216_Cell32-G12


title: T-aSLAM cell 233 [062216_Cell30-C12]

description: run1646_lane1_read1_indexN709-S506=062216_Cell30-C12


title: T-aSLAM cell 232 [062216_Cell3-B2]

description: run1646_lane1_read1_indexN703-S503=062216_Cell3-B2


title: T-aSLAM cell 231 [062216_Cell29-B12]

description: run1646_lane1_read1_indexN708-S505=062216_Cell29-B12


title: T-aSLAM cell 230 [062216_Cell28-A12]

description: run1646_lane1_read1_indexN707-S504=062216_Cell28-A12


title: T-aSLAM cell 228 [062216_Cell26-H10]

description: run1646_lane1_read1_indexN705-S502=062216_Cell26-H10


title: T-aSLAM cell 227 [062216_Cell25-E10]

description: run1646_lane1_read1_indexN704-S517=062216_Cell25-E10


title: T-aSLAM cell 226 [062216_Cell24-D10]

description: run1646_lane1_read1_indexN710-S508=062216_Cell24-D10


title: T-aSLAM cell 229 [062216_Cell27-H11]

description: run1646_lane1_read1_indexN706-S503=062216_Cell27-H11


title: T-aSLAM cell 224 [062216_Cell22-B9]

description: run1646_lane1_read1_indexN708-S506=062216_Cell22-B9


title: T-aSLAM cell 222 [062216_Cell20-G8]

description: run1646_lane1_read1_indexN706-S504=062216_Cell20-G8


title: T-aSLAM cell 223 [062216_Cell21-H8]

description: run1646_lane1_read1_indexN707-S505=062216_Cell21-H8


title: T-aSLAM cell 225 [062216_Cell23-H9]

description: run1646_lane1_read1_indexN709-S507=062216_Cell23-H9


title: T-aSLAM cell 220 [062216_Cell19-E8]

description: run1646_lane1_read1_indexN705-S503=062216_Cell19-E8


title: T-aSLAM cell 221 [062216_Cell2-G1]

description: run1646_lane1_read1_indexN702-S502=062216_Cell2-G1


title: T-aSLAM cell 219 [062216_Cell18-H7]

description: run1646_lane1_read1_indexN704-S502=062216_Cell18-H7


title: T-aSLAM cell 218 [062216_Cell16-B7]

description: run1646_lane1_read1_indexN709-S508=062216_Cell16-B7


title: T-aSLAM cell 217 [062216_Cell15-A7]

description: run1646_lane1_read1_indexN708-S507=062216_Cell15-A7


title: T-aSLAM cell 214 [062216_Cell12-A6]

description: run1646_lane1_read1_indexN705-S504=062216_Cell12-A6


title: T-aSLAM cell 216 [062216_Cell14-F6]

description: run1646_lane1_read1_indexN707-S506=062216_Cell14-F6


title: T-aSLAM cell 215 [062216_Cell13-D6]

description: run1646_lane1_read1_indexN706-S505=062216_Cell13-D6


title: T-aSLAM cell 213 [062216_Cell11-H5]

description: run1646_lane1_read1_indexN704-S503=062216_Cell11-H5


title: T-aSLAM cell 212 [062216_Cell10-G5]

description: run1646_lane1_read1_indexN703-S502=062216_Cell10-G5


title: T-qSLAM cell 209 [Oct10-Cell-55]

description: run0131_lane91_read1_indexN712-S507=Oct10-Cell-55

source_name: T-qSLAM cell


title: T-qSLAM cell 210 [Oct10-Cell-40]

description: run0131_lane91_read1_indexN712-S508=Oct10-Cell-40


title: T-divSLAM cell 295 [062316_Cell86-B11]

description: run1646_lane1_read1_indexN704-S506=062316_Cell86-B11


title: T-qSLAM cell 208 [Oct10-Cell-32]

description: run0131_lane91_read1_indexN711-S508=Oct10-Cell-32


title: T-qSLAM cell 205 [Oct10-Cell-24]

description: run0131_lane91_read1_indexN710-S508=Oct10-Cell-24


title: T-qSLAM cell 207 [Oct10-Cell-39]

description: run0131_lane91_read1_indexN711-S507=Oct10-Cell-39


title: T-qSLAM cell 204 [Oct10-Cell-31]

description: run0131_lane91_read1_indexN710-S507=Oct10-Cell-31


title: T-qSLAM cell 203 [Oct10-Cell-38]

description: run0131_lane91_read1_indexN710-S506=Oct10-Cell-38


title: T-qSLAM cell 202 [Oct10-Cell-53]

description: run0131_lane91_read1_indexN710-S505=Oct10-Cell-53


title: T-qSLAM cell 206 [Oct10-Cell-54]

description: run0131_lane91_read1_indexN711-S506=Oct10-Cell-54


title: T-qSLAM cell 200 [Oct10-Cell-23]

description: run0131_lane91_read1_indexN709-S507=Oct10-Cell-23


title: T-qSLAM cell 199 [Oct10-Cell-30]

description: run0131_lane91_read1_indexN709-S506=Oct10-Cell-30


title: T-qSLAM cell 201 [Oct10-Cell-16]

description: run0131_lane91_read1_indexN709-S508=Oct10-Cell-16


title: T-qSLAM cell 198 [Oct10-Cell-37]

description: run0131_lane91_read1_indexN709-S505=Oct10-Cell-37


title: T-qSLAM cell 194 [Oct10-Cell-22]

description: run0131_lane91_read1_indexN708-S506=Oct10-Cell-22


title: T-qSLAM cell 195 [Oct10-Cell-15]

description: run0131_lane91_read1_indexN708-S507=Oct10-Cell-15


title: T-qSLAM cell 196 [Oct10-Cell-8]

description: run0131_lane91_read1_indexN708-S508=Oct10-Cell-8


title: T-qSLAM cell 197 [Oct10-Cell-52]

description: run0131_lane91_read1_indexN709-S504=Oct10-Cell-52


title: T-qSLAM cell 188 [Oct10-Cell-41]

description: run0131_lane91_read1_indexN712-S517=Oct10-Cell-41


title: T-qSLAM cell 191 [Oct10-Cell-51]

description: run0131_lane91_read1_indexN708-S503=Oct10-Cell-51


title: T-qSLAM cell 193 [Oct10-Cell-29]

description: run0131_lane91_read1_indexN708-S505=Oct10-Cell-29


title: T-qSLAM cell 189 [Oct10-Cell-7]

description: run0131_lane91_read1_indexN707-S507=Oct10-Cell-7


title: T-qSLAM cell 186 [Oct10-Cell-21]

description: run0131_lane91_read1_indexN707-S505=Oct10-Cell-21


title: T-aSLAM cell 211 [062216_Cell1-C1]

description: run1646_lane1_read1_indexN701-S517=062216_Cell1-C1


title: T-qSLAM cell 190 [Oct10-Cell-48]

description: run0131_lane91_read1_indexN707-S508=Oct10-Cell-48


title: T-qSLAM cell 187 [Oct10-Cell-14]

description: run0131_lane91_read1_indexN707-S506=Oct10-Cell-14


title: T-qSLAM cell 184 [Oct10-Cell-35]

description: run0131_lane91_read1_indexN707-S503=Oct10-Cell-35


title: T-qSLAM cell 182 [Oct10-Cell-49]

description: run0131_lane91_read1_indexN706-S517=Oct10-Cell-49


title: T-qSLAM cell 185 [Oct10-Cell-28]

description: run0131_lane91_read1_indexN707-S504=Oct10-Cell-28


title: T-qSLAM cell 180 [Oct10-Cell-6]

description: run0131_lane91_read1_indexN706-S506=Oct10-Cell-6


title: T-qSLAM cell 179 [Oct10-Cell-13]

description: run0131_lane91_read1_indexN706-S505=Oct10-Cell-13


title: T-qSLAM cell 181 [Oct10-Cell-47]

description: run0131_lane91_read1_indexN706-S507=Oct10-Cell-47


title: T-qSLAM cell 178 [Oct10-Cell-20]

description: run0131_lane91_read1_indexN706-S504=Oct10-Cell-20


title: T-qSLAM cell 176 [Oct10-Cell-34]

description: run0131_lane91_read1_indexN706-S502=Oct10-Cell-34


title: T-qSLAM cell 175 [Oct10-Cell-33]

description: run0131_lane91_read1_indexN705-S517=Oct10-Cell-33


title: T-qSLAM cell 177 [Oct10-Cell-27]

description: run0131_lane91_read1_indexN706-S503=Oct10-Cell-27


title: T-qSLAM cell 173 [Oct10-Cell-5]

description: run0131_lane91_read1_indexN705-S505=Oct10-Cell-5


title: T-qSLAM cell 192 [Oct10-Cell-36]

description: run0131_lane91_read1_indexN708-S504=Oct10-Cell-36


title: T-qSLAM cell 172 [Oct10-Cell-12]

description: run0131_lane91_read1_indexN705-S504=Oct10-Cell-12


title: T-qSLAM cell 170 [Oct10-Cell-26]

description: run0131_lane91_read1_indexN705-S502=Oct10-Cell-26


title: T-qSLAM cell 171 [Oct10-Cell-19]

description: run0131_lane91_read1_indexN705-S503=Oct10-Cell-19


title: T-qSLAM cell 168 [Oct10-Cell-45]

description: run0131_lane91_read1_indexN704-S505=Oct10-Cell-45


title: T-qSLAM cell 169 [Oct10-Cell-25]

description: run0131_lane91_read1_indexN704-S517=Oct10-Cell-25


title: T-qSLAM cell 165 [Oct10-Cell-18]

description: run0131_lane91_read1_indexN704-S502=Oct10-Cell-18


title: T-qSLAM cell 166 [Oct10-Cell-11]

description: run0131_lane91_read1_indexN704-S503=Oct10-Cell-11


title: T-qSLAM cell 163 [Oct10-Cell-44]

description: run0131_lane91_read1_indexN703-S504=Oct10-Cell-44


title: T-qSLAM cell 164 [Oct10-Cell-17]

description: run0131_lane91_read1_indexN703-S517=Oct10-Cell-17


title: T-qSLAM cell 162 [Oct10-Cell-3]

description: run0131_lane91_read1_indexN703-S503=Oct10-Cell-3


title: T-qSLAM cell 160 [Oct10-Cell-9]

description: run0131_lane91_read1_indexN702-S517=Oct10-Cell-9


title: T-qSLAM cell 161 [Oct10-Cell-10]

description: run0131_lane91_read1_indexN703-S502=Oct10-Cell-10


title: T-qSLAM cell 159 [Oct10-Cell-43]

description: run0131_lane91_read1_indexN702-S503=Oct10-Cell-43


title: T-qSLAM cell 167 [Oct10-Cell-4]

description: run0131_lane91_read1_indexN704-S504=Oct10-Cell-4


title: T-qSLAM cell 158 [Oct10-Cell-2]

description: run0131_lane91_read1_indexN702-S502=Oct10-Cell-2


title: T-qSLAM cell 183 [Oct10-Cell-50]

description: run0131_lane91_read1_indexN707-S502=Oct10-Cell-50


title: T-qSLAM cell 156 [Oct10-Cell-56]

description: run0131_lane91_read1_indexN701-S508=Oct10-Cell-56


title: T-qSLAM cell 155 [Oct10-Cell-42]

description: run0131_lane91_read1_indexN701-S502=Oct10-Cell-42


title: T-qSLAM cell 157 [Oct10-Cell-1]

description: run0131_lane91_read1_indexN701-S517=Oct10-Cell-1


title: T-qSLAM cell 174 [Oct10-Cell-46]

description: run0131_lane91_read1_indexN705-S506=Oct10-Cell-46


title: divSLAM cell 153 [092415_Cell60-C12]

description: run1315_lane1_read1_indexN711-S504=092415_Cell60-C12

source_name: divSLAM cell


title: divSLAM cell 152 [092415_Cell54-A11]

description: run1315_lane1_read1_indexN712-S506=092415_Cell54-A11


title: divSLAM cell 151 [092415_Cell47-G9]

description: run1315_lane1_read1_indexN712-S507=092415_Cell47-G9


title: divSLAM cell 154 [092415_Cell61-E12]

description: run1315_lane1_read1_indexN712-S505=092415_Cell61-E12


title: divSLAM cell 149 [092415_Cell42-G8]

description: run1315_lane1_read1_indexN707-S502=092415_Cell42-G8


title: divSLAM cell 147 [092415_Cell34-C7]

description: run1315_lane1_read1_indexN706-S502=092415_Cell34-C7


title: divSLAM cell 148 [092415_Cell37-F7]

description: run1315_lane1_read1_indexN709-S505=092415_Cell37-F7


title: divSLAM cell 146 [092415_Cell33-B7]

description: run1315_lane1_read1_indexN705-S517=092415_Cell33-B7


title: divSLAM cell 145 [092415_Cell16-G3]

description: run1315_lane1_read1_indexN709-S508=092415_Cell16-G3


title: divSLAM cell 142 [092415_Cell45-C9]

description: run1315_lane1_read1_indexN710-S505=092415_Cell45-C9


title: divSLAM cell 140 [092415_Cell38-H7]

description: run1315_lane1_read1_indexN710-S506=092415_Cell38-H7


title: divSLAM cell 141 [092415_Cell43-H8]

description: run1315_lane1_read1_indexN708-S503=092415_Cell43-H8


title: divSLAM cell 137 [092415_Cell63-H12]

description: run1315_lane1_read1_indexN702-S507=092415_Cell63-H12


title: divSLAM cell 139 [092415_Cell27-A6]

description: run1315_lane1_read1_indexN706-S503=092415_Cell27-A6


title: divSLAM cell 136 [092415_Cell59-A12]

description: run1315_lane1_read1_indexN710-S503=092415_Cell59-A12


title: divSLAM cell 135 [092415_Cell56-E11]

description: run1315_lane1_read1_indexN702-S508=092415_Cell56-E11


title: divSLAM cell 130 [092415_Cell36-E7]

description: run1315_lane1_read1_indexN708-S504=092415_Cell36-E7


title: divSLAM cell 143 [092415_Cell50-D10]

description: run1315_lane1_read1_indexN708-S502=092415_Cell50-D10


title: divSLAM cell 133 [092415_Cell49-A10]

description: run1315_lane1_read1_indexN707-S517=092415_Cell49-A10


title: divSLAM cell 131 [092415_Cell39-A8]

description: run1315_lane1_read1_indexN711-S507=092415_Cell39-A8


title: divSLAM cell 138 [092415_Cell7-B2]

description: run1315_lane1_read1_indexN707-S507=092415_Cell7-B2


title: divSLAM cell 128 [092415_Cell31-G6]

description: run1315_lane1_read1_indexN710-S507=092415_Cell31-G6


title: divSLAM cell 126 [092415_Cell29-D6]

description: run1315_lane1_read1_indexN708-S505=092415_Cell29-D6


title: divSLAM cell 132 [092415_Cell41-D8]

description: run1315_lane1_read1_indexN706-S517=092415_Cell41-D8


title: divSLAM cell 129 [092415_Cell32-H6]

description: run1315_lane1_read1_indexN711-S508=092415_Cell32-H6


title: divSLAM cell 150 [092415_Cell46-D9]

description: run1315_lane1_read1_indexN711-S506=092415_Cell46-D9


title: divSLAM cell 125 [092415_Cell26-G5]

description: run1315_lane1_read1_indexN705-S502=092415_Cell26-G5


title: divSLAM cell 124 [092415_Cell25-F5]

description: run1315_lane1_read1_indexN704-S517=092415_Cell25-F5


title: divSLAM cell 127 [092415_Cell30-E6]

description: run1315_lane1_read1_indexN709-S506=092415_Cell30-E6


title: divSLAM cell 123 [092415_Cell23-C5]

description: run1315_lane1_read1_indexN709-S507=092415_Cell23-C5


title: divSLAM cell 120 [092415_Cell18-B4]

description: run1315_lane1_read1_indexN704-S502=092415_Cell18-B4


title: divSLAM cell 134 [092415_Cell51-F10]

description: run1315_lane1_read1_indexN709-S503=092415_Cell51-F10


title: divSLAM cell 121 [092415_Cell19-C4]

description: run1315_lane1_read1_indexN705-S503=092415_Cell19-C4


title: divSLAM cell 119 [092415_Cell17-H3]

description: run1315_lane1_read1_indexN703-S517=092415_Cell17-H3


title: divSLAM cell 144 [092415_Cell58-H11]

description: run1315_lane1_read1_indexN709-S502=092415_Cell58-H11


title: divSLAM cell 116 [092415_Cell8-C2]

description: run1315_lane1_read1_indexN708-S508=092415_Cell8-C2


title: divSLAM cell 118 [092415_Cell12-H2]

description: run1315_lane1_read1_indexN705-S504=092415_Cell12-H2


title: divSLAM cell 115 [092415_Cell62-F12]

description: run1315_lane1_read1_indexN701-S506=092415_Cell62-F12


title: divSLAM cell 114 [092415_Cell6-H1]

description: run1315_lane1_read1_indexN706-S506=092415_Cell6-H1


title: divSLAM cell 111 [092415_Cell53-H10]

description: run1315_lane1_read1_indexN711-S505=092415_Cell53-H10


title: divSLAM cell 112 [092415_Cell55-D11]

description: run1315_lane1_read1_indexN701-S507=092415_Cell55-D11


title: divSLAM cell 110 [092415_Cell52-G10]

description: run1315_lane1_read1_indexN710-S504=092415_Cell52-G10


title: divSLAM cell 109 [092415_Cell5-E1]

description: run1315_lane1_read1_indexN705-S505=092415_Cell5-E1


title: divSLAM cell 107 [092415_Cell44-B9]

description: run1315_lane1_read1_indexN709-S504=092415_Cell44-B9


title: divSLAM cell 106 [092415_Cell40-C8]

description: run1315_lane1_read1_indexN712-S508=092415_Cell40-C8


title: divSLAM cell 105 [092415_Cell4-D1]

description: run1315_lane1_read1_indexN704-S504=092415_Cell4-D1


title: divSLAM cell 102 [092415_Cell28-B6]

description: run1315_lane1_read1_indexN707-S504=092415_Cell28-B6


title: divSLAM cell 103 [092415_Cell3-C1]

description: run1315_lane1_read1_indexN703-S503=092415_Cell3-C1


title: divSLAM cell 101 [092415_Cell24-D5]

description: run1315_lane1_read1_indexN710-S508=092415_Cell24-D5


title: aSLAM cell 99 [092415_Cell21-A5]

description: run1315_lane1_read1_indexN707-S505=092415_Cell21-A5

source_name: aSLAM cell


title: aSLAM cell 98 [092415_Cell2-B1]

description: run1315_lane1_read1_indexN702-S502=092415_Cell2-B1


title: divSLAM cell 100 [092415_Cell22-B5]

description: run1315_lane1_read1_indexN708-S506=092415_Cell22-B5


title: divSLAM cell 117 [092415_Cell9-E2]

description: run1315_lane1_read1_indexN702-S517=092415_Cell9-E2


title: aSLAM cell 97 [092415_Cell15-F3]

description: run1315_lane1_read1_indexN708-S507=092415_Cell15-F3


title: aSLAM cell 93 [092415_Cell10-F2]

description: run1315_lane1_read1_indexN703-S502=092415_Cell10-F2


title: divSLAM cell 104 [092415_Cell35-D7]

description: run1315_lane1_read1_indexN707-S503=092415_Cell35-D7


title: divSLAM cell 122 [092415_Cell20-E4]

description: run1315_lane1_read1_indexN706-S504=092415_Cell20-E4


title: aSLAM cell 94 [092415_Cell11-G2]

description: run1315_lane1_read1_indexN704-S503=092415_Cell11-G2


title: aSLAM cell 95 [092415_Cell13-B3]

description: run1315_lane1_read1_indexN706-S505=092415_Cell13-B3


title: aSLAM cell 96 [092415_Cell14-E3]

description: run1315_lane1_read1_indexN707-S506=092415_Cell14-E3


title: aSLAM cell 92 [092415_Cell1-A1]

description: run1315_lane1_read1_indexN701-S517=092415_Cell1-A1


title: aSLAM cell 90 [120215_Cell72-F4]

description: run1315_lane1_read1_indexN704-S508=120215_Cell72-F4


title: aSLAM cell 91 [120215_Cell68-H2]

description: run1315_lane1_read1_indexN712-S504=120215_Cell68-H2


title: divSLAM cell 113 [092415_Cell57-G11]

description: run1315_lane1_read1_indexN708-S517=092415_Cell57-G11


title: aSLAM cell 88 [120215_Cell85-F9]

description: run1315_lane1_read1_indexN703-S505=120215_Cell85-F9


title: aSLAM cell 89 [120215_Cell86-B10]

description: run1315_lane1_read1_indexN704-S506=120215_Cell86-B10


title: aSLAM cell 87 [120215_Cell95-C12]

description: run1315_lane1_read1_indexN706-S507=120215_Cell95-C12


title: aSLAM cell 86 [120215_Cell92-E11]

description: run1315_lane1_read1_indexN703-S504=120215_Cell92-E11


title: divSLAM cell 108 [092415_Cell48-H9]

description: run1315_lane1_read1_indexN701-S508=092415_Cell48-H9


title: aSLAM cell 85 [120215_Cell90-B11]

description: run1315_lane1_read1_indexN701-S502=120215_Cell90-B11


title: aSLAM cell 84 [120215_Cell89-G10]

description: run1315_lane1_read1_indexN712-S517=120215_Cell89-G10


title: aSLAM cell 83 [120215_Cell88-F10]

description: run1315_lane1_read1_indexN706-S508=120215_Cell88-F10


title: aSLAM cell 82 [120215_Cell87-E10]

description: run1315_lane1_read1_indexN705-S507=120215_Cell87-E10


title: aSLAM cell 80 [120215_Cell81-H7]

description: run1315_lane1_read1_indexN711-S517=120215_Cell81-H7


title: aSLAM cell 81 [120215_Cell84-B9]

description: run1315_lane1_read1_indexN702-S504=120215_Cell84-B9


title: aSLAM cell 79 [120215_Cell79-F7]

description: run1315_lane1_read1_indexN704-S507=120215_Cell79-F7


title: aSLAM cell 78 [120215_Cell65-C1]

description: run1315_lane1_read1_indexN709-S517=120215_Cell65-C1


title: aSLAM cell 75 [120215_Cell91-C11]

description: run1315_lane1_read1_indexN702-S503=120215_Cell91-C11


title: aSLAM cell 73 [120215_Cell82-E8]

description: run1315_lane1_read1_indexN712-S502=120215_Cell82-E8


title: aSLAM cell 74 [120215_Cell83-A9]

description: run1315_lane1_read1_indexN701-S503=120215_Cell83-A9


title: aSLAM cell 77 [120215_Cell96-D12]

description: run1315_lane1_read1_indexN707-S508=120215_Cell96-D12


title: aSLAM cell 76 [120215_Cell94-H11]

description: run1315_lane1_read1_indexN705-S506=120215_Cell94-H11


title: aSLAM cell 69 [120215_Cell76-F6]

description: run1315_lane1_read1_indexN701-S504=120215_Cell76-F6


title: aSLAM cell 71 [120215_Cell78-C7]

description: run1315_lane1_read1_indexN703-S506=120215_Cell78-C7


title: aSLAM cell 68 [120215_Cell75-E6]

description: run1315_lane1_read1_indexN712-S503=120215_Cell75-E6


title: aSLAM cell 72 [120215_Cell80-G7]

description: run1315_lane1_read1_indexN705-S508=120215_Cell80-G7


title: aSLAM cell 70 [120215_Cell77-G6]

description: run1315_lane1_read1_indexN702-S505=120215_Cell77-G6


title: aSLAM cell 66 [120215_Cell73-H4]

description: run1315_lane1_read1_indexN710-S517=120215_Cell73-H4


title: aSLAM cell 64 [120215_Cell70-F3]

description: run1315_lane1_read1_indexN702-S506=120215_Cell70-F3


title: aSLAM cell 67 [120215_Cell74-F5]

description: run1315_lane1_read1_indexN711-S502=120215_Cell74-F5


title: aSLAM cell 63 [120215_Cell69-D3]

description: run1315_lane1_read1_indexN701-S505=120215_Cell69-D3


title: aSLAM cell 61 [120215_Cell66-F1]

description: run1315_lane1_read1_indexN710-S502=120215_Cell66-F1


title: aSLAM cell 65 [120215_Cell71-G3]

description: run1315_lane1_read1_indexN703-S507=120215_Cell71-G3


title: aSLAM cell 62 [120215_Cell67-E2]

description: run1315_lane1_read1_indexN711-S503=120215_Cell67-E2


title: aSLAM cell 60 [120215_Cell64-B1]

description: run1315_lane1_read1_indexN703-S508=120215_Cell64-B1


title: sSLAM cell 59 [Lsk.Slam.9]

description: run1033_lane1_read1_indexN702-S517=Grimes_Jun_9_Cell_9

source_name: sSLAM cell


title: sSLAM cell 58 [Lsk.Slam.8]

description: run1033_lane1_read1_indexN708-S508=Grimes_Jun_9_Cell_8


title: sSLAM cell 55 [Lsk.Slam.59]

description: run1033_lane1_read1_indexN709-S503=Grimes_Jun_9_Cell_59


title: sSLAM cell 56 [Lsk.Slam.6]

description: run1033_lane1_read1_indexN706-S506=Grimes_Jun_9_Cell_6


title: sSLAM cell 54 [Lsk.Slam.58]

description: run1033_lane1_read1_indexN708-S502=Grimes_Jun_9_Cell_58


title: sSLAM cell 57 [Lsk.Slam.7]

description: run1033_lane1_read1_indexN707-S507=Grimes_Jun_9_Cell_7


title: sSLAM cell 53 [Lsk.Slam.57]

description: run1033_lane1_read1_indexN707-S517=Grimes_Jun_9_Cell_57


title: sSLAM cell 51 [Lsk.Slam.55]

description: run1033_lane1_read1_indexN712-S507=Grimes_Jun_9_Cell_55


title: sSLAM cell 52 [Lsk.Slam.56]

description: run1033_lane1_read1_indexN701-S508=Grimes_Jun_9_Cell_56


title: sSLAM cell 50 [Lsk.Slam.54]

description: run1033_lane1_read1_indexN711-S506=Grimes_Jun_9_Cell_54


title: sSLAM cell 49 [Lsk.Slam.53]

description: run1033_lane1_read1_indexN710-S505=Grimes_Jun_9_Cell_53


title: sSLAM cell 48 [Lsk.Slam.52]

description: run1033_lane1_read1_indexN709-S504=Grimes_Jun_9_Cell_52


title: sSLAM cell 46 [Lsk.Slam.50]

description: run1033_lane1_read1_indexN707-S502=Grimes_Jun_9_Cell_50


title: sSLAM cell 45 [Lsk.Slam.5]

description: run1033_lane1_read1_indexN705-S505=Grimes_Jun_9_Cell_5


title: sSLAM cell 44 [Lsk.Slam.49]

description: run1033_lane1_read1_indexN706-S517=Grimes_Jun_9_Cell_49


title: sSLAM cell 43 [Lsk.Slam.48]

description: run1033_lane1_read1_indexN707-S508=Grimes_Jun_9_Cell_48


title: sSLAM cell 41 [Lsk.Slam.46]

description: run1033_lane1_read1_indexN705-S506=Grimes_Jun_9_Cell_46


title: sSLAM cell 42 [Lsk.Slam.47]

description: run1033_lane1_read1_indexN706-S507=Grimes_Jun_9_Cell_47


title: sSLAM cell 40 [Lsk.Slam.45]

description: run1033_lane1_read1_indexN704-S505=Grimes_Jun_9_Cell_45


title: sSLAM cell 47 [Lsk.Slam.51]

description: run1033_lane1_read1_indexN708-S503=Grimes_Jun_9_Cell_51


title: hCMEC/D3 cells, NMV 4

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

description:
Gene expression data from human brain endothelial cells
4 MV

hyb_protocol: 12µg of cRNA molecules were heat fragmented and applied to the Human U133 plus 2 GeneChip in a hybridization solution according to the Affymetrix protocol. Hybridization took place overnight in a rotating hybridization platform at 45°C for 16 hours. Post hybridization stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the AGCC software package to prepare the .CEL files

data_processing: The data were analyzed with Transcriptome Analysis Console v4 using RMA as normalization method.

source_name: NMV treated cells

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix IVT protocol

extract_protocol:
[isolation protocol] Peripheral venous blood was collected in tubes containing 3.8% sodium citrate and was separated by density gradient centrifugation using Histopaque-1077. Red blood cells were lysed and isolated neutrophils were stimulated with the bacterial-derived peptide fMLP (10 µmol/L; Sigma) for 1 h (37°C in 5% CO2). Neutrophils and large cell debris were pelleted by centrifugation (500 g for 5 min followed by 1,500 g, 5 mins respectively). The supernatant was centrifuged at 20,000 g for 30 min to pellet NMV. The pelleted NMV were resuspended in 0.2-µm sterile-filtered PBS. The number of NMV from each isolation was determined using a BD LSRII flow cytometer. hCMEC/D3 cells were treated with NMV (300 per ul) for 24h and were collected.
Directzol RNA Extraction kit was used according to manufacturers extraction.

value: brain endothelial cell line hCMEC/D3

tag: treatment

value: NMV


title: Day 28 after AKI (2)

city: Taipei City

first: Yu Hsiang

last: Chou

state: Taiwan

address: No.7, Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University Hospital

description: SAMPLE 11 (#80)

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The file FinalReport-nonormal.txt includes the raw, non-normalized data. FinalReport-quantile.txt includes the quantile normalized data with gene annotation.
The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Kidney

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

growth_protocol: nil, because we extract RNA immediately after isolation of pericytes

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

treatment_protocol: Ischemia-reperfusion renal injury

value: FoxD1-GC;tdTomato; Col1a1-GFP mice

value: Kidney

value: pericyte

tag: time after acute kidney injury (days)


title: Day 56 after AKI (2)

description: SAMPLE 14 (#7)


title: hCMEC/D3 cells, Control 3

description:
Gene expression data from human brain endothelial cells
3 C

source_name: Cells without NMV treatment

value: control


title: Day 56 after AKI (1)

description: SAMPLE 13 (#2)


title: Day 56 after AKI (3)

description: SAMPLE 15 (#28)


title: hCMEC/D3 cells, NMV 2

description:
Gene expression data from human brain endothelial cells
2 MV


title: hCMEC/D3 cells, NMV 1

description:
Gene expression data from human brain endothelial cells
1 MV


title: hCMEC/D3 cells, NMV 5

description:
Gene expression data from human brain endothelial cells
5 MV


title: hCMEC/D3 cells, Control 1

description:
Gene expression data from human brain endothelial cells
1 C


title: hCMEC/D3 cells, NMV 3

description:
Gene expression data from human brain endothelial cells
3 MV


title: hCMEC/D3 cells, Control 4

description:
Gene expression data from human brain endothelial cells
4 C


title: hCMEC/D3 cells, Control 2

description:
Gene expression data from human brain endothelial cells
2 C


title: Day 7 after AKI (1)

description: SAMPLE 7 (D7)


title: Day 28 after AKI (1)

description: SAMPLE 10 (#72)


title: MCF-7-Si

city: Jinan

first: Peng

last: Gao

address: Wenhua Xi Road 44

department: Department of Pathology

institute: Shandong University School of Medicine

description: Gene expression microarray was utilized to screen the differentially expressed genes between MCF-7 cells with or without silencing of OR2T6 gene..

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the mRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and 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 v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, mRNAs that have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: MCF-7 cells

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. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNAs was extracted using TRIzol reagent.Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.RNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

value: breast cancer cell line


title: MCF-7-NC


title: 6b4/SUG6/rdr6

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

country: France

institute: INRA

data_processing:
Remove 3’ adapter with cutadapt version 1.9.1
Map with bowtie version 0.12.7 on the 35S sequence, the GUS sequence, and the RbcS sequence.
Classify the reads (with awk) in 3 overlapping categories, depending on their size: 20-25 (all known short RNAs), 21-22 (miRNAs), 24 (siRNAs)
Count the number of reads in each category.
Genome_build: The reads were not mapped to any genome.
Supplementary_files_format_and_content: the expression of only three genes (or regions) were quantified: 35S, GUS, and RbcS.  The raw counts are provided in the table.

organism: Arabidopsis thaliana

growth_protocol: Seeds were sterilized with bleach and ethanol and grown on S-Medium from Duchefa (http:// www.duchefa-biochemie.com) under 18 h of light and 6 h dark cycles with an average temperature of 22◦C

extract_protocol:
Buffer containing 0.1 M NaCl, 2% SDS, 50 mMTris–HCl (pH 9), 10 mMEDTA (pH 8) and 20 mM ß- mercaptoethanol was added to the frozen powder andRNA was extracted twice with phenol and recovered by ethanol precipitation. For small RNA analysis, total RNA was sep- arated on a 15% denaturing polyacrylamide gel and stained with ethidium bromide.
Library construction has been realized by GATC Biotech
All libraries were pooled together and sequenced on Illumina HiSeq 2000 platform

treatment_protocol: Whole seedlings were collected 11 days after germination and grinded in liquid nitrogen.

tag: ecotype background

tag: transgene

tag: mutation

value: Seedlings


title: Day 28 after AKI (3)

description: SAMPLE 12 (#71)

tag: tissue

tag: cell type


title: Day 2 after AKI (3)

description: SAMPLE 6 (#96)

tag: strain


title: Day 7 after AKI (2)

description: SAMPLE 8 (#87)


title: Day 7 after AKI (3)

description: SAMPLE 9 (#16)


title: Day 2 after AKI (1)

description: SAMPLE 4 (#46)


title: Day 2 after AKI (2)

description: SAMPLE 5 (#85)


title: hCMEC/D3 cells, Control 5

description:
Gene expression data from human brain endothelial cells
5 C

tag: cell line


title: sSLAM cell 38 [Lsk.Slam.43]

description: run1033_lane1_read1_indexN702-S503=Grimes_Jun_9_Cell_43


title: 6b4/SUG6/rdr2rdr6

description: NG-6573_6b4_SUG6_rdr2_rdr6_2_lib21189_1522_7_1

value: rdr2-5 rdr6-1


title: Ctrl(2)

description: SAMPLE 2 (#97)


title: sSLAM cell 39 [Lsk.Slam.44]

description: run1033_lane1_read1_indexN703-S504=Grimes_Jun_9_Cell_44


title: 6b4/SUG6/ago1-27

description: NG-6573_6b4_SUG6_ago1_27_lib20165_1525_7_1


title: 6b4/SUG6/rdr2


title: 6b4/SUG6/dcl2dcl4

description: NG-6573_6b4_SUG6_dcl2_dcl4_lib20164_1525_7_1

value: dcl2(Kas) dcl4-5


title: sSLAM cell 35 [Lsk.Slam.40]

description: run1033_lane1_read1_indexN712-S508=Grimes_Jun_9_Cell_40

value: Bone Marrow


title: 6b4/SUG6/dcl4


title: 6b4/SUG6/dcl2


title: sSLAM cell 34 [Lsk.Slam.4]

description: run1033_lane1_read1_indexN704-S504=Grimes_Jun_9_Cell_4

value: LSK-SLAM Stem cells


title: sSLAM cell 36 [Lsk.Slam.41]

description: run1033_lane1_read1_indexN712-S517=Grimes_Jun_9_Cell_41

value: Fluidigm C1 protocol


title: sSLAM cell 33 [Lsk.Slam.39]

description: run1033_lane1_read1_indexN711-S507=Grimes_Jun_9_Cell_39

value: Nextera XT DNA Library Preparation Kit (Illumina Inc, Santa Clara, CA)


title: Ctrl(1)

description: SAMPLE 1 (#77)


title: sSLAM cell 28 [Lsk.Slam.34]

description: run1033_lane1_read1_indexN706-S502=Grimes_Jun_9_Cell_34


title: sSLAM cell 32 [Lsk.Slam.38]

description: run1033_lane1_read1_indexN710-S506=Grimes_Jun_9_Cell_38


title: sSLAM cell 30 [Lsk.Slam.36]

description: run1033_lane1_read1_indexN708-S504=Grimes_Jun_9_Cell_36


title: sSLAM cell 29 [Lsk.Slam.35]

description: run1033_lane1_read1_indexN707-S503=Grimes_Jun_9_Cell_35


title: L1/rdr2


title: sSLAM cell 27 [Lsk.Slam.33]

description: run1033_lane1_read1_indexN705-S517=Grimes_Jun_9_Cell_33


title: L1/rdr6


title: 6b4

value: WT


title: L1/ago1-27


title: Ctrl(3)

description: SAMPLE 3 (#8)


title: sSLAM cell 26 [Lsk.Slam.32]

description: run1033_lane1_read1_indexN711-S508=Grimes_Jun_9_Cell_32


title: sSLAM cell 24 [Lsk.Slam.30]

description: run1033_lane1_read1_indexN709-S506=Grimes_Jun_9_Cell_30


title: L1/rdr2rdr6


title: sSLAM cell 37 [Lsk.Slam.42]

description: run1033_lane1_read1_indexN701-S502=Grimes_Jun_9_Cell_42


title: L1/e52


title: sSLAM cell 25 [Lsk.Slam.31]

description: run1033_lane1_read1_indexN710-S507=Grimes_Jun_9_Cell_31


title: 6b4/SUG6/ago1-1

description: NG-6573_6b4_SUG6_ago1_1_lib20166_1525_7_1


title: L1/dcl2dcl4

description: NG-6573_L1_dcl2_dcl4_2_lib21185_1522_7_1


title: L1/dcl4


title: L1/dcl2


title: sSLAM cell 22 [Lsk.Slam.29]

description: run1033_lane1_read1_indexN708-S505=Grimes_Jun_9_Cell_29


title: sSLAM cell 31 [Lsk.Slam.37]

description: run1033_lane1_read1_indexN709-S505=Grimes_Jun_9_Cell_37


title: sSLAM cell 21 [Lsk.Slam.28]

description: run1033_lane1_read1_indexN707-S504=Grimes_Jun_9_Cell_28


title: sSLAM cell 20 [Lsk.Slam.27]

description: run1033_lane1_read1_indexN706-S503=Grimes_Jun_9_Cell_27


title: sSLAM cell 23 [Lsk.Slam.3]

description: run1033_lane1_read1_indexN703-S503=Grimes_Jun_9_Cell_3


title: 6b4/SUG6


title: L1


title: SUG6


title: SALINE PFC 12

first: Song-Jun

last: Xu

address: 3400 Civic Center Blvd

data_processing:
RNA-seq reads were aligned against mouse reference genome (mm9, ensemble annotation) using STAR (Version 2.4.1d)
Aligned reads were normalized using different methods including TMM, TMM_CPM, RPKM, EDAseq_UQ , FullQuantile, Median, PoissonSeq, RUV and PORT (https://github.com/itmat/Normalization). Differential gene expression analysis was performed using different models: DEseq2-Wald, EdgeR-Robust-LRT, LimmaVoom, MannWhitney and Parametric t-test. Q-values are determined for each of the 45 combinations of normalization and differential gene expression analysis. Genes with a mean q value smaller than 0.25 were considered a target of differential expression for each combination. A gene is identified as differentially expressed gene if it is detected by the combination of 5 different methods.
Genome_build: mm9
Supplementary_files_format_and_content: *info.txt files: read counts per gene; *fdr.change.txt: DEG summary
D1.NAc.all.info.txt: Generated using Cocaine NAc 1-6
D1.PFC.all.fdr.change.txt: Calculated using Cocaine VTA 1-6 and Saline VTA 1-6
D1.VTA.all.fdr.change.txt: Calculated using Cocaine PFC 1-6 and Saline PFC 1-6
D28.NAc.all.info.txt: Generated using Cocaine NAc 7-12 and Saline NAc 7-12
D28.PFC.all.info.txt: Generated using Cocaine PFC 7-12 and Saline PFC 7-12
D28.VTA.all.info.txt: Generated using Cocaine VTA 7-11 and Saline VTA 7-11

source_name: Prefrontal Cortex

extract_protocol:
For tissue collection, mice were euthanized by cervical dislocation and the brain was placed in ice-cold phosphate buffered saline with protease inhibitor cocktail (Roche cOmplete Protease inhibitor). 1 mm thick sections of prefrontal cortex, nucleus accumbens and ventral tegmental area, brain regions were prepared using a cold tissue matrix and regions were micro-dissected with a 2- or 1.2-mm diameter micro-punch (Harris)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To identify a master regulator of homeostatic gene expression, we profiled global transcriptomic changes in the adult mouse brain, including the NAc, VTA, and PFC, at early (1-day) and late (28-days) abstinence following cocaine self-administration

value: Brain

tag: brain region

value: Prefrontal Cortex

tag: time point

value: 28-days Abstinence

tag: genotype

value: wild type


title: sSLAM cell 19 [Lsk.Slam.26]

description: run1033_lane1_read1_indexN705-S502=Grimes_Jun_9_Cell_26


title: sSLAM cell 18 [Lsk.Slam.25]

description: run1033_lane1_read1_indexN704-S517=Grimes_Jun_9_Cell_25


title: SALINE PFC 7


title: COCAINE PFC 12


title: SALINE PFC 8


title: sSLAM cell 16 [Lsk.Slam.23]

description: run1033_lane1_read1_indexN709-S507=Grimes_Jun_9_Cell_23


title: sSLAM cell 17 [Lsk.Slam.24]

description: run1033_lane1_read1_indexN710-S508=Grimes_Jun_9_Cell_24


title: sSLAM cell 15 [Lsk.Slam.22]

description: run1033_lane1_read1_indexN708-S506=Grimes_Jun_9_Cell_22


title: SALINE PFC 11


title: SALINE PFC 9


title: SALINE PFC 10


title: sSLAM cell 14 [Lsk.Slam.21]

description: run1033_lane1_read1_indexN707-S505=Grimes_Jun_9_Cell_21


title: sSLAM cell 13 [Lsk.Slam.20]

description: run1033_lane1_read1_indexN706-S504=Grimes_Jun_9_Cell_20


title: COCAINE PFC 9


title: sSLAM cell 12 [Lsk.Slam.2]

description: run1033_lane1_read1_indexN702-S502=Grimes_Jun_9_Cell_2


title: COCAINE PFC 11


title: COCAINE PFC 8


title: COCAINE PFC 7


title: sSLAM cell 8 [Lsk.Slam.16]

description: run1033_lane1_read1_indexN709-S508=Grimes_Jun_9_Cell_16


title: SALINE VTA 11

source_name: Ventral Tegmental Area

value: Ventral Tegmental Area


title: sSLAM cell 7 [Lsk.Slam.15]

description: run1033_lane1_read1_indexN708-S507=Grimes_Jun_9_Cell_15


title: SALINE VTA 10


title: sSLAM cell 6 [Lsk.Slam.14]

description: run1033_lane1_read1_indexN707-S506=Grimes_Jun_9_Cell_14


title: sSLAM cell 5 [Lsk.Slam.13]

description: run1033_lane1_read1_indexN706-S505=Grimes_Jun_9_Cell_13


title: SALINE VTA 8


title: sSLAM cell 11 [Lsk.Slam.19]

description: run1033_lane1_read1_indexN705-S503=Grimes_Jun_9_Cell_19


title: COCAINE PFC 10


title: SALINE VTA 9


title: sSLAM cell 10 [Lsk.Slam.18]

description: run1033_lane1_read1_indexN704-S502=Grimes_Jun_9_Cell_18


title: sSLAM cell 3 [Lsk.Slam.11]

description: run1033_lane1_read1_indexN704-S503=Grimes_Jun_9_Cell_11


title: SALINE VTA 7


title: sSLAM cell 9 [Lsk.Slam.17]

description: run1033_lane1_read1_indexN703-S517=Grimes_Jun_9_Cell_17


title: COCAINE VTA 12


title: COCAINE VTA 11


title: sSLAM cell 2 [Lsk.Slam.10]

description: run1033_lane1_read1_indexN703-S502=Grimes_Jun_9_Cell_10


title: sSLAM cell 4 [Lsk.Slam.12]

description: run1033_lane1_read1_indexN705-S504=Grimes_Jun_9_Cell_12


title: sSLAM cell 1 [Lsk.Slam.1]

description: run1033_lane1_read1_indexN701-S517=Grimes_Jun_9_Cell_1


title: COCAINE VTA 10


title: COCAINE VTA 9


title: COCAINE VTA 8


title: SB_23

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies) and then loaded onto TruSeq SR v3 flow cells on an Illumina HiSeq 2500 (Illumina) and run for 100 cycles using a paired-read recipe (TruSeq SBS Kit v3, Illumina) according to the manufacturer's instructions.
Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter. Additional quality filtering used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) to keep only reads that have at least 80% of bases with a quality score of 20 or more (conducted by fastq_quality_filter function) and reads left with 10 bases or longer after being end-trimmed with a base quality score of 20 (conducted by fastq_quality_trimmer function).
The RNA-seq reads were mapped using Tophat version 2.0.9(44) supplied by Ensembl annotation file; GRCm38.78.gtf. Read counts were computed using Cufflinks version 2.2.1 supplied by GRCm38.78.gtf.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file, Normalized gene counts

source_name: Sle1b.IFNγR-/--IMQ 3

extract_protocol:
RNA was extracted from spleen tissues by TRIzol as per the manufacturer’s instructions (Ambion). Optical density values of extracted RNA were measured using NanoDrop to confirm an A260:A280 ratio above 1.9. RNA integrity number was measured using BioAnalyzer (Agilent Technologies). RNA 6000 Pico Kit to confirm RIN above 7.
The cDNA libraries were prepared using the Ovation RNA-seq System V2 (NuGEN, San Carlos, CA) as per the manufacturer’s instructions. The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing.

treatment_protocol: B6.Sle1b and Sle1b.IFNγR-/- mice were treated with imiquimod thrice a week (IMQ) for 4 weeks and the splenic tissues were processed for RNA sequencing.

tag: phenotype

value: IFNgR deficient autoimmune prone mice

value: spleen


title: SB_22

source_name: Sle1b.IFNγR-/--IMQ 2


title: COCAINE VTA 7


title: SB_20

source_name: B6.Sle1b-IMQ 3

value: Autoimmune prone control mice


title: SALINE NAC 12

source_name: Nucleus Accumbens

value: Nucleus Accumbens


title: SB_21

source_name: Sle1b.IFNγR-/--IMQ 1


title: Primary Breast Tumor:TN110

type: genomic

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

hyb_protocol: Restored DNA was arrayed using the Illumina Infinium HumanMethylation450K BeadChip Kit (WG-314-1003) in the JHU DNA Microarray Core.

scan_protocol: Arrays were imaged using Illumina iScan with Illumina scanner settings for Infinium chip

data_processing: Raw array file data were imported into Illumina GenomeStudio v2011.1 Illumina, San Diego, CA) without normalization. Probe hybridization and quality control were assessed within GenomeStudio, as was the level of CpG locus methylation, calculated as a β-value, low to high ranging from 0 to 1, respectively. Distributions of methylation levels were visualized using histograms. Data were then imported into the Partek Genomics Suite (Partek, Inc, St. Louis, MO) and analyzed using standard Partek functions as well as GraphPad Prism 5.0 (GraphPad Software, La Jolla, CA) tools.

label: Cy5 and Cy3

source_name: Primary Breast Tumor

label_protocol: The EZ DNA Methylation kit (D5001; ZymoResearch) was used for bisulfite conversion. Bisulfite treated genomic DNA was restored (375 ng in 10 µl; Infinium HD FFPE DNA Restore Kit; WG-321-1002, Illumina, Inc.).

extract_protocol: FFPE tumor tissue sections were deparaffinized with xylene, digested for 24 hours at 56o C with 10 mM Tris pH 8, 150 mM NaCl, 2 mM EDTA, 0.5% SDS containing 4 mg proteinase K, and heated to 90o C. for 10 min.

value: Iowa

value: NoChemo

value: SurgOnly

tag: age

tag: relapse

tag: dfsmo

tag: er

tag: grade

tag: ajcc


title: SB_19

source_name: B6.Sle1b-IMQ 2


title: Primary Breast Tumor:TN151

tag: treatment

value: X


title: SALINE NAC 11


title: Primary Breast Tumor:TN131


title: Primary Breast Tumor:TN002

value: Hopkins

value: IA


title: Primary Breast Tumor:TN042

value: Duke


title: Primary Breast Tumor:TN025


title: Primary Breast Tumor:TN041

value: IIA


title: SALINE NAC 10

value: Brain


title: B220_neg_PC.UTX.Blimp_pos.5

first: Brian

middle: Thomas

last: Gaudette

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

description:
processed data file:
Blimp_reporter_PC_stim.normExp.txt, Blimp_reporter_PC_stim.rawTPM.txt, Blimp_reporter_PC_stim_noIg.normExp.txt, Blimp_reporter_PC_stim_noIg.rawTPM.txt

data_processing:
basecalling: Illumina basespace pipeline (and concatenation of all lanes)
pseudoalignment: Kallisto (param: -b 100 --single -l 250 -s 30 -t 16)
data was analysed both before and after being filtered to remove immunoglobulin transcripts prior to further analysis
differential expression: Voom (normalization), and limma linear fit and Bayesian statistics for differential expression
all data display and additional statistics: R statistical environment
Genome_build: mm10
Supplementary_files_format_and_content: Blimp_reporter_PC_stim.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Blimp_reporter_PC_stim.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol
Supplementary_files_format_and_content: Blimp_reporter_PC_stim_noIg.normExp.txt: tab-delimited text. normalized expression (log2 TPM) for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts
Supplementary_files_format_and_content: Blimp_reporter_PC_stim_noIg.rawTPM.txt: tab-delimited text. raw TPM for all samples and transcripts condensed to official gene symbol and filtered to remove immunoglobulin transcripts

source_name: B220- bone marrow plasma cell

growth_protocol: B6.Blimp1+/GFP mice were maintained in UPENN SPF facilities.

extract_protocol:
Spleens were harvested at time of saccrifice and lypmhocytes were stained and FACS sorted directly into TRIZOL reagent as follows: follicular B cell: live, singlet, CD19+, CD93-, CD23+, CD21/35int.  marginal zone B cell: live, singlet, CD19+, CD93-, CD23-, CD21/35high. immature PC: live, singlet, IgD-, Dump(CD4, CD8a, Ter-119, F4-80)-, GFP(Blimp1)+, CD138high, B220+. long-lived PC:live, singlet, IgD-, Dump(CD4, CD8a, Ter-119, F4-80)-, GFP(Blimp1)+, CD138high, B220-.  In-vitro cultured were FACS sorted by live, singlet, GFP expression and CTV-dilution.
RNA was extracted by TRIZOL protocol and quantified by Qubit.  cDNA was prepared using Takara Clonetech smarter v4 kit by protocol with Illumina Nextera XT reagents for library construction and quantified and equal molar pooled by tape station and qubit analysis.  Plasma cell samples were sequenced 4x deeper than B cell samples to account for Immunoglobulin gene abundance and downstream filtering.

treatment_protocol: In-vivo samples are untreated from SPF mice.  In-vitro cultures from these mice were prepared from marginal zone and follicular B cells stimulated for 48 and 72 hours respectively with CpG DNA (ODN1826) with and without IL-4 and IL-5.

tag: genotype/variation

value: 12 weeks

value: Bone Marrow

value: Bone marrow plasma cell


title: Primary Breast Tumor:TN071


title: Primary Breast Tumor:TN082


title: Primary Breast Tumor:TN083


title: Primary Breast Tumor:TN119


title: Primary Breast Tumor:TN053


title: Primary Breast Tumor:TN067


title: Primary Breast Tumor:TN097


title: Primary Breast Tumor:TN076


title: Primary Breast Tumor:TN088


title: Primary Breast Tumor:TN132


title: Primary Breast Tumor:TN037


title: SALINE NAC 9

value: 28-days Abstinence

value: wild type


title: B220_neg_PC.UTX.Blimp_pos.4


title: Primary Breast Tumor:TN013


title: Primary Breast Tumor:TN099


title: Primary Breast Tumor:TN153


title: Primary Breast Tumor:TN016


title: B220_neg_PC.UTX.Blimp_pos.3


title: SALINE NAC 8


title: SALINE NAC 7


title: COCAINE NAC 12


title: B220_pos_PC.UTX.Blimp_pos.5

source_name: B220+ bone marrow plasma cell


title: Primary Breast Tumor:TN107


title: COCAINE NAC 11


title: Primary Breast Tumor:TN030


title: Primary Breast Tumor:TN152

value: H


title: B220_pos_PC.UTX.Blimp_pos.4


title: COCAINE NAC 10


title: Primary Breast Tumor:TN084


title: Primary Breast Tumor:TN029


title: B220_pos_PC.UTX.Blimp_pos.3


title: COCAINE NAC 9


title: Primary Breast Tumor:TN122


title: COCAINE NAC 8


title: Primary Breast Tumor:TN072


title: Primary Breast Tumor:TN121


title: B220_pos_PC.UTX.Blimp_pos.2


title: Primary Breast Tumor:TN066


title: B220_pos_PC.UTX.Blimp_pos.1


title: Primary Breast Tumor:TN143


title: SB_18

source_name: B6.Sle1b-IMQ 1

value: Autoimmune prone control mice

value: spleen


title: Primary Breast Tumor:TN028


title: marginal_Z_B.C45.Blimp_pos.4

source_name: 4th division GFP+ CpG+IL-4,5-stimulated marginal zone B cell

value: Spleen

value: in-vitro cultured primary B cell


title: SALINE PFC 6

value: Prefrontal Cortex

value: 1-day Abstinence


title: Primary Breast Tumor:TN039

value: Hopkins

value: NoChemo

value: X


title: marginal_Z_B.C45.Blimp_pos.3


title: Primary Breast Tumor:TN106

value: SurgOnly

value: IIA


title: marginal_Z_B.C45.Blimp_pos.2

value: 12 weeks


title: SALINE PFC 5

value: Brain


title: Primary Breast Tumor:TN096

value: Iowa


title: B220_neg_PC.UTX.Blimp_pos.2

value: Bone Marrow

value: Bone marrow plasma cell


title: Primary Breast Tumor:TN052

value: IA


title: marginal_Z_B.CPG.Blimp_pos.4

source_name: 4th division GFP+ CpG-stimulated marginal zone B cell


title: Primary Breast Tumor:TN068


title: SALINE PFC 2

value: wild type


title: Primary Breast Tumor:TN094


title: Primary Breast Tumor:TN069


title: Primary Breast Tumor:TN070


title: SALINE PFC 4


title: marginal_Z_B.CPG.Blimp_pos.3


title: Primary Breast Tumor:TN144


title: Primary Breast Tumor:TN133

value: H


title: Primary Breast Tumor:TN109


title: SALINE PFC 1


title: Primary Breast Tumor:TN115


title: marginal_Z_B.CPG.Blimp_pos.2

value: Spleen


title: Primary Breast Tumor:TN087


title: COCAINE PFC 6


title: Primary Breast Tumor:TN146


title: Primary Breast Tumor:TN108


title: COCAINE PFC 5


title: Primary Breast Tumor:TN130


title: Primary Breast Tumor:TN129


title: marginal_Z_B.C45.Blimp_neg.4

source_name: 3th division GFP- CpG+IL-4,5-stimulated marginal zone B cell

value: in-vitro cultured primary B cell


title: Primary Breast Tumor:TN026

value: IIB


title: COCAINE PFC 4

value: Prefrontal Cortex

value: 1-day Abstinence


title: Primary Breast Tumor:TN140

value: Hopkins

value: NoChemo


title: COCAINE PFC 3


title: Primary Breast Tumor:TN005

value: Duke

value: X


title: Primary Breast Tumor:TN104


title: marginal_Z_B.C45.Blimp_neg.3

value: 12 weeks


title: marginal_Z_B.C45.Blimp_neg.2


title: Primary Breast Tumor:TN001

value: IIA


title: Primary Breast Tumor:TN134

value: Iowa


title: COCAINE PFC 2

value: Brain


title: marginal_Z_B.C45.Blimp_neg.1


title: COCAINE PFC 1


title: COCAINE NAC 7

value: Nucleus Accumbens

value: 28-days Abstinence


title: Primary Breast Tumor:TN103

value: SurgOnly


title: Primary Breast Tumor:TN027

value: IA


title: Primary Breast Tumor:TN120


title: marginal_Z_B.CPG.Blimp_neg.4

source_name: 3th division GFP- CpG-stimulated marginal zone B cell

value: Spleen


title: SALINE VTA 6

value: Ventral Tegmental Area

value: wild type


title: Primary Breast Tumor:TN150


title: SALINE VTA 5


title: marginal_Z_B.CPG.Blimp_pos.1

value: in-vitro cultured primary B cell


title: Primary Breast Tumor:TN060


title: marginal_Z_B.CPG.Blimp_neg.2


title: marginal_Z_B.CPG.Blimp_neg.1


title: SALINE VTA 4

value: 1-day Abstinence


title: marginal_Z_B.C45.Blimp_pos.1


title: Primary Breast Tumor:TN073


title: Primary Breast Tumor:TN118

value: Hopkins


title: Primary Breast Tumor:TN080

value: NoChemo


title: SALINE VTA 3


title: Primary Breast Tumor:TN032


title: Primary Breast Tumor:TN101


title: SALINE VTA 2


title: marginal_Z_B.UTX.Blimp_neg.5

source_name: marginal zone B cell

value: Splenic B cell


title: Primary Breast Tumor:TN012

value: IIB


title: Primary Breast Tumor:TN058


title: marginal_Z_B.UTX.Blimp_neg.4

value: 12 weeks


title: SALINE PFC 3

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: marginal_Z_B.CPG.Blimp_neg.3


title: Primary Breast Tumor:TN033

value: Iowa


title: marginal_Z_B.UTX.Blimp_neg.2


title: Primary Breast Tumor:TN047


title: SALINE VTA 1

source_name: Ventral Tegmental Area

value: Brain


title: marginal_Z_B.UTX.Blimp_neg.3


title: Primary Breast Tumor:TN135

value: X

value: IIA


title: COCAINE VTA 6


title: Primary Breast Tumor:TN049

value: XH


title: Primary Breast Tumor:TN007

value: SurgOnly


title: COCAINE VTA 4


title: Primary Breast Tumor:TN138


title: Primary Breast Tumor:TN061

value: IA


title: COCAINE VTA 3

value: Ventral Tegmental Area


title: follicular_B.C45.Blimp_pos.4

source_name: 5th division GFP+ CpG+IL-4,5-stimulated follicular B cell

value: Spleen


title: COCAINE VTA 2

value: wild type


title: follicular_B.C45.Blimp_pos.3

value: in-vitro cultured primary B cell


title: Primary Breast Tumor:TN125


title: follicular_B.C45.Blimp_pos.5


title: Primary Breast Tumor:TN148

value: Hopkins


title: Primary Breast Tumor:TN114

value: NoChemo


title: Primary Breast Tumor:TN046

value: Duke


title: COCAINE VTA 1

value: 1-day Abstinence


title: Primary Breast Tumor:TN137


title: Primary Breast Tumor:TN055


title: SALINE NAC 6

value: Nucleus Accumbens


title: Primary Breast Tumor:TN043

value: IIIA


title: SALINE NAC 5


title: follicular_B.C45.Blimp_pos.1

value: 12 weeks


title: follicular_B.C45.Blimp_pos.2


title: Primary Breast Tumor:TN035

value: Iowa


title: follicular_B.C45.Blimp_neg.5

source_name: 4th division GFP- CpG+IL-4,5-stimulated follicular B cell


title: Primary Breast Tumor:TN081

value: IIB


title: SALINE NAC 4

value: Brain


title: follicular_B.C45.Blimp_neg.4


title: Primary Breast Tumor:TN010

value: IIA


title: SALINE NAC 2


title: Primary Breast Tumor:TN091

value: SurgOnly


title: follicular_B.C45.Blimp_neg.3


title: SALINE NAC 3


title: Primary Breast Tumor:TN008

value: H


title: COCAINE VTA 5

value: Ventral Tegmental Area


title: Primary Breast Tumor:TN044


title: Primary Breast Tumor:TN136

value: X

value: IA


title: Primary Breast Tumor:TN019


title: follicular_B.C45.Blimp_neg.2

value: Spleen

value: in-vitro cultured primary B cell


title: marginal_Z_B.UTX.Blimp_neg.1

value: Splenic B cell


title: Primary Breast Tumor:TN090

value: Hopkins

value: NoChemo


title: COCAINE NAC 6

value: Nucleus Accumbens

value: 1-day Abstinence

value: wild type


title: Primary Breast Tumor:TN123


title: Primary Breast Tumor:TN022

value: Iowa


title: follicular_B.CPG.Blimp_neg.5

source_name: 4th division GFP- CpG-stimulated follicular B cell

value: 12 weeks


title: follicular_B.C45.Blimp_neg.1


title: COCAINE NAC 5

source_name: Nucleus Accumbens

value: Brain


title: Primary Breast Tumor:TN021

value: IIA


title: Primary Breast Tumor:TN089

value: Duke

value: SurgOnly


title: Primary Breast Tumor:TN034


title: Primary Breast Tumor:TN054

value: IIB


title: COCAINE NAC 4


title: Primary Breast Tumor:TN020

value: X


title: follicular_B.CPG.Blimp_neg.3


title: Primary Breast Tumor:TN111


title: COCAINE NAC 2


title: Primary Breast Tumor:TN147


title: follicular_B.CPG.Blimp_neg.4


title: COCAINE NAC 1


title: Primary Breast Tumor:TN092

value: IA


title: Primary Breast Tumor:TN031


title: follicular_B.UTX.Blimp_neg.5

source_name: follicular B cell

value: Spleen


title: Primary Breast Tumor:TN024

source_name: Primary Breast Tumor


title: Primary Breast Tumor:TN112


title: follicular_B.CPG.Blimp_neg.1

value: in-vitro cultured primary B cell


title: COCAINE NAC 3


title: Old 3

city: Guangzhou

first: Zhongwu

last: Su

address: 107 West Yan Jiang Road

institute: Sun Yat-sen Memorial Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Clean data were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data, then were aligned to the reference genome (GRCm38) using TopHat v2.0.9.
The mapped reads of each sample were then assembled by Cufflinks (v2.1.1) in a reference-based approach.
CNCI (Coding-Non-Coding-Index) (v2), CPC (Coding Potential Calculator) (0.9-r2), Pfam Scan (v1.3) and CPAT (Coding Potential Assessment Tool) (v1.2.1) were used for coding potential analysis of each transcript.
Cuffdiff (v2.1.1) was used to calculate FPKMs (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of transcripts in each sample and to analyze the differential expression.
Genome_build: GRCm38
Supplementary_files_format_and_content: excel file include FPKM values for each Sample

source_name: cochlea

growth_protocol: Mice were housed in a specific pathogen-free animal facility under a 12-hour light-dark pattern and had free access to water and food.

extract_protocol:
Cochlear basilar membranes were dissected from cochleas, snap frozen in liquid nitrogen, and RNA were harvested using Trizol reagent.
Sequencing libraries were generated using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: Mice were deeply anesthetized and decapitated, then cochleas were removed.

value: cochlea

value: 12-month old


title: Primary Breast Tumor:TN009

value: NoChemo


title: Fmr1-KO rep3

city: East Lansing

first: Zhuang

last: Miao

state: Michigan

address: 567 Wilson Road

department: Physiology

institute: Michigan State University

data_processing:
Raw data were processed through adaptor cleaning (with Fastx Clipper), trimming (with sickle, https://github.com/najoshi/sickle)
Junk sequence removal, mapping clean reads to the mouse reference genome (version: GRCm38) using TopHat2, and gene construction with Cufflinks
Differentially expressed genes (DEGs) between WT and Fmr1 KO samples were assessed with Cuffdiff
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include  RPKM values for each sample, differentially expressed genes (DEGs) between WT and Fmr1 KO samples

source_name: Hippocampal neuron

extract_protocol:
Total RNA was extracted by the TRIzol method (Invitrogen) followed by purification with RNAeasy kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hippocampus


title: Primary Breast Tumor:Case_24

value: Hopkins

value: Chemo

value: RC

value: IIIA


title: Primary Breast Tumor:TN062

value: Iowa


title: follicular_B.UTX.Blimp_neg.4

value: 12 weeks

value: Splenic B cell


title: Primary Breast Tumor:Case_26

value: IIA


title: Old 2


title: Primary Breast Tumor:TN126

value: H

value: IIB


title: Fmr1-KO rep2


title: Fmr1-KO rep1


title: Old 1


title: follicular_B.UTX.Blimp_neg.3


title: Primary Breast Tumor:Case_23


title: Yound 3

value: 1-month old


title: follicular_B.UTX.Blimp_neg.2

value: Spleen


title: follicular_B.UTX.Blimp_neg.1


title: Primary Breast Tumor:Case_21

value: DSC

value: IIIC


title: Primary Breast Tumor:Case_19

value: CB


title: WT rep3

value: WT


title: Primary Breast Tumor:Case_15

value: IIIB


title: WT rep1

value: hippocampus


title: Primary Breast Tumor:Case_20

value: Hopkins

value: Chemo

value: C


title: 18LCO128_tumor

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

description:
Tumors_Cdh1_Trps1_log2_norm_counts.txt
Tumors_Cdh1_Trps1_subgroup_one_diff_expr_analysis.txt
Tumors_Cdh1_Trps1_subgroup_two_diff_expr_analysis.txt

data_processing:
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)
Sequencing data was aligned to or GRCm38 using TopHat and number of reads per gene were measured with HTSeq count.
Read counts were corrected for differences in sequencing depth by using DESeqs median-of-ratios and the normalized counts were log2-transformed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Log2_norm_counts files contain expression tables of samples (columns) by transcript (rows) reporting normalized counts. Diff_expr_analysis files contain differential gene expression analysis per transcript (rows)

source_name: Mouse mammary tumor

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.).

value: Primary mouse mammary tumor cells

tag: genotype/strain


title: 18LCO114_tumor


title: Primary Breast Tumor:Case_25


title: TAB182_KD-repeat_2

city: Birmingham

first: Nafiseh

last: Chalabi

state: West Midland

address: Vincent Drive

department: Cancer and Genomic Sciences

institute: University of Birmingham

description:
gene_count_matrix.csv
transcript_count_matrix.csv
condition_TAB_KD_vs_Control_KD_trans.tsv
condition_TAB_KD_vs_Control_KD_gene.tsv

data_processing:
HiSeq 4000 with two lanes in 2x150 mode was used for sequencing.
The raw FASTQ files are trimmed for the presence of Illumina adapter sequences using Cutadapt version 1.2.1. The option -O 3 was used, so the 3' end of any reads which match the adapter sequence for 3 bp. or more are trimmed. The reads are further trimmed using Sickle version 1.200 with a minimum window quality score of 20. Reads shorter than 20 bp. after trimming were removed. Statistics were generated using fastq-stats from EAUtils.
FastQC was used to do some quality control checks on raw sequence data.
FastQ Screen was used to determine if there was sequence contamination.
Reads were aligned by HISAT2 in spliced-alignment mode with these parameters: --max-intronlen 741000 --rna-strandness RF --dta-cufflinks -k 22 --secondary
RNA-Seq alignments were assembled into potential transcripts using StringTie 1.3.6 with these parameters: -G Homo_sapiens.GRCh38.97.gtf --rf -m 30 -e
Raw read count tables were generated using StrinTie's prepDE.py with this parameter: -l 30
Differential gene expression analysis was used using DESeq2.
Genome_build: H. sapiens, GRCh38
Supplementary_files_format_and_content: assembled_genes.tab: is a tab delimited file containing assembled reads (using StringTie) to genes with three values: coverage, FPKM and RPKM
Supplementary_files_format_and_content: assembled_transcripts.gtf: a Gene Transfer Format (GTF) file that contains details of the transcripts that StringTie assembles from RNA-Seq data
Supplementary_files_format_and_content: gene_count_matrix.csv: matrix of raw gene counts for each sample using StringTie with Ensembl IDs
Supplementary_files_format_and_content: transcript_count_matrix.csv: matrix of raw transcript counts for each sample using StringTie with Ensembl IDs
Supplementary_files_format_and_content: condition_Treatment_vs_Control_HU.tsv: these tab-delimited files contains differential transcript/gene expression analysis using DESEq2 for a treatment vs control comparison

source_name: HeLa cell line

growth_protocol: 1* 10^7 HeLa cells per 6 cm dish were pelleted  and grown in Dulbecco’s Modified Eagle’s Medium-high glucose (Sigma) with 10% FCS (Sigma) in 5% 〖CO〗_2 at 37 °C.

extract_protocol:
TotalRNA was extracted using RNeasy Plus Mini (Qiagen). Cells were pelleted and washed once with PBS. Cell pellets were disrupted by adding 600 μl lysis buffer RLT Plus. Cell lysis was completed by vortexing or vigorous pipetting of the cell lysate. Cells were homogenised by passing the cell lysate a few times through a 20G needle fitted to a syringe. The homogenised lysate was transferred to a gDNA Eliminator spin column placed in a 2 ml collection tube and centrifuged for 1 minute at 13000 rpm. The flow-through in the collection tube was saved and the spin column was discarded. 600 μl of 70% ethanol was added to the flow-through and mixed thoroughly by pipetting. 600 μl of flow-through was transferred to an RNeasy spin column placed in a new 2 ml collection tube and centrifuged for 1 minute at 13000 rpm. This time the flow-through was discarded and spin column was saved. The spin column was washed once with 600 μl buffer RW1, followed by additional two washes with 500 µl Buffer RPE. In order to eliminate residual flow-through the spin column was placed in a new 2 mL collection tube and centrifuged at 16000 rpm for one minute. The spin column was placed in a new 1.5 mL collection tube and 30-50 μl RNAse-free water was directly added to the spin column membrane and left for 2 minutes at room temperature. The spin column was centrifuged for 1 minute at 13000 rpm and eluted RNA was stored at -80 °C.
Dual-indexed, strand-specific RNA-Seq library was prepared from submitted total RNA, using RiboZero (Illumina) rRNA depletion and the NEBNext Ultra Directional RNA library preparation kit (NEB). RNA-Seq was performed on 2 lanes of HiSeq4000 (paired-end, 2x150bp) platform to generate ~80M reads per sample.

treatment_protocol: 24 hours later when cells reached 60-70% confluency they were transfected with scrambled or CNOT1 siRNA (On-target plus siRNA-SMART pools). A transfection complex of 10 µL of siRNA (0.2nmoles) and 8 µL of Oligofectamine was added to 1 mL Opti-MEM® (Invitrogen-31985-047) and mixed thoroughly by pipetting.  Following 30 minutes incubation at room temperature the mixture was added to cells in a 6 cm dish supplemented with 1 mL Opti-MEM. After 5-6 hours, incubation at 37 °C the Opti-MEM transfection mixture was removed and replaced with fresh DMEM medium containing 10% FCS. Cells were incubated until harvested or split. 72 hours post siRNA transfection control and CNOT1-depleted HeLa cells were mock-treated or treated with HU 0.25m, DRB 100µm or MMC 1µm. Cells were collected at indicated timepoints for each treatment.

tag: tissue

value: cervical cancer cells

value: treatment

tag: time stamp

value: 0 hrs


title: Primary Breast Tumor:Case_16

value: RC

value: IA


title: Primary Breast Tumor:TN100

value: Duke

value: NoChemo

value: SurgOnly

value: IIB


title: Primary Breast Tumor:TN057

value: X

value: IIIA


title: Young 1

tag: strain

value: cochlea

value: 1-month old


title: TAB182_KD-repeat_1


title: Primary Breast Tumor:TN045


title: 18LCO046_tumor

tag: cell type


title: Bacteria treated with triclosan, biological rep3

city: Lyngby

first: Malgorzata

last: Ligowska-Marzeta

address: Søltofts Plads 221

country: Denmark

institute: Technical University of Denmark

description: Gene expression data from E. coli CFT073 at exponential phase, grown with triclosan at a subinhibitory concentration (0.125xMIC)

hyb_protocol: Hybridization was performed for 16 hours at 45C on the GeneChip® E. coli Genome 2.0 Array. Washing and staining was performed according to the manual (Expression Analysis Technical Manual version P/N 702232 Rev. 3, Affymetrix), using the Affymetrix Fluidics Station 400

scan_protocol: GeneChip® Scanner 3000 was used to scan the microarray chips.

data_processing: The expression values from the microarrays were obtained using dChip software package. The invariant set normalization method was used and probe selection and computation of expression values was performed using model-based (PM-only) method. Permutation was used to estimate the empirical false discovery rate (FDR) of differentially expressed genes.

organism: Escherichia coli CFT073

source_name: Bacterial cells, mid-exponential growth phase

label_protocol: Fragmented biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual version P/N 702232 Rev. 3, Affymetrix).

growth_protocol: Cultures from all samples were grown for 16-18 hours at 37C at 200 rpm prior to biocide treatment. Cultures were transferred to a new medium and treated with biocides. All the cultures were then grown for 18-20 hours and transferred into a fresh medium with biocides. They were cultivated until they reached mid-exponential phase (OD600=0.6). The control sample was grown like the other samples, but never treated with biocides.

extract_protocol: The bacterial pellets were lysed using 0.2 mg lysozyme per sample and RNA was extracted using the Rneasy Mini Kit (Qiagen), according to manufacturer's instructions, including the on-column DNase digestion.

treatment_protocol: Double volume of RNA Protect reagent (Qiagen) was added to 2 ml culture from each sample. Each sample was then briefly vortexed and incubated for 5 minutes at room temperature. The supernatant was decanted and the pellets were stored at -20C until RNA extraction.

tag: agent


title: follicular_B.CPG.Blimp_neg.2

value: 12 weeks

value: Spleen

value: in-vitro cultured primary B cell


title: 18LCO052_tumor

description:
Tumors_Cdh1_Trps1_log2_norm_counts.txt
Tumors_Cdh1_Trps1_subgroup_three_diff_expr_analysis.txt

value: Primary mouse mammary tumor cells


title: Primary Breast Tumor:Case_14

value: Hopkins

value: Chemo

value: C

value: IIA


title: WT rep2

value: hippocampus

value: WT


title: Primary Breast Tumor:Case_22

value: RC


title: 18LCO027_tumor

description:
Tumors_Cdh1_Trps1_log2_norm_counts.txt
Tumors_Cdh1_Trps1_subgroup_two_diff_expr_analysis.txt


title: Primary Breast Tumor:Case_18


title: TAB182_KD-24h_post_HU_0_25m-repeat_2

description:
gene_count_matrix.csv
transcript_count_matrix.csv
condition_TAB_HU_vs_Control_HU_trans.tsv
condition_TAB_HU_vs_Control_HU_gene.tsv

value: cervical cancer cells

value: treatment

value: 24 hrs


title: 18LCO025_tumor3


title: Primary Breast Tumor:Case_13

value: IIIA


title: Primary Breast Tumor:Case_11

value: IA


title: SALINE NAC 1

value: Brain

tag: brain region

value: Nucleus Accumbens

tag: time point

value: 1-day Abstinence

value: wild type


title: TAB182_KD-24h_post_HU_0_25m-repeat_1

tag: genotype


title: 18LCO025_tumor2

description:
Tumors_Cdh1_Trps1_log2_norm_counts.txt
Tumors_Cdh1_Trps1_subgroup_one_diff_expr_analysis.txt

value: Primary mouse mammary tumor cells


title: NOT1_KD-repeat_1

description:
gene_count_matrix.csv
transcript_count_matrix.csv
condition_NOT_KD_vs_Control_KD_trans.tsv
condition_NOT_KD_vs_Control_KD_gene.tsv

value: 0 hrs


title: 18LCO025_tumor1


title: NOT1_KD-repeat_2


title: Bacteria treated with triclosan, biological rep2

value: triclosan at a subinhibitory concentration (0.125xMIC)


title: Bacteria treated with hydrogen peroxide, biological rep1

description: Gene expression data from E. coli CFT073 at exponential phase, grown with hydrogen peroxide at a subinhibitory concentration (0.25xMIC)


title: Bacteria treated with hydrogen peroxide, biological rep2

value: hydrogen peroxide at a subinhibitory concentration (0.25xMIC)


title: Bacteria treated with hydrogen peroxide, biological rep3


title: Bacteria treated with triclosan, biological rep1


title: NOT1_KD-4h_post_MMC_1m

description:
gene_count_matrix.csv
transcript_count_matrix.csv
condition_NOT_MMC_vs_Control_MMS_trans.tsv
condition_NOT_MMC_vs_Control_MMS_gene.tsv

value: 4 hrs


title: 17LCO103_tumor


title: NOT1_KD-4h_post_DRB_100m

description:
gene_count_matrix.csv
transcript_count_matrix.csv
condition_NOT_DRB_vs_Control_DRB_trans.tsv
condition_NOT_DRB_vs_Control_DRB_gene.tsv


title: Primary Breast Tumor:Case_08

value: Hopkins

value: Chemo

tag: age


title: 17LCO102_tumor


title: Control-repeat_2

value: control


title: Primary Breast Tumor:Case_03

value: RHC

tag: relapse

value: IIIC


title: Bacteria treated with chlorhexidine, biological rep3

description: Gene expression data from E. coli CFT073 at exponential phase, grown with chlorhexidine at a subinhibitory concentration (0.25xMIC)


title: Control-repeat_1

value: cervical cancer cells


title: 18LCO003_tumor


title: Control-4h_post_MMC_1m


title: Bacteria treated with chlorhexidine, biological rep2

value: chlorhexidine at a subinhibitory concentration (0.25xMIC)


title: HC11_TSA_repl3

description:
HC11_TSA_vs_DMSO_log2_norm_counts.txt
HC11_TSA_vs_DMSO_diff_expr_analysis.txt

source_name: Mammary epithelial cell line

tag: cell line

value: Mammary epithelial cells

value: 300nM Trichostatin A (24 hours)


title: Bacteria treated with benzalkonium chloride, biological rep3

description: Gene expression data from E. coli CFT073 at exponential phase, grown with benzalkonium chloride at a subinhibitory concentration (0.25xMIC)


title: Bacteria treated with chlorhexidine, biological rep1


title: HC11_DMSO_repl3

value: DMSO


title: HC11_TSA_repl2


title: Bacteria treated with benzalkonium chloride, biological rep2

value: benzalkonium chloride at a subinhibitory concentration (0.25xMIC)


title: Bacteria treated with benzalkonium chloride, biological rep1


title: Control-24h_post_HU_0_25m-repeat_2

value: 24 hrs


title: Primary Breast Tumor:Case_09

value: C

tag: dfsmo

tag: er

value: IA


title: Untreated bacteria, biological rep3

description: Gene expression data from E. coli CFT073 at exponential phase, grown without biocides


title: Control-24h_post_HU_0_25m-repeat_1


title: Primary Breast Tumor:Ctrl_41

tag: grade

tag: ajcc

value: IIIA


title: HC11_DMSO_repl2

tag: treatment


title: Control-4h_post_DRB_100m


title: Primary Breast Tumor:Ctrl_42

value: DSRC


title: HC11_TSA_repl1


title: Young 2

value: cochlea

value: 1-month old


title: HC11_DMSO_repl1


title: Primary Breast Tumor:Case_12

value: Hopkins

value: Chemo

value: RC

value: IIIB


title: Untreated bacteria, biological rep2


title: Primary Breast Tumor:Case_01

value: IIA


title: Primary Breast Tumor:Ctrl_43


title: Primary Breast Tumor:Case_02


title: ultra-low primed 6

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

description: BV2_RNA6_1 fg/mL

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4
The reads were mapped to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release 85) with TopHat2 v2.1.0 (parameters: -x 1 --no-coverage-search –no-novel-juncs --no-novel-indels -T)
All reads mapped to an Ensembl gene were counted using FeatureCounts v1.5.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: xls file containing reads counts, RPMs and RPKMs per gene over all samples

extract_protocol:
Total RNA was extracted from microglial cells using QIAzol Lysis Reagent (#79306) purchased from Qiagen (Hilden, Germany). RNA concentration and quality were checked by using the Nanodrop ND-1000 machine (Peqlab, Erlangen, Germany).
Preparation of libraries was done using Illumina‘s TruSeq stranded mRNA Kit according the manufacturer‘s description

value: immortalized murine microglial cell line

tag: treatment agent

value: LPS

tag: no. of treatments

value: twice

tag: concentration treatment one

tag: concentration treatment two

value: 100 ng/mL


title: NHF1CPD12minR1

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: replicate 1

data_processing:
Library strategy: XR-seq
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: dm6 and hg38
Supplementary_files_format_and_content: bigWig

source_name: normal human fibroblast cells

extract_protocol:
S2-DGRC cells were obtained from the Drosophila Genetic Resources Center. Cells were cultured in Schneider’s medium at 27 degrees with heat inactivated FBS at 10% (v/v).  For UV treatments, cells were inoculated into R-150 plates and grown to about 25 to 80 percent confluence.  Media was gently removed from the semi-adherent monolayer, cells were irradiated with UV-C, and then fresh media containing sterilized, conditioned media was added to cells, and cells were incubated at 27 degrees.  XR-seq assays employed 20 Jm-2.    Following predetermined repair times, plates were placed on ice and cooled cells were harvested by scraping and rinsing with ice-cold PBS. Cells were pelleted, transferred to Eppendorf tubes, washed with cold PBS, and resuspended in 320 to 340 ul of cold TE.  Samples were processed using 5 ul RNase A and proteinase K.
Samples were immunoprecipitated with anti-CPD antibody, and then ligated to adapters and processed for sequencing (XR-seq).  One plate of S2 cells per repair time point was sufficient for XR-seq assay.  Drosophila possesses photolyases, so cells were kept in the dark or under dim yellow illumination from the time of irradiation to the time of addition of NaCl to cell lysates. After PCR amplification, libraries wrere sequencing on HS4000.

value: normal human fibroblast cells

tag: genotype/variation

value: wild type

value: UV

tag: repair time


title: NHF1CPD36minR1

description: replicate 1


title: Untreated bacteria, biological rep1

tag: strain

tag: agent


title: ultra-low primed 5

description: BV2_RNA5_1 fg/mL

tag: cell type


title: Primary Breast Tumor:Ctrl_38

tag: age

value: IA


title: Primary Breast Tumor:Ctrl_40

value: C

tag: relapse


title: high primed 6

description: BV2_RNA6_100 ng/mL

tag: cell line

value: 1 fg/mL


title: Primary Breast Tumor:Ctrl_39

tag: dfsmo