title: NOD TCR Beta-chain GFP negative Replicate 1

city: Toulouse

first: Joost

last: van Meerwijk

address: CHU PURPAN

country: France

institute: INSERM CPTP

data_processing:
Library strategy: TCR-seq
High quality selection with pRESTO-FilterSeq
Indexing and annotation UMI pRESTO-MaskPrimers and PairSeq
Construction concensus pRESTO-BuildConsensus
Aligned F and R pRESTO-AssemblePairs
Aligment to TCR end table export MiXCR-align-assemble-exportClones
Genome_build: mm10
Supplementary_files_format_and_content: Number of UMI, CDR3 sequence, and VJ segments

source_name: Thymic regulatory T cells

growth_protocol: NA, Sorting

extract_protocol:
RNA was extracted by Nucleospin RNA XS (Macherey-Nagel)
Libraries for TCR-sequencing (TCR-seq), the cDNA synthesis and library preparation were performed as previously described (Feng et al., 2015), and was adjusted to our different conditions.) the RNA had a high quality (RIN>8)

value: NOD

value: eight-week-old

tag: Sex

value: female

value: WT

tag: sorting

value: GFP negative


title: NOD TCR Beta-chain GFP negative Replicate 3

status: Public on May 31 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age

tag: genotype/variation

tag: cell type


title: B6 TCR Alpha-chain GFP negative Replicate 3


title: NOD TCR Alpha-chain GFP negative Replicate 3


title: NOD TCR Beta-chain GFP negative Replicate 2


title: B6 TCR Beta-chain GFP negative Replicate 2


title: B6 TCR Beta-chain GFP negative Replicate 1


title: ST_PB6_B

city: Ithaca

first: Charles

middle: G.

last: Danko

state: NY

address: Hungerford Hill Rd.

department: Baker Institute for Animal Health, College of Veterinary Medicine

country: USA

institute: Cornell University

description:
nascent RNA
pooled sample B
ST_PB6_all_R1.B6.bowtie.gz
ST_PB6_all_R1.CAST.bowtie.gz
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
ST_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

data_processing:
Library strategy: ChRO-Seq
For ChRO-seq reads, adaptor sequences were trimmed with the cutadapt 1.16. PCR duplicates were removed using unique molecular identifiers (UMIs) in the sequencing data with prinseq-lite.pl. The reads were seperated with a custom J-barcode. The processed reads were then aligned with bowtie to to the diploid genome as input for AlleleDB.
The first base of nascent RNA in B6-specific, CAST-specific, or identical reads without SNPs was liftover to ref genome (mm10), and shown as bigwig files
Genome_build: mm10
Supplementary_files_format_and_content: ChRO-seq data are provided in standard bigWig file formats.

source_name: Stomach

extract_protocol: ChRO-seq library preparation: ChRO-seq libraries were prepared following a recent protocol (Mahat et al., 2016). We prepared some libraries to achieve single nucleotide resolution for the Pol II active site. In these cases, the chromatin pellet was incubated with 2x run-on buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2,1 mM DTT, 300 uM KCl, 20 uM  Biotin-11-ATP (Perkin Elmer, NEL544001EA), 200 uM Biotin-11-CTP (Perkin Elmer, NEL542001EA), 20 uM Biotin-11-GTP (Perkin Elmer, NEL545001EA), 200 uM Biotin-11-UTP (Perkin Elmer, NEL543001EA)) for 5 minutes at 37 C. In some libraries we modified the run-on buffer to extend the length of reads for more accurate allelic mapping at the expense of single nucleotide resolution for the Pol II active site. In these cases, the run-on reaction was performed using a different ribonucleotide composition in the nuclear run-on buffer (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2,1 mM DTT, 300 mM KCl, 200 μ M  ATP (New England Biolabs (NEB), N0450S), 200 μ M  UTP, 0.4 μ M CTP, 20 μ  M Biotin-11-CTP (Perkin Elmer, NEL542001EA), 200 μ  M GTP (NEB, N0450S)).The run-on reaction was stopped by adding Trizol LS (Life Technologies, 10296-010) and RNA was pelleted with the addition of GlycoBlue (Ambion, AM9515) to visualize the RNA. RNA pellet was resuspended in diethylpyrocarbonate (DEPC)-treated water. RNA was heat denatured at 65 C for 40 s to remove secondary structure. RNA was fragmented using base hydrolysis (0.2N NaOH on ice for 4 min). RNA was purified using streptavidin beads (NEB, S1421S) and removed from beads using Trizol (Life Technologies, 15596-026). We ligated a 3′ adapter ligation using T4 RNA Ligase 1 (NEB, M0204L). We performed a second bead binding followed by a 5′ decapping with RppH (NEB, M0356S). RNA was phosphorylated on the 5’ end using T4 polynucleotide kinase (NEB, M0201L) then ligated onto a 5’ adapter. A third bead binding was then performed. The RNA was then reverse transcribed using Superscript III Reverse Transcriptase (Life Technologies, 18080-044) and amplified using Q5 High-Fidelity DNA Polymerase (NEB, M0491L) to generate the ChRO-seq libraries. Libraries were sequenced using an Illumina HiSeq by Novogene.

value: Castaneus x C57BL/6 F1 hybrid

tag: tissue

value: Stomach

value: post natal day 25

tag: gender

value: male


title: SP_PB6_D

description:
nascent RNA
pooled sample D
SP_PB6_all_R1.B6.bowtie.gz
SP_PB6_all_R1.CAST.bowtie.gz
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Spleen

value: Spleen

value: post natal day 24


title: SP_PB6_E

description:
nascent RNA
pooled sample E
SP_PB6_all_R1.B6.bowtie.gz
SP_PB6_all_R1.CAST.bowtie.gz
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: NOD TCR Alpha-chain GFP negative Replicate 1


title: ST_MB6_A

description:
nascent RNA
pooled sample A
ST_MB6_all_R1.B6.bowtie.gz
ST_MB6_all_R1.CAST.bowtie.gz
ST_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
ST_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
ST_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: C57BL/6 x Castaneus F1 hybrid

value: post natal day 23


title: ST_MB6_F

description:
nascent RNA
pooled sample F
ST_MB6_all_R1.B6.bowtie.gz
ST_MB6_all_R1.CAST.bowtie.gz
ST_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
ST_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
ST_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 22


title: SP_PB6_C

description:
nascent RNA
pooled sample C
SP_PB6_all_R1.B6.bowtie.gz
SP_PB6_all_R1.CAST.bowtie.gz
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: SP_PB6_B

description:
nascent RNA
pooled sample B
SP_PB6_all_R1.B6.bowtie.gz
SP_PB6_all_R1.CAST.bowtie.gz
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SP_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: NOD TCR Beta-chain Replicate 3

value: Thymic regulatory T cells


title: KD_MB6_F

description:
nascent RNA
pooled sample F
KD_MB6_all_R1.B6.bowtie.gz
KD_MB6_all_R1.CAST.bowtie.gz
KD_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
KD_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
KD_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
KD_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Kidney

value: Kidney


title: B6 TCR Beta-chain Replicate 3


title: NOD TCR Beta-chain Replicate 2


title: SP_MB6_G

description:
nascent RNA
pooled sample G
SP_MB6_all_R1.B6.bowtie.gz
SP_MB6_all_R1.CAST.bowtie.gz
SP_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SP_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SP_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: B6 TCR Beta-chain Replicate 2


title: p53-knockout, non-binding control, SLC7A11experiment-2

type: RNA

city: Bedford Park

first: George

last: Mayne

state: SA

address: Room 3D213, Dept of Surgery, Flinders Medical Center

department: Surgery

country: Australia

institute: Flinders University of South Australia

description:
Control
SLC7A11 non-binding control expt-2

data_processing:
Fluorescence data was exported to comma delimited text files and then analysed using R statistical software (version 3.4.3), and Microsoft Excel for Mac (version 16). The cycle threshold (Ct) value for each PCR assay was determined using the qpcR package v1.4 in R (https://cran.r-project.org/web/packages/qpcR/index.html). The relative levels of the miRNAs were determined using the formula 2^(40-Ct), and were normalized using the geometric means of the relative levels of selected House Keeping Genes (HKGs).  The HKGs used in this study are included in a file on the series record named "Selected HKGs for p53-KO manuscript .xlsx".
normalized_data includes House Keeping Gene normalised miRNA relative levels

label: FAM

organism: Homo sapiens

source_name: JH-EsoAd1 cell line derived from a patient with Barrett-associated adenocarcinoma, which has a missense c797G>A mutation in TP53 resulting in an amino acid change of G266E

label_protocol: For cell line experiments, high throughput QuantStudio™ 12K Flex OpenArray® PCR custom made plates were used for miRNA profiling. These arrays were comprised of a panel of 112 miRNA probes (miRBase version 22 miRNA names, seed sequences, and miRBase accession numbers are in Supplementary file 2) that were selected based upon their abundance in OAC patient samples from our previous study on serum small extracellular vesicle associated miRNAs [94]. For each sample, 3.35 μl of RNA was reverse transcribed using a matching Custom OpenArray® miRNA RT pool (Life Technologies cat # A25630) and the TaqMan® microRNA Reverse Transcription Kit (Life Technologies cat # 4366596). cDNA Pre-amplifications were carried out with a matching Custom OpenArray® PreAmp pool (Life Technologies cat # 4485255) and TaqMan PreAmp Master Mix (Life Technologies cat # 4488593) on 7.5 μl complementary DNA (cDNA)/sample for each pool. The pre-amplified products (4 μl per sample) were diluted at the recommended 1:40 dilution with 156 μl of RNase-free ultra pure water before mixing with TaqMan OpenArray Real-Time PCR Master Mix (Life Technologies cat # 4462164) and loading onto a 384-well TaqMan OpenArray loading plate. PCR runs were performed using a QuantStudio™ 12K Flex Real-Time PCR System.

growth_protocol: All cell lines were cultured using (phenol red free) RPMI 1640 medium  supplemented with 10 % fetal bovine serum (FBS) , 50 U/ml penicillin , 50 µg/ml streptomycin , and 100 µg/ml normocin.

extract_protocol: Total RNA isolation from untreated cell samples at time of treatment, including DNase digestion, was performed using the miRNeasy Mini Kit (Qiagen, #217004, Chadstone, Australia) and RNase-free DNase Set (Qiagen, #79254, Chadstone, Australia) as instructed by the manufacturer.

treatment_protocol:
The samples were collected from co-cultured cells prior to their counterparts being treated with drugs or irradiation.
SLC7A11 transfections: media was changed 24 h prior to transfection to antibiotic-free charcoal-stripped FCS. Cells were then transfected using Lipofectamine 2000 (Invitrogen, cat #11668019, Scoresby, Australia) in a pooled setting as described above. After harvesting of the cells, 2.04x 106 cells were placed in T25 flasks which resulted in 30-50% confluency after 6 h. Cells were transiently transfected with SLC7A11 siRNA (ON-TARGETplus Human SLC7A11 (23657) siRNA-SMARTpool, Dharmacon / Horizon, cat #L-007612-01-0010, Cambridge, UK) or control siRNA (ON-TARGETplus Non-targeting Pool, Dharmacon / Horizon, cat #D-001810-10-05, Cambridge, UK) to inhibit expression of SLC7A11 or not, respectively. The final siRNA concentration was 100 nM.

tag: cell line

tag: genotype

value: p53 KO with control siRNA


title: NOD TCR Alpha-chain GFP negative Replicate 2

value: NOD


title: B6 TCR Beta-chain GFP negative Replicate 3

value: eight-week-old


title: ST_MB6_G

description:
nascent RNA
pooled sample G
ST_MB6_all_R1.B6.bowtie.gz
ST_MB6_all_R1.CAST.bowtie.gz
ST_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
ST_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
ST_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
ST_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: B6 TCR Beta-chain Replicate 1

value: female


title: B6 TCR Alpha-chain Replicate 3

value: WT


title: NOD TCR Alpha-chain Replicate 3


title: NOD TCR Alpha-chain Replicate 2


title: SP_MB6_A

description:
nascent RNA
pooled sample A
SP_MB6_all_R1.B6.bowtie.gz
SP_MB6_all_R1.CAST.bowtie.gz
SP_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SP_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SP_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: SP_MB6_F

description:
nascent RNA
pooled sample F
SP_MB6_all_R1.B6.bowtie.gz
SP_MB6_all_R1.CAST.bowtie.gz
SP_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SP_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SP_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SP_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: B6 TCR Alpha-chain GFP negative Replicate 2

value: GFP negative


title: SK_PB6_C

description:
nascent RNA
pooled sample C
SK_PB6_all_R1.B6.bowtie.gz
SK_PB6_all_R1.CAST.bowtie.gz
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Skeletal muscle

value: Castaneus x C57BL/6 F1 hybrid

value: Skeletal muscle


title: B6 TCR Alpha-chain Replicate 2


title: NOD TCR Beta-chain Replicate 1


title: SK_PB6_B

description:
nascent RNA
pooled sample B
SK_PB6_all_R1.B6.bowtie.gz
SK_PB6_all_R1.CAST.bowtie.gz
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 25


title: SK_PB6_E

description:
nascent RNA
pooled sample E
SK_PB6_all_R1.B6.bowtie.gz
SK_PB6_all_R1.CAST.bowtie.gz
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: male


title: SK_PB6_D

description:
nascent RNA
pooled sample D
SK_PB6_all_R1.B6.bowtie.gz
SK_PB6_all_R1.CAST.bowtie.gz
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SK_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: B6 TCR Alpha-chain Replicate 1


title: SK_MB6_A

description:
nascent RNA
pooled sample A
SK_MB6_all_R1.B6.bowtie.gz
SK_MB6_all_R1.CAST.bowtie.gz
SK_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: SK_MB6_F

description:
nascent RNA
pooled sample F
SK_MB6_all_R1.B6.bowtie.gz
SK_MB6_all_R1.CAST.bowtie.gz
SK_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: LV_PB6_E

description:
nascent RNA
pooled sample E
LV_PB6_all_R1.B6.bowtie.gz
LV_PB6_all_R1.CAST.bowtie.gz
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Liver

value: Liver


title: SK_MB6_G

description:
nascent RNA
pooled sample G
SK_MB6_all_R1.B6.bowtie.gz
SK_MB6_all_R1.CAST.bowtie.gz
SK_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
SK_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
SK_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
SK_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 24


title: Mdmx C462A no treatment rep2

city: Boston

first: Zhi-Min

last: Yuan

state: Massachusetts

address: 677 Huntington Ave.

department: Environmental Sciences

institute: Harvard University

hyb_protocol: Contained within publication; detailed protocols are available upon request

data_processing: The resultant dataset from the GeneChip™ Mouse Gene 2.0 array was performed in the Transcriptome Analysis Console (v4.0). This software was used for the creation of scatterplots, volcano plots, and hierarchical clustering. From these plots, the threshold for log fold change in gene expression was set at ± 2.0, with statistical significance cutoffs at or below a p-value of 0.05. Using these differentially expressed genes, the software MetaCore+MetaDrug™ (v20.2; build 70100) was used to perform pathway enrichment (PE) as well as gene ontology (GO) analyses (all p-values used were ≤ 0.05). Microsoft Excel was used to transform these results into 1/FDR (false discovery rate) as well as to create the combined figure.

label: biotin

source_name: MEFs

value: MEFs

value: Mdmx C462A


title: B6 TCR Alpha-chain GFP negative Replicate 1


title: LV_PB6_D

description:
nascent RNA
pooled sample D
LV_PB6_all_R1.B6.bowtie.gz
LV_PB6_all_R1.CAST.bowtie.gz
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: Wildtype no treatment rep3

scan_protocol: Contained within publication; detailed protocols are available upon request

value: Wildtype


title: NOD TCR Alpha-chain Replicate 1

value: Thymic regulatory T cells


title: LV_PB6_C

description:
nascent RNA
pooled sample C
LV_PB6_all_R1.B6.bowtie.gz
LV_PB6_all_R1.CAST.bowtie.gz
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: Wildtype no treatment rep2

label_protocol: Contained within publication; detailed protocols are available upon request


title: Wildtype no treatment rep1

growth_protocol: Contained within publication; detailed protocols are available upon request


title: LV_MB6_G

description:
nascent RNA
pooled sample G
LV_MB6_all_R1.B6.bowtie.gz
LV_MB6_all_R1.CAST.bowtie.gz
LV_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
LV_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
LV_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: C57BL/6 x Castaneus F1 hybrid


title: LV_MB6_F

description:
nascent RNA
pooled sample F
LV_MB6_all_R1.B6.bowtie.gz
LV_MB6_all_R1.CAST.bowtie.gz
LV_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
LV_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
LV_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 22


title: Wildtype JBL5 treatment rep3

extract_protocol: Contained within publication; detailed protocols are available upon request


title: Wildtype JBL5 treatment rep2

treatment_protocol: Contained within publication; detailed protocols are available upon request


title: Wildtype JBL5 treatment rep1


title: Wildtype DMSO treatment rep3


title: Mdmx C462A no treatment rep1


title: Wildtype DMSO treatment rep2


title: Wildtype DMSO treatment rep1


title: Mdmx C462A no treatment rep3


title: HT_PB6_DE2

description:
nascent RNA
pooled sample D and E
HT_PB6_all_R1.B6.bowtie.gz
HT_PB6_all_R1.CAST.bowtie.gz
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Heart

value: Heart

value: post natal day 23


title: HT_PB6_E

description:
nascent RNA
pooled sample E
HT_PB6_all_R1.B6.bowtie.gz
HT_PB6_all_R1.CAST.bowtie.gz
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: Mdmx C462A PMA treatment rep3


title: Mdmx C462A PMA treatment rep2


title: Mdmx C462A PMA treatment rep1


title: LV_PB6_B

description:
nascent RNA
pooled sample B
LV_PB6_all_R1.B6.bowtie.gz
LV_PB6_all_R1.CAST.bowtie.gz
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
LV_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: Wildtype PMA treatment rep3


title: Wildtype PMA treatment rep2


title: LV_MB6_A

description:
nascent RNA
pooled sample A
LV_MB6_all_R1.B6.bowtie.gz
LV_MB6_all_R1.CAST.bowtie.gz
LV_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
LV_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
LV_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
LV_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: CCM3_Ammo_300

city: Nashville

first: Benjamin

last: Reisman

state: TN

address: 1234 Stevenson Center Dr. Rm 7330

department: Chemistry

institute: Vanderbilt University

description: processed data file: gatk_counts_H293.csv

library_source: genomic

data_processing:
library strategy:  Targeted amplifaction
Adapter trimming and QC with fastp v 0.20.0
Alignment using bwa-mem 0.7.17 w/ -O 100
Generate bam/sam using samtools v1.10
Count variants using gatk v.4.1.8.1 AnalyzeSaturationMutagenesis
Collate data and tidy using R 4.0.4
Genome_build: NA
Supplementary_files_format_and_content: gatk_counts_library.csv - variant frequency in the library as a csv, chain = gene, aa.residue = WT residue/position, aa = amino acid, residue = position, count = num of counts of that variant observed in the data, clen = chain length, frac = fraction of library composed of the variant
Supplementary_files_format_and_content: gatk_counts_H293.csv - variant frequency recovered from cells as a csv, sample = replicate, compound = compound and dose, chain = gene, aa.residue = WT residue/position, aa = amino acid, residue = position, count = num of counts of that variant observed in the data, clen = chain length, frac = fraction of library composed of the variant

molecule: genomic DNA

source_name: Synthetic sequence

growth_protocol: HEK293 cells were maintained in glucose free Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/mL Penicillin, 100 μg/mL Streptomycin, 10 mM galactose. After addition of the attB plasmid library, media was supplemented with 1 μg/mL doxycycline and successfully recombined cells were selected with 100 μg/mL Blasticidin S, 10 nM Rimiducid for 7 days.

extract_protocol:
Confluent cells from 6 well dishes were scraped from the plate, pelleted at 800 g for 5 min, and genomic DNA was extracted using the Qiagen DNAeasy kit per manufactures protocols, and eluted in 100 μL of low EDTA TE buffer. The transgene region was amplified using primers targeted to the tetracycline promoter (located in the attP landing pad) and the IRES site (located in the attB plasmid), such that only successful integrated transgenes were amplified. PCR was carried out at 100 μL scale using NEB Q5 high fidelity polymerase per manufacturers protocols using 5 μL of genomic DNA, an annealing temperature of 68 °C, and a 3 min extension time to limit bias towards shorter products (ATP5C) for a total of 30 cycles. PCR amplicons were purified using the NEB Monarch PCR clean-up kit per manufactures protocols.
Nextera Flex library prepration on PCR amplicons

treatment_protocol: After selection with Blasticidin/Rimiducid, cells were transferred to 6 well plates for drug selection with ammocidin A or apoptolidin A added as a 1000x stock in DMSO. Cells were treated for four days and allowed to recover for three days, in two cycles. After treatment, cells were expanded, and genomic DNA extracted as below.

tag: treatment

tag: library

value: CCM

tag: molecule subtype

value: PCR from gDNA


title: WT_Parental

value: WT


title: CCM3_Ammo_30


title: CCM3_Apo_1000


title: Wildtype PMA treatment rep1


title: CCM3_Apo_100


title: WT_Apo_100


title: CCM3_Vehicle

value: Vehicle


title: HT_PB6_C

description:
nascent RNA
pooled sample C
HT_PB6_all_R1.B6.bowtie.gz
HT_PB6_all_R1.CAST.bowtie.gz
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: Castaneus x C57BL/6 F1 hybrid


title: HT_MB6_F

description:
nascent RNA
pooled sample F
HT_MB6_all_R1.B6.bowtie.gz
HT_MB6_all_R1.CAST.bowtie.gz
HT_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: HT_PB6_B

description:
nascent RNA
pooled sample B
HT_PB6_all_R1.B6.bowtie.gz
HT_PB6_all_R1.CAST.bowtie.gz
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 25


title: HT_MB6_G

description:
nascent RNA
pooled sample G
HT_MB6_all_R1.B6.bowtie.gz
HT_MB6_all_R1.CAST.bowtie.gz
HT_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: male


title: HT_PB6_D

description:
nascent RNA
pooled sample D
HT_PB6_all_R1.B6.bowtie.gz
HT_PB6_all_R1.CAST.bowtie.gz
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: CCM3_Ammo_3


title: CCM2_Apo_1000


title: CCM3_Parental


title: GI_PB6_B

description:
nascent RNA
pooled sample B
GI_PB6_all_R1.B6.bowtie.gz
GI_PB6_all_R1.CAST.bowtie.gz
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Large intestine

value: Large intestine


title: Rep 2; CD8+ T cells; intermingled island culture; Ag- area; plate 1

city: Amsterdam

first: Anne

middle: Magdalena

last: van der Leun

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
MARS seq
AB9308_SB390

data_processing:
bcl2fastq/2.15.0.4
Note: Second read contained only cell and molecule barcodes. This information was appended to the fastq entry header
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: Meta data file associating each single cell with its amplification batch and index sorting readouts

molecule: polyA RNA

source_name: CD8+ T cells

growth_protocol: OVCAR5 cells were plated in small droplets (±5,000 cells per 5ul droplet) on polymer or glass bottom 8 well m-slides. After 3-5 days of OVCAR5 culture, CD8+ T cells labeled with the PsT were added to the tumor cell cultures and co-cultured for 4 hours.

extract_protocol:
Tumor and CD8+ T cells were harvested by trypsinization. Cell suspensions were stained with FACS antibodies and CD8+ T cells were sorted using index sorting into 384-well plates containing 2 ml of lysis solution with barcoded poly(T) reverse-transcription (RT) primers.
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol: Where indicated, specific regions of the cultures were exposed to 405nm light using a confocal microscope.

tag: tumor areas

value: Intermingled Ag+ and Ag- islands

tag: exposed tumor area

value: Ag-

tag: primary cells (sequenced)

value: CD8+ T cells

tag: tumor cell line (not sequenced)

tag: selection markers

value: CD3+ CD8+ IRdye-


title: Rep 2; CD8+ T cells; intermingled island culture;  non-exposed control; plate 1

description:
MARS seq
AB9310_SB390

value: non-exposed


title: Rep 2; CD8+ T cells; intermingled island culture; Ag- area & non-exposed control; plate 1

description:
MARS seq
AB9309_SB390

value: Ag- & non-exposed


title: GI_MB6_G

description:
nascent RNA
pooled sample G
GI_MB6_all_R1.B6.bowtie.gz
GI_MB6_all_R1.CAST.bowtie.gz
GI_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
GI_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
GI_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: C57BL/6 x Castaneus F1 hybrid

value: post natal day 24


title: GI_PB6_C

description:
nascent RNA
pooled sample C
GI_PB6_all_R1.B6.bowtie.gz
GI_PB6_all_R1.CAST.bowtie.gz
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: HT_MB6_A

description:
nascent RNA
pooled sample A
HT_MB6_all_R1.B6.bowtie.gz
HT_MB6_all_R1.CAST.bowtie.gz
HT_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
HT_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
HT_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
HT_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: Heart

value: post natal day 23


title: GI_PB6_E

description:
nascent RNA
pooled sample E
GI_PB6_all_R1.B6.bowtie.gz
GI_PB6_all_R1.CAST.bowtie.gz
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: Rep 2; CD8+ T cells; intermingled island culture; Ag+ area; plate 2

description:
MARS seq
AB9307_SB390

value: Ag+


title: GI_PB6_D

description:
nascent RNA
pooled sample D
GI_PB6_all_R1.B6.bowtie.gz
GI_PB6_all_R1.CAST.bowtie.gz
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
GI_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: GI_MB6_F

description:
nascent RNA
pooled sample F
GI_MB6_all_R1.B6.bowtie.gz
GI_MB6_all_R1.CAST.bowtie.gz
GI_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
GI_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
GI_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 22


title: CCM2_Ammo_300

value: CCM

value: PCR from gDNA


title: CCM2_Apo_100


title: CCM2_Ammo_30


title: BN_PB6_E

description:
nascent RNA
pooled sample E
BN_PB6_all_R1.B6.bowtie.gz
BN_PB6_all_R1.CAST.bowtie.gz
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

source_name: Brain

value: Castaneus x C57BL/6 F1 hybrid

value: Brain


title: GI_MB6_A

description:
nascent RNA
pooled sample A
GI_MB6_all_R1.B6.bowtie.gz
GI_MB6_all_R1.CAST.bowtie.gz
GI_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
GI_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
GI_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
GI_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: Large intestine

value: male


title: Rep 2; CD8+ T cells; intermingled island culture; Ag+ area; plate 1

description:
MARS seq
AB9306_SB390

value: Intermingled Ag+ and Ag- islands


title: Rep 2; CD8+ T cells; Ag- control culture; non-exposed control ; plate 1

description:
MARS seq
AB9305_SB390

value: Ag- cells only

value: CD8+ T cells


title: Rep 2; CD8+ T cells; Ag- control culture; Ag- area; plate 1

description:
MARS seq
AB9303_SB390

value: Ag-

value: CD3+ CD8+ IRdye-


title: BN_PB6_D

description:
nascent RNA
pooled sample D
BN_PB6_all_R1.B6.bowtie.gz
BN_PB6_all_R1.CAST.bowtie.gz
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw


title: BN_PB6_B

description:
nascent RNA
pooled sample B
BN_PB6_all_R1.B6.bowtie.gz
BN_PB6_all_R1.CAST.bowtie.gz
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 25


title: CCM2_Parental

description: processed data file: gatk_counts_H293.csv


title: CCM2_Vehicle

value: Vehicle


title: BN_PB6_C

description:
nascent RNA
pooled sample C
BN_PB6_all_R1.B6.bowtie.gz
BN_PB6_all_R1.CAST.bowtie.gz
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
BN_PB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: post natal day 24


title: Rep 2; CD8+ T cells; Ag+ control culture; Ag+ area; plate 1

description:
MARS seq
AB9302_SB390

value: Ag+ cells only


title: Rep 2; CD8+ T cells; Ag+ control culture; non-exposed control; plate 1

description:
MARS seq
AB9304_SB390

value: non-exposed


title: BN_MB6_G

description:
nascent RNA
pooled sample G
BN_MB6_all_R1.B6.bowtie.gz
BN_MB6_all_R1.CAST.bowtie.gz
BN_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
BN_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
BN_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: C57BL/6 x Castaneus F1 hybrid


title: CCM1_Apo_1000

value: CCM


title: CCM1_Apo_100

value: PCR from gDNA


title: Rep 2; CD8+ T cells; island culture; non-exposed control; plate 3

description:
MARS seq
AB9301_SB390

value: Single Ag+ island surrounded by Ag- islands


title: Rep 2; CD8+ T cells; island culture; Ag- area & non-exposed control; plate 1

description:
MARS seq
AB9300_SB390

value: Ag- & non-exposed


title: CCM2_Ammo_3


title: CCM1_Ammo_30


title: Rep 2; CD8+ T cells; island culture; Ag- area; plate 3

description:
MARS seq
AB9299_SB390


title: BN_MB6_F

description:
nascent RNA
pooled sample F
BN_MB6_all_R1.B6.bowtie.gz
BN_MB6_all_R1.CAST.bowtie.gz
BN_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
BN_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
BN_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

value: Brain

value: post natal day 22


title: CCM1_Ammo_3


title: CCM1_Vehicle


title: M2

city: Farmington

first: Marmar

last: Moussa

state: CT

address: Farmington

department: School of Medicine

institute: University of Connecticut

description:
10X single cell RNA sequencing
processed data file: CRISPR_COMBINED_N_filtered_feature_bc_matrix.h5
M2_N

data_processing:
Data processing steps follow in general the 10x Genomics pipeline with default params, and in detail: cell ranger v. 3.0.2 is used to generate the 10x output files, rad data from 10x BAM is converted to FASTQ format for new /reproducing analyses using the 10x tool bamtofastq. 10x BAMs contain all the reads from the FASTQ(s), alignment information, and necessady metadata. cellranger count is used to obtain UMI counts and cellranger aggr is used to compare samples. Sample DMSO_Control1, Alms1MUT, Ccdc85cMUT, and DMSO_Control2 constitute one set, processed (aggr) into MethA_filtered_feature_bc_matrix in that order, where as M1, Rev, and M2 constitute another set into processed matrix CRISPR_COMBINED_N_filtered_feature_bc_matrix.
filtered_feature_bc_matrix output files from 10x Genomics pipeline are used for further downstream analyses using QC metrics of min 500 genes per cell and 15% mitochondrial content.
Genome_build: mm10
Supplementary_files_format_and_content: h5

extract_protocol:
Tumors were harvested 10 days after tumor challenge and CD45+ cells were sorted to be analyzed with 10x
Twelve thousand tumor infiltrating immune cells were loaded for capture, using a Chromium Single Cell 3′ Reagent Kits v2 Chemistry (10× Genomics). Following capture and lysis, complementary DNA was synthesized and amplified (12 cycles) as per the manufacturer’s protocol. The amplified cDNA was used to construct Illumina sequencing libraries and was sequenced on a HiSeq4000 system (Illumina). The Cell Ranger Single-Cell Software Suite v.3.0 (10× Genomics) was used to perform sample demultiplexing, barcode processing and single-cell 3′ counting.

value: BALB/cJ

tag: immunization

value: Not Immunized

tag: crispr edited


title: BN_MB6_A

description:
nascent RNA
pooled sample A
BN_MB6_all_R1.B6.bowtie.gz
BN_MB6_all_R1.CAST.bowtie.gz
BN_MB6_all_R1.B6.specific.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.B6.specific.5prime.1bp.map2ref_minus.bw
BN_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.CAST.specific.5prime.1bp.map2ref_minus.bw
BN_MB6_all_R1.identical.5prime.1bp.map2ref_plus.bw
BN_MB6_all_R1.identical.5prime.1bp.map2ref_minus.bw

tag: strain

tag: age

value: post natal day 23

value: male


title: Rep 2; CD8+ T cells; island culture; Ag- area; plate 2

description:
MARS seq
AB9298_SB390

value: Ag-

value: CD8+ T cells

value: CD3+ CD8+ IRdye-


title: Rep 2; CD8+ T cells; island culture; Ag- area; plate 1

description:
MARS seq
AB9297_SB390


title: Rev

description:
10X single cell RNA sequencing
processed data file: CRISPR_COMBINED_N_filtered_feature_bc_matrix.h5
Rev_N

source_name: Rev

value: REV


title: CCM1_Parental


title: M1

description:
10X single cell RNA sequencing
processed data file: CRISPR_COMBINED_N_filtered_feature_bc_matrix.h5
M1_N

value: No (MUT1)


title: DMSO_Control1

description:
10X single cell RNA sequencing
processed data file: MethA_filtered_feature_bc_matrix.h5
PS17022_DMSO

value: BMDCs

value: No


title: Rep 2; CD8+ T cells; island culture; Ag+ area; plate 2

description:
MARS seq
AB9293_SB390

value: Ag+


title: Rep 2; CD8+ T cells; island culture; non-exposed control; plate 1

description:
MARS seq
AB9295_SB390

value: non-exposed


title: Ccdc85cMUT

description:
10X single cell RNA sequencing
processed data file: MethA_filtered_feature_bc_matrix.h5
PS17019_1038

value: Ccdc85cMUT peptidepulsed BMDCS


title: Rep 2; CD8+ T cells; island culture; Ag+ area; plate 3

description:
MARS seq
AB9294_SB390

value: Single Ag+ island surrounded by Ag- islands


title: Alms1MUT

description:
10X single cell RNA sequencing
processed data file: MethA_filtered_feature_bc_matrix.h5
PS17024_1036

value: Alms1MUT peptide pulsed BMDCs


title: CCM1_Ammo_300

value: CCM

value: PCR from gDNA


title: Rep 2; CD8+ T cells; island culture; non-exposed control; plate 2

description:
MARS seq
AB9296_SB390


title: A18

city: Brussels

first: Lila

last: Gannoun

address: Avenue Hippocrate 75

department: Institut de Duve

country: Belgium

institute: Université Catholique de Louvain

description:
Transgenic mice
TPM_E16_E18_cholangiocytes.tsv

data_processing:
RNA sequencing using Illumina HiSeq 2x150bp configuration with estimated data output ≥350M raw paired-end reads per lane.
The reads quality control was performed using FastQC software v0.11.7 (Babraham Institute, Cambridge, UK).
Paired-end reads were aligned by HISAT2 software v2.1.0 (Johns Hopkins University School of Medicine, Center for Computational Biology, Baltimore, MD, USA) against the mm10 genome build using the bowtie1 aligner24 option.
Gene counts were generated using HTSeq-count (v0.5.4p3) software and gencode.vM15.annotation.gtf annotation file and raw counts were further converted in transcripts per million (TPM).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: TPM_E16_E18_cholangiocytes.tsv: Tab-delimited text file includes TPM values for each sample.

source_name: Bile ducts

growth_protocol: Mus musculus CD-1 model: Sox9-GFP.

extract_protocol:
RNA extraction of embryonic cholangiocytes: The supernatant was removed and RNA from cells pellets was extracted using RNAqueous™-Micro Total RNA Isolation Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s protocol.
RNA libraries were generated using the TruSeq total stranded RNA-seq kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Purification of embryonic cholangiocytes (E16 and E18): Livers were dissociated using collagenase IV and Dispase. Then, GFP positive cells were selected using a cell sorter (FACSAria II, BD, Franklin Lakes, USA), harvested in an individual microtube and centrifugated at 1000 rpm during 5 min.

tag: cell type

value: Cholangiocytes from liver

tag: developmental stage

value: Embryonic day 18


title: C18


title: Rep 1; CD8+ T cells; Ag- control culture; Ag- area; plate 1

description:
MARS seq
AB9290_SB390

value: Ag- cells only


title: Rep 1; CD8+ T cells; Ag+ control culture; Ag+ area; plate 1

description:
MARS seq
AB9289_SB390

value: Ag+ cells only


title: B18


title: B16

value: Embryonic day 16


title: Rep 2; CD8+ T cells; island culture; Ag+ area; plate 1

description:
MARS seq
AB9292_SB390

value: CD8+ T cells

value: CD3+ CD8+ IRdye-


title: Rep 1; CD8+ T cells; island culture; Ag+ area;  plate 5

description:
MARS seq
AB9291_SB390


title: Rep 1; CD8+ T cells; island culture; Ag- area; plate 4

description:
MARS seq
AB9288_SB390

value: Ag-


title: C16


title: Rep 1; CD8+ T cells; island culture; Ag- area; plate 3

description:
MARS seq
AB9287_SB390


title: Input_AG_male_midgut_Rep2

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
Parkour-ID A887
Input

data_processing:
Paired-end reads were mapped to AgamP4_ensembl with bowtie2 (Galaxy version v2.2.6.2) using default parameters. To generate readCount normalized coverage bigwig files, we calculated the log2 ratio versus the Input using a binsize of 5 bp with deepTools bamCompare v2.4.2. Duplicate reads and reads with a mapping quality <10 were removed, the X chromosome was ignored for scaling.
Genome_build: AgamP4_ensembl
Supplementary_files_format_and_content: bigWig files of uniquely mapped reads.

organism: Anopheles gambiae

source_name: Dissected midgut

growth_protocol: A. gambiae mosquitoes were maintained in standard insectary conditions (28°, 75–80% humidity, 12-hr/12-hr light/dark cycle).

extract_protocol:
Anopheles gambiae midguts were dissected and fixed in PBS containing 0.2% Formaldehyde (15 min at RT). Chromatin was extracted using a sucrose cushion followed by Micrococcal Nuclease treatment and 10 cycles of sonication in a Bioruptor Pico. The lysate was clarified by centrifugation before immunoprecipitation, washes, elution by reverse crosslinking at 65deg for 14h. After RNaseA and ProteinaseK treatment, the DNA from Input and Immunoprecipitation was purified using Phenol-Chloroform Extraction and Ethanol precipitation.
NEB Next Ultra II.

treatment_protocol: Male and female Anopheles were collected and anesthetized with CO2. Midguts were dissected.

tag: genotype/variation

value: wild-type

tag: gender

value: male

tag: tissue

value: Dissected midgut

tag: chip antibody


title: Input_AG_male_midgut

description:
Parkour-ID A747
Input


title: Input_AG_female_midgut_Rep2

description:
Parkour-ID A747
Input

value: female


title: NTG_Old+CP2.15

city: Rochester

first: Mrunal

middle: Kishor

last: Dehankar

state: MN

address: 200 First St. SW

department: Computational genomics

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat (https://ccb.jhu.edu/software/tophat/index.shtml)
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include Raw counts and FPKM values for each gene per sample

extract_protocol:
Brains were removed, cross-sectional brain region encompassing hippocampal and cortical tissue was flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA isolation using miRNeasy (Qiagen cat. # 217004)  was used with 200 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: NTG_Adult mice were treated with either vehilce or CP2 (25 mg/kg/day in 0.1% PEG dissolved in drinking water ad lib) or vehicle-containing water (0.1% PEG) starting at 9 months of age. Young NTG mice were untreated.

value: brain

value: 23 months

tag: genotype

value: wild type


title: A16


title: DMSO_Control2

description:
10X single cell RNA sequencing
processed data file: MethA_filtered_feature_bc_matrix.h5
PS17017_DMSO

value: BALB/cJ

value: BMDCs

value: No


title: Rep 1; CD8+ T cells; island culture; Ag- area; plate 1

description:
MARS seq
AB9285_SB390

value: Single Ag+ island surrounded by Ag- islands


title: K562 Treated rep3

city: Maywood

first: Jiwang

last: Zhang

state: Illinois

address: 2160 S. 1st Ave

institute: Loyola University Medical Center

data_processing:
RNA-seq reads were aligned to the hg38 genome using IGV software (version 2.7.2).
For the samples with biological replicates, Novogene performed differential expression significant analysis of two conditions/groups by using the DESeq2 R package, while the significant criterion is padj<0.05.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM values for all differentially-expressed genes in each individual cell type and replicate

source_name: Chronic myeloid leukemia

growth_protocol: Molm-13 and MV4:11 cells grown in RPMI 1640, HL-60 and K562 cells grown in DMEM; 10% FBS for Molm-13, MV4:11, K562; 20% FBS for HL-60; 1% Penicillin/Streptomycin for all

extract_protocol:
RNA was extracted from each replicate separately using TRI reagent; QIAGEN Rneasy Mini Kit (Cat#74104) was then used following kit protocol.
RNA libraries were prepared using standard Novogene mRNA-seq protocols.

treatment_protocol: 5x10^5 cells/mL treated per replicate, 6 hrs 100 nM GEX1A; controls treated with plain RPMI (vehicle)

tag: mutations

value: BCR-ABL1, TP53

tag: treatment

value: 100 nM GEX1A, 6hr

tag: cell line


title: Rep 1; CD8+ T cells; island culture; Ag+ area; plate 4

description:
MARS seq
AB9284_SB390

tag: tumor areas

tag: exposed tumor area

value: Ag+

tag: primary cells (sequenced)


title: NTG_Old+CP2.13


title: Input_AG_female_midgut

description:
Parkour-ID A747
Input


title: NTG_Old+CP2.12


title: H4K16acChIP_AG_male_midgut_Rep2

description: Parkour-ID A887

value: H4K16ac (Merck Millipore, 07-329)


title: K562 Treated rep2


title: Rep 1; CD8+ T cells; island culture; Ag+ area; plate 3

description:
MARS seq
AB9283_SB390

value: CD8+ T cells

tag: tumor cell line (not sequenced)

tag: selection markers

value: CD3+ CD8+ IRdye-


title: H4K16acChIP_AG_male_midgut

description: Parkour-ID A747

value: wild-type


title: Rep 1; CD8+ T cells; island culture; Ag+ area; plate 2

description:
MARS seq
AB9282_SB390


title: K562 Control rep3

value: Vehicle (RPMI)


title: NTG_Old+CP2.11

tag: strain


title: NTG_Old.10

tag: age


title: H4K16acChIP_AG_female_midgut_Rep2

description: Parkour-ID A747

value: Dissected midgut


title: NTG_Old.9


title: Rep 1; CD8+ T cells; island culture; Ag- area; plate 2

description:
MARS seq
AB9286_SB390

value: Ag-


title: HUVEC-C2_d74

city: Fujisawa

first: Momoko

last: Ohori

state: Kanagawa

address: 26-1, Muraokashicashi2

country: Japan

institute: Takeda pharmaceutical company

description: Sample 8

data_processing:
Illumina mRNA-Seq reads were aligned to hg19 (GRCh37) reference genome assembly using the GSNAP aligner.
Aligned libraries had mate-pair information fixed, were removed of potential PCR duplicates.
Cufflinks was used to quantify gene expression FPKM values.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: HUVEC

growth_protocol: HUVECs (Lonza, Basel, Switzerland) were cultured using an EBM-2 Bullet Kit (Lonza) and passaged for indicated periods.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: HUVEC

tag: clone

tag: culture periods

value: 74 days


title: K562 Control rep1


title: K562 Control rep2


title: H3ChIP_AG_male_midgut_Rep2

description: Parkour-ID A887

tag: genotype/variation

tag: gender

value: male

value: Histone H3 antibody (mAb), MABI 0301 (39763 Active Motif)


title: HUVEC-C2_d61

description: Sample 7

value: 61 days


title: H4K16acChIP_AG_female_midgut

description: Parkour-ID A747

value: female

tag: tissue

tag: chip antibody


title: NTG_Old.7

value: brain

value: 23 months

tag: genotype

value: wild type


title: NTG_Old.8


title: K562 Treated rep1

tag: mutations

value: BCR-ABL1, TP53

tag: treatment

value: 100 nM GEX1A, 6hr


title: HUVEC-C2_d20

description: Sample 6

value: 20 dyas


title: HL-60 Treated rep2

source_name: Acute myeloid leukemia

value: KRAS, TP53, CDKN2A

tag: cell line


title: NTG_Young.5

value: 3 months


title: H3ChIP_AG_male_midgut

description: Parkour-ID A747

value: wild-type


title: HL-60 Treated rep1


title: HUVEC-C2_d5

description: Sample 5

value: 5 days


title: H3ChIP_AG_female_midgut_Rep2

description: Parkour-ID A747

value: Dissected midgut


title: H3ChIP_AG_female_midgut

description: Parkour-ID A747


title: Rep 1; CD8+ T cells; island culture; Ag+ area; plate 1

description:
MARS seq
AB9281_SB390

tag: tumor areas

value: Single Ag+ island surrounded by Ag- islands

tag: exposed tumor area

value: Ag+

value: CD8+ T cells

value: CD3+ CD8+ IRdye-


title: HL-60 Control rep3

value: Vehicle (RPMI)


title: NTG_Young.1


title: HL-60 Control rep2


title: HUVEC-C1_d60

description: Sample 3

value: HUVEC

value: 60 days


title: NTG_Young.3

value: brain


title: HUVEC-C1_d74

description: Sample 4

value: 74 days


title: AG_mixed_R9_wt_7h_A3

description:
Parkour-ID 130_Keller_Akhtar
processed data file: RNAseq_AGAP_counts.txt

data_processing:
For quality control, we used FastQC version: v0.11.3. For RNA-seq, paired-end reads were mapped with RNA STAR (Galaxy version 2.5.2b-0) to AgamP4_ensembl or dm6_ensembl with default parameters. The raw read counts per gene were obtained with featureCounts (1.4.6.p5) followed by differential expression analysis with DESeq2, R version 3.0.2.
Genome_build: BDGP6 (dm6, Release 6 plus ISO1 MT), AgamP4_ensembl
Supplementary_files_format_and_content: *_counts.txt: Tab-delimited featureCounts count table output.

source_name: Embryo

growth_protocol: Drosophila melanogaster were reared on a cornflour-molasses fruit fly medium [1l water, 12g agar-agar threads, 18g bakery yeast, 10g soya flour, 80g corn flour, 22g molasses, 80g malt extract, 2.4g 4-hydroxibenzoic acid methylester (Nipagin), 6.25ml propionic acid] at 25C, 70% relative humidity and 12 hr dark/12 hr light cycle. A. gambiae mosquitoes were maintained in standard insectary conditions (28°, 75–80% humidity, 12-hr/12-hr light/dark cycle).

extract_protocol:
Samples were homogenized in TRIzol™ Reagent (Thermo Fisher 15596026) followed by RNA purification using a Direct-zol™ RNA MiniPrep kit (Zymo Research, R2050) according to the manufacturer's instruction.
TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Non-fluorescent embryos were collected from over-night collections of msl-2.227/CyO-GFP D. melanogaster. For A. gambiae, vasa-Cas9 mothers were crossed with msl-2 gRNA or control gRNA fathers. Embryos were collected from egg dishes at indicated times after egg laying.

value: vasa-Cas9 x ctrlgRNA

value: control

tag: developmental stage

value: 6-7h embryo

value: whole body


title: HL-60 Control rep1

value: KRAS, TP53, CDKN2A


title: HUVEC-C1_d18

description: Sample 2

value: 18 days


title: HL-60 Treated rep3

value: 100 nM GEX1A, 6hr


title: AG_mixed_R9_wt_6h_A1


title: HUVEC-C1_d5

description: Sample 1

value: 5 days


title: MV4:11 Treated rep3

source_name: Acute monocytic leukemia

value: MLL-AF4, FLT3-ITD


title: AG_mixed_R9_wt_24h_A11

value: 24h embryo


title: MV4:11 Treated rep2


title: AG_mixed_R9_wt_15h_A7

value: 15h embryo


title: HEK293T flow through RNA (FT)

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce Street

institute: the wistar institute

description:
column label is FT
flow through RNA

data_processing:
the sequence corresponding to 5’ adapter was first removed from raw 3’READS reads using Cutadapt (1.18). Reads with short inserts (<25 nt) were discarded.
The retained reads were then mapped to the human genome (hg19) using bowtie2 (local mode) (2.2.9). The six random nucleotides at the 5’ end of reads 1 derived from the 3’ adapter were removed before mapping using the setting "-5 6" in bowtie2. Reads with a mapping quality score (MAPQ) <10 were discarded.
Reads with ≥2 non-genomic 5’ Ts after alignment were called PASS reads. PASs within 24 nt from each other were clustered as previously described
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including reads count for each pAs/gene

source_name: HEK 293T

growth_protocol: Human HEK293T cells were cultured in high glucose DMEM with 10% FBS (Gibco) and 1% Penicillin/Streptomycin solution (Sigma).

extract_protocol:
RNA was harvested with Trizol (Sigma)
0.2-2ug of input RNA was captured using oligo(dT)25 magnetic beads and fragmented on beads with RNAse III. Partially digested poly(A)+ RNA fragments were ligated to 5’ adapter (5′-CCUUGGCACCCGAGAAUUCCANNNN) with T4 RNA ligase 1. The ligation products were incubated with biotin-T15-(T)5 LNA and digested by RNase H. Digested products were ligated to 3’ adapter with T4 RNA ligase 2. The final ligation products were reverse transcribed and subjected for PCR amplification with index primers for multiplex sequencing. PCR products were size selected with AMPure XP beads (Beckman) and subjected to quality control with ScreenTape (Agilent). Libraries were sequenced on llumina HiSeq (2 x 150 paired end reads).
OTHER: 3'READS+ (3' end biased RNA-Seq)

treatment_protocol: cells were cultures with 50uM of 4-thiouridine (Sigma) for 1 hours. 100ug of total RNA was biotinylated with biotin-HPDP, and subsequently captured by Streptavidin C1 Dynabeads (ThermoFisher). The unbound flow-through (FT) fraction was also collected to represent pre-existing RNAs.

value: HEK 293T

tag: metabolic labeling

value: 4sU treated

tag: fraction

value: 4sU-biotin flowthrough


title: NTG_Young.4

tag: strain

tag: age

value: 3 months

value: wild type


title: MV4:11 Treated rep1


title: HEK293T 4sU RNA (4sU)

description:
column label is 4sU
4sU labeled RNA

tag: cell type

value: 4sU-biotin pull down


title: DM_mixed_msl2_710_CyOGFP_embryoON_C5

description:
Parkour-ID 130_Keller_Akhtar
processed data file: RNAseq_Dmel_counts.txt

organism: Drosophila melanogaster

value: CRISPR knock-out allele, Valsecchi et al. (2018)

value: over night collection embryo


title: MV4:11 Control rep2

value: Vehicle (RPMI)


title: DM_mixed_msl2_710_CyOGFP_embryoON_C4

value: whole body


title: MV4:11 Control rep1


title: AG_mixed_R9_wt_7h_A9

value: vasa-Cas9 x ctrlgRNA

value: control

value: 6-7h embryo


title: AG_mixed_R9_gMSL2_7h_A4

value: vasa-Cas9 x msl-2gRNA

value: msl-2 knock-out


title: HEK293T 4sU RNA (H293T_E)

description:
column label is H293T_E
4sU labeled RNA


title: DM_mixed_msl2_710_CyOGFP_embryoON_C3


title: Molm-13 Treated rep3

value: MLL-AF9, FLT3-ITD

value: 100 nM GEX1A, 6hr


title: Hep3B_si-SMARCA4_2

city: Seoul

first: Sang Yean

last: Kim

state: Select

address: 222 BANPO-DAERO SEOCHO-GU, SEOUL

country: South Korea

institute: The Catholic university of korea

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using star method.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg 19
Supplementary_files_format_and_content: FPKMs

source_name: HCC cell line

growth_protocol: Hep3B cells were maintained using EMEM media supplemented with 10% Fetal Bovine Serum(ATCC, Manassas, VA, USA) and 1% Penicillin Streptomycin.

extract_protocol:
RNA was extracted with Trizol reagent (Invitrogen, Carlsbad, CA, USA) followed by clean-up and DNase I treatment, The quality of total RNA was analyzed with the RNA StdSens Chips on the Experion system.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OPTI-MEM I (Gibco, MA, USA) 1.6ml and mi

value: HCC cell line Hep3B

value: si-SMARCA4 transfected cells


title: RAW264.7_SMARTpool_siRvbl2_DMSO

city: Hong Kong

first: Kwong Wai

last: CHOY

address: Hong Kong

department: O and G

country: Hong Kong

institute: CUHK

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent Hi-RPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 8x60K Microarray (G4852B) for 16 hours at 65°C in a rotating Agilent hybridization oven at 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0(Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Macrophage cell line RAW264.7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Agilent One-Color Quick Amp labeling kit according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: RAW 264.7 macrophages (American Type Culture Collection) were grown in DMEM(Gibco), supplemented with 10% heat-inactivated fetal bovine serum (Gibco).

extract_protocol: Total RNA extraction was performed using TRIzol® Reagent (Invitrogen, Carlsbad, CA) and the extraction was done according to the manufacturer’s instructions. The quantity and quality of each RNA sample was determined using NanoDrop ND-2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) RNA Pico Kit.

treatment_protocol: Cells were transfected with the respective siRNA duplexes by using NeonTM transfection system(ThermoFisher) (1720V, 10ms, 2 pulses)or TransInTM EL Transfection Reagent (Transgen Biotech).Cells were analyzed after two days of transfection.


title: AG_mixed_R9_gMSL2_6h_A2


title: Hep3B_si-SMARCA4_3


title: HEK293T Total RNA (H293T_T)

description:
column label is H293T_T
Total RNA

value: HEK 293T

value: untreated


title: RAW264.7_SiControl_DMSO


title: RAW264.7_SiControl_Lipopolysaccharides


title: RAW264.7_SMARTpool_siRvbl2_Lipopolysaccharides


title: Molm-13 Treated rep2


title: AG_mixed_R9_gMSL2_15h_A8

value: 15h embryo


title: Molm-13 Treated rep1


title: Hep3B_si-SMARCA4_1


title: AG_mixed_R9_gMSL2_24h_A12

value: 24h embryo


title: AG_mixed_R9_wt_15h_A5


title: MV4:11 Control rep3

value: MLL-AF4, FLT3-ITD


title: DM_mixed_msl2_7_10_embryoON_C8

description:
Parkour-ID 130_Keller_Akhtar
msl-2∆7 / msl-2∆10
processed data file: RNAseq_Dmel_counts.txt

value: CRISPR knock-out allele, Valsecchi et al. (2018)

value: msl-2<delta>7 / msl-2<delta>10

value: over night collection embryo


title: HEK293T flow through RNA (H293T_FT)

description:
column label is H293T_FT
flow through RNA

value: 4sU treated

value: 4sU-biotin flowthrough


title: AG_mixed_R9_gMSL2_15h_A6

value: whole body


title: Molm-13 Control rep3

value: Vehicle (RPMI)


title: DM_mixed_msl2_7_10_embryoON_C7


title: Hep3B_si-Cont_3

value: si-cont transfected cells


title: WT_Plasmid

description:
ATP synthase pool including ATP5F1A, ATP5F1B, ATP5F1C
processed data file: gatk_counts_library.csv

organism: Escherichia coli

tag: library

value: WT

tag: molecule subtype

value: PCR from plasmid


title: DM_mixed_msl2_710_CyOGFP_embryoON_C2

tag: genotype/variation


title: Hep3B_si-Cont_2

value: HCC cell line Hep3B


title: Molm-13 Control rep2

value: MLL-AF9, FLT3-ITD


title: DM_mixed_msl2_7_10_embryoON_C9

tag: tissue


title: Hep3B_si-Cont_1


title: Molm-13 Control rep1


title: CCM_Plasmid

description:
ATP synthase variant library generated using comprehensive codon mutagenesis (PMID 33659364)
processed data file: gatk_counts_library.csv

value: XL-1 Blue

value: CCM


title: NJA02402.O18

status: Public on May 30 2021

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
Sequencing reads were trimmed, adapter sequences removed
Reads aligned to the mm10 reference assembly using STAR with default parameters
Duplicate reads were removed using picard
Transcript counts were obtained using HTSeq35 and mm10 UCSC exon/transcript annotations
Single cell profiles with the following features were deemed to be of poor quality and removed: 1) cells with less than a specified total number of valid counts in exonic regions (1.8x104 and 4x104 for the mouse gut and sorted multiplets dataset, respectively), 2) cells with low actin TPM, and 3) cells with high fractions of ERCC reads. To determine a cut-off for actin TPM, we used the normal distribution with empirical mean and standard deviation from log2 transformed actin TPM, which is normally distributed in successful experiments. The cut-off was set to the 0.01 quantile (eg. the lower 0.01 % of the bell curve). A similar strategy was used for fractions of ERCC reads, samples with a log2 transformed fraction of ERCC reads above the 0.99 % quantile were rejected.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: htseq-format of raw counts

source_name: spleen

growth_protocol: Small intestine and colon were removed from C57BL/J wild-type mice and kept on ice in phosphate buffered saline (PBS). Lumina of colon and small intestine were washed three times with PBS and adipose tissue connected to the exterior of the small intestine or colon was removed. Colon and small intestine were opened longitudinally, and any remaining mucous on covering the epithelial layer was gently rubbed off. Tissues were washed once in PBS before being cut into 0.5 - 1 mm long fragments. Colon fragments were immersed in 10mM EDTA-PBS and incubated for 105 minutes on ice, with shaking every 15 minutes. Small intestinal fragments were similarly immersed in 10mM EDTA-PBS on ice and shaken. After 15 minutes, small intestinal fragments were allowed to settle at the bottom and the supernatant was discarded and replaced with new 10mM EDTA-PBS and shaken vigorously. This procedure was repeated 1-2 times, with supernatant fractions investigated through light microscopy before discarding, in order to enrich for crypts. Small intestinal fragments were then incubated on ice for 45-60 minutes for a total of 105 minutes. Following EDTA-PBS treatment fractions were triturated 10-15 times. Colon fractions were strained through a 100 um filter while small intestinal fractions were strained through a 70 um filter. Fractions were centrifuged at 300g for 5 minutes and dissociated using TrypLE Express (Invitrogen) at 37°C for 15-20 minutes. Enzymatic dissociation was supervised using light microscopy during regular intervals to obtain an appropriate amount of single cells and multiplets. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer's protocol before staining for FACS sorting was performed.

extract_protocol:
For mouse intestine, cells were stained with FITC anti-CD326 and 7AAD (Sony Biotechnology) in order to monitor number of epithelial cells and select live cells. Additionally, paneth cells were enriched using Brilliant Violent anti-CD24. For spleen, cells were sorted with only 7AAD to remove dead cells, not other antibodies. Single cells were distinguished from multiplets using FSC-H and FSC-W gating and the gating scheme was visually confirmed via phase contrast microscopy (Fig. 1a). Cells were sorted into 384- or 96-well plates containing hypotonic lysis buffer using a SH800S FACS sorter (Sony). Plates were sealed immediately after sorting with microseal F foil (Biorad) and centrifuged at 4000g at 4°C for 5 min before being frozen on dry ice and stored at -80°C.
Single-cell and multiplet RNA-Seq libraries were generated as described. Briefly, single-cells collected in 384-well plates were lysed, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analysed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (Illumina) according to the manufacturer's instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq 500 instrument.

value: spleen

tag: facs cellnumber

value: Multiplet

tag: age (days)


title: NJA02402.O15

value: Singlet


title: NJA02402.O16


title: NJA02402.O19


title: NJA02402.O17


title: NJA02402.O14


title: NJA02402.O21


title: AG_mixed_R9_gMSL2_7h_A10

value: vasa-Cas9 x msl-2gRNA

value: msl-2 knock-out

value: 6-7h embryo


title: NJA02402.O20


title: NJA02402.O22


title: NJA02402.O12


title: NJA02402.O05


title: NJA02402.O09


title: NJA02402.O23


title: NJA02402.O08


title: NJA02402.O10


title: NJA02402.O11


title: NJA02402.O06


title: NJA02402.O07


title: NJA02402.O04


title: NJA02402.O03


title: NJA02402.O02


title: NJA02402.N21


title: NJA02402.N22


title: NJA02402.N19


title: NJA02402.N20


title: NJA02402.N15


title: NJA02402.N17


title: NJA02402.O13


title: NJA02402.N14


title: NJA02402.N13


title: NJA02402.N07


title: NJA02402.N04


title: NJA02402.N06


title: NJA02402.N10


title: NJA02402.N08


title: NJA02402.N03


title: NJA02402.M18


title: NJA02402.M21


title: NJA02402.M20


title: NJA02402.N02


title: NJA02402.M23


title: NJA02402.M22


title: NJA02402.M17


title: NJA02402.M13


title: NJA02402.M09


title: NJA02402.M06


title: NJA02402.M07


title: NJA02402.M12


title: NJA02402.M19


title: NJA02402.M11


title: NJA02402.M10


title: NJA02402.M05


title: NJA02402.N12


title: NJA02402.N11


title: NJA02402.N05


title: NJA02402.M15


title: NJA02402.M14


title: NJA02402.M04


title: NJA02402.M03


title: NJA02402.M01


title: NJA02402.L23


title: NJA02402.L21


title: NJA02402.L16


title: NJA02402.L22


title: NJA02402.L17


title: NJA02402.L19


title: NJA02402.L18


title: NJA02402.M02


title: NJA02402.L24


title: NJA02402.L01


title: NJA02402.K23


title: NJA02402.L05


title: NJA02402.L12


title: NJA02402.L04


title: NJA02402.L13


title: NJA02402.L02


title: NJA02402.K24


title: NJA02402.L07


title: NJA02402.K21


title: NJA02402.K22


title: NJA02402.L08


title: NJA02402.L20


title: NJA02402.L11


title: NJA02402.L10


title: NJA02402.L14


title: NJA02402.L06


title: NJA02402.L03


title: NJA02402.L15


title: NJA02402.K20


title: NJA02402.K16


title: NJA02402.K17


title: NJA02402.K14


title: NJA02402.K11


title: NJA02402.K13


title: NJA02402.K08


title: NJA02402.K06


title: NJA02402.K09


title: NJA02402.K07


title: NJA02402.K05


title: NJA02402.K02


title: NJA02402.J24


title: NJA02402.K19


title: NJA02402.K04


title: NJA02402.J22


title: NJA02402.J20


title: NJA02402.K01


title: NJA02402.K18


title: NJA02402.J23


title: NJA02402.K03


title: NJA02402.J18


title: NJA02402.J16


title: NJA02402.J15


title: NJA02402.J13


title: NJA02402.J10


title: NJA02402.J17


title: NJA02402.J14


title: NJA02402.J06


title: NJA02402.J12


title: NJA02402.J08


title: NJA02402.J07


title: NJA02402.J21


title: NJA02402.J11


title: NJA02402.J05


title: NJA02402.J04


title: NJA02402.J03


title: NJA02402.J09


title: NJA02402.I24


title: NJA02402.J01


title: NJA02402.J02


title: NJA02402.I20


title: NJA02402.I23


title: NJA02402.I21


title: NJA02402.I16


title: NJA02402.I17


title: NJA02402.I14


title: NJA02402.I22


title: NJA02402.I18


title: NJA02402.I15


title: NJA02402.I12


title: NJA02402.I11


title: NJA02402.I09


title: NJA02402.I05


title: NJA02402.I10


title: NJA02402.I07


title: NJA02402.I03


title: NJA02402.I08


title: NJA02402.I04


title: NJA02402.I13


title: NJA02402.I02


title: NJA02402.I06


title: NJA02402.I19


title: NJA02402.I01


title: NJA02402.H23


title: NJA02402.H24


title: NJA02402.H20


title: NJA02402.H22


title: NJA02402.H19


title: NJA02402.H21


title: NJA02402.H17


title: NJA02402.H15


title: NJA02402.H16


title: NJA02402.H18


title: NJA02402.H12


title: NJA02402.H10


title: NJA02402.H11


title: NJA02402.H09


title: NJA02402.H07


title: NJA02402.H14


title: NJA02402.H06


title: NJA02402.H01


title: NJA02402.G21


title: NJA02402.H03


title: NJA02402.H04


title: NJA02402.G24


title: NJA02402.G23


title: NJA02402.G20


title: NJA02402.G19


title: NJA02402.G18


title: NJA02402.H08


title: NJA02402.G17


title: NJA02402.G15


title: NJA02402.G16


title: NJA02402.G14


title: NJA02402.G13


title: NJA02402.H02


title: NJA02402.G12


title: NJA02402.H05


title: NJA02402.G06


title: NJA02402.G08


title: NJA02402.G05


title: NJA02402.G07


title: NJA02402.G10


title: NJA02402.G03


title: NJA02402.G04


title: NJA02402.G11


title: NJA02402.G02


title: NJA02402.F24


title: NJA02402.G22


title: NJA02402.G01


title: NJA02402.F23


title: NJA02402.F20


title: NJA02402.F21


title: NJA02402.F22


title: NJA02402.F19


title: NJA02402.F16


title: NJA02402.F17


title: NJA02402.F18


title: NJA02402.G09


title: NJA02402.F15


title: NJA02402.F14


title: NJA02402.F12


title: NJA02402.F10


title: NJA02402.F11


title: NJA02402.F09


title: NJA02402.F08


title: NJA02402.F07


title: NJA02402.F05


title: NJA02402.F06


title: NJA02402.E23


title: NJA02402.F02


title: NJA02402.E24


title: NJA02402.F03


title: NJA02402.F04


title: NJA02402.F01


title: NJA02402.E22


title: NJA02402.E20


title: NJA02402.E18


title: DM_mixed_msl2_7_10_embryoON_C6

value: CRISPR knock-out allele, Valsecchi et al. (2018)

value: msl-2<delta>7 / msl-2<delta>10

value: over night collection embryo


title: NJA02402.E17


title: NJA02402.E16


title: NJA02402.E14


title: NJA02402.E15


title: NJA02402.E13


title: NJA02402.E12


title: NJA02402.E11


title: NJA02402.E10


title: NJA02402.E09


title: NJA02402.E08


title: NJA02402.E07


title: NJA02402.E05


title: NJA02402.E04


title: NJA02402.E03


title: NJA02402.E01


title: NJA02402.E02


title: NJA02402.E21


title: NJA02402.D22


title: NJA02402.D17


title: NJA02402.D11


title: NJA02402.D16


title: NJA02402.D14


title: NJA02402.D18


title: NJA02402.D12


title: NJA02402.D09


title: NJA02402.D15


title: NJA02402.D13


title: NJA02402.D06


title: NJA02402.D03


title: NJA02402.D04


title: NJA02402.D07


title: NJA02402.D08


title: NJA02402.D02


title: NJA02402.C24


title: NJA02402.C23


title: NJA02402.E06


title: NJA02402.D01


title: NJA02402.C21


title: NJA02402.C22


title: NJA02402.C18


title: NJA02402.C20


title: NJA02402.C16


title: NJA02402.C19


title: NJA02402.C17


title: NJA02402.D10


title: NJA02402.C15


title: NJA02402.C14


title: NJA02402.C13


title: NJA02402.C10


title: NJA02402.C08


title: NJA02402.C09


title: NJA02402.C11


title: NJA02402.D05


title: NJA02402.C12


title: NJA02402.C05


title: NJA02402.C03


title: NJA02402.C06


title: NJA02402.C04


title: NJA02402.B22


title: NJA02402.B24


title: NJA02402.B20


title: NJA02402.B19


title: NJA02402.B15


title: NJA02402.B18


title: NJA02402.B17


title: NJA02402.B14


title: NJA02402.B13


title: NJA02402.B11


title: NJA02402.B10


title: NJA02402.B07


title: NJA02402.B09


title: NJA02402.B08


title: NJA02402.C07


title: NJA02402.B06


title: NJA02402.C02


title: NJA02402.A20


title: NJA02402.B03


title: NJA02402.B04


title: NJA02402.B02


title: NJA02402.C01


title: NJA02402.A19


title: NJA02402.A17


title: NJA02402.A22


title: NJA02402.A15


title: NJA02402.A16


title: NJA02402.A13


title: NJA02402.A12


title: NJA02402.A10


title: NJA02402.A08


title: NJA02402.A18


title: NJA02402.B12


title: NJA02402.A09


title: NJA02402.A14


title: NJA02402.A11


title: NJA02402.A05


title: NJA02402.A06


title: NJA02402.B05


title: NJA02402.B01


title: NJA02402.A04


title: NJA02402.A03


title: NJA02401.P01


title: NJA02402.A02


title: NJA02401.O23


title: NJA02401.O22


title: NJA02401.O20


title: NJA02401.O18


title: NJA02401.O19


title: NJA02401.O21


title: NJA02402.A01


title: NJA02401.O17


title: NJA02401.O15


title: NJA02401.O14


title: NJA02401.O13


title: NJA02401.O12


title: NJA02401.O11


title: NJA02401.O10


title: NJA02401.O09


title: NJA02401.O07


title: NJA02401.O05


title: NJA02401.O06


title: NJA02401.O04


title: NJA02401.O03


title: NJA02401.N23


title: NJA02401.N22


title: NJA02401.N20


title: NJA02401.N19


title: NJA02401.O16


title: NJA02401.N18


title: NJA02401.N17


title: NJA02401.O01


title: NJA02401.N16


title: NJA02401.N15


title: NJA02401.N14


title: NJA02401.N11


title: NJA02401.N06


title: NJA02401.N08


title: NJA02401.N12


title: NJA02401.N10


title: NJA02401.O08


title: NJA02401.O02


title: NJA02401.N07


title: NJA02401.N03


title: NJA02401.N04


title: NJA02401.M23


title: NJA02401.M22


title: NJA02401.M21


title: NJA02401.N21


title: NJA02401.N02


title: NJA02401.M20


title: NJA02401.M19


title: NJA02401.M18


title: NJA02401.M16


title: NJA02401.M15


title: NJA02401.N13


title: NJA02401.M17


title: NJA02401.M12


title: NJA02401.M13


title: NJA02401.M11


title: NJA02401.M10


title: NJA02401.M07


title: NJA02401.M09


title: NJA02401.N09


title: NJA02401.M05


title: NJA02401.M04


title: NJA02401.M03


title: NJA02401.M02


title: NJA02401.M01


title: NJA02401.L24


title: NJA02401.N01


title: NJA02401.L23


title: NJA02401.N05


title: NJA02401.L20


title: NJA02401.L21


title: NJA02401.L19


title: NJA02401.M14


title: NJA02401.L15


title: NJA02401.L14


title: NJA02401.L13


title: NJA02401.L11


title: NJA02401.L12


title: NJA02401.L10


title: NJA02401.M08


title: NJA02401.L08


title: NJA02401.L09


title: NJA02401.M06


title: NJA02401.L05


title: NJA02401.L02


title: NJA02401.L03


title: NJA02401.L04


title: NJA02401.K22


title: NJA02401.K23


title: NJA02401.L01


title: NJA02401.K21


title: NJA02401.K19


title: NJA02401.K20


title: NJA02401.K12


title: NJA02401.K16


title: NJA02401.K14


title: NJA02401.K15


title: NJA02401.K07


title: NJA02401.K09


title: NJA02401.K11


title: NJA02401.K10


title: NJA02401.L07


title: NJA02401.L06


title: NJA02401.K03


title: NJA02401.K05


title: NJA02401.L22


title: NJA02401.K06


title: NJA02401.K01


title: NJA02401.J24


title: NJA02401.K02


title: NJA02401.K13


title: NJA02401.J23


title: NJA02401.J22


title: NJA02401.J21


title: NJA02401.J20


title: NJA02401.J19


title: NJA02401.J18


title: NJA02401.J17


title: NJA02401.J15


title: NJA02401.J16


title: NJA02401.L16


title: NJA02401.J13


title: NJA02401.J11


title: NJA02401.J12


title: NJA02401.J10


title: NJA02401.J09


title: NJA02401.J08


title: NJA02401.J07


title: NJA02401.J04


title: NJA02401.J05


title: NJA02401.J06


title: NJA02401.J02


title: NJA02401.J03


title: NJA02401.J01


title: NJA02401.I22


title: NJA02401.I21


title: NJA02401.I24


title: NJA02401.I20


title: NJA02401.K08


title: NJA02401.J14


title: NJA02401.I18


title: NJA02401.I19


title: NJA02401.I17


title: NJA02401.I14


title: NJA02401.I12


title: NJA02401.I13


title: NJA02401.I11


title: NJA02401.I15


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