title: 218_pos_2

description:
location of sense strand RNA: R2
070717_218_pos_2_S11
08081717_218_pos_2_S11


title: 256_pos_1

status: Public on Apr 01 2021

type: SRA

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

country: USA

institute: Yale University School of Medicine

description:
location of sense strand RNA: R2
070717_256_pos_1_S8
08081717_256_pos_1_S8

library_source: transcriptomic

data_processing:
Paired-end 150nt sequencing on Illumina NextSeq 500
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
Read alignment to homo sapiens sequence GRCh38 with CLCGenomicsServer 8.5.3 with: Mismatchh cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer 8.5.3 as above
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v6.6
Genome_build: HIV-1 (K03455.1, downloaded 24 Sep 2017), Human GRCh38 transcriptome of April 2017
Supplementary_files_format_and_content: FPKMs

molecule: total RNA

organism: Homo sapiens

source_name: Resting CD4+ T cells following ex vivo PMA/ionomycin activation

growth_protocol: Resting CD4+ T cells were isolated from ART-treated, virally suppressed, HIV-1-infected individuals using magnetic negative selection.

extract_protocol:
Cells were sorted by HIV-1 RNA SortSeq into bulk (8-30 cells per sample) or single cells into RNA preserving buffer. RNA was reverse crosslinked with proteinase K and SDS under 50°C for 1 hour. RNA was extracted by Quick-RNA Microprep (Zymo Research) with a built-in on-column DNase treatment step.
Total RNA was extracted followed by a ribosomal RNA depletion step using the SMARTer Stranded Total RNA-Seq Kit v1 (individuals 21, 108, 159, 361) and v2 (individuals 154, 218, 256, 381) - Pico Input Mammalian (Pico v2).
Samples with different barcodes were pooled into one high-output NextSeq 400M 2x150 platform, targeting an estimated reads of 20-40 million per sample.

treatment_protocol: Cells were treated with PMA (1 µg/ml) and ionomycin (1 µM) for 16-18 hours in the presence of enfurvitide to induce HIV-1 RNA expression without causing new rounds of infection in vitro.

tag: disease state

tag: cell type

value: Resting CD4+ T cells

tag: treatment

value: PMA/ionomycin for 16-18 hours under enfurvitide

tag: individual


title: 218_pos_1

description:
location of sense strand RNA: R2
070717_218_pos_1_S10
08081717_218_pos_1_S10


title: 256_pos_2

description:
location of sense strand RNA: R2
070717_256_pos_2_S9
08081717_256_pos_2_S9


title: 154_pos_8

description:
location of sense strand RNA: R2
070717_154_pos_8_S3
08081717_154_pos_8_S3


title: 348_pos_3

description:
location of sense strand RNA: R2
070717_348_pos_3_S15
08081717_348_pos_3_S15


title: RNAseq_Lung_CCNETA_1

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

data_processing:
Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14  to the reference genome UCSC mm10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts in tab-delimited text file

organism: Mus musculus

source_name: Whole tissue, lung

extract_protocol:
RNA was column-extracted using Rneasy Mini kit (qiagen)
RNA-seq libraries were prepared from 100-200 ng high-quality RNA using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: Tet-inducible Ccne1; rtTA (CCNE-TA) mice and rtTA control (TA) mice were treated with doxycyclin (dox) from weaning age (3wks) onwards. Mice were euthanized at 4 months of age and tissues were subjected to RNA-sequencing.

tag: tissue

value: lung

tag: background strain

tag: condition

value: CCNE-TA

tag: age

value: 4 months


title: 154_pos_17

description:
location of sense strand RNA: R2
070717_154_pos_17_S5
08081717_154_pos_17_S5


title: 154_pos_12

description:
location of sense strand RNA: R2
070717_154_pos_12_S4
08081717_154_pos_12_S4


title: 154_pos_18

description:
location of sense strand RNA: R2
070717_154_pos_18_S6
08081717_154_pos_18_S6


title: RNAseq_Liver_TA_3

source_name: Whole tissue, liver

value: liver

value: TA


title: RNAseq_Lung_CCNETA_2


title: 159_pos_9

description:
location of sense strand RNA: R1
159_PI_Pos_9_S9


title: 218_pos_5

description:
location of sense strand RNA: R2
070717_218_pos_5_S13
08081717_218_pos_5_S13


title: RNAseq_Liver_TA_2


title: H3K9me3_ChIPseq_Tex191ESC_Het1IP

city: Edinburgh

first: Ian

last: Adams

address: Crewe Road

department: Genome Regulation

country: United Kingdom

institute: MRC Human Genetics Unit

description: IP DNA

library_source: genomic

data_processing:
Sequences aligned to the mouse mm10 reference genome with Bowtie2 v2.2.6 using settings: -X 500 --sensitive.
The alignment maps were converted into tag directories using HOMER v4.8 makeTagDirectory using settings: -sspe -unique. Peaks were found from the 'IP' sample relative to its 'Input DNA' sample for each replicate using HOMER v4.8 findPeaks using settings: -style histone.
Peaks common to at least two replicates of the same genotype were identified and merged using BEDTools v2.25.0.
Read coverage for the peak intervals was determined using HOMER v4.8 annotatePeaks using settings: -size given.
Read counts were normalised to the number of mapped reads (CPM, counts per million mapped reads) and low coverage peaks (CPM<1 in more than half the IP samples) were removed. Differential enrichment analysis of read counts was performed using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by edgeR that include CPM values in each Sample, logCPMs for all samples, and logFCs, P values and FDR-adjusted P values for the Tex19.1-/- vs Tex19.1+/- comparison.

molecule: genomic DNA

growth_protocol: Mouse embryonic stem cells derived from the parental E14Tg2a line were cultured in gelatinised flasks in Glasgow Modified Eagle’s Media (GMEM), 10% foetal calf serum, 1% non-essential amino acid, 1% sodium pyruvate, 1% penicillin-streptomycin, 1% L-glutamine, 0.001% β-mercaptoethanol, and 0.2% leukaemia inhibitory factor-conditioned media at 37°C in 5% CO2 and passaged using 0.05% trypsin, 0.02% EDTA in PBS.

extract_protocol:
Embryonic stem cells were detached from 70% confluent T75 flasks by scraping and resuspended in ice-cold PBS. Cross-linked ChIP was then performed essentially as previously described (Mortazavi et al., 2006, Genome Res. 16, 1208–1221) by fixing cells with formaldehyde, collecting nuclei from lysates, sonicating then isolating histone-DNA complexes with anti-histone H3K9me3 antibody (Abcam ab8898). Samples of input DNA were removed prior to the addition of anti-histone H3K9me3 antibodies.
Libraries were prepared using an NEBNext Ultra ChIPseq kit and sequenced using an Illumina HiSeq 4000 75PE sequencing system.

tag: strain background

value: Embryonic stem cells

tag: passages

tag: genotype/variation

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: 159_pos_8

description:
location of sense strand RNA: R1
159_PI_Pos_8_S8


title: RNAseq_Liver_TA_1


title: 154_pos_7

description:
location of sense strand RNA: R2
070717_154_pos_7_S2
08081717_154_pos_7_S2


title: 159_pos_7

description:
location of sense strand RNA: R1
159_PI_Pos_7_S7


title: RNAseq_Liver_CCNETA_3


title: RNAseq_Liver_CCNETA_2


title: RNAseq_Liver_CCNETA_1


title: RNAseq_Lung_TA_1


title: 159_pos_bulk_20

description:
control
location of sense strand RNA: R1
159_PI_Pos_20_S3


title: 159_pos_bulk_29

description:
control
location of sense strand RNA: R1
159_PI_Pos_29_S2


title: 159_pos_11

description:
location of sense strand RNA: R1
159_PI_Pos_11_S11


title: RNAseq_Kidney_TA_1

source_name: Whole tissue, kidney

value: kidney


title: RNAseq_Kidney_TA_2


title: 361_pos_bulk

description:
control
location of sense strand RNA: R1
361PI_pos_S3


title: 159_pos_12

description:
location of sense strand RNA: R1
159_PI_Pos_12_S12


title: 159_pos_10

description:
location of sense strand RNA: R1
159_PI_Pos_10_S10


title: RNAseq_Kidney_CCNETA_2


title: RNAseq_Kidney_TA_3


title: TET3

city: New York

first: Daniel

middle: Fernando

last: Zegarra-Ruiz

state: NY

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

description: SFB-colonized mice

data_processing:
The output data (FASTQ files) are mapped to the target genome using the rnaStar aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done.
The expression count matrix from the mapped reads was computed using HTSeq (www-huber.embl.de/users/anders/HTSeq) and processed using DESeq (www-huber.embl.de/users/anders/DESeq) to normalize the full dataset and analyze differential expression between sample groups.
Genome_build: mm10
Supplementary_files_format_and_content: excel file includes a matrix table with normalized gene abundance for each sample

source_name: Thymus CD4 single positive cells

extract_protocol:
Tet+ and Tet- CD4 single positive thymic cells were sorted into Trizol LS.RNA was extracted using RNeasy mini kit (Qiagen) per manufacturer instructions. After ribogreen quantification and quality control by Agilent BioAnalyzer, total RNA was amplified using the SMART-seq V4 (Clonetech) ultralow input RNA kit for sequencing (12 cycles of amplification for 2–10 ng of total RNA).
10 ng of amplified cDNA was used to prepare Illumina Hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR. Samples were barcoded and run on a Hiseq 4000, in a 50-bp/50-bp paired-end run, using the TruSeq SBS Kit v3 (Illumina).

treatment_protocol: Mice from the TET group were colonized with SFB at weaning. Two weeks later SFB-Tetramer+ CD4 thymic cells were sorted into Trizol LS and compared with age-matched CD4 thymic cells from CTRL mice for RNA-seq.

tag: strain

value: Thymus

value: 5 weeks of age


title: K1092SAL

city: Seattle

first: Justin

last: Norton

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality as well as those with better alignment to mm9 were omitted prior to alignment to hg19 using STAR v2.5.2a. Counts were generated from STAR alignments at the gene-level using featureCounts v1.6.0.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts genreated at the gene-level by featureCounts.

source_name: human SCLC derived PDX

extract_protocol:
Tumor tissue was lysed in TRIzol reagent with RNA isolated following manufacturers instructions.
RNA-seq libraries were prepared using theNEBNext Ultra RNA Library Prep Kit for Illumina (catalog E7530L). Briefly, 500 ng total RNA was used to isolate mRNA with the NEB Next Oligo dT Magnetic Isolation Module (catalog E7490L). The isolated mRNA undergoes fragmentation, priming, cDNA synthesis and end repair/dA-tail. Individual index primers for multiplexing were added during PCR library enrichment after adaptor ligation.

value: PDX

tag: tumor type

value: human SCLC

tag: pdx

value: Vehicle


title: RNAseq_Kidney_CCNETA_3


title: RNAseq_Kidney_CCNETA_1


title: K1082SAL


title: TET2

description: SFB-colonized mice


title: 21_pos_bulk

description:
control
location of sense strand RNA: R1
21PI_pos_S1


title: 108_pos_bulk

description:
control
location of sense strand RNA: R1
108PI_pos_S2


title: K1070SAL


title: TET1

description: SFB-colonized mice


title: K1067SAL


title: 159_pos_bulk_30

description:
control
location of sense strand RNA: R1
159_PI_Pos_30_S1


title: K1079MLN


title: Pt.CrAT.Het_2_5

city: Baton Rouge

first: Krisztian

last: Stadler

state: LA

address: 6400 Perkins Rd

institute: Pennington Biomedical Research Center

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, 3.5.2(2018-12-2), Rstudio V1.2.1511 and biomaRt V2.38.0
DESeq2  V1.22.2 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Genome_build: Rnor_6.0

source_name: kidney cortex

extract_protocol:
RNA was isolated by the TRIzol method.
Lexogen - QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina

tag: cre promoter

value: Ggt

tag: Sex

value: female

tag: genotype

value: Pt-CrAT Het


title: fl.plus_2054

value: fl/fl


title: Pt.CrAT.Het_1_16


title: K1075MLN


title: fl.plus_1_18


title: K1069MLN


title: fl.plus_1_19

value: male


title: K1076MLN


title: Pt.CrAT.Het_1_07


title: Pt.CrAT.Het_1_02


title: Pt.CrAT.Het_1_10


title: Pt.CrAT.Het_1_03


title: H9270vehicle

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality as well as those with better alignment to mm9 were omitted prior to alignment to hg19 using TopHat v2.0.12. Counts were generated from Tophat alignments at the gene-level employing the "intersection-strict" overlap mode in HTSeq v0.6.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include counts genreated by HTSeq count

source_name: human extrapulmonary small cell carcinoma derived PDX

value: extrapulmonary small cell carcinoma


title: H9507vehicle


title: fl.fl_3_21


title: H9506vehicle


title: H9271vehicle


title: H9509MLN


title: Pt.CrAT.Het_3_10


title: H9266vehicle


title: H9508MLN


title: Pt.CrAT.Het_3_6


title: K3325MLN


title: H9272MLN


title: H9265MLN


title: fl.fl_3_3


title: Pt.CrAT.Het_2_19


title: H9263MLN


title: Pt.CrAT.Het_2_18


title: H8828vehicle


title: H8827vehicle


title: BMDMs LPS/IFN-g WT rep4 [WT_treated_4]

city: Indianapolis

first: Mircea

last: Ivan

state: IN

address: 980 W. Walnut St.

department: HEMATOLOGY/ONCOLOGY

institute: Indiana University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic version 0.38 with parameters LEADING:20 TRAILING:20 SLIDINGWINDOW:3:20 MINLEN:20, then mapped to GRCm38.p6 using STAR version STAR_2.5.2b with parameters --outFilterMultimapNmax 20 --seedSearchStartLmax 16 --twopassMode Basic
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes using featureCounts tool of subread package (version 2.0.0) (Liao et al. 2014) with parameters "-s 2 -p -B -C" using Gencode vM17 as the annotation
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Raw counts of reads mapped to genes using Gencode M17 as the annotation

source_name: BMDMs LPS/IFN-g WT

growth_protocol: Macrophages were derived from BM precursors from WT and miR-210 KO mice. Briefly, BM precursor (up to 10 x106 cells) were cultured in a volume of 6 ml in a 10 cm Petri dish (non-treated culture dishes, bacterial grade) in DMEM high glucose (41965039 – Gibco) supplemented with 20% FBS, 30% L929 conditioned medium as a source of M-CSF, 25 mM HEPES, 2 mM L- Glutamine and Pen/Strep. After 3 days of culture, an additional 3 ml of differentiation medium was added. At day 7, bone marrow-derived macrophages (BMDMs) were detached with ice cold PBS. The resulting BMDMs were plated for 42 hours with LPS (100 ng/ml) + IFN-γ (20 ng/ml) in in DMEM high glucose (41965039 – Gibco), 10% FBS, 2 mM L-Glutamine and Pen/Strep.

extract_protocol:
QIAzol lysis reagent was added to the plates in order to obtain cell lysates. After, total RNA was extracted using miRNeasy kit following manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LPS (100 ng/ml) + IFN-γ (20 ng/ml)

value: wild type

tag: cell type

value: murine bone marrow-derived macrophages (BMDMs)

value: LPS (100 ng/ml) + IFN-g (20 ng/ml)


title: BMDMs LPS/IFN-g WT rep2 [WT_treated_2]

tag: treatment


title: BMDMs LPS/IFN-g WT rep3 [WT_treated_3]


title: H8820vehicle


title: H8821vehicle


title: Pt.CrAT.Het_3_11


title: H8829MLN


title: fl.fl_3_8


title: H8825MLN


title: BMDMs untreated WT rep3 [WT_notreated_3]

source_name: BMDMs untreated WT

value: untreated


title: BMDMs LPS/IFN-g WT rep1 [WT_treated_1]


title: BMDMs untreated WT rep1 [WT_notreated_1]


title: BMDMs untreated WT rep2 [WT_notreated_2]


title: H8826MLN


title: BMDMs LPS/IFN-g KO rep4 [KO_treated_4]

source_name: BMDMs LPS/IFN-g KO

value: miR-210 deletion


title: BMDMs LPS/IFN-g KO rep2 [KO_treated_2]


title: BMDMs LPS/IFN-g KO rep3 [KO_treated_3]


title: HeLa cells, Cisplatin 3

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

data_processing:
Quality check by FastQC
Adapter trimming by Cutadapt
Ribosomal RNA filtering by sortMeRNA
Reference genome alignment with STAR-aligner
Counting of mapped reads with featureCounts.  The counting was performed with ensembl transcript ID's and by allowing counting of multiple mapped reads.
Differential expression analysis with DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: counts, log2FoldChange

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in RPMI medium supplemented with 10% FBS and 1 % penicillin-streptomycin

extract_protocol:
Total RNA was extracted by TRIzol Reagent
RNA samples were subjected to DNAse treatment

treatment_protocol: Hela cells were treated with 80 uM cisplatin and 0.1 % DMSO for 16 h

tag: cell line

value: HeLa

value: cervix epithelial

value: Cisplatin 80 uM 16h


title: BMDMs untreated WT rep4 [WT_notreated_4]


title: HeLa cells, Cisplatin 2


title: H8822MLN

tag: tissue

value: PDX


title: HeLa cells, Cisplatin 1


title: BMDMs LPS/IFN-g KO rep1 [KO_treated_1]


title: HeLa cells, DMSO 3


title: BMDMs untreated KO rep4 [KO_notreated_4]

source_name: BMDMs untreated KO


title: HeLa cells, DMSO 2


title: H8733vehicle

value: human SCLC


title: BMDMs untreated KO rep2 [KO_notreated_2]


title: BMDMs untreated KO rep3 [KO_notreated_3]


title: HeLa cells, DMSO 1


title: BMDMs untreated KO rep1 [KO_notreated_1]


title: H8823MLN


title: LuCaP_173_2_s2_ET292 [173_2_s2_ET292]

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

institute: Fred Hutchinson Cancer Center

description: LuCaP 173.2 PDX tumor

data_processing:
PDX Sequencing reads were mapped to the hg38 human and mm10 mouse genomes using STAR.v2.7.3a. Sequences aligning to the mouse genome deriving from potential contamination with mouse tissue were removed from the analysis using XenofiltR . PrEC Cell line sequencing reads were mapped to the hg38 human genome only using STAR.v2.7.3a.
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: LuCaP 173.2 PDX tumor

growth_protocol: LuCaP xenograft lines were established from specimens acquired at either radical prostatectomy or at autopsy, implanted, and maintained by serial passage in intact immune compromised male mice (PMID 28156002.)

extract_protocol:
Total RNA was isolated from flash frozen LuCaP xenograft tissue with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) utilizing the manufacturer’s recommended in solution DNase digestion (Qiagen).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 or NovaSeq generating 50 bp paired end reads.

tag: gender

value: prostate cancer


title: LuCaP_173_1_s6_ET289 [173_1_s6_ET289]

description: LuCaP 173.1 PDX tumor

source_name: LuCaP 173.1 PDX tumor


title: LuCaP_173_2_s2_ET223 [173_2_s2_ET223]

description: LuCaP 173.2 PDX tumor


title: LuCaP_173_1_s6_ET222 [173_1_s6_ET222]

description: LuCaP 173.1 PDX tumor


title: Aged_ENR6

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

country: Germany

institute: German Center for Neurodegenerative Diseases (DZNE)

description: Methylated cytosines converted to uracil by treatment with sodium bisulfite

data_processing:
Fastq reads were trimmed using Trim Galore 0.4.0 and the function Cutadapt 1.8.1. To remove cytosines that were filled in during ends preparation, an additional 2 bp were cut off from every sequence with detected adapter.
Trimmed reads were mapped against mm10 using Bismark 0.16.1
Base calling was performed using MethylKit 1.5.2.
Genome_build: mm10
Supplementary_files_format_and_content: Methylation percentages of cytosines for all samples. Comma-delimited text file exported from Methylkit.

source_name: Dentate gyrus

growth_protocol: Mice housed in 12:12 light:dark cycle under SPF conditions and given ad libitum access to mouse chow and water.

extract_protocol:
Dentate gyrus was micro-dissected from the brain.
Genomic DNA was isolated using the QIAamp DNA Micro Kit (QIAGEN) following the manufacturer’s manuals. RRBS libraries were prepared using the Premium RRBS Kit (Diagenode) and purified twice using Agencourt AMPure XP beads (Beckman Coulter; 1X bead volume). Quality and concentration of RRBS libraries were determined using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical) and a fragment analyzer with capillary size of 33 cm (Advanced Analytical).

treatment_protocol: Mice were housed in either standard cages or in an enriched environment.

value: Dentate gyrus

value: 17 months

value: Female

tag: housing

value: Environmental enrichment


title: Aged_ENR5

tag: age


title: Aged_ENR4


title: Aged_ENR7


title: LuCaP_147CR_s3 [147CR_s3]

description: LuCaP 147CR PDX tumor

source_name: LuCaP 147CR PDX tumor

value: male


title: LuCaP_145_2_p9s26n3 [145_2_p9s26n3]

description: LuCaP 145.2 PDX tumor

source_name: LuCaP 145.2 PDX tumor


title: Aged_ENR3


title: LuCaP_147CR_s23n2_ET2390 [147CR_s23n2_ET2390]

description: LuCaP 147CR PDX tumor


title: Aged_ENR2


title: LuCaP_145_1_p2s18n5 [145_1_p2s18n5]

description: LuCaP 145.1 PDX tumor

source_name: LuCaP 145.1 PDX tumor


title: LuCaP_145_2_p9s25n3 [145_2_p9s25n3]

description: LuCaP 145.2 PDX tumor


title: Aged_STD7

value: Standard housing


title: Aged_STD6


title: LuCaP_145_1_p25s19n5 [145_1_p25s19n5]

description: LuCaP 145.1 PDX tumor


title: LuCaP_136CR_s4_2 [136CR_s4_2]

description: LuCaP 136CR PDX tumor

source_name: LuCaP 136CR PDX tumor


title: Aged_ENR8


title: Aged_STD5


title: LuCaP_136CR_s4_1 [136CR_s4_1]

description: LuCaP 136CR PDX tumor


title: Aged_STD4


title: LuCaP_96CR_s41n1_ET2411 [96CR_s41n1_ET2411]

description: LuCaP 96CR PDX tumor

source_name: LuCaP 96CR PDX tumor


title: LuCaP_105CR_s11_ET78 [105CR_s11_ET78]

description: LuCaP 105CR PDX tumor

source_name: LuCaP 105CR PDX tumor


title: Aged_STD8


title: LuCaP_105CR_s7 [105CR_s7]

description: LuCaP 105CR PDX tumor


title: Aged_STD2


title: LuCaP_96CR_s40n1_ET1784 [96CR_s40n1_ET1784]

description: LuCaP 96CR PDX tumor


title: LuCaP_96CR_s39n1_ET1173 [96CR_s39n1_ET1173]

description: LuCaP 96CR PDX tumor


title: Aged_STD1


title: Aged_STD3


title: LuCaP_93_p39s31n6 [93_p39s31n6]

description: LuCaP 93 PDX tumor

source_name: LuCaP 93 PDX tumor


title: Young_STD7

value: 3 months


title: LuCaP_93_p39s22n6 [93_p39s22n6]

description: LuCaP 93 PDX tumor


title: LuCaP_81CR_s5 [81CR_s5]

description: LuCaP 81CR PDX tumor

source_name: LuCaP 81CR PDX tumor


title: Young_STD8


title: Aged_ENR1


title: Young_STD5


title: Young_STD6


title: Young_STD2


title: LuCaP_77CR_s18n2_ET232 [77CR_s18n2_ET232]

description: LuCaP 77CR PDX tumor

source_name: LuCaP 77CR PDX tumor


title: LuCaP_77CR_s18n2_ET414 [77CR_s18n2_ET414]

description: LuCaP 77CR PDX tumor


title: Young_STD4


title: LuCaP_78CR_s2 [78CR_s2]

description: LuCaP 78CR PDX tumor

source_name: LuCaP 78CR PDX tumor


title: Young_STD3


title: LuCaP_70CR_s3 [70CR_s3]

description: LuCaP 70CR PDX tumor

source_name: LuCaP 70CR PDX tumor


title: LuCaP_73CR_s4n1_020713 [73CR_s4n1_020713]

description: LuCaP 73CR PDX tumor

source_name: LuCaP 73CR PDX tumor


title: ATAC-Seq WT2

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

institute: University of Duesseldorf

description: For ATAC-Seq, BM-derived pDCs (CD3-CD19-CD11c+CD11blowB220+SiglecH+mPDCA1+) were FACS purified using FACS Aria III (BD).

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cut off of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include average values for each sample and one file containing the peak values and associated genes for each merged region.

source_name: bone marrow

growth_protocol: BM-derived Flt3-L cultured cDCs and pDCs were generated as previously described (Scheu et al, PNAS 2008).

extract_protocol: Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: The pDCs were left untreated or stimulated with 1µM CpG 2216 (Tib Molbiol, Nr. 930507l) complexed to transfection reagent DOTAP (Roche) for 2 hours.

value: pDC

tag: condition

value: naïve

value: wild type


title: ATAC-Seq WT2CpG2h

value: CpG 2h


title: ATAC-Seq WT1CpG2h


title: LuCaP_35CR_s59n1 [35CR_s59n1]

description: LuCaP 35CR PDX tumor

source_name: LuCaP 35CR PDX tumor


title: LuCaP_73CR_s9n1_ET2068 [73CR_s9n1_ET2068]

description: LuCaP 73CR PDX tumor


title: LuCaP_70CR_s6 [70CR_s6]

description: LuCaP 70CR PDX tumor


title: LuCaP_35CR_s54 [35CR_s54]

description: LuCaP 35CR PDX tumor


title: LuCaP_81CR_s9_ET1092 [81CR_s9_ET1092]

description: LuCaP 81CR PDX tumor


title: ATAC-Seq WT1


title: LuCaP_35CR_s37 [35CR_s37]

description: LuCaP 35CR PDX tumor


title: LuCaP_78CR_s5 [78CR_s5]

description: LuCaP 78CR PDX tumor


title: Apc fl/+ tumour - 3

city: Glasgow

first: Andrew

last: Campbell

address: Switchback Road

institute: CRUK Beatson Institute

description: Adenoma grown from small intestinal tissue subjected to tamoxifen induced genetic recombination in vivo

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Matrix of raw counts

source_name: Small Intestine

extract_protocol:
RNA extraction perfomed with Qiagen RNeasy kit using Qiagen protocols
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

treatment_protocol: Where stated, antibiotic treatment (ampicillin (1g/L) neomycin trisulphate (1g/L) vancomycin (500mg/L) metronidazole (1g/L)) was given in drinking water from the first day after tamoxifen injection, and was refreshed three times a week. Sulindac treatment (0.4g/L) was given in drinking water from the first day after tamoxifen injection for 14 days, before switching to normal drinking water.

value: VilCreER+ Apcfl/+

tag: sample type

value: Primary Tumour

tag: genetic background

tag: drug treatment


title: Apc fl/+ tumour - 4


title: Apc fl/+ tumour - 5


title: Young_STD1

tag: strain


title: WT SI - 3

description: Small intestinal tissue subjected to tamoxifen induced genetic recombination in vivo

value: VilCreER+

value: Tissue sample


title: LuCaP_23.1CR3_s7_ET1838 [23.1CR3_s7_ET1838]

description: LuCaP 23.1CR3 PDX tumor

source_name: LuCaP 23.1CR3 PDX tumor


title: Apc fl/+ tumour - 1


title: Apc fl/+ tumour - 2


title: LuCaP_23.1CR3_s10_ET2785 [23.1CR3_s10_ET2785]

description: LuCaP 23.1CR3 PDX tumor


title: SkCaP-1 [SkCaP_71R]

description: SkCaP-1 PDX tumor

source_name: SkCaP-1 PDX tumor

growth_protocol: Triple immune‐deficient NSG (i.e. NOD.Cg‐PrkdcScidIl2rgtm1Wji/Szj), adult (>8 week old) male mice obtained from the Sidney Kimmel Comprehensive Cancer Center (SKCCC) Animal Core Facility were used for xenografting. For each line tested, 100 μl of sterile saline containing 2 x 106 cancer cells was mixed at 4˚C with 100 μl of Matrigel obtained from BD Biosciences and then the mixture inoculated subcutaneously in the flank of 5 intact and 5 castrated adult male NSG mice.

extract_protocol:
Total RNA was extracted from flash-frozen xenograft tissue using the Qiagen RNeasy Kit, (Qiagen Inc.), according to the manufacturer's protocol. On-column DNase digestion was performed.
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on the Illumina HiSeq 2500 or NovaSeq generating 50 bp paired end reads.


title: WT SI - 2


title: WT SI - 1


title: SkCaP-1R [SkCaPcast_448c]

description: SkCaP-1R PDX tumor

source_name: SkCaP-1R PDX tumor


title: Day 30 Wild type – 4

description: Proximal colon tissue subjected to tamoxifen induced genetic recombination in vivo

source_name: Proximal colon

value: Day30 post-induction tissue sample

value: Mixed C57BL/6J N6


title: SkCaP-1 [SkCap_479]

description: SkCaP-1 PDX tumor

value: prostate cancer


title: Day 30 Wild type – 2


title: Day 30 Wild type – 3


title: PLNCaP-1 [PLNCaP_51L_v2]

description: PLNCaP-1 PDX tumor

source_name: PLNCaP-1 PDX tumor


title: PC-82 [PC-82_95]

description: PC-82 PDX tumor

source_name: PC-82 PDX tumor


title: Day 30 Alk5 fl/fl – 3

value: VilCreER+ Alk5fl/fl


title: Day 30 Wild type – 1


title: Day 30 Alk5 fl/fl – 4


title: LuCaP_23.1CR3_s9_ET2651 [23.1CR3_s9_ET2651]

description: LuCaP 23.1CR3 PDX tumor


title: LvCaP-3 [LVCaP-3_48]

description: LvCaP-3 PDX tumor

source_name: LvCaP-3 PDX tumor


title: SkCaP-1R [SkCaPcast_665c_v2]

description: SkCaP-1R PDX tumor


title: LvCaP-2 [LVCaP-2_485]

description: LvCaP-2 PDX tumor

source_name: LvCaP-2 PDX tumor


title: LvCaP-2R [LVCaP-2cast_518R]

description: LvCaP-2R PDX tumor

source_name: LvCaP-2R PDX tumor


title: LvCaP-1R [LVCaP-1cast_45i]

description: LvCaP-1R PDX tumor

source_name: LvCaP-1R PDX tumor


title: LvCaP-2 [LVCaP-2_413]

description: LvCaP-2 PDX tumor


title: LvCaP-2R [LVCaP-2cast_450c]

description: LvCaP-2R PDX tumor


title: Day 30 Alk5 fl/fl sulindac – 3

value: Sulindac (0.4g/L)


title: LvCaP-1 [LVCaP-1_428]

description: LvCaP-1 PDX tumor

source_name: LvCaP-1 PDX tumor


title: Day 30 Alk5 fl/fl sulindac – 2


title: Day 30 Alk5 fl/fl – 1


title: LNCaP-95 [LN95_214]

description: LNCaP-95 PDX tumor

source_name: LNCaP-95 PDX tumor


title: Day 30 Alk5 fl/fl sulindac – 1


title: PLNCaP-1 [PLNCaP_52R]

description: PLNCaP-1 PDX tumor


title: LvCaP-1 [LVcaP-1_414]

description: LvCaP-1 PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl antibiotic – 3

value: VilCreER+ BrafV600E/+ Alk5fl/fl

value: ampicillin (1g/L) neomycin trisulphate (1g/L) vancomycin (500mg/L) metronidazole (1g/L)


title: Day 30 Braf V600E/+ Alk5 fl/fl antibiotic – 4


title: LvCaP-3 [LVCaP-3_48_v2]

description: LvCaP-3 PDX tumor

value: male


title: LgCaP-1 [LGCaP-1_50R]

description: LgCaP-1 PDX tumor

source_name: LgCaP-1 PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl antibiotic – 5


title: LgCaP-1 [LGCaP-1_49R]

description: LgCaP-1 PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl antibiotic – 2


title: Day 30 Alk5 fl/fl – 2


title: CWR22-RH [CWR-H_65]

description: CWR22-RH PDX tumor

source_name: CWR22-RH PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl antibiotic – 1


title: Day 30 Alk5 fl/fl sulindac – 4


title: CWR22 [CWR22_Px7]

description: CWR22 PDX tumor

source_name: CWR22 PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl – 5


title: CWR22-RH [CWR-H_563]

description: CWR22-RH PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl – 4


title: CWR22 [CWR22_Px2]

description: CWR22 PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl – 3


title: BCaP-1 [BCaP_502]

description: BCaP-1 PDX tumor

source_name: BCaP-1 PDX tumor


title: Day 30 Braf V600E/+ Alk5 fl/fl – 2


title: WT tiss – 3


title: 160701_SND393_B_L002_3_GDU-39

data_processing:
3’ adapter removal by Trimmomatic
Mapping to the genome by Bowtie, Tophat and Samtools
Quantification, expression estimation, normalization and comparison via Cufflinks. Transcript abundances was measured in FPKM
Genome_build: Ensembl GRCh37

source_name: HeLa cells

extract_protocol:
Total RNA was extracted by TRIzol Reagent
RNA samples were subjected to DNAse treatment and poly(A) enrichment

treatment_protocol: Hela cells were treated with 40 nM Negative GapmeR and DR5-AS GapmeR for 72h.

value: HeLa

value: cervix epithelial

tag: passages

value: DR5-AS GapmeR


title: WT tiss – 2


title: 160701_SND393_B_L002_3_GDU-37


title: WT tiss – 1


title: Braf V600E/+ Alk5 fl/fl -4


title: Braf V600E/+ Alk5 fl/fl -3


title: WT - 6

source_name: Small Intestine

value: Day4 post-induction tissue sample


title: Braf V600E/+ Alk5 fl/fl -2


title: Braf V600E/+ Alk5 fl/fl -1


title: PROseq_K562_s_pC40_rep2

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

description:
3' barcode:
TCAAGTC
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC40_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC40_BRs_pl.bigWig

data_processing:
Library strategy: PRO-seq
Paired-end sequencing data is provided, but please note that only read1 was analysed for each sample in this study. These analyses follow the same logic as for related samples GSE127844 and GSE128160 which were SE75 sequenced.
Samples from replicate 2 were sorted into individual files using barcode splitter (http://hannonlab.cshl.edu/fastx_toolkit/)
The reads were collapsed using fastx collapser (http://hannonlab.cshl.edu/fastx_toolkit/).
The 3' UMIs (rep1), 3' barcodes (rep2), as well as the 5' UMIs (reps 1 and 2) were removed using fastx trimmer (http://hannonlab.cshl.edu/fastx_toolkit/)
Adapters (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) were removed using cutadapt (Marcel, 2011)
Complements of reads were generated using fastx (http://hannonlab.cshl.edu/fastx_toolkit/).
The reads were aligned to combined hg19-dm3 genome using Bowtie2 (Langmead et al., 2009).
Reads that uniquely mapped to hg19 were processed to bed, bedgraph and bigWig files. The number of uniquely mapping reads to Drosophila genome (whole-genome invariant spike-in) was used for sample normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized and replicate-combined bigWig files. Since PRO-seq reports positions of transcription complexes strand-specifically, the plus strand and minus strand are given in separate bigWig files.

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma), containing 10% fetal calf serum, 2 mM L-glutamate, 100 μg/ml streptomycin, and 100 U/ml penicillin. The cells were grown below 5x10^5 cells/ml confluency.

extract_protocol:
After treatments, the cells were harvested by centrifugation, and washed twice with PBS. Chromatin was isolated as in Chu et al., 2018, Nature Genetics, 50: 1553–1564 and run-on reactions performed with biotinylated nucleotides as described by Kwak et al., 2013, Science, 339:950-953. The run-on reaction was conducted in the presence of chromatin from S2 cells, which provides an invariant whole-genome spike-in control between samples.
The libraries were generated using TruSeq small-RNA adaptors. Half of the libraries were amplified for 12 cycles, after which the libraries were purified and size-selected with Ampure XP beads. Distinct libraries were combined for HiSeq (Illumina, Novogene) sequencing.

treatment_protocol: Preconditioning of K562 cells was conducted by submerging the cells into a 42°C heat bath for 1-hour, and allowing the cells to recover 48h in a 37°C incubator. Kinetics of transcriptional response to an additional heat shock was measured by collecting the cells at 12.5-minute, 25-minute, and 40-minute heat shock time points. To measure rapid kinetics, the additional  heat shock was conducted by centrifuging the cells, removing the supernatant and adding preconditioned media (cell-free media isolated from the same culture right before the treatment) that was prewarmed to 42C. Once suspended into the prewarmed preconditioned media, the cell suspension was placed to 42C water bath for the indicated time point. Cells with no (additional) heat shock treatment (uC0 and p0) were subjected to the same conditions, but 37C preconditioned media was used and the cells maintained at 37C.

tag: preconditioning

value: 1h heat shock at 42°C water bath, followed by 48 h recovery at 37 °C

tag: heat shock (additional to preconditioning)

value: 40 min at 42°C water bath (initiated with prewarmed preconditioned media)

tag: sequenced molecule

value: nascent RNA


title: PROseq_K562_s_pC40_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC40_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC40_BRs_pl.bigWig


title: PROseq_K562_s_pC25_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC25_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC25_BRs_pl.bigWig

value: 25 min at 42°C water bath (initiated with prewarmed preconditioned media)


title: WT - 5

tag: genotype

value: VilCreER+


title: WT - 1


title: WT - 3


title: WT - 4


title: WT - 2


title: PROseq_K562_s_pC12p5_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC12p5_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC12p5_BRs_pl.bigWig

value: 12.5 min at 42°C water bath (initiated with prewarmed preconditioned media)


title: Day 30 Braf V600E/+ Alk5 fl/fl – 1

value: Day30 post-induction tissue sample

value: Mixed C57BL/6J N6


title: PROseq_K562_s_pC0_rep2

description:
3' barcode:
CACTGTC
3' UMI:
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC0_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC0_BRs_pl.bigWig

value: no additional heat shock  applied


title: APCfl/fl - 10

value: VilCreER+ APCfl/fl


title: PROseq_K562_s_pC0_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC0_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC0_BRs_pl.bigWig

value: no additional heat shock applied


title: 160701_SND393_B_L002_3_GDU-38

tag: cell type


title: PROseq_K562_s_pC12p5_rep2

description:
3' barcode:
ATTGGCC
3' UMI:
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC12p5_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC12p5_BRs_pl.bigWig


title: PROseq_K562_s_uC40_rep2

description:
3' barcode:
TGGTCAC
3' UMI:
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC40_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC40_BRs_pl.bigWig


title: BCaP-1 [BCaP_497i]

description: BCaP-1 PDX tumor

value: prostate cancer


title: APCfl/fl - 9


title: APCfl/fl - 8


title: PROseq_K562_s_uC40_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC40_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC40_BRs_pl.bigWig


title: APCfl/fl - 6


title: PROseq_K562_s_uC25_rep2

description:
3' barcode:
GCCTAAC
3' UMI:
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC25_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC25_BRs_pl.bigWig


title: PROseq_K562_s_uC25_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC25_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC25_BRs_pl.bigWig


title: APCfl/fl - 7


title: PROseq_K562_s_uC12p5_rep2

description:
3' barcode:
ACATCGC
3' UMI:
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC12p5_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC12p5_BRs_pl.bigWig


title: APCfl/fl - 4


title: APCfl/fl - 3


title: PROseq_K562_s_uC0_rep2

description:
3' barcode:
CGTGATC
3' UMI:
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC0_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC0_BRs_pl.bigWig

value: no heat stress applied


title: APCfl/fl - 5


title: PROseq_K562_s_uC12p5_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC12p5_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC12p5_BRs_pl.bigWig


title: APCfl/fl - 2


title: PROseq_K562_s_pC25_rep2

description:
3' barcode:
CTCTACC
3' UMI:
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_pC25_BRs_mn.bigWig
Normalized_PROseq_K562_s_pC25_BRs_pl.bigWig


title: PROseq_K562_s_uC0_rep1

description:
3' barcode:
3' UMI:
6nt + C (7 nt in total)
5' UMI:
6nt + C (7 nt in total)
Normalized_PROseq_K562_s_uC0_BRs_mn.bigWig
Normalized_PROseq_K562_s_uC0_BRs_pl.bigWig


title: APCfl/fl - 1

description: Small intestinal tissue subjected to tamoxifen induced genetic recombination in vivo


title: EdUseq-HU of LY2090314-treated BRCA1-/- RPE1 cells 20 h after mitotic shake-off

city: Paris

first: Emilia

last: Puig Lombardi

address: 24 Boulevard du Montparnasse

department: INSERM UMR1163 - Bioinformatics Core

country: France

institute: Institut Imagine

data_processing:
Library strategy: EdUseq-HU
Sequence reads were aligned to the masked human genome assembly hg19 using BWA
Only reads with base quality scores ≥ 60 were retained
Each chromosome (1-22) was split into 10 kb bins and the number of reads for each bin was calculated
Sigma (σ) values for each genomic bin were calculated (where sigma is the normalized number of sequence reads per bin, divided by its standard deviation)
Genome_build: hg19 (masked)
Supplementary_files_format_and_content: CSV files containing sigma (σ) values for each chromosome and each genomic bin, formatted as follows: 25,000 lines correspond to 25,000 bins of 10 kb each; each column contains data (for chr 1-22) as: chr_1_variable_1, chr_1_variable_2, chr_1_variable_n,, chr_2_variable_1, chr_2_variable_2, chr_2_variable_n,, etc. These files can be directly used for visualization (as described in Macheret & Halazonetis, 2019, PMID: 30487655).

source_name: RPE1 cell line

extract_protocol:
Genomic DNA was sonicated to a size range of 100–500 bp with a bioruptor sonicator. EdU-labelled DNA fragments were then isolated using Dynabeads MyOne streptavidin C1, as follows: for each sample, the beads were washed 3 times with Binding and Washing Buffer 1× (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCL, 0.5% Tween-20) using a magnet. After washing, the beads were resuspended to twice the original volume with Binding and Washing Buffer 2×, mixed with an equal volume of sonicated EdU-labelled DNA and incubated for 15 min on a rotating wheel at room temperature. The beads were then washed three times with Binding and Washing Buffer 1× and once with TE (10 mM Tris- HCl pH 8, 1 mM EDTA) using the magnet. The EdU-labelled DNA was eluted by incubating the streptavidin beads with 2% β-mercaptoethanol for 1 h at room temperature.
The eluted DNA for EdUseq-HU was directly used for library preparation using the TruSeq ChIP Sample Prep Kit (Illumina, Cat. No. IP-202-1012)

tag: brca1/2 status

tag: treatment


title: wt_2

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

data_processing:
CTSS finding based on scripts available on Akahashi, H., Lassmann, T., Murata, M. et al. 5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc 7, 542–561 (2012).
Average CTSS were acquired by awk '{ total += $4; count++ } END { print total/count }'
CTSS were filtered by tag>8 by awk '{ if ($4 >= 8) { print } }'
CTSS bed files are converted to bw files by bedtools 2.29.2 and ucsc-bedgraphtobigwig 377
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files showing distribution of CTSS with tag>8.

source_name: Lung smooth muscle cells

extract_protocol:
RNA was isolated from sorted smooth muscle cells using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
CAGE library preparation, sequencing, mapping and motif discovery analysis were performed by DNAFORM (Life Science Research Center, Japan).
RNA quality was assessed by Bioanalyzer (Agilent) to ensure a RIN (RNA integrity number) >7.0, and A260/280 and 260/230 ratios >1.7. First strand cDNA was transcribed to the 5’ end of capped RNAs, attached to CAGE “bar code” tags.

value: WT

value: Lung smooth muscle cells


title: EdUseq-HU of DMSO-treated BRCA1+/+ RPE1 cells 10 h after mitotic shake-off

tag: cell line

value: DMSO


title: EdUseq-HU of DMSO-treated BRCA1-/- RPE1 cells 20 h after mitotic shake-off


title: EdUseq-HU of LY2090314-treated BRCA1+/+ RPE1 cells 10 h after mitotic shake-off


title: wt_1


title: EdUseq-HU/release of LY2090314-treated H1299 BRCA2-deficient cells 16 h HU arrest and release for 2 h

source_name: H1299 cell line


title: BalbC Female #1

city: Louisville

first: Michele

middle: M.

last: Kosiewicz

state: Kentucky

address: 505 S. Hancock St., Room 609

department: Microbiology & Immunology

institute: University of Louisville

data_processing:
Base calling was done with Illumina NextSeq Real Time Analysis (version 2.0) and reads were trimmed for adapter sequences
Quality control of reads was done with FastQC (version 0.10.1)
Reads were aligned to the Mus musculus genome (mm10 reference assembly) using STAR (version 2.6)
Read counts were normalized using the Relative Log Expression method
Filtered out genes with less than 20 cumulative read counts among all samples
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Splenic macrophages

extract_protocol:
Spleens were diced and digested with collagenase (Sigma Type VIII) and CD11b+F4/80+, cells were sorted by FACS, RNA was extracted using the Qiagen Rneasy plus mini kit (#74134), and rRNA was depleted using the NEBNext rRNA depletion kit (#E6310)
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library prep kit (#E7775) and indexed using NEBNext Multiplex Oligos for Illumina (#E7335, E7500)

tag: tissue

value: Spleen

value: Macrophage

value: BALB/c

tag: Sex

value: Female


title: mut_1

value: TET3 KO


title: EdUseq-HU/release of DMSO-treated H1299 BRCA2-deficient cells 16 h HU arrest and release for 2 h


title: EdUseq-HU of LY2090314-treated BRCA2-deficient H1299 cells 16 h after mitotic shake-off


title: BWF1 Female #3

value: NZB x NZW F1


title: BWF1 Female #2


title: BWF1 Female #1


title: EdUseq-HU/release of LY2090314-treated H1299 BRCA2-proficient cells 12 h HU arrest and release for 2 h


title: EdUseq-HU of DMSO-treated BRCA2-deficient H1299 cells 16 h after mitotic shake-off


title: BWF1 Male #3

value: Male


title: BalbC Female #2


title: BWF1 Male #2


title: EdUseq-HU of LY2090314-treated BRCA2-proficient H1299 cells 12 h after mitotic shake-off


title: BalbC Female #3


title: BWF1 Male #1


title: EdUseq-HU/release of LY2090314-treated H1299 BRCA2-deficient cells 20 h HU arrest and release for 3 h


title: mut_2


title: EdUseq-HU of LY2090314-treated BRCA2-deficient H1299 cells 20 h after mitotic shake-off


title: EdUseq-HU/release of DMSO-treated H1299 BRCA2-proficient cells 12 h HU arrest and release for 2 h


title: LymphNodeH_single-cell

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2218 Biological Sciences III

department: Developmental and cell biology

country: Canada

institute: University of California at Irvine

data_processing:
Bulk RNA-seq quantification and mapping was done USING STAR and RSEM, GENCODE v21
Single-cell processing was done using ddseeker and Kallisto, GENCODE v21.  Single-cell pipeline assigns samplename_cellnumber but not barcodes per se in the naming.
Genome_build: mm10
Supplementary_files_format_and_content: CSV table format;TPM for bulk RNA-seq and raw counts for single-cell RNA-seq

source_name: Cell line derived from lymph node of metastasic mice CD44 signature high

extract_protocol: QIAGEN RNAeasy

treatment_protocol: A suite of organ-derived metastatic cell lines were harvested from 10 female PyMT mice and used for transcriptome profiling. The cells were first extracted from mouse organs with metastatic disease. Tissues were processed into single cell suspensions. Cancer cells were isolated and sorted based on the expression of specific cell surface markers. Cells exhibiting CD44low/EpCAMhigh or CD44high/EpCAMhigh profiles were collected

value: metastatic,  derived from lymph node of metastatic mice CD44 signature high


title: EdUseq-HU of DMSO-treated BRCA2-deficient H1299 cells 20 h after mitotic shake-off


title: LungL_rep1_single-cell

source_name: Cell line derived from lung of metastasic mice CD44 signature low

value: metastatic,  derived from lung of metastatic mice CD44 signature low


title: MFP2

source_name: Primary tumor mammary fat pad

value: Primary tumor mammary fat pad


title: EdUseq-HU/release of DMSO-treated H1299 BRCA2-proficient cells 10 h HU arrest and release for 3 h


title: LungH_rep1_single-cell

source_name: Cell line derived from lung of metastasic mice CD44 signature high

value: metastatic,  derived from lung of metastatic mice CD44 signature high


title: MFP1


title: EdUseq-HU of LY2090314-treated BRCA2-proficient H1299 cells 10 h after mitotic shake-off


title: EdUseq-HU/release of LY2090314-treated H1299 BRCA2-proficient cells 10 h HU arrest and release for 3 h


title: Lun1High


title: EdUseq-HU of DMSO-treated BRCA2-proficient H1299 cells 10 h after mitotic shake-off


title: Lun2low

source_name: Cell line derived from lung node of metastasic mice CD44 signature low

value: metastatic,  derived from lung node of metastatic mice CD44 signature low


title: Lun2High


title: EdUseq-HU of DMSO-treated BRCA2-proficient H1299 cells 12 h after mitotic shake-off


title: NB4-KO-H3K4me3_ChIP

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

data_processing:
The FASTQ data were trimmed adaptor by trim_galore (bioinformatics.babraham.ac.uk)
ChIP-seq data mapped to human genome hg19 with Bowtie  in single-end mode.
ChIP-seq peaks were called by MACS2 .
RNA-seq data were mapped to human genome hg19 using STAR  (020201) and assembled by Homer get Homer tags.
Use Homer to get RNA-seq raw counts, counts per million (CPM), and differential expressed genes were generated by DEseq2 size-factor normalized log2(CPM), with fold change > 2 and p < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files for ChIP-seq peaks in sample 1 to sample 6. An Excel file for H3K4me2 ChIP-seq up-regulated peaks in KDM5A-KO vs scramble (sample 4 vs sample 3). A tab-delimited text file and an excel file for RNA-seq log2(CPM), log2(fold change) and p value for sample 7 to sample 10.

growth_protocol: Human AML cell lines, NB4 (kindly provided by Dr. Kankan Wang, Ruijin Hospital), THP-1 (American Type Culture Collection, Manassas, VA, USA), HL-60 (American Type Culture Collection, Manassas, VA, USA), MV4-11(American Type Culture Collection, Manassas, VA, USA) were cultured in RPMI 1640 supplemented with 10% FBS (Sigma), penicillin (100 U/ml) and streptomycin (10 mg/ml) at 37C in a 5% CO 2 humidified atmosphere.

extract_protocol:
For histone modification, 3 × 10 6 cells per IP and primary antibody (4 mg/ml) were used; for KMD5A ChIP, 40 × 10 6 cells per IP were used (10 mg/ml). The obtained DNA was then quantified by PicoGreen and processed for ChIP-seq library preparation (as described for the Illumina protocol) or used for qPCR.
For libraries preparation, 2 ng of immunoprecipitated DNA was used. Antibodies used for ChIP are as follows:  H3K4me2 (Abcam, no. 32356), H3K4me3 (Active Motif, no. 39159), KDM5A (Bethyl Laboratories, A300-897A), and immuno-globulin G rabbit (Jackson ImmunoResearch, lot no. 134230).

treatment_protocol: CRISPR-Cas9 gene knockout was carried out using lentiCRISPR V2 system  and acted as protocol recommended. sgRNAs target KDM5A were designed as followed: KDM5A-sgRNA1: TATCGGCCGCATCCGGCCTT, KDM5A-sgRNA2: GGCCTTTGGCGGAGAAAAC. GFP-control-sgRNA1: AGCTGGACGGCGACGTAAA, GFP-control-sgRNA2: GTGAACCGCATCGAGCTGA. The lentiCRISPR v2 was a gift from Feng Zhang (Addgene plasmid # 52961; http://n2t.net/addgene:52961; RRID: Addgene_52961).

value: leukemia

tag: wt or kdm5a ko

value: KDM5A KO

tag: antibody

value: H3K4me3 (Active Motif, no. 39159)


title: EdUseq-HU/release of DMSO-treated H1299 BRCA2-deficient cells 20 h HU arrest and release for 3 h


title: Lun1low


title: NB4-KO-H3K4me2_ChIP


title: NB4-SCR-H3K4me3_ChIP

value: CRISPR scramble


title: LN2High


title: NB4-SCR-H3K4me2_ChIP


title: NB-WT-KDM5A_ChIP

value: WT

value: KDM5A (Bethyl Laboratories, A300-897A)


title: LN1low

source_name: Cell line derived from lymph node of metastasic mice CD44 signature low

value: metastatic,  derived from lymph node of metastatic mice CD44 signature low


title: LN2low


title: BM2High

source_name: Cell line derived from bone marrow of metastasic mice CD44 signature high

value: metastatic,  derived from bone marrow of metastatic mice CD44 signature high


title: RE_N822K_1_RNAseq

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

institute: University of Birmingham

description: CD34+ human cord blood cells

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using STAR
The  aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph

source_name: RE_N822K RNAseq replicate1

growth_protocol: Cells were maintained in a humidified incubator at 37 °C with 5% CO2. RE/CB, RE/WT and RE/N cells were cultured in Iscove modified Dulbecco medium with 20% BIT Serum Substitute (Stemcell Technologies #9500), supplemented with 10 ng/ml stem cell factor (SCF), thrombopoietin (TPO), FLT3 ligand, interleukin-3 (IL-3) and IL-6.

extract_protocol:
RNA-Seq libraries were prepared with a Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina, USA) according to manufacturer’s instructions with the following alterations: 15 cycles of PCR was undertaken to amplify the library and adaptors for multiplexing were used at a 1:4 dilution. Library quality was checked by running the samples on a Bioanalyser and libraries were quantified using a Kapa library quantification kit (Kapa Biosystems, USA) and run in a pool of eight indexed libraries in two lane of a HiSeq 2500 (Illumina, USA) using rapid run chemistry with 100 bp paired end reads.
RNA-seq libraries were prepared with a Total RNA Ribo-zero library preparation kit (with ribosomal RNA depletion) (Illumina, USA) as previously described in Loke, J. et al 2017

treatment_protocol: Cells were transduced with retrovirus expressing RE and either WT cKIT or N822K cKIT

value: CD34+ human

value: N822K cKIT mutant


title: BM1High


title: BM2low

source_name: Cell line derived from bone marrow of metastasic mice CD44 signature low

value: metastatic,  derived from bone marrow of metastatic mice CD44 signature low


title: RE_WT_2_RNAseq

description: CD34+ human cord blood cells

source_name: RE_WT RNAseq replicate2

value: wild type cKIT mutant


title: RE_CB_2_RNAseq

description: CD34+ human cord blood cells

source_name: RE_CB RNAseq replicate2

value: control untreated


title: RE_CB_1_RNAseq

description: CD34+ human cord blood cells

source_name: RE_CB RNAseq replicate1


title: WT2_tail_tip_fibroblasts

first: Sha

last: Sun

state: CA

address: 4232 McGaugh Hall

department: Development and cell biology

institute: University of california Irvine

data_processing:
index building, alignement and generation of count table was perform with Rsubread package version 1,24,2
Differential analysis expression was perform on Rstudio with the package DeSeq version 1,26,0
FPKM result was perform on Rstudion with counttofpkm package version 1,0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Tail tip fibroblasts

growth_protocol: Tail tip fibroblasts (TTF) were isolated from tail tip tissues of transgenic and wildtype mice from the same litter and grown in DMEM medium containing 10% FBS supplemented with MEM non-essential amino acids, 25mM HEPES pH 7.2-7.5, 0.1mM 2-mercaptoethanl, penicillin, and streptomycin. TTFs were then immortalized with Simian virus 40 large T cDNA following the protocol as previously described (Brown et al. 1986). Transgenic samples and wildtype (control) samples were processed in parallel following the same procedure.

extract_protocol:
Total RNA was extracted from cells grown on a 15cm tissue culture plate using Trizol (ThermoFisher), followed by DNase treatment using TURBO DNA-freeTM Kit (ThermoFisher). Polyadenylated mRNA was isolated from total RNA using DynabeadsTM mRNA Purification Kit (ThermoFisher). RNA integrity was checked by Bioanalyzer (Agilent 2100), followed by fragmentation with Mg2+- catalyzed hydrolysis.
cDNA library was constructed as previously described (Mortazavi et al. 2008). In brief, the first-strand cDNA was reverse transcribed with random primers, followed by dA addition and adaptor ligation. Then an RNA gel-purified was performed for size selection of 300 bp, follow by UNG treatment for strand specificity and PCR amplification. cDNA sequencing was performed as previously reported (Mortazavi et al. 2008). DNA quality and size were checked by Bioanalyzer (Agilent 2100), quantified by KAPA Library quantification Kit (Illumina), followed by sequencing on NextSeq500 (Illumina) using paired-end mode.

value: Immortalized fibroblasts


title: TG1_tail_tip_fibroblasts


title: TG2_tail_tip_fibroblasts


title: WT1_tail_tip_fibroblasts


title: LN1High

value: metastatic,  derived from lymph node of metastatic mice CD44 signature high


title: GATA2_RE_CB_ChIP

description: CD34+ human cord blood cells

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained and duplicate reads were removed from the aligned data using Picard tools.
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools
Genome_build: hg38
Supplementary_files_format_and_content: wiggle

extract_protocol:
Each aliquot of 1x10^7 cells was resuspended in 600 μl of sonication buffer (Tris- HCL pH8 25 mM, NaCl 150 mM, EDTA 2 mM, Triton 100x 1%, SDS 0.25%, PIC 1x). 300 μl of nuclei in sonication buffer was placed in each polystyrene tube and sonicated at 15 cycles: 30s on and 30s off per cycle (Bioruptor, Diagenode, Belgium). Subsequently, 1.2 ml of dilution buffer (Tris-HCL pH8 25 mM, NaCl 150 mM, EDTA 2 mM, Triton 100x 1%, glycerol 7.5%, PIC 1x) was added to the pooled post sonication material. This was divided equally between four immunoprecipitations (with 5% of input taken for validation).   15 μl protein G beads (Diagenode, Belgium) were washed twice with 500 μl of 50 mM citrate phosphate buffer and once with 100 mM sodium phosphate). Antibody was added to 10 μl 100 mM sodium phosphate, 0.5% BSA and incubated with protein G beads at 4 °C for 1 hour. Chromatin was then added to the protein G beads with antibody and returned to 4 °C for 4 hours. Unbound chromatin was separated from the beads by magnet and the attached beads were washed by buffer 1 (Tris HCL 20 mM, NaCl 150 mM, EDTA 2 mM, Triton x100 1%, SDS 0.1%), twice with buffer 2 (Tris HCL 20 mM, NaCl 500 mM, EDTA 2 mM, Triton x100 1%, SDS 0.1%), LiCl buffer (Tris HCL 10 mM, LiCl 250 mM, EDTA 1 mM, NP40 0.5%, sodium deoxychlolate 0.5%) and finally twice with wash buffer 4 (Tris HCL pH8, 10 mM, NaCl 50 mM, EDTA 1 mM). The column was eluted twice with 50 μl buffer (NaHCO3 100 mM and SDS 1%) and the eluent containing the chromatin was pooled. Crosslinks were reversed by incubating the samples at 65 °C overnight in 500 mM NaCl, 500 μg/ml proteinase K. DNA was purified by Ampure beads (Beckman Coulter, USA), as above, with the DNA eluted off with 50 μl water. Validation of the ChIP was performed by qPCR using a standard curve of genomic DNA from untreated cells (10 ng/μl followed by serial 1:5 dilutions). The input material was diluted 1:5 with water and qPCR was performed as above with primers listed in appendix. Validation was analysed as a ratio of the qPCR signal from the ChIP material over the input.
Libraries for high throughput sequencing were prepared using the Kapa HyperPrep kit (Kapa biosystems, USA), as per manufacturer’s protocol. 16 cycles of PCR was performed and 200-400 bp fragments were size selected by running the samples in an agarose gel. Libraries were validated by qPCR, with an analysis of the ChIP signal of a positive control region (e.g. PU.1 14 3H enhancer) over a negative control region (e.g. IVL). Finally, libraries were quantified by Kapa library quantification kit (Kapa biosystems, USA) and run in a pool of four indexed libraries in one lane of a HiSeq 2500 (Illumina, USA) or 12 indexed libraries in one lane of a NextSeq 500 (Illumina, USA) using 50 cycle single-end reads.

tag: company

value: R&D systems


title: rrTAPS

city: Oxford

first: Jingfei

last: Cheng

state: Oxfordshire

address: Roosevelt Drive

institute: University of Oxford

description: Reduced representation TAPS

data_processing:
Library strategy: rrTAPS
For eeTAPS, raw sequenced reads were processed with TrimGalore to perform adapter and quality trimming with the following parameters: --paired --length 35. For rrTAPS, raw reads were processed with seqtk trimfq -b 2 to trim 2 bp from the left of each read.
For eeTAPS, cleaned reads were aligned using bwa mem 0.7.17-r1188 with default parameters. For rrTAPS, cleaned reads were aligned using astair align 3.2.7.
For eeTAPS, only properly mapped read pairs (Read 1 with flag assigned as 83 or 99) were extracted to compute coverage with bedtools coverage for both endpoints and read-through of the whole fragments, and un-cleaved sites were also taken into consideration when calculating the cleavage efficiency. The detailed computational pipeline to analyse eeTAPS can be found here https://gitlab.com/jfeicheng/userenrich. For rrTAPS, methylated CpGs were extracted with astair call.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: For eeTAPS, tab-delimited text files include position, # total, # cleaved, # uncleaved and methylation level.
Supplementary_files_format_and_content: For rrTAPS, tab-delimited text file includes position, # methylated, # total, and methylation level.

source_name: E14 mESC

growth_protocol: E14 mESC cells were cultured on gelatin-coated 100 mm plates in Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen) supplemented with 15% FBS (GIBCO), 2 mM L-glutamine (Gibco), 1% non-essential amino acids (Gibco), 1% penicillin/streptavidin (Gibco), 0.1 mM β-mercaptoethanol (Sigma), 1000 units/mL LIF (Millipore), 1 μM PD0325901 (Stemgent), and 3 μM CHIR99021 (Stemgent). Cultures were maintained at 37°C and 5% CO2 and passaged every 2 days.

extract_protocol:
Confluent E14 mESC were dissociated from the plates and collected by centrifugation for 5 min at 1000 xg. Genomic DNA was extracted from 40 mln cells with Quick-DNA Plus kit (Zymo Research) according to manufacturer’s protocol.
To prepare eeTAPS libraries, DNA was converted with TAPS protocol, digested by USER enzyme and size selected to retain fragments 200-1000 bp. Final sequencing libraries were prepared with KAPA HyperPlus kit according to the manufacturer’s protocol. The final sequencing libraries were amplified with KAPA HiFi HotStart ReadyMix for 6 cycles (200 ng input), 8 cycles (50 ng input), 10 cycles (10 ng input) or 14 cycles (1 ng input). For control library untreated DNA was digested by USER enzyme and used for library construction as described above. Final library was amplified for 6 cycles. To prepare rrTAPS library DNA was first digested by MspI enzyme then used for End-repair and A-tailing reaction and ligation of Illumina Multiplexing adapters were prepared with NEBNext® Ultra™ II DNA Library Prep Kit according to the manufacturer’s protocol. DNA fragments from 100-400 bp were cut out of the gel and purified by Monarch® DNA Gel Extraction Kit following manufacturer’s protocol. Adapter-ligated sample was TAPS-converted and amplified with KAPA HiFi Uracil (+) Master Mix for 6 cycles.

value: embryonic stem cell line


title: JUND_RE_N822K_ChIP

description: CD34+ human cord blood cells

value: JUND

value: Santa Cruz


title: eeTAPS ctrl

description: Endonuclease enrichment TAPS

data_processing:
Library strategy: eeTAPS
For eeTAPS, raw sequenced reads were processed with TrimGalore to perform adapter and quality trimming with the following parameters: --paired --length 35. For rrTAPS, raw reads were processed with seqtk trimfq -b 2 to trim 2 bp from the left of each read.
For eeTAPS, cleaned reads were aligned using bwa mem 0.7.17-r1188 with default parameters. For rrTAPS, cleaned reads were aligned using astair align 3.2.7.
For eeTAPS, only properly mapped read pairs (Read 1 with flag assigned as 83 or 99) were extracted to compute coverage with bedtools coverage for both endpoints and read-through of the whole fragments, and un-cleaved sites were also taken into consideration when calculating the cleavage efficiency. The detailed computational pipeline to analyse eeTAPS can be found here https://gitlab.com/jfeicheng/userenrich. For rrTAPS, methylated CpGs were extracted with astair call.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: For eeTAPS, tab-delimited text files include position, # total, # cleaved, # uncleaved and methylation level.
Supplementary_files_format_and_content: For rrTAPS, tab-delimited text file includes position, # methylated, # total, and methylation level.


title: NB-WT-Input

value: leukemia


title: JUND_RE_CB_ChIP

description: CD34+ human cord blood cells


title: eeTAPS 200ng rep1

description: Endonuclease enrichment TAPS


title: ETO_RE_N822K_ChIP

description: CD34+ human cord blood cells

value: ETO

value: Diagenode


title: eeTAPS 200ng rep2

description: Endonuclease enrichment TAPS


title: eeTAPS 1ng

description: Endonuclease enrichment TAPS


title: ETO_RE_CB_ChIP

description: CD34+ human cord blood cells


title: eeTAPS 50ng

description: Endonuclease enrichment TAPS


title: RE_N822K_2_RNAseq

description: CD34+ human cord blood cells

source_name: RE_N822K RNAseq replicate2


title: RE_N822K_ATAC

description: CD34+ human cord blood cells

data_processing:
Quality of reads was verified using FASTQC analysis
Sequences reads in fastq format were mapped onto the reference human genome version hg38, Genome Reference Consortium GRCh38. The Illumina reads were aligned to the human genome using Bowtie2
Reads that were uniquely aligned to chromosomal positions were retained for downstream analysis
The filtered aligned reads were used to generate density profiles using “genomeCoverageBed” function from bedtools
Genome_build: hg38
Supplementary_files_format_and_content: wiggle

extract_protocol:
ATAC-seq was performed in RE/CB, RE/WT and RE /N cells essentially as described in Corces et al. 20162. Briefly, cells were harvested and 50,000 cells pelleted prior to resuspension in 50 µl ATAC transposition reaction mix containing 2x Tagment DNA Buffer (Illumina), Tn5 transposase (Illumina) and 0.5 µl 1% Digitonin (Promega). DNA was purified using a MinElute Reaction Clean up kit (Qiagen). DNA was PCR amplified using Nextera custom primers and saturation of the PCR reaction avoided by monitoring the reaction to prevent overamplification as described in Buenrostro et al.3,4. Amplified DNA was subsequently purified using MinElute columns or Ampure Beads (Beckman Coulter) prior to validation. Libraries were sequenced in a pool of 12 indexed libraries using a NextSeq 500/550 High Output Kit v2 (150 cycles) for paired end sequencing (Illumina) at the Genomics Birmingham sequencing facility.
ATAC-seq was performed on 50,000 cells. ATAC-seq libraries were prepared essentially as described in Corces, M. R. et al. 2016 and in Buenrostro et al.2015. Libraries were sequenced in a pool of 12 indexed libraries using a NextSeq 500/550 High Output Kit v2 (150 cycles) for paired end sequencing (Illumina) at the Genomics Birmingham sequencing facility.


title: RUNX1_RE_N822K_ChIP

description: CD34+ human cord blood cells

value: RUNX1 (C-terminal epitope)

value: Abcam


title: BM1low


title: eeTAPS 10ng

description: Endonuclease enrichment TAPS


title: KhetA20#4

city: Vienna

first: Herwig

middle: P

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

data_processing:
fastq generation, bcl2fastq via Basespace
alignment and extraction of counts/gene, Tophat (version 2.1.0) and Bowtie2 (version 2.2.6) aligners via Basespace,
differential gene expression analysis, DESeq2 (1.6.3) via Basespace
Genome_build: UCSC mm10
Supplementary_files_format_and_content: plain text, raw counts per gene, one file per sample

source_name: lung adenocarcinoma tissue

extract_protocol:
Lung tumors were macroscopically dissected and snap frozen in liquid nitrogen. Subsequently, RNA was isolated using RNeasy isolation kit with on-column DNase digestion  (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: timepoint

value: 10 weeks

value: KRASG12D mutated, p53 and A20 deficient

tag: tissues

value: lung adenocarcinoma tissue


title: RE_WT_1_RNAseq

description: CD34+ human cord blood cells

source_name: RE_WT RNAseq replicate1

value: CD34+ human


title: RE-CB_ATAC

description: CD34+ human cord blood cells


title: GATA2_RE_N822K_ChIP

description: CD34+ human cord blood cells

value: N822K cKIT mutant


title: RE_WT_ATAC

description: CD34+ human cord blood cells

value: wild type cKIT mutant


title: KhetA20#3

tag: strain


title: KhetA20#2


title: Tet2KO CMML without antibiotics treatment 2

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

description: Tet2KO_CMML_vehicle 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bowtie2 was used to map RNAseq to hg19 with default parameters.
RPKM was calculated to measure the genes expression level.
DESeq2 was used to call differential expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include the RPKM for each gene in each sample

source_name: CMML cell + Vehicle

growth_protocol: CD4+ T cells or CD4+ lymphoma cells were isolated from spleen and lymph node of normal or sick Tet2KO mice with CD4+ T cell isolation kit. CMML cells were isolated from sick Tet2KO mice using Mac1 and Gr1 enrichment.

extract_protocol:
RNA were extracted with qiagent RNAeasy mini isolation kit.
RNAseq libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: Tet2KO CD4+ lymphoma cells or Tet2KO CMML cells were injected into to CD45.1 recipient mice followed by antibiotics cocktail treatment for 10 days and cessation for 20 days before analysis.

value: CMML cell

value: without antibiotics treatment


title: Tet2KO CMML without antibiotics treatment 1

description: Tet2KO_CMML_vehicle 1


title: Tet2KO CMML with antibiotics treatment 2

description: Tet2KO_CMML_abx 2

source_name: CMML cell + ABX

value: with antibiotics treatment


title: Tet2KO CMML with antibiotics treatment 1

description: Tet2KO_CMML_abx 1


title: Tet2KO lymphoma without antibiotics treatment 2

description: Tet2KO_lymphoma_vehicle 2

source_name: CD4+ lymphoma cell + Vehicle

value: CD4+ lymphoma cell


title: KhetA20#1


title: Tet2KO lymphoma with antibiotics treatment 2

description: Tet2KO_lymphoma_abx 2

source_name: CD4+ lymphoma cell + ABX


title: Tet2KO lymphoma without antibiotics treatment 1

description: Tet2KO_lymphoma_vehicle 1


title: RUNX1_RE_CB_ChIP

description: CD34+ human cord blood cells

value: control untreated


title: Tet2KO lymphoma with antibiotics treatment 1

description: Tet2KO_lymphoma_abx 1


title: Tet2KO normal CD4 T cell 1

source_name: Normal CD4+ T cell

value: Normal CD4+ T cell


title: Tet2KO lymphoma 1

description: Tet2KO_lymphoma 1

source_name: CD4+ lymphoma cell


title: Tet2KO normal CD4 T cell 2


title: EBs.index08.BC_380

city: Utrecht

first: Isabel

last: Guerreiro

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Transcriptome measurement of sample EBs.index08.BC_380

data_processing:
Demultiplexing of raw data (previously demultiplexed on Illumina index) was done using barcodes. Read1 measurements contain in read1, from 5’ to 3’: a 6nt UMI, an 8nt barcode, followed by unalignable sequence, usually polyT. Read2 of the transcriptomic measurements contains the mRNA sequence.
mRNA reads (in read2) were aligned using tophat2 (v2.1.1) using parameters ‘--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200’ to a transcriptome (options ‘--GTF’ and ‘--transcriptome-index’) obtained from GENCODE (v26) supplemented with ERCC mRNA spike-in sequences.
Reads and unique UMIs were counted per gene (according to the “intersection-strict” algorithm of `htseq-count` [http://htseq.readthedocs.io/en/master/count.html]). For each gene, the number of unique observed UMIs was trimmed by starting at the UMI with highest read count and setting UMIs with Hamming distance of 1 to zero, and iteratively filtering all UMI sequences (in case of equal read counts for a UMI, ties were broking by lexicographic sorting of the UMIs). The number of observed distinct UMIs after trimming was taken as the transcript count for that gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tables are provided with the number of transcripts per gene.

molecule: polyA RNA

source_name: embryoid bodies from mouse ESCs

growth_protocol: Expansion medium: ESC were expanded for minimally 2 passages on gelatin-coated tissue-culture plastic in B27N2 medium supplemented with 3 μM CHIR99021 (AxonMed 1386), 1 μM 10 ng/mL Lif (Merck Millipore ESG1106), PD0325901 (1 μM, AxonMed 1408). PrE-induction medium: An average of 10 ESC per microwell was seeded in high-glucose DMEM containing sodium pyruvate and Glutamax (Thermo Fisher, 10569010), supplemented with 10% serum, 10 mM Non-essential amino acids, 10 mM HEPES and penicillin/streptomycin. This medium was supplemented with 10 ng/mL Lif (Merck Millipore ESG1106) and 2 µM Y27632 (AxonMed 1683). PrE-induction supplements were 3 μM CHIR99021 (AxonMed 1386), 50 ng/mL Fgf4 (RnD systems, 5846-F4-025), 10 nM RA (Sigma R2625), 1 mM 8Br-cAMP (Biolog, B007-50E), 1 µg/mL heparin (Sigma) and 50 µM 2-mercaptoethanol (Gibco 11528926).

extract_protocol:
EBs were washed twice in PBS-0 and collagenase IV (600U/ml) was added. Plates were shaken at 350RPM for 30 minutes. EBs were then transferred to TrypleE 10X (no dilution) and shaken for 20 minutes. EBs were dissociated into single cell suspensions using a small capillary. The resulting suspension was quenched using PBS with 50% FBS, centrifuged and resuspended in 230 ul of PBS0 with 10% FBS. Cells were stained with PDGFRA antibody (1:150 dilution) for 30 min at 4°C followed by three PBS (+10%FBS) washes, secondary antibody incubation (1:400) for 30 min. Cells were washed three times in PBS0 and sorted for further processing.
Library construction was done following the Sort-seq protocol as previously described [Muraro, T. et al. A Single-Cell Transcriptome Atlas of the Human Pancreas. Cell Systems 3, 385–394.e3 (2016).]
Library preparation was done as previously described[Hashimshony, T. et al. CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq. Genome biology 17, 77, (2016).] using 5 μL of aRNA and 8 PCR cycles. Libraries were run on the Illumina NextSeq platform with high output 75 bp paired-end sequencing.

value: embryoid bodies from mouse ESCs

tag: celseq2 adapter

tag: pdgfra staining

value: negative


title: EBs.index08.BC_384

description: Transcriptome measurement of sample EBs.index08.BC_384


title: EBs.index08.BC_374

description: Transcriptome measurement of sample EBs.index08.BC_374


title: EBs.index08.BC_372

description: Transcriptome measurement of sample EBs.index08.BC_372


title: EBs.index08.BC_370

description: Transcriptome measurement of sample EBs.index08.BC_370


title: EBs.index08.BC_362

description: Transcriptome measurement of sample EBs.index08.BC_362


title: EBs.index08.BC_326

description: Transcriptome measurement of sample EBs.index08.BC_326


title: EBs.index08.BC_320

description: Transcriptome measurement of sample EBs.index08.BC_320


title: EBs.index08.BC_322

description: Transcriptome measurement of sample EBs.index08.BC_322


title: EBs.index08.BC_280

description: Transcriptome measurement of sample EBs.index08.BC_280


title: EBs.index08.BC_240

description: Transcriptome measurement of sample EBs.index08.BC_240


title: EBs.index08.BC_284

description: Transcriptome measurement of sample EBs.index08.BC_284


title: EBs.index08.BC_278

description: Transcriptome measurement of sample EBs.index08.BC_278


title: EBs.index08.BC_282

description: Transcriptome measurement of sample EBs.index08.BC_282


title: EBs.index08.BC_192

description: Transcriptome measurement of sample EBs.index08.BC_192


title: EBs.index08.BC_230

description: Transcriptome measurement of sample EBs.index08.BC_230


title: EBs.index08.BC_238

description: Transcriptome measurement of sample EBs.index08.BC_238


title: EBs.index08.BC_186

description: Transcriptome measurement of sample EBs.index08.BC_186


title: EBs.index08.BC_178

description: Transcriptome measurement of sample EBs.index08.BC_178


title: EBs.index08.BC_180

description: Transcriptome measurement of sample EBs.index08.BC_180


title: Tet2KO lymphoma 2

description: Tet2KO_lymphoma 2


title: EBs.index08.BC_176

description: Transcriptome measurement of sample EBs.index08.BC_176


title: X6_M_3

city: Harbin

first: Jian

address: 600 Changjiang Road

country: China

institute: Northeast Agricultural University

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: GCF_000188115.4_SL3.0
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: susceptible cultivar

growth_protocol: Tomatoes grow naturally in the greenhouse.All tomato tissues were collected and used to RNA sequencing.

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: Tomatoes grow naturally in the greenhouse.All tomato tissues were infected with Fusarium oxysporum for 0,3 or 6 h,respectively.

value: leaf

value: infected with Fusarium oxysporum for 6h

tag: cultivar

value: FORL susceptible


title: X6_M_2


title: EBs.index08.BC_174

description: Transcriptome measurement of sample EBs.index08.BC_174


title: EBs.index08.BC_172

description: Transcriptome measurement of sample EBs.index08.BC_172


title: EBs.index08.BC_144

description: Transcriptome measurement of sample EBs.index08.BC_144


title: X6_M_1


title: X3_M_3

value: infected with Fusarium oxysporum for 3h


title: EBs.index08.BC_132

description: Transcriptome measurement of sample EBs.index08.BC_132


title: X3_M_2


title: EBs.index08.BC_288

description: Transcriptome measurement of sample EBs.index08.BC_288


title: X3_M_1


title: EBs.index08.BC_096

description: Transcriptome measurement of sample EBs.index08.BC_096


title: X0_M_1

value: infected with Fusarium oxysporum for 0h


title: EBs.index08.BC_094

description: Transcriptome measurement of sample EBs.index08.BC_094


title: X6_Frl_1

source_name: resistant cultivar

value: FORL resistant


title: X0_M_3


title: EBs.index08.BC_088

description: Transcriptome measurement of sample EBs.index08.BC_088


title: X6_Frl_3


title: X6_Frl_2


title: EBs.index08.BC_082

description: Transcriptome measurement of sample EBs.index08.BC_082


title: X0_M_2


title: EBs.index08.BC_048

description: Transcriptome measurement of sample EBs.index08.BC_048


title: EBs.index08.BC_188

description: Transcriptome measurement of sample EBs.index08.BC_188


title: X3_Frl_2


title: X0_Frl_3


title: X0_Frl_2


title: X3_Frl_3


title: X3_Frl_1


title: X0_Frl_1


title: EBs.index08.BC_036

description: Transcriptome measurement of sample EBs.index08.BC_036


title: EBs.index08.BC_042

description: Transcriptome measurement of sample EBs.index08.BC_042


title: EBs.index07.BC_383

description: Transcriptome measurement of sample EBs.index07.BC_383


title: EBs.index07.BC_381

description: Transcriptome measurement of sample EBs.index07.BC_381


title: EBs.index07.BC_379

description: Transcriptome measurement of sample EBs.index07.BC_379


title: EBs.index07.BC_373

description: Transcriptome measurement of sample EBs.index07.BC_373


title: EBs.index07.BC_367

description: Transcriptome measurement of sample EBs.index07.BC_367


title: PD-1+TIM-3+CD8+ TILs_IL-10/Fc_rep4

city: Lausanne

first: Li

last: Tang

state: Vaud

address: MED 1 2826, Station 9, CH-1015 Lausanne

department: Institute of Bioengineering (IBI) / Institute of Materials (IMX)

country: Switzerland

institute: École polytechnique fédérale de Lausanne (EPFL)

data_processing:
Illumina Casava1.8.2 software used for basecalling.Base calls were subsequently converted into multiplexed, unaligned BAM format before demultiplexing into sample-specific, unaligned BAM files.
NGS reads were trimmed based on quality and adapter sequence content with Trimmomatic in single-end (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10:1:true, SLIDINGWINDOW:4:15, MINLEN:20).
NGS reads passing vendor quality filtering were aligned to the UCSC Genome Browser [mm10] flavour of the Genome Reference Consortium [GRCm38] assembly with TopHat2 (v2.1.1), a splice junction mapper utilising the Bowtie2 (v2.2.9) short read aligner.
Before differential expression calling with Cuffdiff (included in Cufflinks v2.2.1), transcriptome sets of each sample of each group were combined via the Cuffmerge algorithm.
The Bioconductor DESeq2 package was then used to model the expression data set and call differentially expressed genes.
Genome_build: Mus musculus genome assembly GRCm38/mm10.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM counts for each sample.

source_name: Terminally exhausted CD8+ T-cells

extract_protocol:
Thy1.1+PD-1+TIM-3+CD8+ TILs (500 cells, purity > 99%) were sorted into Hard-Shell® 96-Well PCR Plates (Bio-Rad, Hercules, CA, USA) containing Triton X-100 (0.2%) with RNase inhibitor (Takara) and stored at −80°C until library preparation. Total RNA was extracted using the protocol for low input RNA sequencing provided by Research Center for Molecular Medicine of the Austrian Academy of Sciences.
RNA libraries were prepared for sequencing using Smart-Seq2 Illumina protocol.

treatment_protocol: Mice were sublethally lymphodepleted by total body irradiation (4 Gy) on day -4, followed by i.v. adoptive transfer of Thy1.1+ naïve PMEL T-cells (2 million) on day -3, and inoculation with B16F10 tumour cells on day 0. On day 10, mice were treated with i.v. adoptive transfer of Thy1.2+ activated PMEL CD8+ T-cells (5 million) prepared as described above, followed by p.t. administration of IL-10/Fc (20 µg) or PBS control every other day starting from day 10 (4 doses in total). On day 18, mice were sacrificed and TILs were isolated.

value: B16F10 tumor

tag: tumor stage

value: post inoculation day 18

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

value: peritumoral injection of IL-10/Fc


title: PD-1+TIM-3+CD8+ TILs_IL-10/Fc_rep3

tag: genotype


title: EBs.index07.BC_335

description: Transcriptome measurement of sample EBs.index07.BC_335


title: PD-1+TIM-3+CD8+ TILs_IL-10/Fc_rep2


title: PD-1+TIM-3+CD8+ TILs_PBS_rep2

value: peritumoral injection of PBS


title: EBs.index07.BC_333

description: Transcriptome measurement of sample EBs.index07.BC_333


title: RNA-seq mouse Control rep1

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: RNA-seq mouse Control rep1

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie2 and Tophat2
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes among different conditions.
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs

source_name: spleens

growth_protocol: Naïve T cells were isolated from Thy1.1+ BALB/c mice by EasySepTM mouse T cell isolation kit (STEMCELL). Thy1.1+ T cells were suspended into serum free PBS and labeled with CellTraceTM Violet (Invitrogen) for 5 min at 37℃. Thy1.1+ T cells were co-cultured with Foxp3GFP+ Tregs transduced with oIL-2Rβ at 1:1 ratio together with same number of CD3/CD28 beads (1 × 105). 1 ug IL-2 (both wt and ortho)= 16,300 U, and 1 ug MSA-IL-2 is 3200 U. Cytokine was added at 1e+03 - 1e+06 IU /mL and replenished on day 2. Four days later, recovered cells were stained with CD4, CD25, and ICOS mAb for 15 min at 4℃. Cells were acquired by LSRII (BD) and data was analyzed with FlowJo software (BD). Cell number in each well was calculated from the count of Precision counting beads (BioLegend) according to the manufacturer’s instructions.

extract_protocol:
RNA-seq, RNA was extracted using the Zymo RNA miniprep kit (Zymo Research), and 500 ng RNA was used for library preparation with the Kapa mRNA HyperPrep Kit (KK8580, Kapa Biosystems) and indexed with NEXTflex DNA Barcodes-24. After the final amplification, samples were loaded onto 2% E-Gel pre-cast gels (ThermoFisher), and 250 to 400 bp DNA fragments were recovered and purified with Zymoclean Gel DNA Recovery Kit (Zymo Research).
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina HiSeq3000 system.

treatment_protocol: Transduced Foxp3GFP+ Tregs were inoculated with CD3/CD28 beads and 1,000 IU/mL hIL-2. 48 hrs later, cells were recovered and hEGFR-oIL-2Rβ+ cells were isolated by magnetic isolation. Sorted cells were incubated overnight in the conditioning media without hIL-2. After IL-2 starvation, cells were incubated for 4 hrs with 2e+04 IU/mL wt IL-2 or 2e+06 IU/mL ortho IL-2. Control cells were incubated without IL-2 (no IL-2).

value: BALB/c

tag: cell type

value: Tregs

value: Control


title: EBs.index07.BC_329

description: Transcriptome measurement of sample EBs.index07.BC_329


title: PD-1+TIM-3+CD8+ TILs_IL-10/Fc_rep1


title: EBs.index08.BC_044

description: Transcriptome measurement of sample EBs.index08.BC_044


title: RNA-seq mouse Control rep2

description: RNA-seq mouse Control rep2


title: RNA-seq mouse Control rep3

description: RNA-seq mouse Control rep3


title: EBs.index07.BC_331

description: Transcriptome measurement of sample EBs.index07.BC_331


title: RNA-seq mouse WT-IL2 rep3

description: RNA-seq mouse WT-IL2 rep3


title: RNA-seq mouse WT-IL2 rep2

description: RNA-seq mouse WT-IL2 rep2


title: RNA-seq mouse WT-IL2 rep1

description: RNA-seq mouse WT-IL2 rep1


title: PD-1+TIM-3+CD8+ TILs_PBS_rep1


title: EBs.index07.BC_325

description: Transcriptome measurement of sample EBs.index07.BC_325


title: EBs.index07.BC_279

description: Transcriptome measurement of sample EBs.index07.BC_279


title: RNA-seq mouse ortho-IL2 rep1

description: RNA-seq mouse ortho-IL2 rep1


title: cL15 w/o FBS +100µM FAC replicate 3

city: College Station

first: Zach

last: Adelman

state: TX

address: 370 Olsen Blvd

department: Entomology

institute: Texas A&M University

description: Aag2 cells incubated with serum deficient media (L15) plus 100µM Ferric Ammonium Citrate (FAC) for 48hrs

data_processing:
Aligning reads to reference genome: Reads were aligned to the Ae. aegypti reference genome AaegL3 and the reference genome AaegL5 (www.vectorbase.org) using HISAT2 v2.1.0
Cleaning up mapped files: SAMtools view and SAMtools sort commands v1.7 were used to sort the mapped files and remove low quality mapping scores
Counting number of reads per transcript: BEDtools suite v2.19.1 used to calculate the number of reads per mRNA transcript
Merging Count tables: Counts data was merged from all samples into one file for each genome assembly
EdgeR analysis: ;The counts tables was analyzed in EdgeR (Robinson et al, 2010)
Genome_build: AaegL3 & AaegL5 (www.vectorbase.org)
Supplementary_files_format_and_content: tab delimited text files containing the raw counts data, one for each genome version

organism: Aedes aegypti

growth_protocol: Aag2 cells were maintained in Leibovitz’s L-15 (L15) medium (Thermo Fisher) supplemented with 10% FBS (Atlanta Biological), 2% tryptose phosphate broth (Thermo Fisher) and 1% penicillin/streptomycin (hereafter “complete” L15 = cL15) at 28 °C in closed flasks

extract_protocol:
After 48 h cells were harvested and RNA was extracted from cells using TRIzol (Life Technologies), according to the manufacturer’s instructions
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, NEB) and multiplexed into 3 lanes of an Illumina HiSeq 2500.

treatment_protocol: Aag2 cells were seeded in triplicate T-25 flasks and then the following day the medium was replaced with either cL15, cL15 without any FBS, cL15 without FBS supplemented with 50 µM deferoxamine (DFO), or cL15 without FBS supplemented with 100 µM ferric ammonium citrate (FAC).


title: cL15 w/o FBS +100µM FAC replicate 1

source_name: Aag2 cells incubated with serum deficient media (L15) plus 100µM Ferric Ammonium Citrate (FAC) for 48hrs


title: cL15 w/o FBS +100µM FAC replicate 2


title: EBs.index07.BC_283

description: Transcriptome measurement of sample EBs.index07.BC_283


title: RNA-seq mouse ortho-IL2 rep2

description: RNA-seq mouse ortho-IL2 rep2


title: EBs.index07.BC_371

description: Transcriptome measurement of sample EBs.index07.BC_371


title: RNA-seq mouse ortho-IL2 rep3

description: RNA-seq mouse ortho-IL2 rep3


title: cL15 w/o FBS +50µM DFO replicate 3

description: Aag2 cells incubated with serum deficient media (L15) plus 50µM deferoxamine (DFO) for 48hrs


title: cL15 w/o FBS +50µM DFO replicate 1

source_name: Aag2 cells incubated with serum deficient media (L15) plus 50µM deferoxamine (DFO) for 48hrs


title: cL15 w/o FBS +50µM DFO replicate 2


title: EBs.index07.BC_275

description: Transcriptome measurement of sample EBs.index07.BC_275


title: cL15 without FBS replicate 3

description: Aag2 cells incubated with serum deficient media (L15) for 48hrs


title: cL15 without FBS replicate 2

source_name: Aag2 cells incubated with serum deficient media (L15) for 48hrs


title: EBs.index07.BC_327

description: Transcriptome measurement of sample EBs.index07.BC_327


title: EBs.index07.BC_229

description: Transcriptome measurement of sample EBs.index07.BC_229


title: cL15 without FBS replicate 1


title: EBs.index07.BC_227

description: Transcriptome measurement of sample EBs.index07.BC_227


title: HepV_O3 rep5

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

data_processing:
Reads Trimmed, aligned with STAR default parameters, and quantified to the PARTEK E/M Annotation model at the GENE level
Extracted Gene Counts rounded to nearest Integer for DESeq Analysis
Removed Genes without at least 1 count in at least 10 of the samples
Removed Two samples from Analysis (not uploaded) with abberant PCA clustering of top 500 expressed genes
DESeq2 Normalization provided in processed files
Genome_build: Rattus norvegicus rn6 with Annotation = Ensembl Transcripts Release 90
Supplementary_files_format_and_content: normalized count matrix from DESeq2

organism: Rattus norvegicus

source_name: Liver

growth_protocol: 10-11 Week old purchased and housed hardwood chip bedding under controlled conditions (21°C, 50-65% relative humidity and 12h light/dark cycle); Rats were provided with standard Purina (5001) rat chow (Brentwood, MO) and water ad libitum

extract_protocol:
10-20mg similar location liver  extracted with Rneasy minikit (Qiagen, Valencia, CA)
hepatic RNA samples were indexed using the PrepXTM RNA-Seq for Illumina Library Kit (Takara Bio Inc.; Kusatsu, Japan) with SuperScript III Reverse Transcriptase (ThermoFisher) and AMPure XP beads (Agilent) on the Apollo324 system (Takara Bio Inc.) using the recommended protocols developed by Takara Bio.

treatment_protocol:
12wk old rats underwent either Sham or Hepatic Vagotomy surgery and were allowed to recover 5-6 days
Air or Ozone (1.0ppm) for 4 hours, for 1 or 2 days and necropsied within 2 hours after exposure


title: HepV_O3 rep3


title: HepV_O3 rep4