title: T47D_HA_GATA3_wt_aHA_siNT_rep1


title: T47D_HA_GATA3_TR1_aHA_rep2

status: Public on Jun 12 2019

type: SRA

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

library_source: genomic

data_processing:
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (v1.5) and MACS (v1.4) peak caller. Only peaks called by both algorithms were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: filtered.intersect files contain peaks called by both peak calling algorithms in bed format

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Chromatin immunoprecipitations were performed as described previously, with adaptations (Schmidt et al., 2009). In short, cells were crosslinked in solution A (pH 7.4, 50mM Hepes, 100mM NaCl, 1mM EDTA, 0.5M EGTA) containing 2mM DSG for 35 minutes, then formaldehyde was added to a final concentration of 1% and incubated for another 10 minutes. After addition of Glycine to a final concentration of 125mM to quench the crosslinking reaction and washing with PBS, cells were collected. The Bioruptor Pico (Diagenode) was used for sonication. For ChIP, antibodies were used to detect the HA-tag (25mg, 05-904, Millipore) and GATA3 (10 mg, sc-268, Santa Cruz) with 100 ml Protein A magnetic beads (Thermo Scientific).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

tag: cell line

tag: cell type

value: Breast cancer cell line

tag: chip antibody

value: aHA (05-904, Millipore)

tag: plasmid

value: HA_GATA3_TR1 plasmid


title: T47D_HA_GATA3_TR2_aHA_rep1

value: HA_GATA3_TR2 plasmid


title: T47D_aGATA3

value: aGATA3 (sc-268, Santa Cruz)


title: T47D_HA_GATA3_TR1_aHA_rep1


title: T47D_HA_GATA3_wt_aHA_rep1

value: HA_GATA3_wt plasmid


title: T47D_EV_aHA_rep2

value: control plasmid


title: T47D_HA_GATA3_wt_aHA_rep2


title: T47D_EV_aHA_rep1


title: T47D_HA_GATA3_TR1_aHA_siNT_rep2

tag: sirna

value: siNT


title: T47D_HA_GATA3_TR1_aHA_siFOXA1_rep1


title: T47D_EV_aHA_siNT_rep1


title: PNET_FFPE_2 H3K4me2

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
ChIP-seq reads were aligned to the reference genome (hg19) using BWA 0.7.10. Reads with mapping scores <10 were discarded, and those aligned to the same position and strand were only counted once. Density signals were calculated by igvtools, and converted to bigWigs with bedGraphToBigWig. Peaks were called with HOMER 4.6, using parameters -style histone -L 0.
Genome_build: hg19

source_name: pancreatic neuroendocrine tumors

extract_protocol:
For FiT-seq, we macrodissected FFPE sections to obtain >80% tumor cell enrichment and used 10 sections, each 10 μm thick. Sections were washed 3 times with xylenes to remove paraffin, rehydrated in an ethanol/water series, and prepared as described17, with modified sonication conditions (Covaris E220 instrument, 20 min, 5% duty cycle, 105 Peak Incident Power, 200 Cycles per burst, 1mL AFA Fiber milliTUBEs).
Soluble chromatin (5 µg) was immunoprecipitated with 10 μg H3K4me2 (Millipore 07-030). Libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) following the manufacturer's protocols. 36-bp paired-end reads were sequenced on a HiSeq 2500 instrument (Illumina).

tag: pnet subtype

value: A


title: PNET_FFPE_1 H3K4me2

value: C


title: PNET_12 H3K4me2

extract_protocol:
30-μm sections from frozen samples with >90% tumor enrichment were collected in microtubes, washed in phosphate-buffered saline (PBS), cross-linked with 1% formaldehyde for 5 min, and quenched with 0.125 M glycine for 5 min at room temperature. Cross-linked material was resuspended in 0.1% SDS (50 mM Tris-HCl pH8, 10 mM EDTA) and sonicated for 40 min in a Covaris E210 instrument (duty cycle 20%; intensity 8; cycles per burst 200).
Soluble chromatin (5 µg) was immunoprecipitated with 10 μg H3K4me2 (Millipore 07-030) or H3K27ac (Active Motif 39133) antibodies (Ab). ChIP-seq libraries were constructed by end repair (Epicentre ER0720) of precipitated DNA, base extension with Klenow fragment (New England Biolabs M0212L), and ligation (New England Biolabs M220S) of Y-form sequencing adapters (Illumina), followed by 14 cycles of PCR. Between enzymatic steps, fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter).

value: B


title: PNET_11 H3K4me2


title: PNET_FFPE_7 H3K4me2


title: PNET_FFPE_8 H3K4me2


title: PNET_FFPE_5 H3K4me2


title: PNET_FFPE_6 H3K4me2


title: PNET_9 H3K4me2


title: PNET_10 H3K4me2


title: PNET_6 H3K27ac


title: PNET_5 H3K4me2


title: PNET_6 H3K4me2


title: PNET_8 H3K27ac


title: PNET_7 H3K27ac


title: PNET_7 H3K4me2


title: PNET_8 H3K4me2


title: PNET_4 H3K27ac


title: PNET_3 H3K27ac


title: PNET_1 H3K4me2


title: PNET_1 H3K27ac


title: PNET_2 H3K27ac


title: PNET_4 H3K4me2


title: CAR_20 H3K27ac

source_name: carinoids


title: PNET_2 H3K4me2


title: CAR_19 H3K27ac


title: CAR_A_22 H3K27ac


title: PNET_5 H3K27ac


title: PNET_FFPE_3 H3K4me2


title: CAR_21 H3K27ac


title: PNET_3 H3K4me2


title: CAR_16 H3K27ac


title: CAR_17 H3K27ac


title: CAR_14 H3K27ac


title: CAR_15 H3K27ac


title: CAR_13 H3K27ac


title: CAR_18 H3K27ac


title: CAR_11 H3K27ac


title: CAR_12 H3K27ac


title: CAR_9 H3K27ac


title: CAR_7 H3K27ac


title: CAR_4 H3K27ac


title: CAR_8 H3K27ac


title: CAR_10 H3K27ac


title: CAR_5 H3K27ac


title: CAR_1 H3K27ac


title: CAR_3 H3K27ac


title: HA_negative

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

data_processing:
ChIP-seq:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Two technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Sequenced reads were mapped to the human reference genome hg19 using bowtie 1.0.0 with arguments -m 1 --strata --best -y -S -l 40
Mapped SAM-files were used for peak calling using the Homer package {Heinz, 2010}
Homer was used to generated bedgraphs with bp resolution with counts normalised to 10 million reads
Genome_build: hg19

RNA-seq:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Two technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Raw fastq files were then trimmed of poly-A using  cutadapt
Processed fastq files were mapped using STAR with custome hg38 build which contains ERCC as well as mouse-Mitf
Counts per gene from STAR were used as input for differential gene expression analysis using EdgeR.
Reads for each sample set were first filtered for genes whose expression is  count-per-million prior to glmQLFTest.
Supplementary_files_format_and_content: bedgraph of normalised counts for uniqely aligned reads

source_name: 501mel_Negative control for MITF

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
ChIP-seq: 3x-15cm dishes of 501mel cells were fixed in 0.4% PFA then cheared with a Covaris S220 for 15 minutes (160 W peak incident power, 5% duty cycle and 200 cycles per burst). The sonicated chromatin were precleared and ChIP was performed using 80ug of the indicated antivodies. Purification of the ChIP-DNA was done using QIAGEN PCR clean-up column
RNA-seq: RNA-samples were extracted using QIAGEN RNeasy kit
ChIP-seq: Libraries were prepared using recommended Illumina protocols
RNA-seq: Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

treatment_protocol:
ChIP-seq: Cells were treated for 16h at 1% O2 level in hypoxia chamber, fixation started in the chamber before moving out into the rocker outside the chamber
RNA-seq: Cells were treated at 1% O2 level in hypoxia chamber for the indicated time

value: melanoma cell line

tag: treated with

value: 1% O2 level for 16hrs

tag: chip antibody cat. #


title: HIF1a

value: Rabbit Polyclonal in whole antiserum (antigen:HIF1a)

tag: chip antibody vendor

value: home-made


title: TU0137_CD8_LTBI

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

country: USA

institute: La Jolla Institute for Immunology

library_source: transcriptomic

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] abundance measurements as a matrix table

molecule: polyA RNA

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 or memory CD8 T cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Microscaled (SmartSeq2) cDNA amplification.
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: disease state

value: Latent tuberculosis infection

tag: cell subset

value: Memory CD3+CD8+ T cells


title: TU0137_CD4_LTBI

value: Memory CD3+CD4+ T cells


title: TU0040_CD8_LTBI


title: TU0036_CD4_LTBI


title: TU0036_CD8_LTBI


title: TU0040_CD4_LTBI


title: TU0011_CD4_LTBI


title: CAR_6 H3K27ac


title: TU0011_CD8_LTBI


title: TU0002_CD8_LTBI


title: HA

value: Monoclonal mouse IgG2b

value: Roche


title: HIF2a

value: Rabbit Polyclonal in whole antiserum (antigen:HIF2a)


title: XT0131_CD8_HC

value: Healthy


title: XT0131_CD4_HC


title: XT0141_CD8_HC


title: XT0141_CD4_HC


title: TU0002_CD4_LTBI


title: HIF1b

value: Rabbit Polyclonal in whole antiserum (antigen:HIF1b)

value: Novus Biologicals


title: XT0127_CD8_HC


title: XT0127_CD4_HC


title: XT0115_CD8_HC


title: XT0115_CD4_HC


title: XT0108_CD8_HC


title: TU0078_CD8_LTBI


title: TU0078_CD4_LTBI


title: TU0081_CD4_LTBI


title: XT0108_CD4_HC


title: TU0081_CD8_LTBI


title: TU0064_CD8_LTBI


title: TU0064_CD4_LTBI


title: TU0025_CD4_LTBI


title: TU0023_CD8_LTBI


title: XT0133_CD8_HC


title: TU0023_CD4_LTBI


title: TU0025_CD8_LTBI


title: XT0133_CD4_HC


title: XT0130_CD4_HC


title: XT0130_CD8_HC


title: TU0054_CD8_HC


title: TU0054_CD4_HC


title: TU0051_CD4_HC


title: TU0049_CD8_HC


title: TU0051_CD8_HC


title: TU0049_CD4_HC


title: MC57G cells, nontargeting siRNA, R443I infection Rep 2 [input DNA]

city: Berkeley

first: Britt

middle: A

last: Glaunsinger

state: CA

address: 565 Li Ka Shing Center

department: Molecular and Cellular Biology

institute: University of California Berkeley

description:
MC57G cells, nontargeting siRNA, R443I infection Rep 2
input DNA

data_processing:
Quality assessment with FastQC
Reads were trimmed with Sickle
Data were aligned to the mm10 genome and the MHV68 genome (custome index was used that combines both) with Bowtie2 (2.3.0)
Tag pileups around TSS, TTS and gene bodies with HOMER
Genome_build: mm10 + NM052517
Supplementary_files_format_and_content: tdf

organism: Mus musculus

growth_protocol: Thawed cells from ATCC were mainted in DMEM + 10% FBS, split every 2-3 days and kept below passage 18

extract_protocol:
Lysates were clarified from sonicated nuclei and PolII-DNA complexes were isolated with antibody.
Libraries were prepared using the KAPA Hyper prep Kit (KAPA KK8504). Briefly, 20ng of ChIP'd or input DNA for each sample was subjected to end repair and A-tailing. Illumina adapters were ligated and then the samples were PCR amplified with Illumina primers for 15 cycles. The purified DNA was sequenced on a Hi Seq 4000

treatment_protocol: Cells were infected at a MoI of 5 with either MHV68 WT or R443I virus. For knockdown experiments, Cells were nucleofected with 20umols of siRNA twice over a 48h period prior to infection

value: B6 mouse fibroblasts

tag: passages

tag: strain


title: MC57G cells, Xrn1 siRNA, mock infection Rep 1 [RNA Polymerase II ChIP seq]

description:
MC57G cells, Xrn1 siRNA, mock infection Rep 1
RNA Polymerase II ChIP seq

value: Rpb1 (BioLegend, 8WG16)


title: MC57G cells, nontargeting siRNA, MHV68 infection Rep 2 [input DNA]

description:
MC57G cells, nontargeting siRNA, MHV68 infection Rep 2
input DNA


title: MC57G cells, Xrn1 siRNA, MHV68 infection Rep 2 [RNA Polymerase II ChIP seq]

description:
MC57G cells, Xrn1 siRNA, MHV68 infection Rep 2
RNA Polymerase II ChIP seq


title: MC57G cells, Xrn1 siRNA, MHV68 infection Rep 1 [RNA Polymerase II ChIP seq]

description:
MC57G cells, Xrn1 siRNA, MHV68 infection Rep 1
RNA Polymerase II ChIP seq


title: MC57G cells, Xrn1 siRNA, mock infection Rep 1 [input DNA]

description:
MC57G cells, Xrn1 siRNA, mock infection Rep 1
input DNA


title: MC57G cells, nontargeting siRNA, R443I infection Rep 2 [RNA Polymerase II ChIP seq]

description:
MC57G cells, nontargeting siRNA, R443I infection Rep 2
RNA Polymerase II ChIP seq


title: MC57G cells, Xrn1 siRNA, MHV68 infection Rep 1 [input DNA]

description:
MC57G cells, Xrn1 siRNA, MHV68 infection Rep 1
input DNA


title: MC57G cells, nontargeting siRNA, MHV68 infection Rep 1 [input DNA]

description:
MC57G cells, nontargeting siRNA, MHV68 infection Rep 1
input DNA


title: MC57G cells, nontargeting siRNA, mock infection Rep 2 [RNA Polymerase II ChIP seq]

description:
MC57G cells, nontargeting siRNA, mock infection Rep 2
RNA Polymerase II ChIP seq


title: MC57G cells, nontargeting siRNA, R443I infection Rep 1 [input DNA]

description:
MC57G cells, nontargeting siRNA, R443I infection Rep 1
input DNA


title: MC57G cells, nontargeting siRNA, mock infection Rep 1 [input DNA]

description:
MC57G cells, nontargeting siRNA, mock infection Rep 1
input DNA


title: MC57G cells, nontargeting siRNA, MHV68 infection Rep 2 [RNA Polymerase II ChIP seq]

description:
MC57G cells, nontargeting siRNA, MHV68 infection Rep 2
RNA Polymerase II ChIP seq


title: MC57G cells, nontargeting siRNA, mock infection Rep 2 [input DNA]

description:
MC57G cells, nontargeting siRNA, mock infection Rep 2
input DNA


title: MC57G cells, nontargeting siRNA, R443I infection Rep 1 [RNA Polymerase II ChIP seq]

description:
MC57G cells, nontargeting siRNA, R443I infection Rep 1
RNA Polymerase II ChIP seq


title: MC57G cells, nontargeting siRNA, mock infection Rep 1 [RNA Polymerase II ChIP seq]

description:
MC57G cells, nontargeting siRNA, mock infection Rep 1
RNA Polymerase II ChIP seq


title: MC57G cells, nontargeting siRNA, MHV68 infection Rep 1 [RNA Polymerase II ChIP seq]

description:
MC57G cells, nontargeting siRNA, MHV68 infection Rep 1
RNA Polymerase II ChIP seq


title: MM5 WT5

city: San Francisco

first: Michelle

middle: Amy

last: Mintz

address: 513 Parnassus Ave

department: Microbiology and Immunology

institute: University of California San Francisco

data_processing:
Base calling performed using RTA (Real-time Analysis), demultiplexed FASTQ files generated using CASAVA
RNA-seq paired end reads were aligned using Tophat (ver. 2.0.8b, Linux) to output read alignments that map once to the genome; other parameters were set as default
Aligned reads were then analyzed for differential expression using cufflinks (ver. 2.1.1).
Cufflinks output was transferred to excel file and then formatted.
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet containing gene expression matrix reported as FPKM values

molecule: total RNA

source_name: Germinal Center B cells WT

extract_protocol:
Mice were euthanized and 5x10^4 GC B cells were FACS sorted for purity (B220+IgDloCD38loGL7+Fas+), flash frozen and RNA from extracted using Qiagen RNeasy Micro Kit
Ovation RNA-seq System V2 from Nugen for amplification, KAPA Hyper prep labeling kit and NEXTFlex DNA barcodes adapter from Bioo Scientific to label the adaptors.

treatment_protocol: Bone marrow chimeras were generated, reconstituted for 8 weeks, immunized with NP-CGG alum, and analyzed at day 11.

value: Germinal Center B cells

tag: genotype

value: WT

tag: background strain


title: MM6 KO6

source_name: Germinal Center B cells HVEM KO

value: HVEM KO

value: HVEM KO C57BL/6 CD45.2


title: MM3 WT3


title: MM1 WT1


title: MM2 KO2


title: MM4 KO4


title: MC57G cells, Xrn1 siRNA, mock infection Rep 2 [RNA Polymerase II ChIP seq]

description:
MC57G cells, Xrn1 siRNA, mock infection Rep 2
RNA Polymerase II ChIP seq


title: RHB7025

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

data_processing:
Raw reads were aligned to the human reference genome GRCh38 from GENCODE using RSEM program version 1.3.0 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the human GENCODE annotation version 25.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: human peripheral blood dendritic cells and monocytes

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll-Paque (GE Healthcare) density gradient centrifugation of whole blood form a human donor
Single cell cDNA libraries were made using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modification: Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina, San Diego, CA, USA) (300 samples/lane).
Single Cell RNA-Seq

value: dendritic cells and monocytes


title: RHB7031


title: RHB7027


title: RHB7026


title: RHB7028


title: RHB7024


title: RHB7030


title: RHB7029


title: RHB7023


title: RHB7022


title: RHB7021


title: RHB7016


title: RHB7018


title: RHB7019


title: RHB7017


title: RHB7014


title: RHB7013


title: RHB7020


title: RHB7010


title: RHB7011


title: RHB7012


title: RHB7009


title: RHB7008


title: RHB7003


title: RHB7005


title: RHB7004


title: RHB7007


title: RHB7006


title: RHB7015


title: RHB7000


title: RHB7001


title: RHB7002


title: RHB6993


title: RHB6999


title: RHB6991


title: RHB6985


title: RHB6988


title: RHB6998


title: RHB6994


title: RHB6996


title: RHB6984


title: RHB6997


title: RHB6983


title: RHB6980


title: RHB6989


title: RHB6986


title: RHB6992


title: RHB6982


title: RHP6537


title: RHB6995


title: RHB6990


title: RHP6535


title: RHB6981


title: RHB6979


title: RHP6536


title: RHP6534


title: RHP6530


title: RHB6987


title: RHP6533


title: RHP6529


title: RHP6532


title: RHP6531


title: RHP6524


title: RHP6525


title: RHP6521


title: RHP6518


title: RHP6519


title: RHP6516


title: RHP6513


title: RHP6515


title: RHP6510


title: RHP6517


title: RHP6509


title: RHP6514


title: RHP6512


title: RHP6511


title: RHP6508


title: RHP6528


title: RHP6505


title: RHP6506


title: RHP6527


title: RHP6523


title: RHP6504


title: RHP6526


title: RHP6500


title: RHP6503


title: RHP6499


title: RHP6502


title: RHP6522


title: RHP6520


title: RHP6497


title: RHP6491


title: RHP6494


title: RHP6501


title: RHP6507


title: RHP6488


title: RHP6496


title: RHP6486


title: RHP6493


title: RHP6495


title: RHP6484


title: RHP6485


title: RHP6483


title: RHP6490


title: RHP6481


title: RHP6480


title: RHP6482


title: RHP6498


title: RHP6477


title: RHP6479


title: RHP6475


title: RHP6478


title: RHP6492


title: RHP6471


title: RHP6474


title: RHP6476


title: RHP6473


title: RHP6468


title: RHP6489


title: RHP6472


title: RHP6487


title: RHP6470


title: RHP6463


title: RHP6469


title: RHP6465


title: RHP6467


title: RHP6466


title: RHP6464


title: RHP6460


title: RHP6452


title: RHP6462


title: RHP6461


title: RHP6451


title: RHP6458


title: RHP6450


title: RHP6457


title: RHP6456


title: RHP6448


title: RHP6447


title: RHP6454


title: RHP6446


title: RHP6453


title: RHP6449


title: RHP6443


title: RHP6442


title: RHP6441


title: RHP6440


title: RHP6439


title: RHP6445


title: RHP6444


title: RHP6459


title: RHP6436


title: RHP6437


title: RHP6455


title: RHP6438


title: RHP6434


title: RHP6433


title: RHP6435


title: RHP6431


title: RHP6432


title: RHP6425


title: RHP6428


title: RHP6422


title: RHP6421


title: RHP6420


title: RHP6430


title: RHP6429


title: RHP6426


title: RHP6416


title: RHP6427


title: RHP6418


title: RHP6419


title: RHP6417


title: CAR_2 H3K27ac


title: RHP6413


title: RHP6414


title: RHP6410


title: RHP6411


title: RHP6403


title: RHP6409


title: RHP6401


title: RHP6399


title: RHP6400


title: RHP6398


title: RHP6397


title: RHP6408


title: RHP6424


title: RHP6402


title: RHP6415


title: RHP6405


title: RHP6423


title: PV3 (RNA-Seq)

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

country: China

institute: Nanjing Normal University

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) including the Q20, Q30 and GC-content of the clean data.
All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content.
Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
All assembled Unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/), Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/) and eggNOG (http://eggnogdb.embl.de/) databases using DIAMOND [3] with a threshold of E-value<0.00001.
Supplementary_files_format_and_content: TPMs

organism: Tachysurus vachellii

source_name: liver

growth_protocol: Parental fish of P. fulvidraco and P. vachelli were obtained from Nanjing Fisheries Research Institute. Fish breeding and cultivation were performed at Nanjing Normal University at Jiangsu Province, China. Artificial fertilization of M ♀ × M ♂, F ♀ × F ♂, and F ♀ × M ♂ were conducted through manually abdominal compression for harvesting eggs from female and stripping sperm from male after hormone injections.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analysed with Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
For nine cDNA library constructions (M1, M2, M3, F1, F2, F3, H1, H2 and H3), approximately 10 μg of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Obtained fertilized eggs (M, F, and H) were incubated at a water temperature of 28°C in flow-through water until hatching. Three lines were fed with live Artemia nauplii to satiation thrice-daily until the mouth gape sizes for all fish matched the size of the artificial compound feed. The feed was slightly over-supplied based on the previous consumption. 600 juvenile fish of M were averagely reared in 3 aquaria (200 individuals / 700 L of volume with bio-filtered water recirculation system) with same stocking density. The treatment procedure for F and H were also followed as the description of M.

tag: developmental stage

value: juvenile fish

tag: tissue

value: liver


title: RHP6406


title: PV2 (miRNA-Seq)

data_processing:
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 21.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤20). (6) number of nucleotides in one bulge in mature region (≤8) (7) number of biased errors in one bulge in mature region (≤4) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤7) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: normalized_counts

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA libraries (M1, M2, M3, F1, F2, F3, H1, H2 and H3) according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.


title: RHP6396


title: RHP6394


title: RHP6391


title: PV2 (RNA-Seq)


title: RHP6412


title: PV1 (RNA-Seq)


title: RHP6407


title: PV3 (miRNA-Seq)


title: RHP6393


title: PV1 (miRNA-Seq)


title: RHP6395


title: RHP6392


title: RHP6404


title: RHP6385


title: RHP6389


title: RHP6388


title: RHP6383


title: RHP6387


title: RHP6384


title: PVAT_S94

city: London

first: Wenduo

last: Gu

state: Select One

address: James Black Centre, 125 Coldharbour Lane

institute: King's College London

data_processing:
l1 and l2 are technical reads and R1 and R2 are biological reads.
Alignment-HiSat2 2.0.5
Sort – SamTools 1.4
Assemble – StringTie 1.3.3
Quality control and data filtering – R package Scater
visualization of clusters – ASAP (automated single cell analysis pipeline)
Genome_build: mm9
Supplementary_files_format_and_content: txt, normalized data

source_name: Peri-aorta adipose tissue

growth_protocol: Primary peri-aorta adipose tissue stromal vascular fraction single cells were isolated with collagenase I and subjected for sequencing

extract_protocol:
lysis buffer Clontech
Labcyte standard protocols
SMARTseq v4

value: normal adipose tissue

tag: sorted cell type

tag: age


title: RHP6390

tag: cell type


title: PVAT_S93


title: RHP6386


title: RHP6382


title: PVAT_S90


title: RHP6378


title: RHP6380


title: Gapmer#4 biological rep 3

type: RNA

city: Halifax

first: Paola

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

department: Pathology

country: Canada

institute: Dalhousie University

hyb_protocol: Hybridized to Affymetrix Human Gene 2.0 ST, 16 hr at 45°C . Washing = FS450_0002

scan_protocol: Affymetrix GeneChip Scanner 3000(Scanner#4)

data_processing: Expression Console

label: Biotin

source_name: breast cancer cells treated with anti-LINC00284 GapmeR

label_protocol: Sample preparaton with Affymetrix WT PLUS Kit and labeled with Biotin Allonamide Triphosphate

growth_protocol: MDA-MB-468 cells were cultured in a humidified incubator at 37oC, with 5% CO2 in DMEM media, supplemented with 10% FBS

extract_protocol: Cells were collected in TRIzol and RNA purified using a PureLink RNA kit (Invitrogen Thermo Fisher Scientific) following the manufacturer’s instructions.

treatment_protocol: MDA-MB-468 cells were treated for 48 hours with 15nM screening-grade modified antisense oligonucleotices GapmeRs, (Qiagen) admixed with TransIT-BrCa (MS Biolnyx) as per the manufacturer’s instructions.

tag: cell line

tag: genotype/variation

value: LINC00284 knockdown


title: RHP6381


title: control biological rep 3

source_name: breast cancer cells treated with control GapmeR

value: control


title: control biological rep 2


title: Gapmer#4 biological rep 1


title: PVAT_S91


title: control biological rep 1


title: Gapmer#4 biological rep 2


title: PVAT_S85


title: PVAT_S89


title: RHP6379


title: RHP6377


title: PVAT_S84


title: PVAT_S88


title: PVAT_S82


title: PVAT_S87


title: PVAT_S86


title: RHP6372


title: RHP6375


title: RHP6376


title: RHP6371


title: RHP6373


title: PVAT_S81


title: WI-38 HRAS(G12v) 2

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: WI-38 oncogene-induced senescence

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program.
The reads were cleaned usning cutadapt program
The reads were aligned using STAR aligner (v2.4) using hg19 Ensembl v82 annotation database
Read counts were generated using featureCounts software
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: Lung

growth_protocol: Cultured in DMEM supplemented with 10% FBS (Gibco), 1% antibiotics, 1% antimycotics, and 1% NEAA (Invitrogen).

extract_protocol:
Standard paired-end illumina preparation: Illumina Hiseq 2x150bp configuration single index per lane, RNA library preparation with rRNA depletion
Total RNA was extracted using TriPure (Roche)
RiboRNA depletion was done using RiboRNA depletion nano kit (Qiagen), cDNA synthesis was made with Ovation RNA-seq System V2 (NuGEN), Library prep was made with TruSeq ChIP Sample Preparation Kit (Illumina), Hiseq PE Cluster Kit (Illumina) and Hiseq SBS Kit (Illumina) was used for clustering and sequencing

value: Human Diploid Lung Fibroblast

value: Lung

tag: treatment

value: Treatment with lentivirus expressing HRASG12V at 10 MOI, and puromycin (1 µg/mL)


title: RHP6370


title: RHP6374


title: PVAT_S79


title: PVAT_S92


title: PVAT_S78


title: WI-38 Dox+ 2

description: WI-38 doxorubicin-induced senescence

value: Treated with 2 µg/mL Dox (Sigma) for 24 h


title: WI-38 EV 1

description: WI-38 empty vector control

value: Treatment with empty vector at 10 MOI, and , and puromycin (1 µg/mL)


title: PVAT_S74


title: PVAT_S77


title: PVAT_S76


title: PVAT_S75


title: WI-38 Dox- 2

description: WI-38 control

value: Control


title: PVAT_S73


title: WI-38 Dox- 1

description: WI-38 control


title: PVAT_S80


title: PVAT_S83


title: PVAT_S71


title: WI-38 HRAS(G12v) 1

description: WI-38 oncogene-induced senescence


title: PVAT_S69


title: WI-38 Dox+ 1

description: WI-38 doxorubicin-induced senescence


title: PVAT_S70


title: IMR-90 IR+ 2

description: IMR-90 IR treatment

value: 10 Gy of ionizing radiation exposure


title: IMR-90 PDL52 2

description: IMR-90  replicative senescence

value: Replicative exhaustion


title: WI-38 EV 2

description: WI-38 empty vector control


title: IMR-90 IR+ 1

description: IMR-90 IR treatment


title: PVAT_S67


title: IMR-90 PDL15 2

description: IMR-90 proliferating control

value: Proliferating cells


title: PVAT_S68


title: IMR-90 PDL52 1

description: IMR-90  replicative senescence


title: PVAT_S64


title: IMR-90 PDL15 1

description: IMR-90 proliferating control


title: PVAT_S66


title: PVAT_S65


title: HUVEC IR+ 3

description: HUVEC IR-induced senescence

source_name: Umbilical

growth_protocol: Cultured in EBM with EGM SingleQuotsTM Kit supplements and growth factors (Lonza).

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: Umbilical

value: 4 Gy of ionizing radiation exposure


title: HUVEC IR+ 2

description: HUVEC IR-induced senescence


title: PVAT_S72


title: PVAT_S62


title: PVAT_S63


title: HUVEC IR+ 1

description: HUVEC IR-induced senescence


title: HUVEC IR- 3

description: HUVEC control


title: PVAT_S60


title: HUVEC IR- 2

description: HUVEC control


title: HAEC IR+ 3

description: HAECs IR-induced senescence

source_name: Aortic

growth_protocol: Cultured in EBM-2 Basal Medium supplemented with EGM-2 SingleQuotsTM Kit supplements and growth factors (Lonza)

value: HAEC

value: Human Aortic Endothelial Cells

value: Aortic


title: PVAT_S59

value: normal adipose tissue


title: PVAT_S61


title: HUVEC IR- 1

description: HUVEC control


title: PVAT_S57


title: PVAT_S54


title: HAEC IR- 1

description: HAECs control


title: BC-3 1uM CC-122 treated Day21 harvest replicate 2

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

description: lentivirally integrated sgRNA casette amplified from gDNA

data_processing:
Library strategy: CRISPR screen
The 5′ and 3′ adapter sequences were removed from demultiplexed sequencing reads
Remaining reads were aligned to the Brunello CRISPR library file using Bowtie
The number of reads per sgRNA were counted and summarized in a read count table
Genome_build: hg19
Supplementary_files_format_and_content: .txt with read count

source_name: Human Primary Effusion Lymphoma cell line BC-3

growth_protocol: Clonal Cas9 expressing BC-3 cells were grown in RPMI + 20% Serum Plus II (Sigma Aldrich) at concentration ranging from 3X10^5 to 9X10^5 cells/ml. The Brunello library was transduced at an MOI of 0.3. 1ug/ml Puromycin was used to select after library transduction

extract_protocol:
Cells pelleted, washed twice with sterile cold PBS and flah frozen in an ethanol-dry ice bath before storing at -80C. gDNA was harvested from frozen cell pellets by following the gDNA extraction protocol mentioned in Manzano et al., Nature Communications, 2018.
Protocol followed for PCR amplification and barcoding of sgRNA inserts is mentioned in Manzano et al., Nature Communications 2018.

treatment_protocol: All compounds were dissolved in DMSO. cells were treated with either 5uM Lenalidomide, 1uM Pomalidomide, 1uM CC-122 or corresponding volume of DMSO. Media was changed and fresh drug was added every two days.

tag: modification 1

value: Lentivirally transduced SpCas9

tag: modification 2

value: lentivirally transduceed Brunello sgRNA library


title: HAEC IR- 2

description: HAECs control


title: PVAT_S56


title: PVAT_S53


title: HAEC IR+ 1

description: HAECs IR-induced senescence


title: PVAT_S55


title: PVAT_S52


title: PVAT_S51


title: PVAT_S48


title: HAEC IR+ 2

description: HAECs IR-induced senescence


title: BC-3 1uM Pomalidomide treated Day21 harvest replicate 2


title: PVAT_S50


title: BC-3 5uM Lenalidomide treated Day21 harvest replicate 2


title: BC-3 1uM Pomalidomide treated Day21 harvest replicate 1


title: PVAT_S49


title: PVAT_S47


title: BC-3 5uM Lenalidomide treated Day21 harvest replicate 1


title: BC-3 1uM CC-122 treated Day21 harvest replicate 1


title: BC-3 DMSO treated Day21 harvest replicate 1


title: BC-3 5uM Lenalidomide treated Day13 harvest replicate 2


title: PVAT_S46


title: BC-3 5uM Lenalidomide treated Day13 harvest replicate 1


title: PVAT_S45


title: BC-3 DMSO treated Day21 harvest replicate 2


title: PVAT_S44


title: BC-3 DMSO treated Day13 harvest


title: PVAT_S58


title: PVAT_S43


title: BC-3 1uM CC-122 treated Day9 harvest replicate 2


title: BC-3 1uM CC-122 treated Day9 harvest replicate 1


title: PVAT_S40


title: BC-3 1uM Pomalidomide treated Day9 harvest replicate 1


title: PVAT_S42


title: BC-3 DMSO treated Day9 harvest


title: BC-3 1uM Pomalidomide treated Day9 harvest replicate 2


title: PVAT_S35


title: PVAT_S39


title: PVAT_S41


title: PVAT_S37


title: siWnk1 Nuclear Extract Rep2

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

data_processing:
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg38
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 1.2
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
BigWig files were generated from the above bedgraph files through the bedGraphToBigWig tool (Kent et al., 2002).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: siWnk1 Nuclear Extract

growth_protocol: Cells were grown in DMEM medium 10% FBS

extract_protocol:
Nuclear and Cytoplasmic fractions were isolated from the cells followed by RNA extraction using Trizol reagent.
library preparation with pA selection, directional. Kit used was  Illumina TruSeq Stranded mRNA Library Prep Kit with standard universal Illumina multiplexing adapters

treatment_protocol: siRNAs were transfected using Lipofectamin RNAimax, as described in the suppliers protocol. Cells were grown for 48 hours before extraction.

value: HeLa

value: WNK1 kinase depleted

tag: fraction

value: Nuclear Extract


title: PVAT_S31


title: siLuc Nuclear Extract Rep2

source_name: siLuc Nuclear Extract

value: control


title: siWnk1 Cytoplasmic Extract Rep1

source_name: siWnk1 Cytoplasmic Extract

value: Cytoplasmic Extract


title: PVAT_S34


title: PVAT_S36


title: siWnk1 Cytoplasmic Extract Rep2


title: PVAT_S38


title: siLuc Cytoplasmic Extract Rep2

source_name: siLuc Cytoplasmic Extract


title: PVAT_S30


title: PVAT_S33


title: siWnk1 Nuclear Extract Rep1


title: siLuc Cytoplasmic Extract Rep1


title: TK6_WT_rep1

city: Mainz

first: Vassilis

last: Roukos

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology gGmbH

data_processing:
Raw sequencing reads were mapped to human Hg19 reference genome with STAR (vSTAR-2.5.3a)
Gene level counting was performed with iRNA-seq pipeline using count mode (iRNA-v1.1)
The count values were normalized based on the mean of the two replicates divided by the length of the gene
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited text file includes the normalized count values for each sample

molecule: nuclear RNA

extract_protocol:
Factory RNA was isolated as described in Melnik et al., Nat Protco, 2016, and subsequently purified using Tri-Zol reagent according to the manufacturers instructions (Thermo Fisher).
RNA libraries were prepared for sequencing using standard Illumina RiboMinus/TruSeq protocols.

value: lymphoblastoid cells


title: PVAT_S29


title: PVAT_S32


title: siLuc Nuclear Extract Rep1


title: TK6_WT_rep2


title: PVAT_S28


title: shHIF1a_t48_R1

description:
processed data file:
edgeR_shHIF1a_hypoxia_t48h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt

value: melanoma cell line

value: HIF1a knockdown

tag: treated with

value: 1% O2 level for 48h (t48)


title: shHIF1a_t24_R3

description:
processed data file:
edgeR_shHIF1a_hypoxia_t24h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt

value: 1% O2 level for 24h (t24)


title: PVAT_S27


title: PVAT_S25


title: PVAT_S26


title: shHIF1a_t24_R2


title: shHIF1a_t24_R1


title: shHIF1a_t12_R3

description:
processed data file:
edgeR_shHIF1a_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt

value: 1% O2 level for 12h (t12)


title: PVAT_S24


title: PVAT_S23


title: PVAT_S21


title: shHIF1a_t0_R1

value: 1% O2 level for 0h (t0)


title: shHIF1a_t12_R2


title: PVAT_S22


title: PVAT_S18


title: shHIF1a_t0_R2


title: shHIF1a_t12_R1


title: PVAT_S19


title: IGR39_t24_R3

description:
processed data file:
edgeR_IGR39_hypoxia_t24h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt


title: PVAT_S20


title: IGR39_t24_R1


title: PVAT_S16


title: IGR39_t12_R3

description:
processed data file:
edgeR_IGR39_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt


title: PVAT_S17


title: shHIF1a_t0_R3


title: PVAT_S14


title: PVAT_S15


title: IGR39_t12_R1


title: IGR39_t12_R2


title: PVAT_S12


title: PVAT_S11


title: IGR39_t0_R1


title: IGR39_t24_R2


title: PVAT_S10


title: IGR39_t0_R2


title: PVAT_S8


title: IGR37_t12_R1

description:
processed data file:
edgeR_IGR37_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt


title: PVAT_S7


title: IGR37_t12_R2


title: PVAT_S9


title: PVAT_S3


title: IGR37_t0_R1


title: PVAT_S6


title: 501_t48_R2

description:
processed data file:
edgeR_501_hypoxia_t48h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt


title: PVAT_S2


title: 501_t48_R3


title: IGR37_t0_R3


title: PVAT_S4


title: 501_t48_R1


title: PVAT_S13


title: IGR37_t0_R2


title: 501_t24_R3

description:
processed data file:
edgeR_501_hypoxia_t24h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt


title: PVAT_S1


title: 501_t24_R2


title: 501_t24_R1


title: 501_t12_R3

description:
processed data file:
edgeR_501_hypoxia_t12h_relative_to_t0_QLF-test_filtered_1cpm_3rep.txt


title: IGR39_t0_R3


title: 501_t12_R2


title: 501_t12_R1


title: IGR37_t12_R3


title: PVAT_S5


title: 501_t0_R2


title: 501_t0_R1


title: PF1 (RNA-Seq)

organism: Tachysurus fulvidraco

value: juvenile fish

value: liver


title: PF2 (RNA-Seq)


title: PF2 (miRNA-Seq)


title: Primary BM monocyte from Trem1-/- mouse 2_27

city: Aachen

first: Oliver

last: Pabst

address: Pauwelsstrasse 30

department: Institute of Molecular Medicine

institute: RWTH Aachen University

description:
TpMono1-2_24
Gene expression of bone marrow monocytes of non-manipulated Trem1-/- mouse

hyb_protocol: Pre-amplified DNA was then hybridized with barcoded target-specific oligonucleotide probe pairs. Hybridization was performed according to manufacturer’s instructions by incubating the reaction tube containing samples, probes and Tagset at 67 oC for 19 hr. After 19 hr of incubation, samples were run in nCounter Prep-station (nanostring technologies inc.) to remove unbound probes and tags, and immobilize hybridized sequences on sample cartridge surface.

scan_protocol: Sample cartridges were scaned and analyzed by nCounter digital analyzer (nanostring technologies inc.).

data_processing: The data were normalized by and analyzed using Qlucore Omics explorer.

source_name: Bone marrow of non-manipulated Trem1-/- mouse

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (TagSet, ELE-P1TS-072, nanostring technologies inc.) were used to label target sequences

extract_protocol: One hundred donor monocyte-derived cells were recovered and FACS-sorted from both non-inflamed and inflamed small intestine of recipient mice at day 1 post-transfer. RNA was reverse-transcribed to cDNA immediately after sorting and stored at -80 oC.

treatment_protocol: The small intestine of recipient mice were surgically manuplated to induce intestinal inflammation one day before adoptive monocyte transfer whereas non-manipulated mice did not undergo any surgical procedure.

tag: cells analyzed

value: Primary monocytes from bone marrow of non-manipulated Trem1-/- mouse

tag: days after transfer

value: day 1

tag: dono mice


title: Primary BM monocyte from WT mouse-1_23

description:
WpMono1-1_23
Gene expression of bone marrow monocytes of non-manipulated WT mouse

source_name: Bone marrow of non-manipulated WT mouse

value: Primary monocytes from bone marrow of non-manipulated WT mouse

value: C57BL/6 WT


title: Primary BM monocyte from Trem1-/- mouse 3_28

description:
TpMono1-3_25
Gene expression of bone marrow monocytes of non-manipulated Trem1-/- mouse


title: Primary BM monocyte from Trem1-/- mouse 1_26

description:
TpMono1-1_23
Gene expression of bone marrow monocytes of non-manipulated Trem1-/- mouse


title: Primary BM monocyte from WT mouse 2_24

description:
WpMono1-2_24
Gene expression of bone marrow monocytes of non-manipulated WT mouse

source_name: Bone marow of non-manipulated WT mouse


title: Primary BM monocyte from WT mouse 3_25

description:
WpMono1-3_25
Gene expression of bone marrow monocytes of non-manipulated WT mouse


title: Trem1-/- donor to manipulated SI day 1 Mouse 7_22

description:
TMSId1-7_22
Gene expression of Trem1-/- donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.

source_name: Small intestine of manipulated mouse

value: Transferred monocytes recovered from inflamed Small intestine of recipient mouse

tag: recipient mice


title: RH-RAS leukemia stem cell line, IBET151_24hr_1

city: Birmingham

first: Rui

last: Lu

state: AL

address: 1824 6th Ave S

institute: Univ of Alabama at Birmingham

hyb_protocol: Samples were hybridized with Affymetrix Mouse Gene 2.1 ST Array Strip (Affymetrix) according to the manifacture's instruction.

scan_protocol: Standard Affymetrix protocol

data_processing:
Hybridization signals were retrieved and normalized, followed by differential expression analysis and statistical analysis using GeneSpring Analysis Platform GX 12.6 (Agilent Technologies).
MoGene-2_1-st.pgf
MoGene-2_1-st.mps

label: biotin

source_name: 100 nM IBET-151, 24 hours

label_protocol: The cDNA was fragmented and terminally labeled with biotin, using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix, Santa Clara, CA)

growth_protocol: Lin- enriched murine hematopoietic stem/progenitor cells leukemia progenitor cell lines were cultured in Opti-MEM base medium supplemented with 10% FBS, 1% antibiotics, 50 μM mercaptoethanol and stem cell factor

extract_protocol: Total RNA was isolated with the Rneasy Plus Miniprep Kit (Qiagen).

treatment_protocol: Primary HSPC Cells were retrovirally infected with NRAS G12D alone (EV-RAS), DNMT3A R882H with NRAS G12D (RH-RAS) or DNMT3A WT with NRAS G12D (WT-RAS)

value: RH-RAS leukemia stem cell lines (transformed by DNMT3A R882H and NRAS G12D)

tag: agent


title: RH-RAS leukemia stem cell line, DMSO_24hr_1

source_name: DMSO, 24 hours

value: DMSO


title: Trem1-/- donor to manipulated SI day 1 Mouse 5_20

description:
TMSId1-5_20
Gene expression of Trem1-/- donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: Trem1-/- donor to manipulated SI day 1 Mouse 6_21

description:
TMSId1-6_21
Gene expression of Trem1-/- donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: 501_t0_R3


title: E12_4C_4C_DFL_Wt_Hoxd4 [re-used]

city: Geneva

first: Eddie

last: Rodríguez-Carballo

address: 4, Boulevard d'Yvoy

department: Department of Genetics and Evolution

country: Switzerland

institute: Université de Genève

data_processing:
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to the mm10 (GRCm38) mouse genome assembly with bowtie2 version 2.2.1 (Langmead et al, 2012) with parameters “--end-to-end --sensitive -k 20”.Hoxd4 viewpoint sequences were as used inAndrey et al et al 2013 (PMID:23744951). Undigested and self-ligated sequences were discarded, which for Hoxd4 were CATGCAGAACGTGACAAGGCCCAGACATTCCACCAATACCTAGAACTCC (un-digested) and CATGGAGCCTGGTTCACTGTGTGCAGGCCTGGTTCATAGAAGGAACTACA(self-ligated) and for CS38 were CATGGTGCCCATAAGTGCTTTTTAGCCACAGAAAGTCAACATGTCACCT (undigested) and (self-ligated).
4C bedgraphs were made through HTSstation: using a running mean algorithm with a window size of eleven fragments. Normalisation was done by dividing the fragment scores by the mean of fragments scores falling into a region defined as +/-5Mb around the centre of the bait coordinates, such as to see only changes in contact distribution and to minimize PCR complexity bias in each sample.
De-multiplexing, mapping and 4C-analysis were performed through HTSstation (David et al, 2014 and http://htsstation.epfl.ch/). Reads were mapped to the mm10 (GRCm38) mouse genome assembly with bowtie2 version 2.2.1 (Langmead et al, 2012) with parameters “--end-to-end --sensitive -k 20”.Hoxd4 viewpoint sequences were as used in Rodríguez-Carballo et al 2017 (PMID:) Undigested and self-ligated sequences were discarded, which are CATGCAGAACGTGACAAGGCCCAGACATTCCACCAATACCTAGAACTCC and CATGGAGCCTGGTTCACTGTGTGCAGGCCTGGTTCATAGAAGGAACTACA respectively for Hoxd4 and CATGGTGCCCATAAGTGCTTTTTAGCCACAGAAAGTCAACATGTCACCTC and CATGTAATAGACAGAGCAGCAGTGTAGAGTGGGTTTAAAAGAGGATCCAG respectively for CS38.
Genome_build: mm10
Supplementary_files_format_and_content: Smoothed/normalized data (bedGraph), one per viewpoint, per tissue.

source_name: Distal forelimb mouse E12.5 4C Wt Hoxd4 viewpoint

extract_protocol:
Micro-dissected proximal and distal segments of E12.5 forelimbs mutant embryos (invHoxD(attP-Itga6)). Tissues were dissected, dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed with 2% formaldehyde (in PBS/10%FBS) for 10 min at room temperature and the reaction was quenched on ice with glycine. Cells were further lysed with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EDTA, 1x Protease inhibitor cocktail to isolate nuclei and stored at -80°C. Nuclei from pools of at least 10 distal or proximal limbs were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Samples were digested again with DpnII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions.
These templates were amplified using Expand long template (Roche) and inversed PCR primers flanked with adaptors allowing multiplexing. The illumina adaptors used were 5'-AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' for the inverse-forward primers located at the NlaIII site and 5'-CAAGCAGAAGACGGCATACGA-3' for the inverse-reverse primers located at the DpnII site. Barcodes (4bp) were added between the illumina adaptor and the specific NlaIII primers when the same viewpoints were multiplexed in the same run.

tag: strain

tag: genotype

value: Wild type

tag: embryonic day

value: Distal Forelimbs


title: E12_4C_4C_PFL_Wt_Hoxd4 [re-used]

source_name: Proximal forelimb mouse E12.5 4C Wt Hoxd4 viewpoint

tag: tissue

value: Proximal Forelimbs


title: E12_4C_4C_DFL_Wt_CS38 [re-used]

source_name: Distal forelimb mouse E12.5 4C Wt CS38 viewpoint


title: E12_4C_DFL_invattp-itga6_Hoxd4

source_name: Distal forelimb mouse E12.5 4C invattp-itga6 Hoxd4 viewpoint


title: Trem1-/- donor to manipulated SI day 1 Mouse 4_19

description:
TMSId1-4_19
Gene expression of Trem1-/- donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: E12_4C_PFL_invattp-itga6_Hoxd4

source_name: Proximal forelimb mouse E12.5 4C invattp-itga6 Hoxd4 viewpoint


title: Trem1-/- donor to manipulated SI day 1 Mouse 3_18

description:
TMSId1-3_18
Gene expression of Trem1-/- donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: PF3 (RNA-Seq)

source_name: liver

tag: developmental stage


title: Trem1-/- donor to manipulated SI day 1 Mouse 2_17

description:
TMSId1-2_17
Gene expression of Trem1-/- donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: RH-RAS leukemia stem cell line, IBET151_24hr_2

tag: cell line


title: E12_4C_DFL_invattp-itga6_CS38

source_name: Distal forelimb mouse E12.5 4C invattp-itga6 CS38 viewpoint


title: Trem1-/- donor to manipulated SI day 1 Mouse 1_16

description:
TMSId1-1_16
Gene expression of Trem1-/- donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: RH-RAS leukemia stem cell line, DMSO_24hr_2


title: PF3 (miRNA-Seq)


title: Trem1-/- donor to non-manipulated SI day 1 Mouse 5_15

description:
TNMSId1-5_15
Gene expression of Trem1-/- donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.

source_name: Small intestine of non-manipulated mouse

value: Transferred monocytes recovered from non-inflamed Small intestine of recipient mouse


title: PF1 (miRNA-Seq)


title: PFL_E12_aR5_delattP-Rel5_RNA-seq

description: Proximal forelimb mouse E12.5_delattp-Rel5_RNA-seq

data_processing:
Analysis was performed using the facilities of the Scientific IT and Application Support Center of EPFL. The gtf used for STAR and cufflinks, based on the version 94 of ensembl annotations, is available on figshare (doi:10.6084/m9.figshare.7775837). Adapters were removed using cutadapt (v1.16) and aligned onto mm10 using STAR with ENCODE parameters.
Strand specific coverage was performed on uniquely mapped reads (tag NH:i:1) with bedtools version 2.27.1
Bedgraphs were normalized to the number of million uniquely mapped reads and replicates were merged using the tool unionbedg (bedtools v2.27).
Genome_build: mm10
Supplementary_files_format_and_content: Mean of normalized bedgraph of the forward or reverse strand unique read coverage.

extract_protocol:
RNA was extracted using the it RNAeasy (Microkit, QIAGEN).
Truseq Stranded mRNA

treatment_protocol: Micro-dissected proximal and distal segments of E12.5 forelimbs either from wild type or mutant embryos (invHoxD(attP-Itga6) and del(HoxD(attP-Rel5)d9lac). Tissues were dissected and placed in RNAlater (invitrogen) and kept at -80ªC until further use.

tag: genotype/variation


title: DFL_E12_aR5_delattP-Rel5_RNA-seq

description: Distal forelimb mouse E12.5_delattp-Rel5_RNA-seq


title: Trem1-/- donor to non-manipulated SI day 1 Mouse 4_14

description:
TNMSId1-4_14
Gene expression of Trem1-/- donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: DFL_E12_aR5_Wt_RNA-seq

description: Distal forelimb mouse E12.5_Wt_RNA-seq

source_name: Distal forelimb mouse E12.5_Wt_RNA-seq

value: wild type


title: PFL_E12_aR5_Wt_RNA-seq

description: Proximal forelimb mouse E12.5_Wt_RNA-seq


title: Trem1-/- donor to non-manipulated SI day 1 Mouse 3_13

description:
TNMSId1-3_13
Gene expression of Trem1-/- donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: WT donor to manipulated SI day 1 Mouse 5_10

description:
WMSId1-5_10
Gene expression of WT donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: PFL_E12_i6a_invattp-itga6_RNA-seq

description: Proximal forelimb mouse E12.5_invattp-itga6_RNA-seq


title: Trem1-/- donor to non-manipulated SI day 1 Mouse 1_11

description:
TNMSId1-1_11
Gene expression of Trem1-/- donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: DFL_E12_i6a_Wt_RNA-seq

description: Distal forelimb mouse E12.5_Wt_RNA-seq


title: DFL_E12_i6a_invattp-itga6_RNA-seq

description: Distal forelimb mouse E12.5_invattp-itga6_RNA-seq


title: PFL_E12_i6a_Wt_RNA-seq

source_name: Proximal forelimb mouse E12.5_Wt_RNA-seq


title: Trem1-/- donor to non-manipulated SI day 1 Mouse 2_12

description:
TNMSId1-2_12
Gene expression of Trem1-/- donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: male p28 WT [698]

city: Safed

first: David

last: Enshell-Seijffers

address: 8 Henrietta Szold

department: The Azrieli Faculty of Medicine

institute: Bar Ilan University

description:
698
Ribosomal depletion was performed

data_processing:
trimmed and quality filtered using Trimmomatic
mapped to the mouse genome (NCBI38/mm10) using Tophat (version 2)
Mapped read for each annotated ENSEMBL gene (GRCm38.p4) were counted using HTSeq-count tool
Read count normalization and differential gene expression analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Read count normalization and differential gene expression

source_name: primary dermal papilla sorted cells

extract_protocol:
Total RNA was purified from FACS-sorted cells utilizing the RNeasy Plus Micro kit (QIAGEN)
Ribosomal depletion was performed on 100 ng of total RNA and libraries for Illumina sequencing were performed using the Nebnext Ultra Directional RNA kit (NEB, #E7420L)

tag: hair cycle stage

value: Anagen VI

tag: Sex

value: male

value: WT


title: male p28 WT [1138]

description:
1138
Ribosomal depletion was performed


title: WT donor to manipulated SI day 1 Mouse 4_09

description:
WMSId1-4_09
Gene expression of WT donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: WT donor to manipulated SI day 1 Mouse 2_07

description:
WMSId1-2_07
Gene expression of WT donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: male p28 Smo* mutant [709]

description:
709
Ribosomal depletion was performed

value: anagen (I-III)

value: Smo* mutant


title: WT donor to manipulated SI day 1 Mouse 3_08

description:
WMSId1-3_08
Gene expression of WT donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: WT donor to manipulated SI day 1 Mouse 1_06

description:
WMSId1-1_06
Gene expression of WT donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: male p28 WT [2648]

description:
2648
Ribosomal depletion was performed


title: male p28 Smo* mutant [2647]

description:
2647
Ribosomal depletion was performed


title: WT donor to non-manipulated SI day 1 Mouse 4_04

description:
WNMSId1-4_04
Gene expression of WT donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: WT donor to non-manipulated SI day 1 Mouse 5_05

description:
WNMSId1-5_05
Gene expression of WT donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: male p28 Smo* mutant [272]

description:
272
Ribosomal depletion was performed


title: WT donor to non-manipulated SI day 1 Mouse 3_03

description:
WNMSId1-3_03
Gene expression of WT donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: WT donor to non-manipulated SI day 1 Mouse 1_01

description:
WNMSId1-1_01
Gene expression of WT donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: WT donor to non-manipulated SI day 1 Mouse 2_02

description:
WNMSId1-2_02
Gene expression of WT donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: female p20 WT [2273]

description:
2273
Ribosomal depletion was performed

value: telogen

value: female


title: female p20 WT [3024]

description:
3024
Ribosomal depletion was performed


title: female p20 WT [1245]

description:
1245
Ribosomal depletion was performed


title: female p20 Smo* mutant [2127]

description:
2127
Ribosomal depletion was performed


title: female p20 Smo* mutant [1244]

description:
1244
Ribosomal depletion was performed


title: Non-manipulated SI (from manipulated WT donor) day 1 Mouse 3_32

description:
mWNMSItd1-3_32
Gene expression of monocyte from manipulated donors that are transferred non-manipulated recipient and recovered from small intestine at day 1 post-transfer.

data_processing: The data were normalized and analyzed using Qlucore Omics explorer.

extract_protocol: One hundred donor monocyte-derived cells were recovered and FACS-sorted from small intestine, liver, spleen and BM of both non-manipulated and manipulated of recipient mice at day 1 post-transfer. RNA was reverse-transcribed to cDNA immediately after sorting and stored at -80 oC.

value: Transferred monocytes recovered from small intestine of non-manipulated recipient

value: day 1

value: C57BL/6 WT (Manipulated)


title: Non-manipulated SI (from manipulated WT donor) day 1 Mouse 2_31

description:
mWNMSItd1-2_31
Gene expression of monocyte from manipulated donors that are transferred non-manipulated recipient and recovered from small intestine at day 1 post-transfer.


title: Primary BM monocyte from non-manipulated mouse 2_28

description:
NMWpMono1-2_28
Gene expression of bone marrow monocytes of non-manipulated mouse

source_name: Bone marrow of non-manipulated mouse

value: Primary monocytes from bone marrow of non-manipulated recipient

value: C57BL/6 WT


title: Non-manipulated SI (from manipulated WT donor) day 1 Mouse 1_30

description:
mWNMSItd1-1_30
Gene expression of monocyte from manipulated donors that are transferred non-manipulated recipient and recovered from small intestine at day 1 post-transfer.


title: Axitinib resistant rep 1

city: Buffalo

first: John

last: Ebos

state: NY

address: Elm & Carlton Streets

department: Department of Cancer Genetics and Genomics

institute: Roswell Park Cancer Institute

data_processing:
Pre-alignment quality control was performed using FASTQC v0.11.5.
Sequenced reads (fastq files) were alinged to the mouse genome GRCm38 M16 (Gencode) using STAR v2.6.0a.
Post-alignment quality control was performed using RSeQC v2.6.5.
Estimated counts at the gene level were quantified using RSEM v1.3.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include RSEM estimated counts at the gene level for all samples

source_name: Breast cancer cells

growth_protocol: Cells were maintained in RPMI supplemented with 5% FBS in the presence of 0.5μM axitinib. Growth media was refreshed every 3-4 days.

extract_protocol:
Total RNA from individual samples was extracted using the RNeasy mini kit (QIAGEN; 74104). Genomic DNA was digested using DNase I (QIAGEN; 79254) as described in the on-column DNase digestion protocol from QIAGEN.
One microgram total RNA was used for library preparation using the TruSeq Stranded mRNA kit (Illumina Inc) following manufacturer's instructions.

tag: variant

value: 4T1 AxR

tag: treatment

value: Axitinib

tag: dose

tag: treatment duration

value: >2 months


title: Manipulated BM day 1 Mouse 3_26

description:
WMBMtd1-3_26
Gene expression of donor monocyte-derived cells in the bone marrow of manipulated recipient at day 1 post-transfer.

source_name: Bone marow of manipulated mouse

tag: cells analyzed

value: Transferred monocytes recovered from bone marrow of manipulated recipient

tag: days after transfer


title: Parental rep 3


title: Primary BM monocyte from non-manipulated Mouse 1_27

description:
NMWpMono1-1_27
Gene expression of bone marrow monocytes of non-manipulated mouse

tag: dono mice


title: Manipulated BM day 1 Mouse 2_25

description:
WMBMtd1-2_25
Gene expression of donor monocyte-derived cells in the bone marrow of manipulated recipient at day 1 post-transfer.

tag: recipient mice


title: Parental rep 2


title: Manipulated Spl day 1 Mouse 3_23

description:
WMSpltd1-3_23
Gene expression of donor monocyte-derived cells in the spleen of manipulated recipient at day 1 post-transfer.

source_name: Spleen of manipulated mouse

value: Transferred monocytes recovered from spleen of manipulated recipient


title: Manipulated Spl day 1 Mouse 2_22

description:
WMSpltd1-2_22
Gene expression of donor monocyte-derived cells in the spleen of manipulated recipient at day 1 post-transfer.


title: Manipulated Spl day 1 Mouse 1_21

description:
WMSpltd1-1_21
Gene expression of donor monocyte-derived cells in the spleen of manipulated recipient at day 1 post-transfer.


title: Manipulated BM day 1 Mouse 1_24

description:
WMBMtd1-1_24
Gene expression of donor monocyte-derived cells in the bone marrow of manipulated recipient at day 1 post-transfer.


title: Axitinib resistant rep 3


title: Non-manipulated SI (from manipulated WT donor) day 1 Mouse 4_33

description:
mWNMSItd1-3_33
Gene expression of monocyte from manipulated donors that are transferred non-manipulated recipient and recovered from small intestine at day 1 post-transfer.


title: female p20 Smo* mutant [3010]

description:
3010
Ribosomal depletion was performed


title: Manipulated Liv day 1 Mouse 2_20

description:
WMLivtd1-2_20
Gene expression of donor monocyte-derived cells in the liver of manipulated recipient at day 1 post-transfer.

source_name: Liver of manipulated mouse

value: Transferred monocytes recovered from liver of manipulated recipient


title: Manipulated Liv day 1 Mouse 1_19

description:
WMLivtd1-1_19
Gene expression of donor monocyte-derived cells in the liver of manipulated recipient at day 1 post-transfer.


title: Cd11cCreKO.H37Rv.mEmNeg.24.AD80

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: processed data file: rawCounts.tsv

data_processing:
Read pairs were aligned to the mouse genome (mm10) + Mtb H37Rv genome using the gsnap aligner (v. 2018-07-04) allowing for novel splicing. (gsnap options: -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1)
Concordantly mapping read pairs (average 15-million / sample) that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Genome_build: mm10 + Mtb H37Rv (NC_000962.3)
Supplementary_files_format_and_content: rawCounts.tsv contains the raw counts for each sample generated by subRead, tab-separated.

source_name: Alveolar macrophages

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
cDNA libraries were constructed and amplified using the SMARTseq v4 mRNASMARTer Kit (Clontech) per the manufacturer's instructions. Libraries were amplified and then sequenced on an Illumina NextSeq (2 x 75, paired-end).

treatment_protocol: Mice were infected with 2000-4000 CFU of mEmerald-H37Rv.

tag: cell type

value: Alveolar macrophages

value: mEmNeg

value: 24 hr


title: Cd11cCreKO.H37Rv.naive.24.AD80

description: processed data file: rawCounts.tsv

value: naive


title: Cd11cCreCntl.H37Rv.mEmPos.24.AD80

description: processed data file: rawCounts.tsv

value: mEmPos


title: Cd11cCreKO.H37Rv.mEmPos.24.AD80

description: processed data file: rawCounts.tsv


title: Primary BM monocyte from manipulated mouse 1_29

description:
MWpMono1-1_29
Gene expression of bone marrow monocytes of manipulated mouse

source_name: Bone marrow of manipulated mouse

value: Primary monocytes from bone marrow of manipulated recipient


title: Axitinib resistant rep 2


title: Cd11cCreCntl.H37Rv.mEmNeg.24.AD80

description: processed data file: rawCounts.tsv


title: Cd11cCreCntl.H37Rv.naive.24.AD80

description: processed data file: rawCounts.tsv


title: Parental rep 1


title: LysMCreKO.H37Rv.mEmPos.24.AD79

description: processed data file: rawCounts.tsv

value: LysMCreKO


title: LysMCreCntl.H37Rv.mEmPos.24.AD79

description: processed data file: rawCounts.tsv

value: LysMCreCntl


title: LysMCreKO.H37Rv.naive.24.AD79

description: processed data file: rawCounts.tsv


title: Manipulated SI day 1 Mouse 2_15

description:
WMSItd1-2_15
Gene expression of donor monocyte-derived cells in the small intestine of manipulated recipient at day 1 post-transfer.

source_name: Small intestine of manipulated mouse

value: Transferred monocytes recovered from small intestine of manipulated recipient

value: day 1


title: Manipulated SI day 1 Mouse 3_16

description:
WMSItd1-3_16
Gene expression of donor monocyte-derived cells in the small intestine of manipulated recipient at day 1 post-transfer.

value: C57BL/6 WT


title: Manipulated SI day 1 Mouse 1_14

description:
WMSItd1-1_14
Gene expression of donor monocyte-derived cells in the small intestine of manipulated recipient at day 1 post-transfer.


title: LysMCreCntl.H37Rv.mEmNeg.24.AD79

description: processed data file: rawCounts.tsv


title: LysMCreCntl.H37Rv.naive.24.AD79

description: processed data file: rawCounts.tsv


title: Non-manipulated BM day 1 Mouse 3_13

description:
WNMBMtd1-3_13
Gene expression of donor monocyte-derived cells in the bone marrow of non-manipulated recipient at day 1 post-transfer.

source_name: Bone marow of non-manipulated mouse

value: Transferred monocytes recovered from bone marrow of non-manipulated recipient


title: Manipulated SI day 1 Mouse 5_18

description:
WMSItd1-5_18
Gene expression of donor monocyte-derived cells in the small intestine of manipulated recipient at day 1 post-transfer.


title: Non-manipulated Spl day 1 Mouse 3_10

description:
WNMSpltd1-3_10
Gene expression of donor monocyte-derived cells in the spleen of non-manipulated recipient at day 1 post-transfer.

source_name: Spleen of non-manipulated mouse

value: Transferred monocytes recovered from spleen of non-manipulated recipient


title: Non-manipulated Spl day 1 Mouse 2_09

description:
WNMSpltd1-2_09
Gene expression of donor monocyte-derived cells in the spleen of non-manipulated recipient at day 1 post-transfer.


title: B6.H37Rv.naive.24.AD47

data_processing:
Stranded paired-end reads of length 76 were preprocessed: The first three nucleotides of R1 (v1 kit) or R2 (v2 kit) were removed as described in the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian User Manual (v1: 112215, v2: 063017) and read ends consisting of 50 or more of the same nucleotide were removed.
The remaining read pairs were aligned to the mouse genome (mm10) + Mtb H37Rv genome using the gsnap aligner (v. 2016-08-24) allowing for novel splicing. (gsnap options: -s Mus_musculus.GRCm38.78.splicesites --filter-chastity=either --max-middle-deletions=3 --max-middle-insertions=3 --query-unk-mismatch=1 )
Concordantly mapping read pairs (average 15-million / sample) that aligned uniquely were assigned to exons using the subRead program and gene definitions from Ensembl Mus_Musculus GRCm38.78 coding and non-coding genes.
Genome_build: mm10 + Mtb H37Rv
Supplementary_files_format_and_content: rawCounts.tsv contains the raw counts for each sample generated by subRead, tab-separated

extract_protocol:
RNA isolation was performed using TRIzol (Invitrogen), two sequential chloroform extractions, Glycoblue carrier (Thermo Fisher), isopropanol precipitation, and washes with 75% ethanol.
cDNA libraries were constructed and amplified using the SMARTer Stranded Total RNA-Seq Kit (v1 or v2) - Pico Input Mammalian (Clontech) per the manufacturers instructions. Libraries were amplified and then sequenced on an Illumina NextSeq (2 x 75, paired-end).

tag: strain/genotype

tag: infectious challenge

tag: infection status

tag: time infected (hrs)

tag: library version

tag: experiment label


title: Nrf2.H37Rv.mEmPos.24.AD54


title: B6.H37Rv.naive.24.AD48


title: Manipulated SI day 1 Mouse 4_17

description:
WMSItd1-4_17
Gene expression of donor monocyte-derived cells in the small intestine of manipulated recipient at day 1 post-transfer.


title: Nrf2.H37Rv.naive.24.AD54


title: Non-manipulated Liv day 1 Mouse 3_07

description:
WNMLivtd1-3_07
Gene expression of donor monocyte-derived cells in the liver of non-manipulated recipient at day 1 post-transfer.

source_name: Liver of non-manipulated mouse

value: Transferred monocytes recovered from liver of non-manipulated recipient


title: Non-manipulated Spl day 1 Mouse 1_08

description:
WNMSpltd1-1_08
Gene expression of donor monocyte-derived cells in the spleen of non-manipulated recipient at day 1 post-transfer.


title: Nrf2.H37Rv.naive.24.AD44


title: Non-manipulated Liv day 1 Mouse 2_06

description:
WNMLivtd1-2_06
Gene expression of donor monocyte-derived cells in the liver of non-manipulated recipient at day 1 post-transfer.


title: LysMCreKO.H37Rv.mEmNeg.24.AD79

description: processed data file: rawCounts.tsv

tag: genotype/variation


title: Nrf2.H37Rv.mEmPos.24.AD44


title: Non-manipulated SI day 1 Mouse 4_04

description:
WNMSItd1-4_04
Gene expression of donor monocyte-derived cells in the small intestine of non-manipulated recipient at day 1 post-transfer.

value: Transferred monocytes recovered from small intestine of non-manipulated recipient


title: Non-manipulated Liv day 1 Mouse 1_05

description:
WNMLivtd1-1_05
Gene expression of donor monocyte-derived cells in the liver of non-manipulated recipient at day 1 post-transfer.


title: B6.H37Rv.mEmPos.240.AD40


title: Non-manipulated BM day 1 Mouse 1_11

description:
WNMBMtd1-1_11
Gene expression of donor monocyte-derived cells in the bone marrow of non-manipulated recipient at day 1 post-transfer.


title: Non-manipulated BM day 1 Mouse 2_12

description:
WNMBMtd1-2_12
Gene expression of donor monocyte-derived cells in the bone marrown of non-manipulated recipient at day 1 post-transfer.


title: Non-manipulated SI day 1 Mouse 3_03

description:
WNMSItd1-3_03
Gene expression of donor monocyte-derived cells in the small intestine of non-manipulated recipient at day 1 post-transfer.


title: 40 przy

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

institute: National Research Institute of Animal Production

data_processing:
Basecalls performed using CASAVA version 1.8.2
The raw sequences were quality controlled using FastQC.
Flexbar software was used to remove Illumina adapters and poly-A sequences
Reads shorter than 36 bp and reads with a quality lower thanthe default of 20 were removed from the dataset.
Cleaned sequences were aligned to the Sus Scrofa genome (assembly Sus Scrofa-11.0) with reference annotation containing more than 25K genes listed in the Ensembl database.
Alignment and estimation of gene expression level were made using the RSEM package supported by STAR aligner.
Differentially expressed genes and their corresponding p-values were determined using the statistical methods DESeq2
Genome_build: Sus_scrofa 11
Supplementary_files_format_and_content: genes.csv.gz: compressed gzip file containing raw genes counts
Supplementary_files_format_and_content: res.csv.gz: compressed gzip file containing DESeq2 results for differential expressed gene analysis for pituitary of cockerels in different point of life.

organism: Sus scrofa

source_name: pituitary

growth_protocol: All pigs were female and they were maintained at Pig Test Station under the same feeding and housing conditions and were slaughtered when they reached 100±2 kg.

extract_protocol:
RNA was isolated by RNA was isolated by the PureLink™ RNA Mini Kit (Ambion, Cambridge, UK) according to the manufacturer’s recommendations. The RIN values were over 7 what was estimated by TapeStation2200 and RNA tapes (Agilent, Palo Alto, USA).
The cDNA libraries were prepared by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to the supplied protocol, and flow cell clustering was performed using a TruSeq SR Cluster Kit v3-cBot HS (Illumina).
RNA-seq. The libraries were diluted according to a cluster generation protocol and loaded into a v3 Illumina flowcell.

tag: tissue

value: pituitary

tag: breed

value: Zlotnicka white

tag: day

tag: Sex

value: female

tag: shear force

tag: replicate


title: 43 przy


title: 37 przy


title: Non-manipulated SI day 1 Mouse 2_02

description:
WNMSItd1-2_02
Gene expression of donor monocyte-derived cells in the small intestine of non-manipulated recipient at day 1 post-transfer.

tag: cells analyzed

tag: days after transfer


title: B6.H37Rv.mEmNeg.240.AD40

value: Alveolar macrophages

value: mEmNeg


title: 22 przy


title: B6.H37Rv.naive.240.AD40

value: naive


title: 21 przy


title: B6.H37Rv.mEmPos.240.AD39

value: mEmPos


title: 20 przy


title: 9 przy


title: 13 przy


title: 8 przy


title: B6.H37Rv.naive.240.AD39


title: 11 przy


title: 5 przy


title: 3 przy


title: 6 przy


title: B6.H37Rv.mEmNeg.240.AD39


title: Manipulated SI day 5 Mouse 2_25

description:
WMSId5-2_25
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.

extract_protocol: One hundred donor monocyte-derived cells were recovered and FACS-sorted from both non-inflamed and inflamed small intestine of recipient mice at day 1, 2 and 5 post-transfer. RNA was reverse-transcribed to cDNA immediately after sorting and stored at -80 oC.

value: Transferred monocytes recovered from inflamed Small intestine of recipient mouse

value: day 5

tag: donor mice

tag: recipient mice


title: Manipulated SI day 5 Mouse 4_27

description:
WMSId5-4_27
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: Manipulated SI day 5 Mouse 1_24

description:
WMSId5-1_24
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: Manipulated SI day 5 Mouse 3_26

description:
WMSId5-3_26
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: Manipulated SI day 2 Mouse 4_23

description:
WMSId2-4_23
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.

value: day 2


title: 23 przy


title: 2 przy


title: 1 przy


title: B6.H37Rv.naive.240.AD38

tag: cell type

tag: strain/genotype


title: Non-manipulated SI day 1 Mouse 1_01

description:
WNMSItd1-1_01
Gene expression of donor monocyte-derived cells in the small intestine of non-manipulated recipient at day 1 post-transfer.

tag: dono mice


title: B6.H37Rv.mEmPos.96.AD30

tag: infectious challenge

tag: infection status

tag: time infected (hrs)


title: B6.H37Rv.mEmNeg.240.AD38

tag: library version

tag: experiment label


title: B6.H37Rv.mEmPos.240.AD38


title: B6.H37Rv.mEmPos.48.AD30


title: Manipulated SI day 2 Mouse 1_20

description:
WMSId2-1_20
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: B302

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MouseGene1.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite.

source_name: Liver

label_protocol: 100 ng of total RNA is reverse transcribed  following the Ovation Applause kit (Nugen). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 2.5 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen).

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

value: Female

tag: genotype/variation

value: WT


title: B304

value: hepatocyte-specific Lkb1 deficiency, KO


title: NeuNT_MGT_3

city: Portland

first: Tyler

last: Risom

state: Oregon

address: 2730 SW Moody Ave

department: Molecular Medical Genetics

institute: Oregon Health & Science University

data_processing:
Base calling using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
Reads were trimmed by removing low quality score bases (first 4) and alligning next 44 bases.  Trimmed reads were aligned to mm9 with Bowtie version 1.0.0 (allowing up to 3 mismatches, but requiring unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models.
Genome_build: mm9
Supplementary_files_format_and_content: Supplementary files  are tab delimited text files.  The *_FPKM.txt files contain values normalized to aligned Fragments Per Kilobase per Million aligned reads (normalized for gene size and sequencing depth).  The *_Counts.txt files are un-normalized tag counts for each RefSeq gene model (suitable for count based tools such as DESeq2).

source_name: NeuNT mouse Mammary Gland Tumor

growth_protocol: Generate MYC-NeuNT and NeuNT mice, passing two cycles of pregnancy/lactation.  MYC-NeuNT mice developed tumors between 4 and 12 weeks post Blg-Cre activation and NeuNT mice developed tumors between 28 - 44 weeks post Blg-Cre activation.

extract_protocol:
Total RNA was extracted with Trizol according to manufacturer's protocol.
Sequencing libraries were constructed using an Illumina TruSeq RNAseq kit. Briefly, poly(A)+ RNA was isolated from 1ug of total RNA (per sample) using oligo-dT coated magnetic beads. The recovered RNA was then chemically fragmented. First strand cDNA was generated using random hexamers as primers for reverse transcriptase. Following second strand synthesis, the ends of the double stranded fragments were repaired and then a single “A” nucleotide was added to each end. Illumina adaptors were ligated to the cDNAs. Limited round (11-cycle) PCR was used to amplify the material to yield the final libraries. Library concentration was determined using real time PCR with primers complementary to the Illumina adaptors. Sample libraries were diluted and applied to an Illumina single read flow cell at a concentration appropriate to generate about 180 million reads per lane. All  libraries were prepared with indexing barcodes to permit multiplexing in a single lane. 100 cycle single read sequencing was used to generate base call files. Illumina’s CASAVA package was used to assemble the reads into standard fastq formatted data.

treatment_protocol: At 8 weeks of age, start breeding MYC-NeuNT and NeuNT females with male mice through two cycles of pregnancy.  Monitor tumor growth twice every week.

tag: tissue

value: mammary gland tumor

tag: tumor size (diameter)

tag: genotype

value: NeuNT


title: B305

tag: Sex


title: B6.deltaRD1.mEmPos.24.AD26


title: Manipulated SI day 1 Mouse 5_19

description:
WMSId1-5_19
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.

tag: cells analyzed

value: day 1

value: C57BL/6 WT


title: Normal_MG_3

source_name: MYC without Blg-Cre mouse Normal Mammary Gland

value: normal mammary  gland

value: MYC without Blg-Cre


title: B6.H37Rv.naive.96.AD30


title: NeuNT_MGT_2


title: B6.H37Rv.mEmPos.12.AD19


title: NeuNT_MGT_4


title: Normal_MG_2


title: Manipulated SI day 2 Mouse 3_22

description:
WMSId2-3_22
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.

tag: days after transfer


title: Manipulated SI day 1 Mouse 4_18

description:
WMSId1-4_18
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.

tag: donor mice


title: Manipulated SI day 1 Mouse 3_17

description:
WMSId1-3_17
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.

tag: recipient mice


title: Manipulated SI day 1 Mouse 2_16

description:
WMSId1-2_16
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: Normal_MG_1


title: Manipulated SI day 2 Mouse 2_21

description:
WMSId2-2_21
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: NeuNT_MGT_1


title: B6.H37Rv.naive.48.AD30

tag: cell type


title: Myc_NeuNT_MGT_14

source_name: MYC-NeuNT mouse Mammary Gland Tumor

value: MYC-NeuNT


title: Myc_NeuNT_MGT_13


title: Manipulated SI day 1 Mouse 1_15

description:
WMSId1-1_15
Gene expression of donor monocyte-derived cells in inflamed small intestine of recipient at day 1 post-transfer.


title: Myc_NeuNT_MGT_12


title: B6.deltaRD1.naive.24.AD26

value: Alveolar macrophages

tag: strain/genotype


title: B253


title: B256


title: B267


title: Non-manipulated SI day 5 Mouse 4_14

description:
WNMSId5-4_14
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.

source_name: Small intestine of non-manipulated mouse

value: Transferred monocytes recovered from non-inflamed Small intestine of recipient mouse


title: Myc_NeuNT_MGT_11


title: B6.H37Rv.naive.12.AD19

value: naive


title: B6.H37Rv.mEmPos.96.AD28

value: mEmPos


title: Myc_NeuNT_MGT_10


title: Myc_NeuNT_MGT_8


title: B6.H37Rv.mEmPos.48.AD28


title: Non-manipulated SI day 5 Mouse 2_11

description:
WNMSId5-2_12
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: Non-manipulated SI day 5 Mouse 3_13

description:
WNMSId5-3_13
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: B6.H37Rv.mEmPos.12.AD18


title: Myc_NeuNT_MGT_7


title: Myc_NeuNT_MGT_3


title: B6.deltaRD1.mEmPos.24.AD25


title: Myc_NeuNT_MGT_4


title: Myc_NeuNT_MGT_5


title: Non-manipulated SI day 2 Mouse 4_09

description:
WNMSId2-4_09
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: Myc_NeuNT_MGT_1


title: Myc_NeuNT_MGT_6


title: Non-manipulated SI day 5 Mouse 1_11

description:
WNMSId5-1_11
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: B6.H37Rv.naive.48.AD28


title: B6.H37Rv.naive.96.AD28


title: Non-manipulated SI day 2 Mouse 5_10

description:
WNMSId2-5_10
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: Non-manipulated SI day 2 Mouse 3_08

description:
WNMSId2-3_08
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: Myc_NeuNT_MGT_9


title: B6.deltaRD1.naive.24.AD25


title: Myc_NeuNT_MGT_2


title: Non-manipulated SI day 2 Mouse 1_06

description:
WNMSId2-1_06
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: Non-manipulated SI day 2 Mouse 2_07

description:
WNMSId2-2_07
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: B6.H37Rv.naive.12.AD18


title: 245_DIFF_24h_c-

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description:
24h c-
245_22

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data were analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using GC-RMA as normalization method.

source_name: d-EpOCs from Ctrl (245), 24h incubation, not stimulated

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Crypts from descending/sigmoid colon samples were isolated by EDTA treatment. Crypt units were embedded in Matrigel, expanded for 3-4 days in stem medium and dissociated. Single epithelial cells were replated in fresh stem medium according to a 1:3 dilution to generate EpOCs. Part of the EpOCs was induced to differentiate (d-EpOCs) by the addition of fresh differentiation medium.

extract_protocol: Total RNA was extracted using Trizol+RNA Cleanup protocol by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: At day 5 of in vitro expansion, EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated. d-EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated.

tag: patient id

value: d-EpOCs

value: c-


title: 245_DIFF_24h_5mM

description:
24h 5 mM
245_24

source_name: d-EpOCs from Ctrl (245), 24h incubation,  5 mM butyrate stimulation


title: 245_DIFF_24h_0,5mM

description:
24h 0.5mM
245_23

source_name: d-EpOCs from Ctrl (245), 24h incubation, 0.5 mM butyrate stimulation


title: B6.H37Rv.mEmPos.48.AD27

tag: infectious challenge


title: Non-manipulated SI day 1 Mouse 5_05

description:
WNMSId1-5_05
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: 245_DIFF_6h_5mM

description:
6h 5 mM
245_21

source_name: d-EpOCs from Ctrl (245), 6h incubation,  5 mM butyrate stimulation


title: B6.H37Rv.mEmPos.96.AD27

tag: infection status


title: Non-manipulated SI day 1 Mouse 4_04

description:
WNMSId1-4_04
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: B6.deltaRD1.mEmPos.24.AD23

tag: time infected (hrs)


title: Non-manipulated SI day 1 Mouse 3_03

description:
WNMSId1-3_03
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: 245_DIFF_3h_5mM

description:
3h 5 mM
245_18

source_name: d-EpOCs from Ctrl (245), 3h incubation,  5 mM butyrate stimulation


title: B6.H37Rv.mEmPos.12.AD15

source_name: Alveolar macrophages

tag: library version


title: 245_DIFF_6h_c-

description:
6h c-
245_19

source_name: d-EpOCs from Ctrl (245), 6h incubation, not stimulated


title: Non-manipulated SI day 1 Mouse 2_02

description:
WNMSId1-2_02
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: 245_DIFF_3h_c-

description:
3h c-
245_16

source_name: d-EpOCs from Ctrl (245), 3h incubation, not stimulated


title: B6.H37Rv.naive.96.AD27

tag: experiment label


title: 245_DIFF_3h_0,5mM

description:
3h 0.5mM
245_17

source_name: d-EpOCs from Ctrl (245), 3h incubation, 0.5 mM butyrate stimulation


title: Non-manipulated SI day 1 Mouse 1_01

description:
WNMSId1-1_01
Gene expression of donor monocyte-derived cells in non-inflamed small intestine of recipient at day 1 post-transfer.


title: DT6D [S142]

city: Charlotte

first: Whitney

middle: at

last: Leach

address: 9201 University City Blvd.

department: Biological Sciences

institute: University of North Carolina at Charlotte

description:
dark:dark, time point 6, replicate D
Sample name in processed data file:
S142

data_processing:
Sequenced reads were concatenated and renamed based on sample ID
Each Illumina read was trimmed of the adapter and PCR duplicates were removed
Quality filtering was performed using fastx_toolkit
Transcriptome mapping was performed using Bowtie2
Genome_build: genome Putnam et al. (2007) is available at:
https://figshare.com/articles/Nematostella_vectensis_transcriptome_and_gene_models_v2_0/807696
Supplementary_files_format_and_content: tab-delimited table of counts per gene for each sample

organism: Nematostella vectensis

source_name: whole-organism

growth_protocol: Animals were maintained as described in Hand et al. (1994)

extract_protocol:
Whole-organism RNA was extracted from animals (that were preserved in RNAlater and stored at -80) using Ambion RNAqueous extraction kit.
Libraries were prepared as in Meyer et al. (2011)

treatment_protocol: Animals were experimentally exposed to one of 4 light conditions: 1) red light:dark 2) blue light:dark 3) green light:dark or 4) dark:dark conditions for 1 month, then sampled every 4 hours for 1 day (24 hours) in replicates of 4

value: whole organism

tag: developmental stage

value: adult

tag: treatment

tag: time point

value: time point 6

tag: replicate

value: replicate D


title: DT6C [S141]

description:
dark:dark, time point 6, replicate C
Sample name in processed data file:
S141

tag: tissue

value: replicate C


title: 245_DIFF_6h_0,5mM

description:
6h 0.5mM
245_20

source_name: d-EpOCs from Ctrl (245), 6h incubation, 0.5 mM butyrate stimulation


title: 245_STEM_24h_5mM

description:
24h 5 mM
245_12

source_name: EpOCs from Ctrl (245), 24h incubation,  5 mM butyrate stimulation

value: Epithelial organoid cultures (EpOCs)


title: 245_DIFF_1h_5mM

description:
1h 5 mM
245_15

source_name: d-EpOCs from Ctrl (245), 1h incubation,  5 mM butyrate stimulation


title: 245_DIFF_1h_0,5mM

description:
1h 0.5mM
245_14

source_name: d-EpOCs from Ctrl (245), 1h incubation, 0.5 mM butyrate stimulation


title: DT6B [S140]

description:
dark:dark, time point 6, replicate B
Sample name in processed data file:
S140

value: replicate B


title: 245_DIFF_1h_c-

description:
1h c-
245_13

source_name: d-EpOCs from Ctrl (245), 1h incubation, not stimulated


title: DT6A [S139]

description:
dark:dark, time point 6, replicate A
Sample name in processed data file:
S139

value: replicate A


title: B6.H37Rv.naive.12.AD15


title: B6.H37Rv.mEmPos.24.AD14


title: GT6D [S138]

description:
green light:dark, time point 6, replicate D
Sample name in processed data file:
S138

value: green light:dark


title: B6.H37Rv.mEmPos.24.AD09


title: 245_STEM_24h_0,5mM

description:
24h 0.5mM
245_11

source_name: EpOCs from Ctrl (245), 24h incubation, 0.5 mM butyrate stimulation


title: 245_STEM_6h_5mM

description:
6h 5 mM
245_9

source_name: EpOCs from Ctrl (245), 6h incubation,  5 mM butyrate stimulation


title: 245_STEM_24h_c-

description:
24h c-
245_10

source_name: EpOCs from Ctrl (245), 24h incubation, not stimulated


title: GT6C [S137]

description:
green light:dark, time point 6, replicate C
Sample name in processed data file:
S137


title: B6.deltaRD1.naive.24.AD23


title: B6.bead.beadPos.24.AD62817

value: bead

value: beadPos


title: 245_STEM_6h_c-

description:
6h c-
245_7

source_name: EpOCs from Ctrl (245), 6h incubation, not stimulated


title: 245_STEM_3h_5mM

description:
3h 5 mM
245_6

source_name: EpOCs from Ctrl (245), 3h incubation,  5 mM butyrate stimulation


title: B6.H37Rv.naive.48.AD27

value: Alveolar macrophages


title: GT6B [S136]

description:
green light:dark, time point 6, replicate B
Sample name in processed data file:
S136


title: 245_STEM_6h_0,5mM

description:
6h 0.5mM
245_8

source_name: EpOCs from Ctrl (245), 6h incubation, 0.5 mM butyrate stimulation


title: B6.bead.naive.24.AD62817


title: 245_STEM_3h_c-

description:
3h c-
245_4

source_name: EpOCs from Ctrl (245), 3h incubation, not stimulated


title: GT6A [S135]

description:
green light:dark, time point 6, replicate A
Sample name in processed data file:
S135


title: 245_STEM_3h_0,5mM

description:
3h 0.5mM
245_5

source_name: EpOCs from Ctrl (245), 3h incubation, 0.5 mM butyrate stimulation


title: B6.H37Rv.mEmNeg.24.AD14

source_name: Alveolar macrophages

value: mEmNeg


title: BT6D [S134]

description:
blue light:dark, time point 6, replicate D
Sample name in processed data file:
S134

value: blue light:dark


title: B6.H37Rv.mEmNeg.24.AD09


title: BT6C [S133]

description:
blue light:dark, time point 6, replicate C
Sample name in processed data file:
S133


title: B6.H37Rv.naive.24.AD14

value: naive


title: SAMPLE 35 TF-1 R882H M IDH mut rep 2

type: genomic

description: SAMPLE 37

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using Illumina standard protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software version V2011.1

label: Cy5 and Cy3

source_name: TF-1 cells

label_protocol: Standard Illumina labelling protocol.

growth_protocol: The TF-1 human erythroleukemic cell line was obtained from ATCC and cultivated in the RPMI 1640 base medium (Invitrogen) supplemented with 10% of FBS and 2 ng/ml of recombinant human GM-CSF (R&D Systems).

extract_protocol: Genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen), and 1µg genomic DNA was subject to bisulfite conversion using EZ DNA methylation gold kit (Zymo Research) according to manufacturer's instructions.

treatment_protocol: TF-1 cell lines with stable expression of wild-type (WT) or mutant DNMT3A were established by MSCV-based retrovirus packaged in HEK293 cells.

tag: gene expressed

value: DNMT3A R882H GFP medium/IDH1 R132H


title: 245_STEM_1h_c-

description:
1h c-
245_1

source_name: EpOCs from Ctrl (245), 1h incubation, not stimulated

value: c-


title: SAMPLE 34 TF-1 R882H M IDH mut rep 1

description: SAMPLE 36


title: B6.H37Rv.naive.24.AD09