title: ChIP_ ZfSp5

description: Cells were transfected with the ZfWnt3 promoter

source_name: Immunoprecipitated Chromatin from Hek cells transfected with ZfSp5 expression plasmid

value: anti-HA (Novus biologicals NB600-363)


title: BFUE_70

status: Public on Mar 01 2019

type: SRA

city: Cambridge

first: Hojun

last: Li

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute for Biomedical Research

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-TATGCA-s_2

library_source: transcriptomic

data_processing:
Reads were mapped against the GRCm38 mouse genome using STAR version 2.4, gene annotations from ENSEMBL version 87 (using only canonical chromosomes) and the overhang parameter from STAR set to 100
Read counts per gene were obtained with featureCounts using the option –p and the same GTF file used to map the reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file with gene counts per gene.

molecule: polyA RNA

organism: Mus musculus

source_name: burst forming unit-erythroid

growth_protocol: Erythroid progenitor cell isolation. Fetal liver was dissected from embryonic day 14.5 mice and disrupted and homogenized with manual pipetting, followed by lysis of mature red blood cells with ammonium chloride solution (Stem Cell Technologies).  Remaining fetal liver cells were stained with biotinylated antibodies against the following surface proteins: CD3e, CD45R, Ly-6G, CD11b, Ter119 (all 5 from the BD-Pharmingen biotin mouse linage depletion panel), Ly-6A/E (i.e. Sca-1, cloned D7, E-Biosciences), CD16/32 (clone 93, E-Biosciences), CD41 (clone EbioMWReg30, E-Biosciences), and Ter119 (E-biosciences). Cells were then incubated with streptavidin-labeled magnetic beads (BD) to deplete cells labeled with biotinylated antibodies.  Remaining unlabeled cells were then purified by FACS (staining procedure described below) on a FACS Aria sorter (BD).

extract_protocol:
FACS selection protocol: Antibody staining and FACS.For FACS purification of erythroid progenitors, lineage-depleted fetal liver cells were stained with the following: Propidium Iodide (Sigma), APC or PE-Cy7 anti-CD117 (clone ACK2, E-Biosciences), PE anti-CD71 (clone R127217, E-Biosciences), PE anti-CD24 (clone M1/69, E-biosciences), FITC streptavidin (E-Biosciences).   Flow cytometry for erythroid differentiation markers was performed on a FACS Fortessa cytometer (BD)
Single cell transcriptome library preparation.  SmartSeq2 library prep was performed by depositing single cells in PCR plate wells by FACS.  Single cells were lysed in TCL buffer (Qiagen), containing RNase inhibitor (Clontech), Oligo-dT (5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’, IDT), and dNTPs (Invitrogen).  Lysates were then reverse transcribed at 42 deg C with SuperScript II reverse transcriptase (Invitrogen) in the presence of First-Strand Buffer (Invitrogen) containing DTT (Invitrogen), betaine (Sigma), magnesium chloride (Sigma), and template switching oligonucleotide (5’ -AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ where rG = riboguanosine, and +G = LNA-modified guanosine, Exiqon/Qiagen).  Reverse-transcribed products were then amplified using Kapa HiFi Hotstart PCR master mix (Kapa) and an IS PCR oligo primer (5’ -AAGCAGTGGTATCAACGCAGAGT-3’, IDT). Amplified double-stranded cDNA libraries were then purified using Agencourt Ampure XP beads (Beckman Coulter), followed by DNA concentration quantification using the Qubit dsDNA HS kit (Life Technologies).  0.2 ng of double-stranded cDNA was used in a tagmentation reaction using the Nextera XT DNA sample preparation kit (Illumina) per manufacturers protocol. Tagmented transcriptomes were then indexed using the Nextera XT 96-index kit for 384 samples (Illumina) per manufacturers instructions, and samples were then sequenced on a HiSeq 2500 sequencer (Illumina).

tag: strain

tag: cell type

value: BFUE


title: BFUE_68

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-CTCCTT-s_2


title: POI female [BPOF-121]

type: genomic

city: Pittsburgh

first: Svetlana

middle: A

last: Yatsenko

state: PA

address: 300 Halket St

institute: University of Pittsburgh

description: copy number

hyb_protocol: According to Agilent protocol

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
normalized log2 ratio (Cy5/Cy3) representing test/reference

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: According to Agilent protocol

growth_protocol: uncultured

extract_protocol: Genomic DNA extracted using Puregene Kit following manufacturer's instructions

tag: gender

value: Female

tag: tissue

value: peripheral blood

source_name: Promega

tag: reference dna gender

tag: reference dna cell line

value: pooled


title: BFUE_77

description:
BFUE_CFUE.counts.txt.gz
TAAGGCG-TACTCC-s_2


title: POI female [BPOF-105]

description: copy number


title: POI female [BPOF-110]

description: copy number


title: BFUE_67

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-ATAGAG-s_2


title: POI female [BPOF-103]

description: copy number


title: BFUE_66

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-AGGCTT-s_2


title: 014_03d_nanos_medGFP_B

city: Geneva

first: Yvan

last: Wenger

state: Geneva

address: 30 Quai Ernest-Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: 3 days starvation, medium GFP selection

data_processing:
Adapter and removal of known trans-spliced leader: Cutadapt 1.11 (--trim-n -m 50 -q 5)
Generation of pseudo counts: Salmon 0.7.2 (--libType SR --seqBias --gcBias)
Normalization using DESeq2
Reference transcriptome (Fasta): Hv_AEP_transcriptome.fasta.gz
Genome_build: Hv_AEP_transcriptome.fasta.gz
Supplementary_files_format_and_content: counts2017_stem.csv.gz: Raw abundance measurements (estimated counts)
Supplementary_files_format_and_content: normacounts_stem2017.csv.gz: Normalized abundance measurements (estimated counts)

organism: Hydra vulgaris

source_name: Central body column (no apical/basal regions), FACS

growth_protocol: 3 feedings per weeks

extract_protocol:
Qiagen RNeasy, followed by polyA enrichment
Illumina TruSeq, directional

treatment_protocol: No treatment

value: AEP

tag: transgenics

tag: egfp expression

value: ISC (interstitial stem cells)

tag: time point

value: 3 days starvation, medium GFP selection


title: POI female [BPOF-104]

description: copy number


title: 013_05d_nanos_medGFP_A

description: 5 days starvation, medium GFP selection

value: 5 days starvation, medium GFP selection


title: BFUE_65

description:
BFUE_CFUE.counts.txt.gz
GTAGAGG-AGAGGA-s_2


title: POI female [BPOF-102]

description: copy number


title: POI female [BPOF-098]

description: copy number


title: 012_05d_nanos_hiGHP_D

description: 5 days starvation, high GFP selection

value: 5 days starvation, high GFP selection


title: POI female [BPOF-097]

description: copy number


title: 011_03d_nanos_hiGHP_C

description: 3 days starvation, high GFP selection

value: 3 days starvation, high GFP selection


title: BFUE_64

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TCTTAC-s_2


title: POI female [BPOF-096]

description: copy number


title: BFUE_61

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TACTCC-s_2


title: BFUE_63

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TCTACT-s_2


title: 009_02d_nanos_hiGHP_A

description: 2 days starvation, high GFP selection

value: 2 days starvation, high GFP selection


title: POI female [BPOF-094]

description: copy number


title: POI female [BPOF-095]

description: copy number


title: BFUE_60

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-CTCCTT-s_2


title: 007_03d_endo_hiGFP_B

description: 3 days starvation, high GFP selection

value: gESC (gastrodermal epithelial stem cells)


title: 010_03d_nanos_hiGHP_B

description: 3 days starvation, high GFP selection


title: BFUE_59

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-ATAGAG-s_2


title: 008_03d_endo_hiGFP_C

description: 3 days starvation, high GFP selection


title: 006_03d_endo_hiGFP_A

description: 3 days starvation, high GFP selection


title: 015_03d_nanos_medGFP_C

description: 3 days starvation, medium GFP selection


title: BFUE_58

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-AGGCTT-s_2


title: POI female [BPOF-086]

description: copy number


title: POI female [BPOF-084]

description: copy number


title: 005_03d_ecto_hiGFP_C

description: 3 days starvation, high GFP selection

value: eESC (epidermal epithelial stem cells)


title: 004_03d_ecto_hiGFP_B

description: 3 days starvation, high GFP selection


title: POI female [BPOF-083]

description: copy number


title: 003_03d_ecto_hiGFP_A

description: 3 days starvation, high GFP selection


title: POI female [BPOF-082]

description: copy number


title: BFUE_57

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-AGAGGA-s_2


title: POI female [BPOF-074]

description: copy number


title: POI female [BPOF-075]

description: copy number


title: BFUE_53

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TACTCC-s_2


title: 032_COL_10D_C

description: 1 period of 8 hours treatment

data_processing:
Adapter and removal of known trans-spliced leader: Cutadapt 1.11 (--trim-n -m 50 -q 5)
Generation of pseudo counts: Salmon 0.7.2 (--libType SR --seqBias --gcBias)
Normalization using DESeq2
Reference transcriptome (Fasta):Hv_Jussy_transcriptome.fasta.gz
Supplementary_files_format_and_content: counts2017_drugs.csv.gz: Raw abundance measurements (estimated counts)
Supplementary_files_format_and_content: Hv_Jussy_transcriptome.fasta.gz: Fasta reference transcriptome
Supplementary_files_format_and_content: normacounts_drugs2017.csv.gz: Normalized abundance measurements (estimated counts)

source_name: Central body column (no apical/basal regions)

growth_protocol: 3 feedings per weeks, no feeding upon start of the experiment

treatment_protocol: Described above

tag: treatments

value: Colchicine 0.4%

tag: days after beginning of treatment

value: 9 days

tag: days of starvation

value: 11 days


title: BFUE_54

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TATGCA-s_2


title: POI female [BPOF-065]

description: copy number


title: POI female [BPOF-062]

description: copy number


title: 031_COL_10D_B

description: 1 period of 8 hours treatment


title: 001_10d_gastric_ecto

description: 10 days starvation (no FACS)

value: 10 days starvation (no FACS)


title: POI female [BPOF-061]

description: copy number


title: BFUE_51

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-ATAGAG-s_2

value: BFUE


title: POI female [BPOF-060]

description: copy number

value: Female


title: BFUE_49

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-AGAGGA-s_2


title: POI female [BPOF-057]

description: copy number

value: peripheral blood


title: BFUE_50

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-AGGCTT-s_2


title: 030_COL_10D_A

description: 1 period of 8 hours treatment


title: 029_HS_10D_D

description: 1 period of 62 hours treatment

value: Heat shock 28°C during 62h


title: BFUE_48

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TCTTAC-s_2


title: 028_HS_10D_C

description: 1 period of 62 hours treatment


title: 027_HS_10D_B

description: 1 period of 62 hours treatment


title: 002_10d_gastric_nanos

description: 10 days starvation (no FACS)

value: AEP


title: BFUE_56

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TCTTAC-s_2


title: BFUE_47

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TCTACT-s_2


title: BFUE_55

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-TCTACT-s_2


title: 026_HS_10D_A

description: 1 period of 62 hours treatment


title: BFUE_46

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TATGCA-s_2


title: POI female [BPOF-045]

description: copy number

value: pooled


title: BFUE_52

description:
BFUE_CFUE.counts.txt.gz
GCTACGC-CTCCTT-s_2


title: 025_HU_10D_C

description: 3 periods of 24h treatments separated by 12h in Hydra medium

value: Hydroxurea 10mM


title: BFUE_45

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-TACTCC-s_2


title: POI female [BPOF-042]

description: copy number


title: 024_HU_10D_B


title: POI female [BPOF-028]

description: copy number


title: 023_HU_10D_A


title: BFUE_43

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-ATAGAG-s_2


title: POI female [BPOF-026]

description: copy number


title: 022_HU_6D_C

value: 7 days


title: BFUE_42

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-AGGCTT-s_2


title: POI female [BPOF-025]

description: copy number


title: BFUE_44

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-CTCCTT-s_2


title: BFUE_62

description:
BFUE_CFUE.counts.txt.gz
GGACTCC-TATGCA-s_2


title: BFUE_41

description:
BFUE_CFUE.counts.txt.gz
CTCTCTA-AGAGGA-s_2


title: 020_HU_6D_A


title: POI female [BPOF-048]

description: copy number


title: BFUE_40

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TCTTAC-s_2


title: POI female [BPOF-024]

description: copy number


title: 019_HU_4D_C

value: 5 days


title: BFUE_38

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TATGCA-s_2


title: POI female [BPOF-019]

description: copy number


title: POI female [BPOF-023]

description: copy number


title: POI female [BPOF-017]

description: copy number


title: 017_HU_4D_A


title: 018_HU_4D_B


title: POI female [BPOF-015]

description: copy number


title: BFUE_37

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TACTCC-s_2


title: BFUE_39

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-TCTACT-s_2


title: 016_HU_3D_C

value: 4 days


title: 015_HU_3D_B


title: BFUE_36

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-CTCCTT-s_2


title: POI female [BPOF-013]

description: copy number


title: POI female [BPOF-035]

description: copy number


title: BFUE_35

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-ATAGAG-s_2


title: BFUE_34

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-AGGCTT-s_2


title: BFUE_33

description:
BFUE_CFUE.counts.txt.gz
CGTACTA-AGAGGA-s_2


title: POI female [BPOF-008]

description: copy number


title: POI female [BPOF-006]

description: copy number


title: POI female [BPOF-011]

description: copy number


title: 021_HU_6D_B


title: 012_C_10D_C

description: No treatment

value: Control

value: 11 days (no treatment)


title: BFUE_31

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TCTACT-s_2


title: 011_C_10D_B

description: No treatment


title: POI female [BPOF-003]

description: copy number


title: 010_C_10D_A

description: No treatment


title: BFUE_30

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TATGCA-s_2


title: POI female [BPOF-002]

description: copy number


title: 009_C_6D_C

description: No treatment

value: 7 days (no treatment)


title: KW22c: Sample10-post-ICH

city: Cincinnati

first: Xiaoting

last: Zhu

state: OH

address: 3333 burnet avenue,MLC7024

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Kallisto was used to perform pseudoalignment and to quantify the abundance from fastq files using annotations from Ensembl release 94 for the Sus scrofa 11.1 genome.
Gene counts were normalized and tested for differential expression  by DESeq2 with threshold of |log2FC|>1 and padj <0.1
Genome_build: Sscrofa11.1 (Ensembl release 94)
Supplementary_files_format_and_content: kallisto abundance.tsv files give transcript-level abundances in TPM. Genecounts_kallisto_import.txt gives counts and Log2_fold_changes.txt gives differential gene expression.

molecule: total RNA

organism: Sus scrofa

source_name: PBMC

growth_protocol: Ten female domestic pigs, 80 to 90 days old and 36 to 41 kilograms, were included in the study

extract_protocol:
For each sample, approximately 10 ml of swine peripheral blood was collected and immediately placed into EDTA containing blood collection tubes, inverted multiple times, and processed within one hour. Briefly, Lymphoprep™ (Stemcell Technologies, Cambridge, MA) density gradient medium and SepMate™ (Stemcell Technologies) tubes were used according to the manufacturer’s instructions to isolate PBMCs. The PBMCs were directly lysed with Lysis Buffer from the mirVana miRNA isolation kit (Thermo Fisher, Waltham, MA) to stabilize RNA until the time of RNA extraction as described in the total RNA extraction protocol from the kit.). To isolate the polyA RNA, NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Ipswich, MA) was used with a total of 1 µg of good quality total RNA as input.
The NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs) was used for library preparation.

treatment_protocol: Each pig was sedated by intramuscular injection of tiletamine and zolazepam and then endotracheally intubated and placed under isoflurane general anesthesia. To induce ICH as reported previously,15 a single burr hole craniotomy was performed to pass an angiocatheter and to inject two to four milliliters of autologous blood under pressure control into the frontal white matter. Six hours later, the pig was sacrificed by lethal injection. Peripheral blood was collected immediately prior to ICH induction but after the pig had been placed under general anesthesia for about 2 hours and the angiocatheter was in place. The second sample was collected immediately prior to animal sacrifice.

value: blood

value: PBMC


title: BFUE_28

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-CTCCTT-s_2


title: POI female [BPOF-014]

description: copy number


title: BFUE_29

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TACTCC-s_2


title: 008_C_6D_B

description: No treatment


title: KW21c: Sample10-pre-ICH


title: 014_HU_3D_A

description: 3 periods of 24h treatments separated by 12h in Hydra medium


title: 013_C_10D_D

description: No treatment

value: 11 days


title: BFUE_32

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-TCTTAC-s_2


title: BFUE_27

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-ATAGAG-s_2


title: 006_C_4D_C

description: No treatment

value: 5 days (no treatment)


title: 007_C_6D_A

description: No treatment


title: KW20c: Sample9-post-ICH


title: BFUE_25

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-AGAGGA-s_2

value: BFUE


title: KW19c: Sample9-pre-ICH


title: BFUE_26

description:
BFUE_CFUE.counts.txt.gz
CGAGGCT-AGGCTT-s_2


title: 004_C_4D_A

description: No treatment


title: BFUE_24

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TCTTAC-s_2


title: KW18c: Sample8-post-ICH


title: 003_C_3D_C

description: No treatment

value: 4 days (no treatment)


title: KW17c: Sample8-pre-ICH


title: BFUE_23

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TCTACT-s_2


title: 002_C_3D_B

description: No treatment


title: Genital Skin_Normal4_MtOH_rep1.

type: RNA

city: Setagaya-ku, Okura

first: Kanako

last: Tanase-Nakao

state: Tokyo

country: Japan

institute: National Center for Child Health and Development

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: Genital Skin Fibroblast, Normal 4, MtOH, replicate 1

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Fibroblasts were obtained from surgically removed foreskin. Fibroblasts of each individual were seeded in 10 cm dish (5×105cells /well) and grown in DMEM (Nacalai Tesuque, Kyoto, Japan) containing 1 g/L glucose with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, USA) and penicillin and streptomycin.

extract_protocol: Total RNA was extracted from the fibroblasts using the RNeasy Plus Mini Kit (QIAGEN, Hilden, Germany).

treatment_protocol: After 24 hr incubation, the cells were treated with either dihydrotestosterone (DHT) (final concentration of 1 nM, Sigma-Aldrich) or methanol (MtOH) and maintained for further 72 hr before harvesting.

value: male

tag: age

value: Genital Skin Fibroblast


title: KW16c: Sample7-post-ICH


title: BFUE_22

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TATGCA-s_2


title: KW15c: Sample7-pre-ICH


title: 005_C_4D_B

description: No treatment


title: Genital Skin_Normal3_MtOH_rep1.

source_name: Genital Skin Fibroblast, Normal 3, MtOH, replicate 1


title: 001_C_3D_A

description: No treatment


title: Genital Skin_Normal4_DHT_rep1.

source_name: Genital Skin Fibroblast, Normal 4, DHT, replicate 1


title: Genital Skin_Normal3_DHT_rep1.

source_name: Genital Skin Fibroblast, Normal 3, DHT, replicate 1


title: Genital Skin_Normal2_DHT_rep1.

source_name: Genital Skin Fibroblast, Normal 2, DHT, replicate 1


title: Genital Skin_Normal1_MtOH_rep1.

source_name: Genital Skin Fibroblast, Normal 1, MtOH, replicate 1


title: BFUE_21

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-TACTCC-s_2


title: KW14c: Sample6-post-ICH


title: BFUE_20

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-CTCCTT-s_2


title: Genital Skin_Normal2_MtOH_rep1.

source_name: Genital Skin Fibroblast, Normal 2, MtOH, replicate 1


title: 098_Intact_000_B

description: Full intact animal, replicate B

data_processing:
Adapter and removal of known trans-spliced leader: Cutadapt 1.11 (--trim-n -m 50 -q 5)
Generation of pseudo counts: Salmon 0.7.2 (--libType SR --seqBias --gcBias)
Normalization using DESeq2
Genome_build: Hv_Jussy_transcriptome.fasta.gz
Supplementary_files_format_and_content: counts2017_reg.csv.gz: Raw abundance measurements (estimated counts)
Supplementary_files_format_and_content: normacounts_reg2017.csv.gz: Normalized abundance measurements (estimated counts)

source_name: Intact homeostatic animals

growth_protocol: 3 feedings per week

extract_protocol:
Qiagen RNeasy, polyA enrichment
Illumina TruSeq,  directional

value: Jussy

value: Full intact animal


title: 099_Intact_000_C

description: Full intact animal, replicate C


title: KW13c: Sample6-pre-ICH


title: KW12c: Sample5-post-ICH


title: 097_Intact_000_A

description: Full intact animal, replicate A


title: BFUE_19

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-ATAGAG-s_2


title: BFUE_18

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-AGGCTT-s_2


title: ANTI-CD22-7

city: palo alto

first: John

last: Pluvinage

state: California

address: 3801 Miranda Ave Rm D3-131

institute: Stanford

data_processing:
bcl2fastq
STAR
SummarizedExperiment
DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: .csv normalized counts

source_name: microglia

extract_protocol:
Primary mouse microglia were isolated by gentle dounce homogenization of the brain, magentic myelin removal, and FACS-purification of ~20,000 live CD11b+CD45lo cells. Microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according the manufacturer’s protocol. RNA integrity was assessed on a Bioanalyzer (Agilent), and high quality samples were used for library preparation.
cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina). After normalization and pooling, libraries were sequenced on a Hiseq 4000 (Illumina) using paired-end 100bp reads.

treatment_protocol: To assess the transcriptional effects of CD22 blockade, we implanted aged mice with osmotic pumps to continuously infuse a CD22 blocking antibody or an IgG control antibody directly into the cerebrospinal fluid for one month. Following one month of continuous infusion, we performed RNA-seq on purified microglia from the hemi-brains of these mice contralateral to the cannulation site to minimize injury-induced confounding factors.

value: 18 months old


title: Genital Skin_hypospadias_MtOH_rep1.

source_name: Genital Skin Fibroblast, hypospadias, MtOH, replicate 1


title: Genital Skin_Normal1_DHT_rep1.

source_name: Genital Skin Fibroblast, Normal 1, DHT, replicate 1


title: KW10c: Sample4-post-ICH


title: 096_Head_000_C

description: Homeostatic apical region (subtentacular cut), replicate C

source_name: Homeostatic apical region (head), subtentacular section


title: KW11c: Sample5-pre-ICH


title: Genital Skin_hypospadias_DHT_rep1.

source_name: Genital Skin Fibroblast, hypospadias, DHT, replicate 1


title: Genital Skin_PAIS_MtOH_rep1.

source_name: Genital Skin Fibroblast, PAIS, MtOH, replicate 1


title: BFUE_17

description:
BFUE_CFUE.counts.txt.gz
CAGAGAG-AGAGGA-s_2

source_name: burst forming unit-erythroid


title: ANTI-CD22-6


title: BFUE_16

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TCTTAC-s_2


title: 095_Head_000_B

description: Homeostatic apical region (subtentacular cut), replicate B


title: 094_Head_000_A

description: Homeostatic apical region (subtentacular cut), replicate A


title: KW9c: Sample4-pre-ICH


title: BFUE_15

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TCTACT-s_2


title: BFUE_14

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TATGCA-s_2


title: KW6c: Sample3-post-ICH


title: 093_Foot_000_C

description: Homeostatic basal disk and lower peduncle, replicate C


title: ANTI-CD22-5


title: ANTI-CD22-2


title: ANTI-CD22-4


title: 091_Foot_000_A

description: Homeostatic basal disk and lower peduncle, replicate A


title: BFUE_13

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-TACTCC-s_2


title: ANTI-CD22-3


title: KW4c: Sample2-post-ICH


title: KW5c: Sample3-pre-ICH


title: KW3c: Sample2-pre-ICH


title: BFUE_12

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-CTCCTT-s_2


title: BFUE_11

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-ATAGAG-s_2


title: 089_H8_480_B

description: 48 hours post amputation, replicate B

source_name: Regenerating tip, apical reg. 80%

value: 48 hours post amputation


title: 090_H8_480_C

description: 48 hours post amputation, replicate C


title: Genital Skin_PAIS_DHT_rep1.

source_name: Genital Skin Fibroblast, PAIS, DHT, replicate 1


title: IGG-7


title: KW1c: Sample1-pre-ICH

source_name: PBMC


title: IGG-6


title: 092_Foot_000_B

description: Homeostatic basal disk and lower peduncle, replicate B


title: BFUE_9

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-AGAGGA-s_2


title: 087_H8_360_C

description: 36 hours post amputation, replicate C

value: 36 hours post amputation


title: BFUE_8

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TCTTAC-s_2


title: 086_H8_360_B

description: 36 hours post amputation, replicate B


title: IGG-5


title: IGG-4


title: BFUE_7

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TCTACT-s_2


title: IGG-3


title: isolated_rep3

city: Bielefeld

first: Steven

last: Ramm

address: Konsequenz 45

country: Germany

institute: Bielefeld University

description: Mlig-SocialRNASeq-Processed.txt, header = 12_1.3

data_processing:
Real-time base-calling on the HiSeq computer (Fasteris)
Sequencing reads were mapped to the M. lignano de novo transcriptome assembly MLRNA110815 using bowtie v. 0.12.7 with parameters “-n 2 -e 99999999 -l 16 -a -m 200 --best –strata”
Transcript expression levels were derived from the read mapping data by RSEM v1.1.19
Genome_build: M. lignano transcriptome assembly MLRNA110815
Supplementary_files_format_and_content: Matrix table containing all prcoessed data is a tab-delimited text file; raw files are in FASTQ format

organism: Macrostomum lignano

source_name: Whole flatworms

growth_protocol: Standard culturing procedures for M. lignano, 32‰ salinity artificial sea water, fed with diatoms (Nitzschia curvilineata), 14:10 light:dark cycle at 20°C and 60% relative humidity. Different group sizes according to treatment.

extract_protocol:
Standard TRIzol extraction protocol for liquid samples
mRNA standard Illumina protocol (Fasteris)

treatment_protocol: No additonal treatment beyond the differing group sizes between treatments (see individual sample descriptions)

tag: developmental stage

value: adult

tag: group size

value: isolated


title: 085_H8_360_A

description: 36 hours post amputation, replicate A


title: isolated_rep2

description: Mlig-SocialRNASeq-Processed.txt, header = 8_1.2


title: BFUE_6

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TATGCA-s_2


title: IGG-2


title: ANTI-CD22-1


title: 084_H8_240_C

description: 24 hours post amputation, replicate C

value: 24 hours post amputation


title: BFUE_5

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-TACTCC-s_2


title: KW2c: Sample1-post-ICH


title: 088_H8_480_A

description: 48 hours post amputation, replicate A


title: IGG-1


title: joined_rep3

description: Mlig-SocialRNASeq-Processed.txt, header = 11_J.3

value: joined


title: BFUE_10

description:
BFUE_CFUE.counts.txt.gz
AGGCAGA-AGGCTT-s_2


title: 083_H8_240_B

description: 24 hours post amputation, replicate B


title: isolated_rep4

description: Mlig-SocialRNASeq-Processed.txt, header = 16_1.4


title: joined_rep4

description: Mlig-SocialRNASeq-Processed.txt, header = 15_J.4


title: 082_H8_240_A

description: 24 hours post amputation, replicate A


title: SCC_1_shPixt1_3_K27Ac_ChIP

city: New York

first: Markus

last: Schober

state: NY

address: 550 First Ave, Smilow 407

department: Dermatology

institute: New York University School of Medicine

library_source: genomic

data_processing:
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
Sequences with MAPQ scores <30 were removed with samtools50 and duplicates were removed with picard-tools version 1.88
IGV viewer files were generated with igvtools count -z 5 -w 25 -e 250.
ChIP-seq peaks were called with MACS51 version 2.1.0 in comparison to input controls with the parameters -q 0.001 --nomodel --extsize 400.
Motif discovery was performed with MEME-ChIP52,53 using 200bp sequence surrounding peak summits.
Motif containing ChIP-seq peaks were analyzed with the GREAT: Genomic Regions Enrichment of Annotations Tool54, using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 peak calling from the common peaks conserve in shScr and shPitx1 technical replicates (linked to the corresponding rep1 sample records)

growth_protocol:
Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions, and infected with shPitx1 lentiviruses.
Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions. For in vivo ChIP, 15,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 1x10^5 cells were sorted gatting in integrin α6 and integrin b1 high or low expression

extract_protocol:
Chromatin was prepared from 1x10^6 SCC cells or2x10^6 sorted cells  using the ChIPmentation protocol described in Schmidl et. al, Nat Methods. 2015 Oct; 12(10): 963–965, DOI: 10.1038/nmeth.3542  using 4ug of anti-Pitx1 (Santa Cruz, 18922), anti-Klf4 (R&D, AF3758) and anti-H3K27Ac (Abcam, ab4729).
Library prep was performed acording to Schmidl et. al, Nat Methods. 2015 Oct; 12(10): 963–965, DOI: 10.1038/nmeth.3542, using Tn5 to tagment the DNA fragments previous elution of the DNA.

treatment_protocol: For shScr and shPitx1 H3K27Ac ChIP-Seq experiments, SCC cells were infected with shScr and shPitx1 lentiviruses, and the cell were collected 48 hours after the infection.

tag: strain background

value: skin

value: squamous cell carcinoma (SCC)

tag: genotype/variation

value: shPitx1 lentiviruses

tag: chip antibody

value: anti-H3K27Ac (Abcam, ab4729)


title: SCC_1_shPitx1_4_K27Ac_ChIP

tag: cell type


title: 081_H8_160_C

description: 16 hours post amputation, replicate C

tag: strain

value: 16 hours post amputation


title: SCC_1_shPitx1_2_K27Ac_ChIP

tag: tissue


title: joined_rep2

description: Mlig-SocialRNASeq-Processed.txt, header = 7_J.2


title: isolated_rep1

description: Mlig-SocialRNASeq-Processed.txt, header = 4_1.1


title: BFUE_2

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-AGGCTT-s_2

value: BFUE


title: paired_rep4

description: Mlig-SocialRNASeq-Processed.txt, header = 14_2.4

value: paired


title: KO SVZ 3

city: Birmingham

first: Kushani

last: Shah

state: AL

address: 1825 University Blvd.

department: Biochemistry & Molecular Genetics

institute: University of Alabbama at Birmingham

data_processing:
Basecalls performed using CASAVA version 1.8.4
For RNA-seq, data analysis was performed using TruSeq Stranded RNA-Seq Pipeline in Partek Flow with some parameter modifications. Briefly, low quality mapped reads (MQ < 30) were removed from the analysis, mapped to the mouse reference genome (GRCm38/mm10) using TopHat2 (v2.1.0), and annotated using Gencode v20 (changed parameter “Strand Specificity” set to “Auto detect”). Read counts were normalized by TMM then FPKM and differential gene expression analyses (GSA) were performed to identify genes differentially expressed between Control and KO tissues. Gene ontology analysis was performed with DAVID 6.7 (https://david-d.ncifcrf.gov/), GSEA was performed at http://software.broadinstitute.org/gsea/index.jsp.
Genome_build: mm10
Supplementary_files_format_and_content: Count tables (transcript counts for genomic features)

source_name: SVZ Tissue

extract_protocol:
For samples 1-12, total RNAs were isolated using Direct-zol RNA Extraction Kit (Zymo Research).
Library preparation and sequencing for RNA samples were performed at the Genomic Services Lab at HudsonAlpha Institute for Biotechnology (Huntsville, AL). Briefly, the quality of the total RNA was assessed using the Agilent 2100 Bioanalyzer. Two rounds of polyA+ selection was performed for RNA samples, followed by conversion to cDNAs. The mRNA library generation kits (Agilent, Santa Clara, CA) was used generate sequencing libraries per manufacturer’s instructions. The indexed DNA libraries were quantitated using qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit for library quantitation (Kapa Biosystems, Woburn, MA) prior to cluster generation. Clusters were generated to yield approximately 725 K to 825 K clusters/mm2. Cluster density and quality were determined during the run after the first base addition parameters were assessed.

value: NSC/NPC & surrounding cells in Subventricular zone (SVZ)

tag: genotype


title: 079_H8_160_A

description: 16 hours post amputation, replicate A

value: Jussy


title: 080_H8_160_B

description: 16 hours post amputation, replicate B


title: joined_rep1

description: Mlig-SocialRNASeq-Processed.txt, header = 3_J.1


title: KO SVZ 2


title: SCC_1_shScr_2_K27Ac_ChIP

growth_protocol:
Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions, and infected with shScr lentiviruses.
Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions. For in vivo ChIP, 15,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 1x10^5 cells were sorted gatting in integrin α6 and integrin b1 high or low expression

value: shScr lentiviruses


title: BFUE_4

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-CTCCTT-s_2


title: SCC_1_shPixt1_1_K27Ac_ChIP


title: 078_H8_080_C

description: 8 hours post amputation, replicate C

value: 8 hours post amputation


title: BFUE_1

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-AGAGGA-s_2


title: SCC_1_shScr_1_K27Ac_ChIP


title: 077_H8_080_B

description: 8 hours post amputation, replicate B


title: paired_rep1

description: Mlig-SocialRNASeq-Processed.txt, header = 2_2.1


title: BFUE_3

description:
BFUE_CFUE.counts.txt.gz
AAGAGGC-ATAGAG-s_2


title: octet_rep4

description: Mlig-SocialRNASeq-Processed.txt, header = 13_8.4

value: octet


title: SCC_1_invivo_Klf4_Low_ChIP

growth_protocol:
5,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 1x10^6 cells were sorted gatting in integrin α6 and integrin b1 low expression
Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions. For in vivo ChIP, 15,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 1x10^5 cells were sorted gatting in integrin α6 and integrin b1 high or low expression

value: anti-Klf4 (R&D, AF3758)


title: paired_rep2

description: Mlig-SocialRNASeq-Processed.txt, header = 6_2.2

value: adult


title: Con SVZ 3


title: SCC_1_invivo_Klf4_High_ChIP

growth_protocol:
5,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 1x10^6 cells were sorted gatting in integrin α6 and integrin b1 high expression
Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions. For in vivo ChIP, 15,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 1x10^5 cells were sorted gatting in integrin α6 and integrin b1 high or low expression


title: KO SVZ 1


title: 075_H8_040_C

description: 4 hours post amputation, replicate C

value: 4 hours post amputation


title: Con SVZ 2


title: 074_H8_040_B

description: 4 hours post amputation, replicate B


title: paired_rep3

description: Mlig-SocialRNASeq-Processed.txt, header = 10_2.3


title: Con SVZ 1


title: SCC_1_invivo_Pitx1_Low_ChIP

value: anti-Pitx1 (Santa Cruz, 18922)


title: 073_H8_040_A

description: 4 hours post amputation, replicate A


title: octet_rep1

description: Mlig-SocialRNASeq-Processed.txt, header = 1_8.1


title: KO DG 3

source_name: DG Tissue

value: NSC/NPC & surrounding cells in Dentate Gyrus (DG)


title: KO DG 2


title: SARM1 KO-RML-2

city: Zurich

first: Caihong

address: Schmelzbergstrasse 12

institute: Institute of Neuropathology

data_processing:
Reads were quality-checked with FastQC. For RNAseq data analysis, we used RSEM to perform RNAseq read alignment and expression estimation
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-separated value files with the output from RSEM (transcriptCounts, TPM, FPKM) and posterior estimates

source_name: Brain_prion infected

extract_protocol:
Brains were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent and cleaned up using RNeasy kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 500ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice at 6-8 weeks old were intracerebrally (i.c) inoculated with 30 ul of brain homogenate diluted in PBS with 5% BSA and containing 3 x 105LD50 units of the RML6 (RML6, Rocky Mountain Laboratories scrapie strain passage 6). Scrapie was diagnosed according to clinical criteria (ataxia, kyphosis, priapism, and hind leg paresis). Mice were sacrificed on the day of onset of terminal clinical signs of scrapie.

tag: background strain

value: Brain

tag: infected with

value: prion


title: SARM1 KO-RML-4


title: 071_H8_020_B

description: 2 hours post amputation, replicate B

value: 2 hours post amputation


title: SARM1 KO-RML-3


title: 076_H8_080_A

description: 8 hours post amputation, replicate A


title: KO DG 1


title: 070_H8_020_A

description: 2 hours post amputation, replicate A


title: SARM1 KO-RML-1


title: Con DG 3


title: WT-RML-4

value: Wild type


title: Con DG 2


title: 069_H8_010_C

description: 1 hour post amputation, replicate C

value: 1 hour post amputation


title: 068_H8_010_B

description: 1 hour post amputation, replicate B


title: Con DG 1


title: octet_rep3

description: Mlig-SocialRNASeq-Processed.txt, header = 9_8.3


title: WT-RML-3


title: octet_rep2

description: Mlig-SocialRNASeq-Processed.txt, header = 5_8.2


title: WT-RML-2


title: 067_H8_010_A

description: 1 hour post amputation, replicate A


title: 072_H8_020_C

description: 2 hours post amputation, replicate C


title: WT-RML-1


title: 066_H8_005_C

description: 0.5 hour post amputation (30min), replicate C

value: 0.5 hour post amputation (30min)


title: 065_H8_005_B

description: 0.5 hour post amputation (30min), replicate B


title: SARM1 KO-4

value: not infected


title: SARM1 KO-3


title: 064_H8_005_A

description: 0.5 hour post amputation (30min), replicate A


title: 063_H8_000_C

description: 0 hours post amputation, replicate C

value: 0 hours post amputation


title: SCC_2_Pitx1_KO_ChIP

data_processing:
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
Sequences with MAPQ scores <30 were removed with samtools50 and duplicates were removed with picard-tools version 1.88
IGV viewer files were generated with igvtools count -z 5 -w 25 -e 250.
ChIP-seq peaks were called with MACS51 version 2.1.0 in comparison to input controls with the parameters -q 0.001 --nomodel --extsize 400.
Motif discovery was performed with MEME-ChIP52,53 using 200bp sequence surrounding peak summits.
Motif containing ChIP-seq peaks were analyzed with the GREAT: Genomic Regions Enrichment of Annotations Tool54, using default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bed

source_name: squamous cell carcinoma

growth_protocol: Cells were grown in low calcium (50uM) conditions or 15,000 cells were injected intradermally to form tumor allografts

extract_protocol:
Chromatin was prepared from 2x10^7 SCC cells or 1x10^6 sorted cells using the ChIP-IT High Sensitivity kit (53040, Active Motif) according to manufacturers instructions.
Library prep was performed with ThruPLEX DNA-seq kit (Rubicon Genomics, R400427) using 200pg of ChIP DNA or KAPA Hyper Prep kit (KAPA, KK8505) using 1ng of ChIP DNA

value: skin

tag: antibody

value: anti-Pitx1 (Santa Cruz, 18922), 4ug

tag: condition

value: Cells were grown in DMEM7F12 media, 50uM Ca2+ and 15% FBS conditions


title: SCC_2_Trp63_ChIP

value: anti-TP63 (Cell Signaling, 13109), 4ug


title: SCC_2_LowCa_Klf4_ChIP

value: anti-Klf4 (R&D, AF3758), 4ug


title: SCC_2_Hi24hCa_Klf4_ChIP

value: Cells were incubated in DMEM7F12 media, 1.5mM Ca2+ and 15% FBS conditions for 24 hours before the chromatin was collected.


title: SCC_2_Sox2_ChIP

value: anti-Sox2 (R&D, AF2018), 4ug


title: Concentration 5, replicate 5

city: Leipzig

first: Stefan

last: Scholz

address: Permoserstr. 15

department: Bioanalytical Ecotoxicology

institute: Helmholtz Centre for Environmental Research

description: Gene expression after exposure to 6.31 µg/L Triclosan

hyb_protocol: 480 ng cy3-labeled fragmented cRNA per sample were hybridized to the microarrays for 17h at 65°C.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 067797_D_F_20140621) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Scenedesmus vacuolatus

source_name: Exposure to 6.63 µg/L of triclosan

label_protocol: 50ng purified RNA was labeled using the Low Input Quick Amp Labeling Kit, one color (Agilent Technologies).

growth_protocol: Cultures of chlorophyte S. vacuolatus (Shih. et Krauss strain 211-15, culture collection Pringsheim (SAG Göttingen, Germany)) were grown in a sterile inorganic medium (pH 6.4) at 28°C by using a 14:10-h light:dark cycle as describe by Altenburger et al. (Environ. Sci. Toxicol., 23, 6353-6362).

extract_protocol: Two times 80 mL suspensions of triclosan-exposed cultures for each replicate were harvested by centrifugation (22°C, 10 min, 3300 g). Culture pellets were resuspended in 500µL TRIZOL and stored at -80°C until further analysis. After cell lysis and RNA extraction using a FastPrep®24 homogenizer system (Biomedicals, Santa Ana, USA) and Phase LockTM Gele Tubes (5 Prime GmbH, Hamburg, Germany), total RNA was further purified using a RNeasy®Plant Mini Kit (Quiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA quantity and quality were analyzed using a NanoDrop Spectrophotometer (ND-1000, Peqlab, Erlangen, Germany) and an Agilent 2100 Bioanalyzer (Böblingen, Germany).

treatment_protocol: Scenedesmus vacuolatus cultures were exposed for 14 hours to five concentrations of triclosan (0.690, 1.22, 2.15, 3.77 and 6.63µg/L) and one solvent control (final DMSO concentration of 0.1 %) with 5 replicates.

value: Shih. et Krauss, strain 211-15

tag: exposure duration


title: SARM1 KO-1


title: SARM1 KO-2


title: 062_H8_000_B

description: 0 hours post amputation, replicate B

value: Jussy

tag: time point


title: Concentration 5, replicate 2


title: Concentration 5, replicate 4


title: 061_H8_000_A

description: 0 hours post amputation, replicate A


title: SCC_2_input


title: SCC_2_Pitx1_ChIP


title: Concentration 5, replicate 3


title: Concentration 5, replicate 1


title: Concentration 4, replicate 4

description: Gene expression after exposure to 3.77 µg/L Triclosan

source_name: Exposure to 3.77 µg/L of triclosan


title: Concentration 4, replicate 3


title: WT-4

value: Brain


title: Concentration 4, replicate 5


title: Concentration 4, replicate 1


title: Concentration 4, replicate 2


title: Concentration 3, replicate 5

description: Gene expression after exposure to 2.15 µg/L Triclosan

source_name: Exposure to 2.15 µg/L of triclosan


title: 060_H5_480_C

description: 48 hours post amputation, replicate C

source_name: Regenerating tip, apical reg. 50%

value: 48 hours post amputation


title: WT-3


title: SCC_1_Trp63_ChIP


title: WT-2


title: 059_H5_480_B

description: 48 hours post amputation, replicate B


title: SCC_1_invivo_Pitx1_ChIP

value: 5,000 cells were injected intradermally to form tumor allografts

value: In the end point of the experiment, 1x10^6 cells were sorted gatting in integrin α6 and integrin b1


title: WT-1

value: Wild type


title: SCC_1_Sox2_ChIP


title: 058_H5_480_A

description: 48 hours post amputation, replicate A


title: SCC_1_invivo_input


title: UL_BGB_3

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

description:
Lea18
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt

data_processing:
Reads of murine mRNA were aligned to GRCm38, M13 Gencode release using HISAT2 2.0.5
Aligned reads present within adequate GENCODE gene annotation regions were counted using featureCounts.
Count data were analyzed using the LIMMA package in R Bioconductor (https://www.bioconductor.org/packages/release/ bioc/html/ limma.html).
Preprocessing of count data included log2 transformation and scaling to the library size to obtain log2cpm values (log2 of counts per million).
Voom was applied to estimate non-parametrically the mean-variance trend of the logged read counts and to use this mean-variance relationship to predict the variance of each log2cpm value.
Genome_build: GRCm38, M13 Gencode release
Supplementary_files_format_and_content: Counts_Lea_gencode_vM13_170529.txt: Tab-delimited text file includes annotated genes.
Supplementary_files_format_and_content: log2cpm_ID_220818.txt: Tab-delimited text file includes log2cpm counts for all samples.

source_name: Non-ligated kidney treated with BGB324/Bemcentinib

growth_protocol: Eight- to nine-week-old male C57Bl/6JOlaHSD mice were obtained from Envigo (Horst, The Netherlands). All animals were kept in the local animal facility of the Department of Biomedicine at the University of Bergen, Norway.

extract_protocol:
For RNA extraction from frozen murine tissues, we used the RNeasy mini kit (Qiagen, catalogue number: 74104).
Sequencing libraries of murine tissues were prepared using the TruSeq stranded mRNA library preparation kit (Illumina, USA) and sequenced on an Illumina HiSeq4000 platform.
Paired-end 75bp sequencing.

treatment_protocol: Treatment with BGB324/Bemcentinib or with its vehicle for 2 weeks.

tag: strain/background

tag: Sex

value: Male

value: Non-ligated kidney

tag: treatment


title: 057_H5_360_C

description: 36 hours post amputation, replicate C

value: 36 hours post amputation


title: 055_H5_360_A

description: 36 hours post amputation, replicate A


title: SCC_1_culture_Pitx1_ChIP

value: skin


title: UL_BGB_2

description:
Lea17
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: 056_H5_360_B

description: 36 hours post amputation, replicate B


title: 053_H5_240_B

description: 24 hours post amputation, replicate B

value: 24 hours post amputation


title: UL_BGB_1

description:
Lea16
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: Concentration 3, replicate 3


title: UL_UT_3

description:
Lea15
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt

source_name: Non-ligated kidney treated with vehicle (control, untreated)

value: vehicle


title: Concentration 3, replicate 2


title: Concentration 3, replicate 1


title: UL_UT_2

description:
Lea14
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: Concentration 3, replicate 4


title: Concentration 2, replicate 5

description: Gene expression after exposure to 1.22 µg/L Triclosan

source_name: Exposure to 1.22 µg/L of triclosan


title: Concentration 2, replicate 4


title: 054_H5_240_C

description: 24 hours post amputation, replicate C


title: SCC_1_culture_input


title: 050_H5_160_B

description: 16 hours post amputation, replicate B

value: 16 hours post amputation


title: 052_H5_240_A

description: 24 hours post amputation, replicate A


title: 051_H5_160_C

description: 16 hours post amputation, replicate C


title: Concentration 2, replicate 3


title: Concentration 2, replicate 2


title: Concentration 1, replicate 5

description: Gene expression after exposure to 0.69 µg/L Triclosan

source_name: Exposure to 0.69 µg/L of triclosan


title: 049_H5_160_A

description: 16 hours post amputation, replicate A


title: LIG_BGB_2

description:
Lea8
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt

source_name: Ligated kidney treated with BGB324/Bemcentinib

value: Ligated kidney


title: LIG_BGB_3

description:
Lea9
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: LIG_BGB_4

description:
Lea10
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: LIG_BGB_6

description:
Lea12
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: 048_H5_080_C

description: 8 hours post amputation, replicate C

value: 8 hours post amputation


title: LIG_BGB_1

description:
Lea7
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: UL_UT_1

description:
Lea13
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: Concentration 2, replicate 1


title: 046_H5_080_A

description: 8 hours post amputation, replicate A


title: 045_H5_040_C

description: 4 hours post amputation, replicate C

value: 4 hours post amputation


title: LIG_UT_5

description:
Lea5
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt

source_name: Ligated kidney treated with vehicle (control, untreated)


title: Concentration 1, replicate 4

value: Shih. et Krauss, strain 211-15


title: Concentration 1, replicate 3


title: LIG_UT_4

description:
Lea4
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: LIG_BGB_5

description:
Lea11
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: 044_H5_040_B

description: 4 hours post amputation, replicate B

value: Jussy


title: Concentration 1, replicate 2


title: Control, replicate 4

description: Gene expression after exposure to 0 µg/L Triclosan

source_name: Control


title: Control, replicate 5


title: 047_H5_080_B

description: 8 hours post amputation, replicate B


title: Concentration 1, replicate 1


title: LIG_UT_3

description:
Lea3
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: 042_H5_020_C

description: 2 hours post amputation, replicate C

value: 2 hours post amputation


title: T cell vehicle bulk

city: Denver

first: Rachel

last: Friedman

state: Colorado

address: 1400 Jackson

institute: National Jewish Health

description:
135.07-10-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_020
TCELL_VEH_BUL

data_processing:
Basecalling (Ion Torrent S5)
Alignment (Torrent mapping alignment program)
Quantification (Ion Torrent Ampliseq RNA plugin, unique mapping mode)
Count Normalizaiton (DESeq2)
VST Normalizaiton, blind = TRUE (DESeq2)
Genome_build: AmpliSeq Mouse Transcriptome V1 Reference (based on GRCm38)
Supplementary_files_format_and_content: Count matrices (Raw, Count Normalized, VST Normalized)

source_name: Pancreatic Islets

extract_protocol:
Islets isolated from the pancreases of NOD mice by digest with 0.8% Collagenase P for 11-14 minutes at 37 degrees Celcius, seperated with density gradient, and hand picked. Islets were digested with4 Wunsch units of Collagenase D (Roche) with 250 μg/ml DNAse in HBSS with 10% FBS followed by Cell Dissociation Buffer (Sigma)at 37 degrees Celcius for 30 minutes each.
Sample RNA was isolated using the Quick-RNA Microprep kit (Zymo Research) according to the manufacturer’s protocol. RNA AmpliSeq libraries were constructed and barcoded with the Ion AmpliSeq Transcriptome Mouse Gene Expression Kit and methods.
Amplicon RNA-seq, Unique mapping option

treatment_protocol: Oral saline treatment

value: NOD

tag: age

value: 12-20 weeks pooled

value: T cells

tag: agent

value: vehicle bulk


title: 041_H5_020_B

description: 2 hours post amputation, replicate B


title: CD11c vehicle bulk

description:
135.07-10-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_019
CD11C_VEH_BUL

value: CD11c+ cells


title: LIG_UT_2

description:
Lea2
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt

value: Male


title: LIG_UT_1

description:
Lea1
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: CD11c saline wafergen [134]

description:
134.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_013
CD11C_SAL_WAF

value: saline wafergen


title: 038_H5_010_B

description: 1 hour post amputation, replicate B

value: 1 hour post amputation


title: LIG_UT_6

description:
Lea6
processed data file: log2cpm_ID_220818.txt
processed data file: Counts_Lea_gencode_vM13_170529.txt


title: 037_H5_010_A

description: 1 hour post amputation, replicate A


title: Tcell saline wafergen [134]

description:
134.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_014
TCELL_SAL_WAF


title: Control, replicate 2


title: Control, replicate 1


title: 043_H5_040_A

description: 4 hours post amputation, replicate A


title: O (Yg Het) 3

city: Novato

first: Pedro

last: Sousa-Victor

state: CALIFORNIA

address: 8001 Redwood Blvd.

institute: Buck Institute for Research on Aging

data_processing:
Reads were mapped to the Mouse genome Release mm10 using STAR (v2.4.2a)
Gene expression level was quantified with HTSeq using GENCODE annotation M10, recorded as RPKM
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing RPKM values fro all samples

source_name: Liver

extract_protocol:
Trizol was used to extract RNA from flash frozen tissue
TruSeq Stranded mRNA LT Kit

value: 21 mo

tag: starin

value: WT

tag: parabiosis pair

value: O-YgHet


title: 039_H5_010_C

description: 1 hour post amputation, replicate C


title: O (Yg Het) 2


title: Control, replicate 3


title: O (Yg Het) 5


title: O (Yg Het) 4


title: 035_H5_005_B

description: 0.5 hour post amputation (30min), replicate B

value: 0.5 hour post amputation (30min)


title: Tcell saline wafergen [133]

description:
133.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_014
TCELL_SAL_WAF

tag: cell type


title: CD11c saline wafergen [133]

description:
133.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_013
CD11C_SAL_WAF

tag: strain


title: O (Yg Het) 1


title: O (YgWT) 4

value: O-YgWT


title: 033_H5_000_C

description: 0 hours post amputation, replicate C

value: 0 hours post amputation


title: O (YgWT) 5


title: 034_H5_005_A

description: 0.5 hour post amputation (30min), replicate A


title: Tcell vehicle wafergen (rep2) [133]

description:
133.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_010
TCELL_VEH_WAF

value: vehicle wafergen


title: Tcell vehicle wafergen (rep2) [134]

description:
134.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_010
TCELL_VEH_WAF


title: 031_H5_000_A

description: 0 hours post amputation, replicate A

value: Jussy


title: CD11c vehicle wafergen [133]

description:
133.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_009
CD11C_VEH_WAF


title: O (YgWT) 2


title: CD11c vehicle wafergen [134]

description:
134.06-26-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_009
CD11C_VEH_WAF


title: Tcell vehicle 10x

description:
126.01-05-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_010
TCELL_VEH_10X

value: vehicle


title: O (YgWT) 3


title: 030_F5_480_C

description: 48 hours post amputation, replicate C

source_name: Regenerating tip, basal reg. 50%

value: 48 hours post amputation


title: O-O 4

value: O-O


title: O (YgWT) 1


title: O-O 5


title: Tcell vehicle wafergen (rep 1)

description:
126.01-05-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_004
TCELL_VEH_WAF2

value: NOD

value: 12-20 weeks pooled

value: T cells


title: mx-TCRgd

first: Eleni

last: Mimitou

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
TCRgd transcripts
processed data file:
mx-TCRgd.csv.gz
mx-TCRgd.csv.gz includes: raw counts for gd clonotypes

data_processing:
Library strategy: ECCITE-seq
10x data were processed using cellranger and cellranger vdj pipeline
R1 includes cell barcode, UMI read
R2 is the  biological read
ADT data were mapped to a 12 bases or a 15 bases reference ADT list separately using CITE-seq-count
HTO data were mapped to a 12 bases reference HTO list using CITE-seq-count
GDO data were mapped to a 19 bases reference GDO list using CITE-seq-count
ADT, HTO and GDO sequence lists are available at: https://www.biorxiv.org/content/10.1101/466466v1
Genome_build: hg19 for human only samples
Genome_build: samples with both human and mouse cells were mapped to the hg19-mm10 concatenated reference as provided by cell-ranger
Supplementary_files_format_and_content: tab-delimited text file for 10x data; comma-delimited file for ADT, HTO, GDO and clonotype mapping

organism:
Homo sapiens
Mus musculus

source_name: HEK-293T, NIH-3T3, PBMCs, MyLa, Sez4

extract_protocol:
‘Stained’ and washed cells were loaded into 10x Genomics single cell 5’ system and processed according to manufacturer’s instructions, and the CITE-seq protocols (Stoeckius et al, 2017). For sgRNA capture a custom RT primer was spiked in during the RT reaction.
library construction was performed with the 10x Genomics single cell 5' (VDJ) product.

treatment_protocol: K562, NIH-3T3 and peripheral blood mononuclear cells (PBMCs) were stained as described for CITE-seq (Stoeckius et al, 2017)

value: HEK-293T, NIH-3T3, PBMCs, MyLa, Sez4

tag: antibodies/tag


title: mx-TCRab

description:
TCRab transcripts
processed data file:
mx-TCRab.csv.gz
mx-TCRab.csv.gz includes: raw counts for ab clonotypes


title: 027_F5_360_C

description: 36 hours post amputation, replicate C

value: 36 hours post amputation


title: 040_H5_020_A

description: 2 hours post amputation, replicate A

value: 2 hours post amputation


title: O-O 3

value: 21 mo

tag: genotype


title: 036_H5_005_C

description: 0.5 hour post amputation (30min), replicate C


title: mx-GDO

description:
sgRNAs
processed data file:
mx-GDO-count.csv.gz
mx-GDO-count.csv.gz includes: raw counts for 19 bases GDO

value: 19 bases tag:mNT1, mNT2, mNT3, mNT4, mNT5, mNT6, mNT7, mNT8, mNT9, mNT10


title: O-O 2

value: WT


title: 032_H5_000_B

description: 0 hours post amputation, replicate B


title: 026_F5_360_B

description: 36 hours post amputation, replicate B


title: SCC Replicate 2

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

description: The RNA was extracted from the whole lung tumor.

hyb_protocol: Approximately 480ng of fragmented cRNA samples were loaded onto each of the Mouse G3 8x60K Expression arrays. The arrays were hybridized in an Agilent Hybridization Chamber for 17 hours at 65C with rotation at 10rpm.

scan_protocol: Once dry, the slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.3.1. Data extraction and quality assessment of the microarray data was completed using Agilent Feature Extraction Software Version 11.0.1.1.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using OmicSoft Array Studio (Version 9.0) software.

source_name: Lung tumor

label_protocol: Fifty nanograms of total RNA, combined with RNA spike mix, were reverse transcribed using a T7 Primer Mix to produce cDNA. The cDNA product was transcribed using T7 RNA Polymerase, producing cyanine-3-labeled cRNA. The labeled cRNA was purified using a Qiagen RNeasy Mini Kit. Purified products were quantified using the NanoDrop spectrophotometer for yield and dye incorporation, and tested for integrity on the Agilent Bioanalyzer. Six hundred nanograms of the labeled cRNA were fragmented.

growth_protocol: The mice wre bred in mouse facility following animal protocol approved by NIEHS and Baylor College of Medicine

extract_protocol: Total RNAs were isolated from mouse lungs or lung tumors using TRIzol reagent (Invitrogen) and cleaned by RNeasy kit (QIAGEN, 74104).

treatment_protocol: There is no special treatment for these mice.

tag: genotype/variation

value: 3 months


title: CD11c vehicle 10x

description:
126.01-05-18.S5XL-00648.bcmatrix_submit.txt
IonXpress_075
CD11C_VEH_10X

value: CD11c+ cells


title: O-O 1


title: mx-ADT

description:
antibody oligos
processed data file:
mx-ADT-count.csv.gz
mx-ADT-count.csv.gz includes: raw counts for 12 bases ADT

value: 12 bases tag:hCD29, mCD29


title: 025_F5_360_A

description: 36 hours post amputation, replicate A


title: Yg Het5

value: 5 mo

value: ManfHet

value: O-YgHet


title: mx-HTO

description:
antibody oligos
processed data file:
mx-HTO-count.csv.gz
mx-HTO-count.csv.gz includes: raw counts for 12 bases HTO

value: 12 bases tag:hashtag_1, hashtag_2, hashtag_3, hashtag_A, hashtag_B, hashtag_C, hashtag_D, hashtag_E, hashtag_F, hashtag_G


title: 029_F5_480_B

description: 48 hours post amputation, replicate B

value: Jussy

value: 48 hours post amputation


title: 024_F5_240_C

description: 24 hours post amputation, replicate C

value: 24 hours post amputation


title: 028_F5_480_A

description: 48 hours post amputation, replicate A


title: mx-cDNA

description:
polyA mRNA
processed data file:
mx-cDNA.txt.gz
mx-cDNA.txt.gz includes: raw counts for RNA


title: 023_F5_240_B

description: 24 hours post amputation, replicate B


title: Yg Het4


title: sp-GDO

description:
sgRNAs
processed data file:
sp-GDO.txt.gz
sp-GDO.txt.gz includes: raw counts for 19 bases GDO

source_name: HEK-293T, NIH-3T3

value: HEK-293T, NIH-3T3

value: 19 bases tag:mNT1, mNT2, mNT3, mNT4, mNT5, mNT6, mNT7, mNT8, mNT9, mNT10, hNT1, hNT2, hNT3, hNT4, hNT5, hNT6, hNT7, hNT8, hNT9, hNT10


title: ASC Replicate 2

description: The RNA was extracted from the whole lung.


title: SCC Replicate 1


title: ASC Replicate 3


title: Yg Het3


title: 021_F5_160_C

description: 16 hours post amputation, replicate C

value: 16 hours post amputation


title: sp-ADT

description:
antibody oligos
processed data file:
sp-ADT.txt.gz
sp-ADT.txt.gz includes: raw counts for 12 bases ADT

value: 12 bases tag:hCD29, mCD29, hCD46, hCD13


title: Yg Het2


title: ASC Replicate 1


title: SCC Replicate 3


title: sp-cDNA

description:
polyA mRNA
processed data file:
sp-cDNA.txt.gz
sp-cDNA.txt.gz includes: raw counts for RNA


title: Yg WT5

value: O-YgWT


title: 020_F5_160_B

description: 16 hours post amputation, replicate B


title: Yg Het1


title: 019_F5_160_A

description: 16 hours post amputation, replicate A


title: WT Replicate 3

source_name: Lung

value: wild type (Lkb1f/fPtenf/f)


title: WT Replicate 1


title: WT Replicate 2


title: 018_F5_080_C

description: 8 hours post amputation, replicate C

value: 8 hours post amputation


title: 017_F5_080_B

description: 8 hours post amputation, replicate B


title: Yg WT4

value: WT


title: Yg WT1


title: WHIM30 Normal Adjacent Liver Tissue from mouse 100070

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

description:
Normal liver tissue adjacent to liver metastasis.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Normal.Adjacent.Liver.100070

data_processing:
Alignment: STAR v2.5.2b was used for alignment with the following settings: --outSAMtype BAM Unsorted --outSAMorder Paired --outReadsUnmapped Fastx --quantMode TranscriptomeSAM --outFilterMultimapNmax 1
Read Counting: Salmon v0.8.2 was used for counting reads with the "quant" algorithm and library type set to "IU" using the transcriptome output of STAR.
TPM Calculations: TPM values were calculated using a custom in-house script from the raw read counts and transcript lengths provided by Salmon.  TPM values are raw and have not been log2 transformed or further processed in any way.
Genome_build: A custom reference genome was built by concatenating the following three genome builds: GRCh38 human genome from the Genomic Data Commons (https://gdc.cancer.gov/about-data/data-harmonization-and-generation/gdc-reference-files), GRCm38 M12 Gencode release of the Mouse genome (http://www.gencodegenes.org/mouse_releases/12.html), and the Xenotropic murine leukemia virus accession JF274252.1 (https://www.ncbi.nlm.nih.gov/nuccore/JF274252.1).  Prior to concatenation, human chromosomes were concatenated with "HUMAN_" and mouse chromosomes were concatenated with "MOUSE_".
Supplementary_files_format_and_content: The processed data files contain the output from Salmon and include Salmon calculated TPM, gene lengths, and raw counts for the human and mouse genomes.

source_name: Liver, Human xenograft, Mus musculus

growth_protocol: PDX cells were grown in various organs in NSG mice

extract_protocol:
RNA was harvested from tissue/cell samples using the Qiagen Rneasy Mini Kit.
KAPA Stranded mRNA-Seq Kit was used for library preparation.

treatment_protocol: All samples are untreated and all tissues flash frozen during extraction

tag: histologic subtype

value: Normal adjacent

tag: intrinsic subtype

tag: model type

value: Patient-derived xenograft

tag: pdx model


title: WHIM30 Mammary Gland Tumor from mouse NSG21A

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.NSG21A

source_name: Mammary Gland, Human xenograft, Mus musculus

value: Mammary gland tumor

value: Basal


title: 022_F5_240_A

description: 24 hours post amputation, replicate A

tag: time point


title: WHIM30 Mammary Gland Tumor from Brain Metastasis from mouse 100895

description:
Tissue from mouse brain metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.FromBrainMet.100895


title: 014_F5_040_B

description: 4 hours post amputation, replicate B

value: 4 hours post amputation


title: 015_F5_040_C

description: 4 hours post amputation, replicate C


title: 013_F5_040_A

description: 4 hours post amputation, replicate A


title: 016_F5_080_A

description: 8 hours post amputation, replicate A


title: MANFHet_2

value: 10 mo

value: Manf +/-


title: WHIM30 Normal Adjacent Liver Tissue from mouse 100069

description:
Normal liver tissue adjacent to liver metastasis.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Normal.Adjacent.Liver.100069


title: MANFHet_4


title: MANFHet_3


title: WHIM30 Normal Adjacent Liver Tissue from mouse 100073

description:
Normal liver tissue adjacent to liver metastasis.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Normal.Adjacent.Liver.100073


title: MANFHet_1


title: WHIM30 Mammary Gland Tumor from Brain Metastasis from mouse 100894

description:
Tissue from mouse brain metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.FromBrainMet.100894


title: Yg WT3

value: 5 mo


title: WHIM30 Mammary Gland Tumor from mouse 181040A

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.181040A


title: WT_3

value: Manf +/+


title: WHIM30 Mammary Gland Tumor from mouse 175278A

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.175278A


title: WHIM30 Mammary Gland Tumor from Brain Metastasis from mouse 100893

description:
Tissue from mouse brain metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.FromBrainMet.100893


title: 011_F5_020_B

description: 2 hours post amputation, replicate B

value: Jussy

value: 2 hours post amputation


title: WHIM30 Mammary Gland Tumor from Brain Metastasis from mouse 100542

description:
Tissue from mouse brain metastasis (100218) Long Term Met Line grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.FromBrainMet.100542


title: WHIM30 Mammary Gland Tumor from mouse 182696A

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.182696A


title: Yg WT2


title: WHIM30 Mammary Gland Tumor from Liver Metastasis from mouse 100541

description:
Tissue from mouse liver metastasis (100218) Long Term Met Line grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.FromLiverMet.100541


title: 012_F5_020_C

description: 2 hours post amputation, replicate C


title: Old HTV MANF2

treatment_protocol: Young and old mice received hydrodynamic tail vein injections of EEV plasmids coding hMANF protein or control empty plasmids and were analyzed 5 weeks post intervention.

value: 23 mo

value: hMANF HTV


title: Old HTV MANF3


title: Old HTV MANF1


title: WHIM30 Lung Metastasis from mouse 182835C

description:
Tissue from lung metastsis from tail vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Lung.Met.182835C

source_name: Lung, Human xenograft, Mus musculus

value: Lung metastasis

value: Normal


title: WHIM30 Lung Metastasis from mouse 181658C

description:
Tissue from lung metastasis from Mgmet(180085), which came from Mgmet(178185)
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Lung.Met.181658C


title: 009_F5_010_C

description: 1 hour post amputation, replicate C

value: 1 hour post amputation


title: 003_F5_000_C

description: 0 hours post amputation, replicate C

value: 0 hours post amputation


title: WT_2


title: 007_F5_010_A

description: 1 hour post amputation, replicate A


title: WT_1


title: 002_F5_000_B

description: 0 hours post amputation, replicate B


title: WHIM30 Lung Metastasis from mouse 183303C

description:
Tissue from lung metastsis from tail vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Lung.Met.183303C


title: WT_4


title: WHIM30 Liver Metastasis from mouse 183291B

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.183291B

value: Liver metastasis


title: Old HTV MANF4


title: 004_F5_005_A

description: 0.5 hour post amputation (30min), replicate A

value: 0.5 hour post amputation (30min)


title: 006_F5_005_C

description: 0.5 hour post amputation (30min), replicate C


title: WHIM30 Lung Metastasis from mouse 182837C

description:
Tissue from lung metastsis from tail vein
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Lung.Met.182837C

value: Patient-derived xenograft


title: Old HTV Cntrl1

value: Cntrl HTV


title: OH6 technical replicate 1

data_processing:
bcl2fastq
STAR
samtools
DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: .csv normalized counts

source_name: microglia

extract_protocol:
Primary mouse microglia were isolated by gentle dounce homogenization of the brain, magentic myelin removal, and FACS-purification of ~20,000 live CD11b+CD45lo cells. Microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according the manufacturer’s protocol. RNA integrity was assessed on a Bioanalyzer (Agilent), and high quality samples were used for library preparation.
cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina). After normalization and pooling, libraries were sequenced on a NovaSeq 6000 (Illumina) using paired-end 150bp reads.

value: 20 months old


title: WHIM30 Mammary Gland Tumor from mouse 100431

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.MGT.100431

value: Mammary gland tumor

value: Basal


title: 010_F5_020_A

description: 2 hours post amputation, replicate A


title: 005_F5_005_B

description: 0.5 hour post amputation (30min), replicate B


title: WHIM30 Liver Metastasis from mouse 180090B

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.180090B


title: WHIM30 Liver Metastasis from mouse 178200B

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.178200B


title: Old HTV Cntrl4


title: WHIM30 Lung Metastasis from mouse 100218

description:
Tissue from lung metastasis from Long Term Met Passage Line.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Lung.Met.100218


title: Yg HTV MANF2

value: 5 mo


title: 008_F5_010_B

description: 1 hour post amputation, replicate B


title: OH3 technical replicate 2


title: WHIM30 Lung Metastasis from mouse 100069

description:
Tissue from lung metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Lung.Met.100069

value: LumB


title: 001_F5_000_A

description: 0 hours post amputation, replicate A

value: Jussy


title: Old HTV Cntrl3


title: OH6 technical replicate 2


title: Old HTV Cntrl2


title: OH3 technical replicate 1


title: Yg HTV MANF1


title: WHIM30 Liver Metastasis from mouse 180092B

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.180092B


title: Yg HTV Cntrl3


title: OH4


title: WHIM30 Liver Metastasis from mouse 100521

description:
Tissue from liver metastasis from Cardiac Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.100521


title: Yg HTV MANF4


title: YH5

value: 3 months old


title: WHIM30 Liver Metastasis from mouse 100070

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.100070


title: WHIM30 Liver Metastasis from mouse 100219

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.100219


title: WHIM30 Liver Metastasis from mouse 100220

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.100220


title: WHIM30 Brain Metastasis from mouse 100536

description:
Tissue from brain metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Brain.Met.100536

source_name: Brain, Human xenograft, Mus musculus

value: Brain metastasis


title: YH4 technical replicate 2


title: OH5


title: OH2


title: WHIM30 Brain Metastasis from mouse 100523

description:
Tissue from brain metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Brain.Met.100523


title: pop2 in YPGL

city: Tsukuba

first: Kenji

last: Irie

state: Ibaraki

address: 1-1-1 Tennodai

institute: University of Tsukuba

scan_protocol: GeneChip were scaned by GeneChip Scaner 3000(Affymetrix 690036) using GeneChip Command Console Software ver3.2(Affymetrix 702569). The procedure of scan is followed by  Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）

data_processing: Data is processed by RMA-Skech algorythm using Expression ConsoleTM Softwere ver.1.3（Affymetrix 702387）

label: biotin

organism: Saccharomyces cerevisiae

source_name: pop2 grown in YPGL

label_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）. 100ng Total RNA was used for this assay.

growth_protocol: Yeast cells were grown at 30° in YPD or YPGL.

extract_protocol: Total RNAs were prepared from yeast cells using ISOGEN reagent (Nippon Gene) and the RNeasy Mini kit (Qiagen), following the instructions of the manufacturer.

tag: growth medium

value: YPGL


title: Yg HTV MANF3

value: hMANF HTV


title: mpt5 in YPD

hyb_protocol: The procedure of labeling is followed by Affymetrix GeneChip WT PLUS Reagent Kit User Manuall（Affymetrix 703174 Rev.2）

source_name: mpt5 grown in YPD

value: YPD


title: WHIM30 Liver Metastasis from mouse 100073

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.100073


title: wild type in YPGL

source_name: wild type grown in YPGL

value: wild type


title: Yg HTV Cntrl1


title: BRG1_WT.gene

city: shanghai

first: Yongfeng

address: 320 Yueyang Road, Shanghai, 200025 P.R. China

institute: The Institute of Health Sciences, SIBS, CAS / SJTUSM

data_processing:
Filtering steps are as follows:1) Remove reads with adaptors;2) Remove reads in which unknown bases are more than 10%;3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose  sequencing quality  is no more than 5).
Use  Bowtie2  to map clean reads to reference gene and use  BWA to reference genome.
FPKM  method is used in calculated expression level
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: colon epithelial cells

growth_protocol: no treatment

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 2 weeks prior to isolatation of  the colon epethelial cells WT and Villin-CreERT2 mice are intraperitoneal injected with Tamoxifen and then colon epithelial cells are isolated by EDTA digestion

value: primary colon epithelial cells


title: pbp1 in YPGL

source_name: pbp1 grown in YPGL


title: Yg HTV Cntrl2


title: YH6


title: WHIM30 Liver Metastasis from mouse 100069

description:
Tissue from liver metastasis from Tail Vein Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Liver.Met.100069

value: Liver metastasis


title: YH3


title: OH1


title: YH2 technical replicate 2


title: SBW25 replicate 2

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

institute: Max Planck Institute for Evolutionary Biology

data_processing:
RNA-seq datasets were mapped to the SBW25 genome (downloaded from Genbank under the accession number NC_012660) via Bowtie2 with default settings
The coverage per gene of the genome mapping was determined with HTSeq. The gene annotation for HTSeq was also downloaded from the SBW25 Genbank entry.
Differentially expressed genes were identified by applying DESeq2. The standard workflow in https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf was used, except that the alpha parameter was set to 0.3 to reduce the number of genes that were falsely classified as not significantly differentially expressed between the different morphotypes
Genome_build: ASM922v1
Supplementary_files_format_and_content: The processed data files contain information obtained by running "htseq-count" on the aligned sequence files. The files contain the sequence read coverage for each gene in the Pseudomonas fluorescens SBW25 genome. This data can be used to determine differentially expressed genes by for example DESeq2

organism: Pseudomonas [fluorescens] SBW25

source_name: Microbial cell culture

growth_protocol: Method: 3x single colonies of each of SBW25, 6A4 and 6B4 were grown on KB agar (28˚C, 48 hours), precultured in shaken KB (28˚C, overnight), grown to mid-exponential phase in shaken KB flasks (28˚C, OD600 of 0.4-0.6). SBW25 and 6A4 cultures were used for total RNA extraction; 6B4 cultures were split into cap+ and cap- fractions by centrifugation before total RNA isolation (and are included as separate samples above).

extract_protocol:
RNA extraction and purification was performed using a RiboPureTM Bacteria Kit (Ambion®). RNA libraries were prepared for sequencing using standard Illumina protocols.
Normalized mRNA-seq library preparation was performed by the Australian Genome Research Facility (Brisbane, Australia). AGRF used a TruSeq kit to prep the RNA library, and perforemdd Ribo-Zero Bacteria rRNA Removal (https://sapac.illumina.com/products/scriptseq-bacteria.html). AGRF also performed the Illumina sequencing.

tag: evolved strain

tag: morphotype

value: Non-switcher


title: WHIM2 Mammary Gland Tumor from Lung Metastasis from mouse 100250

description:
Tissue from mouse lung metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.MGT.FromLungMet.100250

value: Mammary gland tumor grown from lung metastasis

value: Patient-derived xenograft


title: atuA regulon in solid culture at 3 days

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Ohnishi

department: Department of Biotechnology

institute: Graduate School of Agriculture and Life Science, The University of Tokyo

hyb_protocol: Labelled cDNA hybridised using Hybstation. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1% SDS) at 42 °C ,  0.1x SSC (+0.05% SDS) and 0.1x SSC, each at 25 °C for 30 sec prior to drying and scanning.

scan_protocol: Arrays scanned using an Affymetrix 428 scanner and Imagene version 6.1 software.

data_processing: Data analysis was carried out using Imagene, version 6.1 (Biodiscovery Inc). The mean values from each channel were normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from biological repeats with all replicates combined. data was compiled from delta atuA mutant and wild-type strains each with a dye-swap replicate, thus providing three biological repeats.

organism: Streptomyces griseus

source_name: delta atuA mutant strain culured in solid YMPD for 3 days

label_protocol: Labelled with Cy3 and Cy5 after cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Strains were cultivated in YMPD solid medium for  2 and 3 days.

extract_protocol: Toral RNA was extracted using ISOGEN (Nippon Gene) and DNA was removed using DNase I.

treatment_protocol: S. griseus strains were grown on a YMPD plate and the temperature maintained at 28 °C.

value: delta atuA mutant

source_name: wild-type strain culured in solid YMPD for 3 days

value: wild-type


title: 6B4-Cap+ replicate 3

value: Switcher


title: YH1

tag: age


title: Yg HTV Cntrl4

source_name: Liver

value: 5 mo

tag: treatment

value: Cntrl HTV


title: BRG1_KO.gene


title: pbp1 in YPD

source_name: pbp1 grown in YPD


title: 6B4-Cap+ replicate 2


title: WHIM30 Brain Metastasis from mouse 100219

description:
Tissue from brain metastasis from tail vein injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM30.Brain.Met.100219


title: SBW25 replicate 3


title: 6B4-Cap+ replicate 1


title: YH4 technical replicate 1


title: atuA regulon in solid culture at 2 days

source_name: delta atuA mutant strain culured in solid YMPD for 2 days

source_name: wild-type strain culured in solid YMPD for 2 days


title: Wildtype S. cerevisiae, biological rep 2

city: Vancouver

first: Peter

last: Stirling

state: BC

address: 675 W 10th Ave

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Research Centre

description: Gene expression data from log phase wildtype cells

hyb_protocol: Hybridization, wash and staining of the arrays were performed using the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix) as per manufacterer’s instructions.

scan_protocol: The hybridized arrays were scanned with the Gene Chip Scanner 3000 7G (Affymetrix) as per manufacterer’s instructions.

data_processing: Expression data was extracted using Expression Console™ Software (Affymetrix) with RMA algorithm. The gene level differential expression analysis was performed using Affymetrix Transcriptome Analysis Console (TAC) Software.

label: Biotin

source_name: Log-phase wildtype cultured at 30°C

label_protocol: Amplification, labeling and fragmentation were performed with Message AmpTMIII RNA Amplification Kit (A&B Applied Biosystems) as per manufacterer’s instructions.

growth_protocol: Strains were cultured in synthetic drop-out media selecting for the DIS3 allele overnight at permissive conditions (30°C). The next morning, the cultures were diluted 1/10 and returned to the incubator until they reached log phase.

extract_protocol: Total RNA was isolated using a RiboPure Yeast kit (A&B Applied Biosystems) as per manufacterer’s instructions.

treatment_protocol: Optical density of each strain was obtained by spectrophotometer and 1 unit of A600 mid-log phase cells was collected by centrifugation. Cell pellets were washed in distilled water, and flash frozen.

tag: background strain

value: Wildtype


title: mpt5 in YPGL

source_name: mpt5 grown in YPGL


title: SBW25 replicate 1


title: YH2 technical replicate 1

first: John

institute: Stanford

value: 3 months old


title: WHIM2 Mammary Gland Tumor from Lung Metastasis from mouse 100321

description:
Tissue from mouse lung metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.MGT.FromLungMet.100321

source_name: Mammary Gland, Human xenograft, Mus musculus

value: Basal


title: 6B4-Cap- replicate 3


title: WHIM2 Mammary Gland Tumor from mouse 100027

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.MGT.100027

value: Mammary gland tumor


title: pop2 in YPD

source_name: pop2 grown in YPD


title: Wildtype S. cerevisiae, biological rep 1


title: wild type in YPD

source_name: wild type grown in YPD


title: mouse  Δ16HER2-MMG KO2

city: Aviano

first: Riccardo

last: Bomben

address: Via Franco Gallini 2

department: D-RT

country: Italy

institute: CRO Aviano

description: Constitutive Gene expression of EOC cells.

hyb_protocol: 1.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent Hi-RPMI hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then scan immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 2um, Dye channel is set to Green and Dynamic Range of Green PMT is set to 100% and 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: mouse mammary glands collected from pre-neoplastic 13 weeks-old STM KO Δ16HER2 transgenic female mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from mammary tissue cells using the TRIZOL Reagent (ThermoFisher) and validated for integrity and purity using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: mammary gland

tag: histotype

value: epithelial

value: STM KO


title: dis3E729K mutant, biological rep 2

description: Gene expression data from log phase dis3E729K mutant cells

source_name: Log-phase dis3E729K mutant cultured at 30°C

value: dis3E729K mutant


title: WHIM2 Mammary Gland Tumor from Liver Metastasis from mouse 100611

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.MGT.FromLiverMet.100611

value: Mammary gland tumor grown from liver metastasis


title: mouse  Δ16HER2-MMG KO1


title: WHIM2 Mammary Gland Tumor from Liver Metastasis from mouse 100609

description:
Tissue from mouse liver metastasis grown in mammary gland.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.MGT.FromLiverMet.100609


title: WHIM2 Mammary Gland Tumor from mouse 100076

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.MGT.100076


title: dis3E729K mutant, biological rep 1


title: mouse  Δ16HER2-MMG WT2

source_name: mouse mammary glands collected from pre-neoplastic 13 weeks-old WT Δ16HER2 transgenic female mice

value: WT


title: mouse  Δ16HER2-MMG WT1


title: WHIM2 Lung Metastasis from mouse 100091

description:
Tissue from lung metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Lung.Met.100091

source_name: Lung, Human xenograft, Mus musculus

value: Lung metastasis


title: 6A4 replicate3

value: Non-switcher


title: 6B4-Cap- replicate 2


title: Alox12b-KO, biological rep.4

city: Heidelberg

first: Thomas

last: Hielscher

address: INF 280

department: Biostatistics

institute: German Cancer Research Center

description: Gene expression data from Alox12b-deficient newborn mouse epidermis

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: The data were analyzed with R/Bioncoductor, using rma (affy package) as normalization method with default settings. Control probes were removed.

source_name: epidermis, Alox12b-KO, biological rep.4

label_protocol: Biotin-labeled single-stranded cRNA was generated from 100 ng of total RNA isolated from epidermal sheets by using the Affymetrix Gene Chip 3´IVT PLUS Reagent kit. 11 ng of fragmented and labeled cRNA were hybridized for 17 hours at 45°C on Affymetrix GeneChip® Mouse Genome U430 2.0 arrays

growth_protocol: Heterozygous Alox12b knockout mice were mated and the offspring animals were sacrified immediately after birth and genotyped.

extract_protocol: Trunk epidermis of newborn mice was separated mechanically from the dermis following submersion in hot phosphate-buffered saline (56°C) for 30 seconds and snap-frozen in liquid nitrogen.

treatment_protocol: Newborn mice were sacrified immediately after birth and skin was harvested


title: WHIM2 Mammary Gland Tumor from mouse 100000

description:
Tissue from mammary tumors grown in mice
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.MGT.100000

value: Patient-derived xenograft


title: WHIM2 Lung Metastasis from mouse 100086

description:
Tissue from lung metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Lung.Met.100086


title: 6A4 replicate 1

source_name: Microbial cell culture


title: WHIM2 Lung Metastasis from mouse 100373

description:
Tissue from lung metastsis from Cardiac Injection
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Lung.Met.100373


title: 6B4-Cap- replicate 1


title: wildtype, biological rep. 5

description: Gene expression data from wildtype newborn mouse epidermis (strain 129S6)

source_name: epidermis, wildtype, biological rep.5


title: 6A4 replicate 2


title: WHIM2 Lung Metastasis from mouse 100084

description:
Tissue from lung metastasis from mammary gland tumor.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Lung.Met.100084


title: WHIM2 Liver Metastasis from mouse 100465

description:
Tissue from liver metastasis from Direct Liver Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Liver.Met.100465

source_name: Liver, Human xenograft, Mus musculus

value: Liver metastasis


title: gRNA-Jnk1/2-3

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

source_name: Mouse lung tumor

label_protocol: Starting with 400ng of total RNA, Cy3 labeled cRNA was produced following the manufacturer’s protocol.

growth_protocol: The culture medium for this mouse SCC cells included RPMI (Life Technologies, 11875-093), 10% FBS (16000-044, Life Technologies), Penicillin (100 IU/ml) and Streptomycin (100 μg/ml) (ATCC® 30-2300™).

extract_protocol: Total RNAs were isolated using RNeasy kit (QIAGEN, 74104).

treatment_protocol: The pooled cells infected by gRNA were collected for Western Blot to confirm the knockout efficiency. Non-infected and gRNA-control-infected cells were used as controls.

tag: cell types

value: Mouse lung squamous cell carcinoma cells


title: wildtype, biological rep. 4

source_name: epidermis, wildtype, biological rep.4


title: gRNA-Jnk1/2-1

description: The pooled cells infected by gRNA were collected for Western Blot to confirm the knockout efficiency


title: wildtype, biological rep. 1

source_name: epidermis, wildtype, biological rep.1


title: WHIM2 Liver Metastasis from mouse 100463

description:
Tissue from liver metastasis from Direct Liver Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Liver.Met.100463


title: gRNA-Jnk1/2-2


title: Alox12b-KO, biological rep.3

source_name: epidermis, Alox12b-KO, biological rep.3


title: wildtype, biological rep.3

source_name: epidermis, wildtype, biological rep.3


title: Alox12b-KO, biological rep.2

source_name: epidermis, Alox12b-KO, biological rep.2


title: WHIM2 Liver Metastasis from mouse 100462

description:
Tissue from liver metastasis from Direct Liver Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Liver.Met.100462


title: wildtype, biological rep. 2

source_name: epidermis, wildtype, biological rep.2


title: gRNA -Control-1


title: Alox12b-KO, biological rep.1

source_name: epidermis, Alox12b-KO, biological rep.1


title: WHIM2 Liver Metastasis from mouse 100374

description:
Tissue from liver metastasis from Cardiac Injection.
TPM_human_AllGenes_AllPDX.txt
TPM_mouse_AllGenes_AllPDX.txt
WHIM2.Liver.Met.100374


title: gRNA -Control-2


title: gRNA -Control-3


title: SCC Replicate 5

description: The RNA was extracted from the whole lung tumor.

source_name: lung tumor

tag: strain

value: 13 months