title: row_RNAi2_rep2

data_processing:
Sequencing was done using Next seq 500 high output kit V2 75 cycles (illumina) on illumina’s NextSeq 500 system
RNA-seq reads were aligned by STAR to the full genome sequences of Drosophila Melanogaster (UCSC version dm3)
Reads were counted per annotated gene using ESET (End Sequencing analysis Toolkit)
Genome_build: dm3
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

source_name: Fly heads

extract_protocol:
The flies were raised for three more days to recover from CO2 exposure and collected using dry ice. RNA was prepared using TRI Reagent (SIGMA) according to the manufacturer’s protocol
3' RNA-seq library was performed based on Guttman’s lab "RNAtag Seq protocol" (Shishkin, A. A. et al. Simultaneous generation of many RNA-seq libraries in a single reaction. Nat. Methods 12, 323–325 (2015).)

value: Fly heads

value: Actin-gal4/+; UAS-rowRNAi2/+


title: Ketamine-anesthesia-treated 4

status: Public on Jul 14 2022

type: SRA

city: Daejeon

first: Woosuk

last: Chung

address: 282, Munhwa-ro

department: Department of Medical Science

country: South Korea

institute: Chungnam National University School of Medicine

library_source: transcriptomic

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.5.3) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Mice were housed at a relative temperature of 22°C and humidity 40%, with a 12-h reverse light/dark cycle and allowed free access to food and water. Mice were weaned at postnatal (PND) 21 days and housed in groups of three to five per cage

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were randomly divided into two groups (saline and ketamine group) at PND 16. Ketamine group mice received a daily intraperitoneal injection of ketamine (i.p., 35 mg/kg) for five consecutive days.  After injection, mice were placed in an empty cage containing fresh bedding (36°C) for at least 30 minutes before returning to its original cage. Mice in the saline group received identical treatment with normal saline.

tag: strain

tag: tissue

value: hippocampus

tag: age

tag: Sex

value: male


title: HUVEC cells, P3, siKLF6 16hr TNF, Biol Rep 2 [KTB_112_081_S21]

city: New Haven

first: Joseph Wayne

middle: Montano

last: Fowler

state: CT

address: 10 Amistad St.

department: Pharmacology

country: USA

institute: Yale University

data_processing:
Reads aligned to hg19 build of human genome with STAR
Quantified to hr19 RefSeq annotation model through Partek E/M
Genes were normalized as counts per million
Assembly: hg19
Supplementary files format and content: tab-delimited text file include cpm values for each Sample

organism: Homo sapiens

source_name: HUVEC

growth_protocol: HUVECs were obtained from the Yale School of Medicine, Vascular Biology and Therapeutics Core facility. Cells were cultured in EGM-2 media (Lonza) with 10% fetal bovine serum (FBS), penicillin/streptomycin and glutamine (2.8 mM) in a 37°C incubator with 5% CO2 supply

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated from control cells using TrueSeq Small RNA Library preparation (Illumina)

treatment_protocol: HUVEC were treated with 20nM of indicated siRNA for 10 hours and refed with fresh media. 48hrs later, HUVEC were treated with 10ng/mL TNF for indicated time.

tag: cell line

value: HUVEC

tag: cell type

value: Primary Endothlelial Cell

tag: genotype

tag: treatment

value: 10ng/mL TNF, 16hr


title: 20 DPH male RA 3

city: Portland

first: Claudio

middle: V

last: Mello

state: OR

address: 3181 SW Sam Jackson Park Rd, L470

department: Behavioral Neuroscience

institute: Oregon Health & Science University

data_processing:
Base calls were made by Illumina's RTA v3.4.4
Quality control and trimming were performed prior to genome alignment using trimmomatic (v0.36, parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36), and no issues were detected from FastQC (v0.11.9) reports.
Splice-aware STAR (v2.6.1, parameters --sjdbOverhang 99 --quantMode GeneCounts) was used to align reads and generate read counts per gene based on the bTaeGut1_v1.p zebra finch assembly (GCF_003957565.1) and associated genome features from the NCBI Taeniopygia guttata Annotation Release 104.
Genome_build: GCF_003957565.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Taeniopygia guttata

source_name: brain

growth_protocol: Birds were sacrificed within 20 min of lights-on and no singing was observed in any individual.

extract_protocol:
Brains were removed, flash frozen in a slurry of dry ice and isopropanol, cryosectioned onto PEN membrane glass slides (Leica, No. 11505158), fixed in 100% cold ethanol, and stained using cresyl violet. Brain nucleus RA was extracted from PEN slides into RLT buffer (Qiagen) using laser capture microdissection (Leica LMD 6500). RNA was isolated using the RNeasy Micro Kit (Qiagen) with on-column DNase digestion.
Using the SmartSeq v4 PLUS Kit (Takara Bio USA), cDNAs were generated from 1 ng total RNA , then the resulting cDNA was bioanalyzed on a High Sensitivity DNA chip, and 5 ng was used as input for the libraries.

value: Male

value: 20 days posthatch

tag: brain id


title: HUVEC cells, P3, siKLF6 16hr TNF, Biol Rep 3 [KTC_100_093_S22]


title: HUVEC cells, P3, siKLF6 0hr TNF, Biol Rep 2 [KXB_148_045_S18]

value: Vehicle


title: 50 DPH male RA 1

value: 50 days posthatch


title: Untreated-control 2


title: HUVEC cells, P3, siKLF6 16hr TNF, Biol Rep 1 [KTA_124_069_S20]


title: Input1_Td_JRY10156

city: Buffalo

first: Laura

middle: N

last: Rusche

state: NY

address: 109 Cooke Hall, UB North/Amherst Campus

department: Biological Sciences

institute: State University of New York at Buffalo

library_source: genomic

data_processing:
T. delbrueckii genome index was built using Bowtie2/2.3.4.1.
ChIP- seq reads for single-end sequencing were aligned to the T. delbrueckii genome index using Bowtie2/2.3.4.1.
ChIP peaks were called using MACS2/2.2.7.1 with the parameters: --nomodel, --extsize 200, --keep-dup 3
Genome_build: CBS1146 (GCA_000243375.1)
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

organism: Torulaspora delbrueckii

source_name: Yeast

growth_protocol: Yeast cells were grown at 30˚C in YPD medium containing 1% yeast extract, 2% peptone, and 2% glucose.

extract_protocol:
Cells were grown in YPD overnight. Following day, cells were diluted at OD600 0.3, grown at 30˚C, and harvested at an OD600 of ∼1.
Libraries were prepared using Takara Bio SMARTer ThruPlex DNA seq kit

treatment_protocol: Cells were cross-linked for 1 hour in 1% formaldehyde. After cell lysis, chromatin was sonicated. Immunoprecipitation was conducted with 10μL Protein A agarose beads and 4 µl of anti MYC (Millipore 06-549) or anti V5 antibody (Millipore AB3792) antibody.

tag: epitope tag

tag: chip antibody


title: Untreated-control 3


title: row_RNAi2_rep3

city: Jerusalem, Kiryat Shemona

first: Neta

last: Herman

address: Kiryat Shemona

department: Gentics, Nutrition

country: Israel

institute: Hebrew University Of Jerusalem, Migal

organism: Drosophila melanogaster

growth_protocol: All flies were raised at 25°C in 12-hour light: 12-hour dark cycles on standard diets


title: Control_actin_ rep2


title: HUVEC cells, P3, siCTRL 16hr TNF, Biol Rep 2 [CTB_184_009_S15]

value: CTRL


title: HUVEC cells, P3, siKLF6 0hr TNF, Biol Rep 3 [KXC_136_057_S19]


title: 50 DPH female RA 1

value: Female


title: row_RNAi1_rep2

value: Actin-gal4/+; UAS-rowRNAi1/+


title: HUVEC cells, P3, siCTRL 16hr TNF, Biol Rep 1 [CTA_101_092_S14]


title: 20 DPH female RA 3


title: hARtg-Osr1Cre_PIN

city: Duarte

first: Zijie

last: Sun

state: CA

address: 1500 E. Duarte Rd.

department: Cancer Biology

institute: City of Hope

data_processing:
The library purity and size was validated by capillary electrophoresis using 2,100 Bioanalyzer (Agilent Technologies)
The library quantity was measured fluorometrically using Qubit dsDNA HS Assay Kit from Invitrogen
The libraries were sequenced with a NovaSeq 6000 instrument (Illumina) to a depth of ~100k reads per cell. Raw sequencing data were processed using the 10x Genomics’ Cell Ranger pipeline (version 3.1.0) to generate FASTQ files and were aligned to the mm10 genome with added hARtg and mGFP sequences to generate gene expression counts
Genome_build: mm10 reference genome with added ARQ and EGFP sequence
Supplementary_files_format_and_content: Txt file with counts for each cell corresponding to each gene

molecule: polyA RNA

source_name: Prostatic intraepithelial neoplasia

extract_protocol:
PIN and PCa tissue were trimmed and dissociated to single cells using collagenase and TrypLE (Gibco)
The library was prepared using 10x Genomics Chromium Single Cell 3' Solution with v2 chemistry following manufacturer protocols (10x Genomics)
scRNAseq

value: Prostate

tag: disease state

value: Prostatic intraepithelial neoplasia


title: row_RNAi2_rep1


title: actin_w1118_rep3

description: genomic DNA-nucleosomes

data_processing:
Mnase-seq reads were aligned by bowtie2 to the full genome sequences of Drosophila Melanogaster (UCSC version dm3)
For visualization, bigwig files were created by deepTools (a python tool) with bamCoverage function and normalization parameter set to RPKM
Genome_build: dm3
Supplementary_files_format_and_content: bigwig file for each replica

extract_protocol: DNA libraries were made as previously described (Blecher-Gonen, R. et al. High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat. Protoc. 8, 539–554 (2013).)


title: HUVEC cells, P3, siCTRL 0hr TNF, Biol Rep 3 [CXC_113_080_S13]


title: actin_w1118_rep2

description: genomic DNA-nucleosomes


title: HUVEC cells, P3, siCTRL 0hr TNF, Biol Rep 2 [CXB_125_068_S12]


title: P35_Prostate

data_processing:
The library purity and size was validated by capillary electrophoresis using 2,100 Bioanalyzer (Agilent Technologies)
The library quantity was measured fluorometrically using Qubit dsDNA HS Assay Kit from Invitrogen
The libraries were sequenced with a NovaSeq 6000 instrument (Illumina) to a depth of ~100k reads per cell. Raw sequencing data were processed using the 10x Genomics’ Cell Ranger pipeline (version 3.1.0) to generate FASTQ files and were aligned to the mm10 genome to generate gene expression counts
Genome_build: mm10 reference genome
Supplementary_files_format_and_content: Txt file with counts for each cell corresponding to each gene

source_name: Prostate

extract_protocol:
Tissues were trimmed and dissociated to single cells using collagenase and TrypLE (Gibco)
The library was prepared using 10x Genomics Chromium Single Cell 3' Solution with v3 chemistry following manufacturer protocols (10x Genomics)
scRNAseq

value: Normal


title: 50 DPH male RA 2


title: actin_w1118_rep1

description: genomic DNA-nucleosomes

value: Fly heads


title: Ketamine-anesthesia-treated 3


title: E18.5_UGS

source_name: E18.5 Male Urogenital Sinus

value: Urogenital Sinus


title: row_RNAi1_rep1


title: Ketamine-anesthesia-treated 1

value: hippocampus


title: 20 DPH male RA 1


title: Ketamine-anesthesia-treated 2

value: male


title: 20 DPH female RA 1


title: HUVEC cells, P3, siCTRL 16hr TNF, Biol Rep 3 [CTC_172_021_S16]

value: HUVEC


title: Untreated cells 3

status: Public on Jul 13 2022

city: Ljubljana

first: Bostjan

last: Markelc

email: bmarkelc@gmail.com, bmarkelc@onko-i.si

state: Ljubljana

address: Zaloska cesta 2

department: Department of Experimental Oncology

country: Slovenia

institute: Institute of Oncology Ljubljana

data_processing:
tophat v2.1.0
cufflinks-2.2.1
htseq  0.9.1
Genome_build: GRCm38 release 88
Supplementary_files_format_and_content: txt

source_name: Tumor endothelial cells

growth_protocol: Murine colon adenocarcinoma cells (MC38) were a gift from Dr. Lee Gorden (Vanderbilt University, Nashville, TN, USA). Cells were transduced with lentiviruses to obtain MC38 mCherry cells. Cells were cultured in DMEM (MC38) supplemented with 10% (v/v) fetal bovine serum and 1% penicillin-streptomycin. All cells were maintained in a humidified incubator with 5% CO2 at 37°C. Cells were used at passage number < 10 and were routinely tested negative for Mycoplasma with MycoAlertTM Mycoplasma Detection Kit (Lonza). A 100 µl of cell suspension in 0.9% NaCl (2.5 x 105 cells) was injected subcutaneously on the right flank.

extract_protocol:
Dissected tumors were finely chopped with scalpels and the obtained fragments digested in HBSS (with Calcium and Magnesium; GIBCO) containing a mix of Collagenases 1 and 3 (Worthington; 3 mg ml−1), dispase II (Roche; 7 mg ml−1), DNase I (Invitrogen; 2 U ml−1) and left at 37 °C with gentle agitation for 20 minutes. A total of 25x106 cells were stained in a final volume of 100 μl of antibody mix for 15-20 minutes, in ice, protected from light. Cells were subsequently washed with 2 ml PBS-5% FBS, centrifuged at 500g for 5 minutes and resuspended in 500 μl PBS-5% FBS. 7-AAD was added right before the sample acquisition. Sorting was performed by using a Fusion cell sorter (BD Biosciences). The dissociated cells were centrifuged at 500g for 5 minutes, resuspended in PBS-5% FBS and filtered through 50 μm cell strainers before being counted and used for flow cytometry. 100 cells per population were sorted in 4 μl of lysis mix (0.4% Triton X + RNAse Inhibitor (1:20), dNTPS (10 mM), Oligo dT (10 μM) - according to the original Smart-seq2 protocol49) for bulk RNAseq, and 1 cell per well of a 96 well plate for single cell RNAseq, and immediately processed for RNA-sequencing or stored at -80 °C.
A 5.7 μl of retro-transcription mix (see reference for details) was added to each sample. Retro-transcription was carried out according to the original Smart-seq2 protocol and cDNA was then pre-amplified for 15 cycles. After PCR pre-amplification, cDNA was purified using Ampure XP magnetic beads according to the manufacturer's instructions, in a ratio of 0.8 to 1 with cDNA, resuspended in 17.5 μl of buffer EB (Qiagen) and stored at –20 °C. Quality and concentration of the cDNA generated were assessed using High-Sensitivity Bioanalyzer kit (Agilent). 1 ng of pre-amplified cDNA was tagmented and indexed with Nextera XT DNA Sample Preparation kit (Illumina) according to the manufacturer's instructions. The product was purified with AMPure XP beads (1:1 ratio) and eluted in 17.5 μl of EB buffer (Qiagen). Samples were loaded on a High-Sensitivity DNA chip (Agilent Technologies) to check for library size and quality and concentration measured with Qubit High-Sensitivity DNA kit (Invitrogen). Libraries were pooled to a final concentration ranging between 2 nM and 10 nM and sequenced with Illumina Hiseq 4000 (25 bp single-end read) at the Wellcome Trust Centre for Human Genetics in Oxford.

treatment_protocol: Once tumors reached 80-100 mm3 mice were randomly assigned to experimental groups. Mice were anesthetized under inhalation with isoflurane and led shielded with only the tumors exposed to radiation. Tumors received  15 Gy X-ray radiation treatment (300 kV, dose rate of 2.25 Gy per minute) delivered to tumors using a Gulmay RS320 irradiation system (Gulmay Medical Ltd).

tag: tumor model

value: colon adenocarcinoma cells (MC38)

value: untreated

tag: time point

tag: experiment type

value: bulk

value: FACS sorted tumor endothelial cells


title: Untreated cells 1


title: Autophagy_KC_KO01

type: RNA

city: Bunkyo-Ku

first: Ge

last: Peng

state: Tokyo

address: 2-1-1 Hongo

country: Japan

institute: Juntendo University Graduate School of Medicine

description: Gene expression data from keratinocytes transfected with Atg3 C264S adeno virus

hyb_protocol: Following fragmentation, 3.5 ug of cDNA were hybridized for 17 hr at 45⁰C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GeneSpring 14.9 software (Agilent Technology, Santa Clara, CA) using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Keratinocytes transfected with Atg3 C264S adeno virus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary normal human epidermal keratinocytes (FC-0007, Kurabo Industries, Osaka, Japan) isolated from neonatal foreskins were cultured in serum-free HuMedia-KG2 keratinocyte growth medium (KK-2150S, Kurabo Industries) containing human epidermal growth factor (0.1 ng/ml), insulin (10 g/ml), hydrocortisone (0.5 g/ml), gentamicin (50 g/ml), amphotericin B (50 ng/ml), and bovine brain pituitary extract (0.4%, v/v) at 37 °C in a humidified atmosphere of 95% air and 5% CO2

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

treatment_protocol: Keratinocytes were plated in 6-well dishes in 2 ml of growth medium 24 hours before infection, and the medium was replaced with fresh medium containing Atg3C264S or Atg3 adenoviruses for 48 hours.

value: Normal human epidermal kerationcyte


title: hARtg-Osr1Cre_PCa

source_name: Prostatic adenocarcinoma

value: Prostatic adenocarcinoma


title: Control_actin_ rep3


title: Sen1_3_G1_R2

city: Paris

first: Odil

last: Porrua Fuerte

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod-CNRS

data_processing:
Reads were demultiplexed using the the pyBarcodeFilter script from the pyCRACutility suite
Adaptor trimming  with cutadapt 1.15
Quality-trimming with trimmomatic
Mapping with bowtie2
Normalized coverage obtained with the bamCoverage tool of deepTools2 package. Normalization to  counts per 10^7 counts. Reads shorter than 20 nt were filtered out.
Genome_build: R64
Supplementary_files_format_and_content: bigwig files for each sample and for each strand (plus or minus)

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Cells grown on CSM-TRP to OD600= 0.6, in the absence or in the presence of 0.5 mM IAA for 1h

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20’ at 20000g at 4°C.IgG and nickel purification steps were performed as previously described in the original protocol (granneman et al., 2009) with minor changes: i) IgG purification steps has been realized using M-280 tosylactivated dynabeads (15mg per samples) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol). Eluates were concentrated in Vivacon® ultrafiltration spin columns 30 KDa MWCO to a final volume of 120 µl. A protein fractionation step was performed using the Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree) system from Expedeon. RNA pol II containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol.
RNA was reverse transcribed using the Reverse transcriptase IV (Invitrogen). The cDNA solution was used to perform multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of each primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per ml of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

treatment_protocol: Cells were submitted to UV crosslink in a UV lamp system (Megatron) for 50 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume / g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

value: W303-derived strain

value: Rpc160-HTP expressing sen1-3


title: P14_Prostate


title: Control_actin_ rep1


title: HUVEC cells, P3, siKLF6 0hr TNF, Biol Rep 1 [KXA_160_033_S17]

value: Primary Endothlelial Cell

value: Vehicle


title: Irradiated cells 3

value: 15 Gy, single dose irradiation

value: 48 h after treatment


title: WT


title: Irradiated cells 2


title: Sen1AID_IAA_R2

value: Rpc160-HTP,Sen1-AID (Auxin Inducible Degron)

value: IAA treatment for 1h


title: Nrd1AID_IAA

value: Rpc160-HTP,Nrd1-AID (Auxin Inducible Degron)


title: Sen1AID_R2


title: Irradiated cells 1


title: Untreated cells 2


title: Sen1_3_R1


title: WT_G1_R2

value: Rpc160-HTP expressing SEN1


title: HUVEC cells, P3, siCTRL 0hr TNF, Biol Rep 1  [CXA_137_056_S11]

value: HUVEC

value: CTRL


title: Sen1_3_G1_R1


title: Nrd1AID


title: WT_G1_R1


title: Sen1_3_R2


title: MN-SC86_S13

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

data_processing:
Fastq generation from BaseSpace Onsite v 3.22.91.158 (Illumina).
For MNase seq experiments, reads were aligned using Bowtie (Langmead et al. 2009) to the S. cereviae SacCer 3 genome version. Alignment files were processed using the NucWave algorithm (Quintales et al. 2015b) to generate the nucleosome occupancy maps. We analyzed biological duplicates of MNase-seq maps of all the strains described in the text.
The DANPOS 2 application (Chen et al. 2013a) was used to calculate the difference in nucleosome fuzziness at genome-wide scale using the dpos utility with a span of 1 bp and a read extension of 50 bp to make it compatible with NucWave maps. We considered significant the level of log2-fold change of fuzziness for each strain relative to its control when the mean of the difference between the two genome-wide maps was above 2σ (σ = 0.1), with an enrichment p-value < 0,05 based on Fisher’s exact test.
Genome_build: sacCer3 (R64-1-1)
Supplementary_files_format_and_content: wig files

source_name: wild type

growth_protocol: Mononucleosomal DNA was isolated as described in Gonzalez et al. (2016). Briefly, S. cerevisiae cultures of 200 mL at 0.8 x 10^7 cells/mL were collected for preparation of mononucleosomal DNA.

extract_protocol:
Mononucleosomal DNA was isolated as described in Gonzalez et al. (2016). Cells were fixed with 1% formaldehyde and treated with 10 mg of Zymolyase 20T for 5 minutes at 30º C to generate spheroplasts. These were resuspended in NP-buffer (1 M Sorbitol; 50 mM NaCl; 10 mM Tris pH7.4; 5 mM MgCl2; 1 mM CaCl2; 0.075% NP-40; 1 mM β-Mercaptoethanol; 500 uM Spermidine) and digested with 300 units/mL of micrococcal nuclease (MNase) at 37 ºC during 10 minutes. The amount of MNase was optimized experimentally for each strain to generate a 80:20 ratio of mononucleosome to dinucleosome fragments.
Libraries of mononucleosomal DNA were constructed following the Illumina protocol and were sequenced in an Illumina NextSeq500 platform using the paired-end protocol. We generated between 13 and 32 million reads of 75 nt per experiment, representing a 83- to 203-fold genome coverage.

treatment_protocol: Those cultures from transformants with RNase H-containing plasmids were considered treated in the case of AID overexpression experiments. For MNase seq experiments, cells were untreated.

tag: strain/background

value: wild type

value: MNase


title: Sen1AID_IAA_R1


title: noXL

description: Sample used as a negative control

value: Cross-linking step ommitted in the procedure.


title: WT_R2


title: MN-SC75_S1


title: WT_R1


title: MN-SC75_S4


title: Autophagy_KC_KO02

value: Normal human epidermal kerationcyte


title: MN-SC89-1_S5


title: MN-SC80_S4


title: MN-SC81_S8


title: Autophagy_KC_WT02

description: Gene expression data from keratinocytes transfected with Atg3 adeno virus

source_name: Keratinocytes transfected with Atg3 adeno virus


title: MN-SC80_S7


title: Sen1AID_R1


title: Autophagy_KC_WT01


title: MN-SC89-2_S6


title: MN-SC79_S6


title: Half-library_A

city: Würzburg

first: Elmar

last: Wolf

address: Am Hubland

department: Chair of Biochemistry and Molecular Biology

country: Germany

institute: University of Würzburg

library_source: other

data_processing:
Fastq files were generated from base calls using bcl2fastq.
Non-sgRNA parts of reads were cut using cutadapt.
Reads were aligned to the combined murine Zhang GeCKO v2 library (including spiked-in sgRNAs targeting the reporters) using bowtie2.
Count tables of sgRNA frequencies were generated using MAGeCK count.
Assembly: Combined murine Zhang GeCKO v2 library (including spiked-in sgRNAs targeting the reporters)
Supplementary files format and content: txt of sgRNA-specific read counts per sample.
Library strategy: CRISPR screen

molecule: other

organism: synthetic construct

growth_protocol: Cells were grown in DMEM + 10% FCS + 1% Pen-Strep

extract_protocol:
Cells were lysed, genomic DNA was sonicated and extracted via phenol-chloroform extraction and isopropanol precipitation.
Sequencing libraries were prepared by PCR amplification of the sgRNAs integrated into the genomic DNA and a second PCR used to incorporate flow cell binding sites into the amplicons.

treatment_protocol: FACS 6 days after viral infection of reporter cell line NIH/3T3-Fbl-GFP;Rpl18-RFP with amplified GeCKO v2 library


title: MN-SC77_S5

source_name: H3 wild-type

value: H3 wild-type


title: Bothdown_Rep3

value: fibroblast

value: sorted for RiBi and RP downregulation, replicate 3


title: MN-SC88_S15

source_name: rnh1∆ rnh201∆

value: RNH-R

value: rnh1{delta} rnh201{delta}


title: MN-SC77_S2


title: MN-SC76_S10


title: MN-SC79_S3


title: Half-library_B_first_amplification


title: RPdown_Rep3

value: sorted for RP downregulation, replicate 3


title: Bothup_Rep3

value: sorted for RiBi and RP upregulation, replicate 3


title: Bothup_Rep2

value: sorted for RiBi and RP upregulation, replicate 2


title: RiBidown_Rep2

value: sorted for RiBi downregulation, replicate 2


title: Bothup_Rep1

value: sorted for RiBi and RP upregulation, replicate 1


title: Bothdown_Rep2

value: sorted for RiBi and RP downregulation, replicate 2


title: unsorted_Rep3

value: unsorted, replicate 3


title: Bothdown_Rep1

value: sorted for RiBi and RP downregulation, replicate 1


title: RPdown_Rep1

value: sorted for RP downregulation, replicate 1


title: RiBidown_Rep3

value: sorted for RiBi downregulation, replicate 3


title: Half-library_B_second_amplification


title: Library

description: Library


title: SAT_obese_80

city: Grand Rapids

first: Luca

last: Fagnocchi

state: MI

address: 333 Bostwick AVE NE

institute: VAI

data_processing:
reads were quality controlled with fastQC
reads were mapped using TopHat v2.0.8b with -G option on Homo   sapiens genome hg38
counts on genomic features were assigned using featureCounts
normalized counts were corrected for both age and sex confounders with comBat
differential expression and Gene Set Enrichment Analysis (GSEA) were performed using DESeq2 and fgsea, respectively
Assembly: hg38
Supplementary files format and content: tab-delimited text counts on genomic features (transcripts) for all samples

source_name: subcutaneous adipose tissue (SAT)

extract_protocol:
Trizol-purified RNA
poly(A)-enriched libraries prepared using the TruSeq Sample Prep v2 kit (Illumina)

value: subcutaneous adipose tissue (SAT)

value: male

value: obese


title: RiBidown_Rep1

value: fibroblast

value: sorted for RiBi downregulation, replicate 1


title: SAT_obese_133


title: SAT_obese_58


title: SAT_obese_127

value: female


title: SAT_obese_118


title: SAT_normal_weight_99


title: RPdown_Rep2

value: sorted for RP downregulation, replicate 2


title: SAT_obese_155


title: SAT_obese_39


title: unsorted_Rep2

value: unsorted, replicate 2


title: SAT_normal_weight_186


title: SAT_obese_43


title: SAT_obese_81


title: SAT_obese_153


title: SAT_normal_weight_139


title: SAT_normal_weight_174


title: SAT_normal_weight_12


title: SAT_normal_weight_67


title: SAT_normal_weight_184


title: SAT_obese_147


title: SAT_normal_weight_56


title: SAT_normal_weight_130


title: unsorted_Rep1

value: unsorted, replicate 1


title: SAT_normal_weight_134


title: SAT_normal_weight_123


title: SAT_normal_weight_34


title: SAT_normal_weight_201


title: SAT_normal_weight_3


title: SAT_normal_weight_78


title: SAT_normal_weight_107


title: SAT_normal_weight_196


title: SAT_normal_weight_144


title: SAT_normal_weight_162


title: SAT_normal_weight_119


title: SAT_normal_weight_95


title: SAT_obese_77


title: SAT_obese_86_1


title: SAT_obese_66


title: SAT_normal_weight_70


title: SAT_obese_53


title: SAT_normal_weight_69


title: SAT_obese_64


title: SAT_normal_weight_4


title: SAT_normal_weight_37


title: SAT_obese_46


title: SAT_obese_24


title: SAT_normal_weight_250


title: SAT_normal_weight_275


title: SAT_normal_weight_219


title: SAT_normal_weight_203


title: SAT_normal_weight_120


title: SAT_normal_weight_160


title: SAT_obese_154


title: SAT_obese_149


title: SAT_normal_weight_143


title: SAT_obese_132_1


title: SAT_normal_weight_42


title: SAT_normal_weight_126


title: SAT_obese_125


title: SAT_obese_122


title: SAT_normal_weight_302


title: SAT_obese_108


title: SAT_obese_226


title: DEHP+KRG

city: Seoul

first: Heewon

last: Song

address: 209, Neungdong-ro, Gwangjin-gu

institute: Sejong Univ

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Ishikawa cell, DEHP 10 µM+KRG 500 µg/mL treatment

growth_protocol: The human endometrial adenocarcinoma Ishikawa cells were maintained in Dulbecco's Modified Eagle Medium (DMEM; WelGENE Inc., Daegu, Korea) containing 10% fetal bovine serum (FBS; GIBCO Invitrogen, NY, USA) and penicillin/streptomycin (GIBCO Invitrogen, NY, USA). The cells were cultured at 37 C in the humidified 5% CO2 atmosphere.

extract_protocol:
RNA was isolated using the Fast HQ RNA Extraction Kit (Intron technology). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Ishikawa cells were pre-treated with KRG for 1 h and treated with DEHP for 8 h.

value: DEHP 10 µM+KRG 500 µg/mL treatment


title: DEHP

source_name: Ishikawa cell, DEHP 10 µM treatment

value: human endometrial adenocarcinoma Ishikawa cells

value: DEHP 10 µM treatment


title: UMHET3, 22, months old, eRapa, F [R7]

city: Boston

first: Anastasia

last: Shindyapina

state: MA

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

description:
Genecounts_Liver.txt
R7

data_processing:
Fastq files were mapped to mm10 (GRCm38.p6) mouse genome. and gene counts were obtained with STAR
Assembly: mm10 (GRCm38.p6)
Supplementary files format and content: tab-delimited text files include raw genecounts for each sample

source_name: liver

extract_protocol:
RNA was extracted using Chemagic 360 instrument
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep Guide, Part #15031048 Rev. E)

treatment_protocol: UMHET pups were subjected to the diet containing encapsulated rapamycin or encapsulating material as a control from birth to 45 days of age.

value: liver

value: eRapa

value: Female


title: UMHET3, 22, months old, Eudragit, F [R9_K]

description:
Genecounts_Kidney.txt
R9_K

source_name: kidney

value: kidney

value: Eudragit


title: UMHET3, 22, months old, eRapa, F [R8]

description:
Genecounts_Liver.txt
R8


title: Control

source_name: Ishikawa cell, Control

value: Control


title: UMHET3, 28, months old, eRapa, F [R6_K]

description:
Genecounts_Kidney.txt
R6_K


title: UMHET3, 22, months old, eRapa, F [R5_K]

description:
Genecounts_Kidney.txt
R5_K


title: UMHET3, 22, months old, eRapa, F [R5]

description:
Genecounts_Liver.txt
R5


title: UMHET3, 22, months old, Eudragit, F [R9]

description:
Genecounts_Liver.txt
R9


title: UMHET3, 2, months old, eRapa, M [R49_K]

description:
Genecounts_Kidney.txt
R49_K

value: Male


title: UMHET3, 22, months old, eRapa, F [R8_K]

description:
Genecounts_Kidney.txt
R8_K


title: UMHET3, 28, months old, eRapa, F [R6]

description:
Genecounts_Liver.txt
R6


title: UMHET3, 22, months old, eRapa, F [R7_K]

description:
Genecounts_Kidney.txt
R7_K


title: UMHET3, 2, months old, eRapa, M [R49]

description:
Genecounts_Liver.txt
R49


title: SAT_obese_16

value: subcutaneous adipose tissue (SAT)

value: obese


title: UMHET3, 2, months old, Eudragit, F [R48_K]

description:
Genecounts_Kidney.txt
R48_K


title: UMHET3, 2, months old, Eudragit, F [R47]

description:
Genecounts_Liver.txt
R47


title: UMHET3, 2, months old, Eudragit, F [R46]

description:
Genecounts_Liver.txt
R46


title: UMHET3, 2, months old, Eudragit, F [R48]

description:
Genecounts_Liver.txt
R48


title: UMHET3, 2, months old, Eudragit, F [R46_K]

description:
Genecounts_Kidney.txt
R46_K


title: UMHET3, 2, months old, eRapa, F [R44_K]

description:
Genecounts_Kidney.txt
R44_K


title: UMHET3, 2, months old, eRapa, F [R44]

description:
Genecounts_Liver.txt
R44


title: UMHET3, 2, months old, eRapa, F [R45]

description:
Genecounts_Liver.txt
R45


title: UMHET3, 2, months old, Eudragit, M [R42_K]

description:
Genecounts_Kidney.txt
R42_K


title: UMHET3, 2, months old, eRapa, F [R43]

description:
Genecounts_Liver.txt
R43


title: UMHET3, 2, months old, eRapa, F [R45_K]

description:
Genecounts_Kidney.txt
R45_K


title: UMHET3, 2, months old, Eudragit, M [R42]

description:
Genecounts_Liver.txt
R42


title: UMHET3, 2, months old, eRapa, M [R39_K]

description:
Genecounts_Kidney.txt
R39_K


title: UMHET3, 2, months old, Eudragit, F [R47_K]

description:
Genecounts_Kidney.txt
R47_K


title: UMHET3, 28.5, months old, eRapa, F [R4]

description:
Genecounts_Liver.txt
R4


title: UMHET3, 2, months old, eRapa, M [R37_K]

description:
Genecounts_Kidney.txt
R37_K


title: UMHET3, 2, months old, Eudragit, M [R40_K]

description:
Genecounts_Kidney.txt
R40_K


title: UMHET3, 28.4, months old, eRapa, M [R36]

description:
Genecounts_Liver.txt
R36


title: UMHET3, 2, months old, Eudragit, M [R41_K]

description:
Genecounts_Kidney.txt
R41_K


title: UMHET3, 2, months old, eRapa, M [R38]

description:
Genecounts_Liver.txt
R38


title: UMHET3, 2, months old, eRapa, M [R39]

description:
Genecounts_Liver.txt
R39


title: UMHET3, 2, months old, eRapa, M [R38_K]

description:
Genecounts_Kidney.txt
R38_K


title: UMHET3, 2, months old, eRapa, M [R37]

description:
Genecounts_Liver.txt
R37


title: UMHET3, 28.4, months old, eRapa, M [R35_K]

description:
Genecounts_Kidney.txt
R35_K


title: UMHET3, 2, months old, Eudragit, M [R40]

description:
Genecounts_Liver.txt
R40


title: UMHET3, 28.4, months old, eRapa, M [R36_K]

description:
Genecounts_Kidney.txt
R36_K


title: UMHET3, 28.4, months old, eRapa, M [R34_K]

description:
Genecounts_Kidney.txt
R34_K


title: UMHET3, 28.4, months old, eRapa, M [R35]

description:
Genecounts_Liver.txt
R35


title: UMHET3, 27.9, months old, Eudragit, F [R32_K]

description:
Genecounts_Kidney.txt
R32_K


title: UMHET3, 27.9, months old, Eudragit, F [R32]

description:
Genecounts_Liver.txt
R32


title: UMHET3, 27.9, months old, Eudragit, F [R31_K]

description:
Genecounts_Kidney.txt
R31_K


title: UMHET3, 28.4, months old, eRapa, M [R34]

description:
Genecounts_Liver.txt
R34


title: UMHET3, 22, months old, Eudragit, F [R3_K]

description:
Genecounts_Kidney.txt
R3_K


title: UMHET3, 27.9, months old, Eudragit, F [R33_K]

description:
Genecounts_Kidney.txt
R33_K


title: UMHET3, 27.9, months old, Eudragit, F [R33]

description:
Genecounts_Liver.txt
R33


title: UMHET3, 28.8, months old, Eudragit, M [R29]

description:
Genecounts_Liver.txt
R29


title: UMHET3, 22, months old, Eudragit, M [R30_K]

description:
Genecounts_Kidney.txt
R30_K


title: UMHET3, 2, months old, eRapa, F [R43_K]

description:
Genecounts_Kidney.txt
R43_K


title: UMHET3, 2, months old, Eudragit, M [R41]

description:
Genecounts_Liver.txt
R41


title: UMHET3, 22, months old, Eudragit, M [R30]

description:
Genecounts_Liver.txt
R30


title: UMHET3, 27.9, months old, Eudragit, F [R31]

description:
Genecounts_Liver.txt
R31


title: UMHET3, 22, months old, Eudragit, M [R25_K]

description:
Genecounts_Kidney.txt
R25_K


title: UMHET3, 28.8, months old, Eudragit, F [R26]

description:
Genecounts_Liver.txt
R26


title: UMHET3, 22, months old, eRapa, M [R23]

description:
Genecounts_Liver.txt
R23


title: UMHET3, 22, months old, Eudragit, F [R3]

description:
Genecounts_Liver.txt
R3


title: UMHET3, 22, months old, eRapa, F [R22_K]

description:
Genecounts_Kidney.txt
R22_K


title: UMHET3, 22, months old, eRapa, F [R22]

description:
Genecounts_Liver.txt
R22


title: UMHET3, 29.2, months old, Eudragit, M [R21]

description:
Genecounts_Liver.txt
R21


title: UMHET3, 29.2, months old, Eudragit, M [R20_K]

description:
Genecounts_Kidney.txt
R20_K


title: UMHET3, 29.2, months old, Eudragit, M [R20]

description:
Genecounts_Liver.txt
R20


title: UMHET3, 28.8, months old, Eudragit, M [R29_K]

description:
Genecounts_Kidney.txt
R29_K


title: UMHET3, 28.8, months old, eRapa, F [R28]

description:
Genecounts_Liver.txt
R28


title: UMHET3, 28.8, months old, eRapa, F [R28_K]

description:
Genecounts_Kidney.txt
R28_K


title: UMHET3, 27.6, months old, eRapa, M [R19_K]

description:
Genecounts_Kidney.txt
R19_K


title: UMHET3, 27.6, months old, eRapa, M [R19]

description:
Genecounts_Liver.txt
R19


title: UMHET3, 22, months old, eRapa, M [R24_K]

description:
Genecounts_Kidney.txt
R24_K


title: UMHET3, 22, months old, eRapa, M [R24]

description:
Genecounts_Liver.txt
R24


title: UMHET3, 20.5, months old, Eudragit, M [R16]

description:
Genecounts_Liver.txt
R16


title: UMHET3, 28.8, months old, eRapa, F [R27]

description:
Genecounts_Liver.txt
R27


title: UMHET3, 28.8, months old, Eudragit, F [R26_K]

description:
Genecounts_Kidney.txt
R26_K


title: UMHET3, 28.8, months old, eRapa, F [R27_K]

description:
Genecounts_Kidney.txt
R27_K


title: UMHET3, 22, months old, eRapa, M [R23_K]

description:
Genecounts_Kidney.txt
R23_K


title: UMHET3, 22, months old, Eudragit, M [R25]

description:
Genecounts_Liver.txt
R25


title: UMHET3, 22, months old, eRapa, M [R14]

description:
Genecounts_Liver.txt
R14


title: UMHET3, 29.2, months old, Eudragit, M [R21_K]

description:
Genecounts_Kidney.txt
R21_K


title: UMHET3, 22, months old, Eudragit, F [R2_K]

description:
Genecounts_Kidney.txt
R2_K


title: UMHET3, 27.9, months old, Eudragit, F [R12_K]

description:
Genecounts_Kidney.txt
R12_K


title: UMHET3, 22, months old, Eudragit, F [R2]

description:
Genecounts_Liver.txt
R2


title: UMHET3, 27.9, months old, Eudragit, F [R11]

description:
Genecounts_Liver.txt
R11


title: UMHET3, 22, months old, Eudragit, F [R10_K]

description:
Genecounts_Kidney.txt
R10_K


title: UMHET3, 22, months old, Eudragit, F [R10]

description:
Genecounts_Liver.txt
R10


title: UMHET3, 27.6, months old, eRapa, M [R18]

description:
Genecounts_Liver.txt
R18


title: UMHET3, 20.5, months old, Eudragit, M [R17_K]

description:
Genecounts_Kidney.txt
R17_K


title: UMHET3, 27.6, months old, eRapa, M [R18_K]

description:
Genecounts_Kidney.txt
R18_K


title: UMHET3, 20.5, months old, Eudragit, M [R17]

description:
Genecounts_Liver.txt
R17


title: UMHET3, 20.5, months old, Eudragit, M [R16_K]

description:
Genecounts_Kidney.txt
R16_K


title: KPC RR ECM G-1

city: La Jolla

first: Hua

last: Su

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
CLC Genomics Workbench v 11.0.1.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05).
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: mm10
Supplementary files format and content: KPC_ECM_lfdr.txt.crdownload.xlsx: Excel file included TPM values for each Sample.

extract_protocol:
Total RNA were extracted using All Prep DNA/RNA Mini Kit (Qiagen). RNA purity was assessed by an Agilent 2100 Bioanalyzer. 500 ng total RNA was used for the construction of sequencing libraries.
500 ng total RNA was enriched for poly-A tailed RNA transcripts by double incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and fragmented for 9 min at 94ºC in 2X Superscript III first-strand buffer containing 10 mM DTT (Invitrogen, #P2325). Reverse-transcription (RT) reaction was performed at 25ºC for 10 min followed by 50ºC for 50 min. RT product was purified with RNAClean XP (Beckman Coulter, #A63987). Libraries were ligated with dual UDI (IDT) or single (Bioo Scientific), PCR-amplified for 11-13 cycles, size-selected using one-sided 0.8× AMPure cleanup beads, quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific), and sequenced on a HiSeq 4000. RNA-seq reads were aligned to the mouse genome (GRCm38/mm10) using STAR.

treatment_protocol: Plated on RR ECM and incubated with low G medium for 24h.

value: mouse pancreatic cancer cell

value: WT

tag: treatment [plate]

value: MMP-resistant Col I ECM

tag: treatment [medium]

value: low glucose for 24h


title: KPC RR ECM Q-1

treatment_protocol: Plated on RR ECM and incubated with low Q medium for 24h.

value: low glutamine for 24h


title: UMHET3, 27.9, months old, eRapa, F [R13_K]

description:
Genecounts_Kidney.txt
R13_K

tag: tissue


title: UMHET3, 22, months old, eRapa, M [R15_K]

description:
Genecounts_Kidney.txt
R15_K

tag: age


title: UMHET3, 22, months old, eRapa, M [R15]

description:
Genecounts_Liver.txt
R15

tag: Sex


title: KPC WT ECM G-3

treatment_protocol: Plated on WT ECM and incubated with low G medium for 24h.

tag: cell line

value: WT ECM


title: UMHET3, 22, months old, eRapa, M [R14_K]

description:
Genecounts_Kidney.txt
R14_K


title: KPC WT ECM Q-2

treatment_protocol: Plated on WT ECM and incubated with low Q medium for 24h.

tag: cell type


title: KPC WT ECM Q-1

tag: genotype


title: KPC WT ECM G-1


title: UMHET3, 27.9, months old, Eudragit, F [R12]

description:
Genecounts_Liver.txt
R12

tag: treatment


title: KPC RR ECM Q-3


title: UMHET3, 27.9, months old, Eudragit, F [R11_K]

description:
Genecounts_Kidney.txt
R11_K


title: UMHET3, 22, months old, Eudragit, F [R1_K]

description:
Genecounts_Kidney.txt
R1_K


title: KPC RR ECM G-3


title: Hep3B in vivo model treated with combo [GS049030]

city: cambridge

first: Kun

last: Yu

state: ma

address: 300 Technology Square City

institute: H3 BIOMEDICINE, INC.

description: 4 different fastq files for 4 lanes

data_processing:
The sequencing reads were produced by the Illumina HiSeq 4000, and aligned with both human reference (GRCh37) and the mouse reference genomes (GRCm38) using STAR
The aligned BAM files were processed by the in-house xenotool to generate the high quality human BAM files and remove mouse reads
The transcripts abundance was calculated using Kallisto
Assembly: GRCh37; GRCm38
Supplementary files format and content: gene_counts

source_name: Hep3B in vivo

growth_protocol: For the Hep3B xenografts, cells were harvested in exponential growth phase, and suspended in a 1:1 mixture of RPMI1640 medium containing 10% fetal bovine serum and Matrigel (Corning) at a final concentration of 5 x 107cells/mL. 0.1 mL of the inoculum was injected subcutaneously into the right flank region of BALB/c nu/nu female mice approximately 8-weeks old.

extract_protocol:
RNA was extracted and purified from 50 to 100 mg tumor fragments using RNeasy reagent (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were randomized into treatment groups when the mean tumor volume (TV) reached approximately 500 mm3, 3 mice per group. Treatment with Vehicle, H3B-6527 (300 mg/kg), Lenvatinib (10 mg/kg) or the combination was administered by oral gavage. Tumors were collected at 8 hour post the 4th dose, once daily.

value: Hep3B cell line xenograft tumor


title: Hep3B in vivo model treated with Lenvatinib [GS049028]

description: 4 different fastq files for 4 lanes

value: Lenvatinib


title: Hep3B in vivo model treated with combo [GS049032]

description: 4 different fastq files for 4 lanes


title: Hep3B in vivo model treated with H3B-6527 [GS049026]

description: 4 different fastq files for 4 lanes


title: Hep3B in vivo model treated with H3B-6527 [GS049025]

description: 4 different fastq files for 4 lanes


title: KPC RR ECM G-2


title: KPC RR ECM Q-2


title: UMHET3, 22, months old, Eudragit, F [R1]

description:
Genecounts_Liver.txt
R1

value: liver


title: KPC WT ECM G-2


title: Hep3B in vivo model treated with vehicle [GS049021]

description: 4 different fastq files for 4 lanes

value: Vehicle


title: Irradiated cell 94 Bio Rep 3

tag: strain

value: colon adenocarcinoma cells (MC38)

value: 15 Gy, single dose irradiation

value: 48 h after treatment

value: single cell

value: FACS sorted tumor endothelial cells


title: KPC WT ECM Q-3


title: Hep3B in vivo model treated with Lenvatinib [GS049027]

description: 4 different fastq files for 4 lanes


title: Hep3B in vivo model treated with combo [GS049031]

description: 4 different fastq files for 4 lanes


title: Hep3B in vivo model treated with H3B-6527 [GS049024]

description: 4 different fastq files for 4 lanes


title: Irradiated cell 92 Bio Rep 3


title: Irradiated cell 93 Bio Rep 2


title: Irradiated cell 92 Bio Rep 2


title: Hep3B in vivo model treated with Lenvatinib [GS049029]

description: 4 different fastq files for 4 lanes


title: Irradiated cell 93 Bio Rep 3


title: Irradiated cell 91 Bio Rep 3


title: Irradiated cell 91 Bio Rep 2


title: Irradiated cell 90 Bio Rep 3


title: Irradiated cell 90 Bio Rep 2


title: Irradiated cell 89 Bio Rep 3


title: Hep3B in vivo model treated with vehicle [GS049023]

description: 4 different fastq files for 4 lanes


title: Irradiated cell 89 Bio Rep 2


title: Hep3B in vivo model treated with vehicle [GS049022]

description: 4 different fastq files for 4 lanes


title: Irradiated cell 88 Bio Rep 3


title: Irradiated cell 85 Bio Rep 2


title: Irradiated cell 88 Bio Rep 2


title: Irradiated cell 86 Bio Rep 2


title: Irradiated cell 87 Bio Rep 3


title: Irradiated cell 86 Bio Rep 3


title: Irradiated cell 87 Bio Rep 2


title: Irradiated cell 84 Bio Rep 3


title: Irradiated cell 84 Bio Rep 2


title: Irradiated cell 83 Bio Rep 3


title: Irradiated cell 83 Bio Rep 2


title: Irradiated cell 81 Bio Rep 3


title: Irradiated cell 82 Bio Rep 3


title: Irradiated cell 82 Bio Rep 2


title: Irradiated cell 81 Bio Rep 2


title: Irradiated cell 80 Bio Rep 3


title: Irradiated cell 78 Bio Rep 3


title: Irradiated cell 80 Bio Rep 2


title: Irradiated cell 78 Bio Rep 2


title: Irradiated cell 85 Bio Rep 3


title: Irradiated cell 77 Bio Rep 3


title: Irradiated cell 76 Bio Rep 3


title: Irradiated cell 75 Bio Rep 3


title: Irradiated cell 79 Bio Rep 2


title: Irradiated cell 77 Bio Rep 2


title: Irradiated cell 76 Bio Rep 2


title: Irradiated cell 72 Bio Rep 3


title: Irradiated cell 74 Bio Rep 3


title: Irradiated cell 73 Bio Rep 2


title: Irradiated cell 75 Bio Rep 2


title: Irradiated cell 74 Bio Rep 2


title: Irradiated cell 79 Bio Rep 3


title: Irradiated cell 73 Bio Rep 3


title: UMHET3, 27.9, months old, eRapa, F [R13]

description:
Genecounts_Liver.txt
R13

value: eRapa

value: Female


title: Irradiated cell 71 Bio Rep 1


title: Irradiated cell 68 Bio Rep 3


title: Irradiated cell 70 Bio Rep 1


title: Irradiated cell 70 Bio Rep 3


title: Irradiated cell 69 Bio Rep 2


title: Irradiated cell 69 Bio Rep 1


title: Irradiated cell 70 Bio Rep 2


title: Irradiated cell 69 Bio Rep 3


title: Irradiated cell 72 Bio Rep 1


title: Irradiated cell 71 Bio Rep 3


title: Irradiated cell 72 Bio Rep 2


title: Irradiated cell 66 Bio Rep 2


title: Irradiated cell 68 Bio Rep 1


title: Irradiated cell 67 Bio Rep 3


title: Irradiated cell 67 Bio Rep 2


title: Irradiated cell 64 Bio Rep 3


title: Irradiated cell 67 Bio Rep 1


title: Irradiated cell 68 Bio Rep 2


title: Irradiated cell 63 Bio Rep 3


title: Irradiated cell 66 Bio Rep 3


title: dsi.KO.eST.rep5

city: Guangzhou

first: Yumei

last: Huang

state: Guangdong

address: Haizhu District Xingangxi Road No. 135

country: China

institute: Sun Yat-sen University

data_processing:
After removing adapters by Trimmomatic (version 0.36, used parameters 2:30:10:1:true MINLEN:75), short reads were mapped to the corresponding reference genomes of D. melanogaster (r6.36) and D. simulans (r2.02), respectively, using HISAT (version 2.2.0, --dta and other default parameters).
Expression abundance of each gene was calculated as FPKM and TPM with StringTie (version 2.1.4, used -e and other default parameters). The annotation files of dmel-all-r6.36.gtf and dsim-all-r2.02.gtf were downloaded from FlyBase (http://flybase.org/) in October 2020.
HTSeq (version 0.6.0, used parameters -f bam -r name -s no -t exon -m union) was applied to count mapped reads for each gene.
Genome_build: D. melanogaster (r6.36) and D. simulans (r2.02)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and TPM values for each gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Drosophila simulans

source_name: Elongating spermatid cyst

growth_protocol: All the flies were raised using cornmeal-sucrose-yeast medium at 25°C with a 12-h light-dark cycle throughout this study.

extract_protocol:
1) For testis samples, adult flies 3-5 days after eclosion were allowed to mate and then testes were dissected in drops of 1× phosphate-buffered saline (PBS) with two pairs of Dumont #5 forceps. For the extraction of total RNA, 20-25 pairs of testes were pooled as a sample. RNeasy Micro Kit (QIAGEN, German) was used for RNA extraction following the manufacturer’s instructions. 2) For single-cyst samples, testes from mated male flies 2-3 days after eclosion were dissected. Two tungsten micro-needles (World Precision Instruments, USA) were used to tear the muscle sheath layer, resulting in germ cell cysts spilling into a drop of 1× phosphate-buffered saline (PBS). The cysts were viewed using an inverted microscope (Leica DMI4000 microscope), and were picked using a glass capillary (BJ-40, Beijing Zhengtian Yi Science and Trade Co. LTD) pulled by a Sutter instrument P-30 with the following parameters: heat#1 = 930; pull = 909. The cysts were staged using the criteria as follows: spermatogonia (SG), 16-cell cysts with cells of <10 μm in diameter for D. melanogaster and < 8 μm in diameter for D. simulans; late primary spermatocytes (pSC), 16-cell cysts with cells of 22-25 μm in diameter; round spermatids (rST), cysts with much more than 32 round or nearly round cells of 14-16 μm in diameter; and elongating spermatids (eST), bundles of 250-350 μm in length. The staged single cyst was transferred into PCR tube by pushing the syringe which was connected with the glass capillary by an infusion tube. Cell lysis, reverse transcription, PCR preamplification and purification of PCR products were conducted using Discover-sc™ WTA Kit V2 (Vazyme Biotech, China) according to the user’s guides.
1) For testis samples, RNA libraries were prepared for sequencing using standard Illumina protocols. 2) For single-cyst samples, RNA-seq libraries were constructed using TruePrep™ DNA Library Prep Kit V2 for Illumina® (Vazyme Biotech, China) and an input of 1 ng amplified cDNAs.

value: 2-3 days after eclosion


title: Irradiated cell 66 Bio Rep 1


title: Irradiated cell 63 Bio Rep 2


title: Irradiated cell 65 Bio Rep 1


title: Irradiated cell 65 Bio Rep 2


title: Irradiated cell 64 Bio Rep 2


title: dsi.KO.eST.rep4


title: dsi.KO.eST.rep6


title: Irradiated cell 64 Bio Rep 1


title: dsi.KO.eST.rep3


title: dsi.KO.eST.rep2


title: dsi.KO.eST.rep1


title: Irradiated cell 62 Bio Rep 3


title: Irradiated cell 65 Bio Rep 3


title: Irradiated cell 61 Bio Rep 2


title: Irradiated cell 61 Bio Rep 1


title: dsi.KO.rST.rep4

source_name: Round spermatid cyst


title: Irradiated cell 62 Bio Rep 1

source_name: Tumor endothelial cells


title: Irradiated cell 62 Bio Rep 2


title: Irradiated cell 60 Bio Rep 3


title: dsi.KO.rST.rep6


title: dsi.KO.rST.rep3


title: Irradiated cell 61 Bio Rep 3


title: dsi.KO.rST.rep2


title: dsi.KO.rST.rep5


title: dsi.KO.rST.rep1


title: Irradiated cell 60 Bio Rep 2


title: Irradiated cell 63 Bio Rep 1


title: dsi.KO.pSC.rep4

source_name: Late primary spermatocyte cyst


title: dsi.KO.pSC.rep3


title: dsi.KO.pSC.rep5


title: Irradiated cell 60 Bio Rep 1


title: Irradiated cell 58 Bio Rep 2


title: Irradiated cell 58 Bio Rep 3


title: Irradiated cell 59 Bio Rep 3


title: Irradiated cell 59 Bio Rep 2


title: Irradiated cell 57 Bio Rep 3


title: Irradiated cell 59 Bio Rep 1


title: dsi.KO.SG.rep6

source_name: Spermatogonion cyst


title: Irradiated cell 58 Bio Rep 1


title: dsi.KO.SG.rep3


title: dsi.KO.SG.rep5


title: dsi.KO.pSC.rep1


title: Irradiated cell 56 Bio Rep 2


title: dsi.WT.eST.rep6


title: Irradiated cell 56 Bio Rep 1


title: dsi.WT.eST.rep3


title: Irradiated cell 56 Bio Rep 3


title: dsi.KO.SG.rep4


title: dsi.WT.eST.rep4


title: dsi.WT.eST.rep5


title: Irradiated cell 57 Bio Rep 1


title: dsi.WT.eST.rep2


title: Irradiated cell 54 Bio Rep 2


title: Irradiated cell 55 Bio Rep 1


title: dsi.KO.pSC.rep2


title: Irradiated cell 57 Bio Rep 2


title: Irradiated cell 55 Bio Rep 2


title: dsi.WT.rST.rep4


title: dsi.WT.eST.rep1


title: dsi.WT.rST.rep3


title: dsi.WT.rST.rep5


title: Irradiated cell 54 Bio Rep 3


title: dsi.KO.SG.rep1


title: Irradiated cell 54 Bio Rep 1


title: Irradiated cell 53 Bio Rep 3


title: dsi.KO.SG.rep2


title: Irradiated cell 53 Bio Rep 2


title: Irradiated cell 55 Bio Rep 3


title: Irradiated cell 53 Bio Rep 1


title: Irradiated cell 52 Bio Rep 3


title: dsi.WT.pSC.rep5


title: dsi.WT.pSC.rep2


title: dsi.WT.pSC.rep4


title: Irradiated cell 52 Bio Rep 1


title: Irradiated cell 51 Bio Rep 3


title: dsi.WT.pSC.rep3


title: dsi.WT.pSC.rep1


title: dsi.WT.rST.rep1


title: dsi.WT.rST.rep2


title: Irradiated cell 51 Bio Rep 1


title: dsi.WT.SG.rep2


title: Irradiated cell 50 Bio Rep 3


title: dsi.WT.SG.rep5


title: dsi.WT.SG.rep4


title: Irradiated cell 49 Bio Rep 2


title: Irradiated cell 50 Bio Rep 1


title: dsi.WT.SG.rep3


title: Irradiated cell 50 Bio Rep 2


title: Irradiated cell 48 Bio Rep 3


title: dsi.WT.SG.rep1


title: dsi.KO.tes.rep2

source_name: Testis

value: 3-5 days after eclosion


title: dsi.KO.tes.rep3


title: Irradiated cell 52 Bio Rep 2


title: dsi.WT.SG.rep6


title: dsi.WT.tes.rep3


title: Irradiated cell 49 Bio Rep 1


title: dsi.KO.tes.rep1


title: Irradiated cell 49 Bio Rep 3


title: Irradiated cell 48 Bio Rep 1


title: Irradiated cell 51 Bio Rep 2


title: Irradiated cell 47 Bio Rep 3


title: Irradiated cell 46 Bio Rep 3


title: Irradiated cell 47 Bio Rep 1


title: dsi.WT.tes.rep1


title: dsi.WT.tes.rep2


title: Irradiated cell 47 Bio Rep 2


title: Irradiated cell 48 Bio Rep 2


title: Irradiated cell 46 Bio Rep 1


title: Irradiated cell 46 Bio Rep 2


title: H446 (parental) 3 [H446 WT 3]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: processed data file: RPKM_H446_for_GEO.txt

data_processing:
Reads were aligned to mouse genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by RPKM (PMID: 18516045) with an in-house script.
Genome_build: hg38
Supplementary_files_format_and_content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

extract_protocol:
RNA from the cell lines was isolated using RNeasy Plus Mini Kit (Qiagen, Hilden, Germany; cat#74104).
RNA-Seq libraries were built using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Wilmington MA, USA; cat#08098093702) with 300 ng of total RNA and 11 cycles of PCR according to manufacturer’s recommendation. The libraries were quantified using Qubit Fluorometer, and the quality of the libraries was determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent, Santa Clara, CA, USA; cat#5067-4626).

treatment_protocol: PC-9 and H446 WT cell lines were initially treated with a low dose (10 µM) of MTI-101.  The surviving or resistant cells were treated each subsequent time with 10 µM MTI-101 until they were able to proliferate at approximately the same rate as the parental WT cell line.  The dose was then increased by 10 µM increments until a stable drug resistant variant emerged.  H446 was able to reach a 40 µM resistant level while PC-9 was stable up to a 60 µM resistant level

value: epithelial

tag: disease

value: Lung small cell carcinoma

tag: culture condition

value: no MTI-101

tag: repeat


title: Irradiated cell 45 Bio Rep 2

tag: tumor model


title: H446 (parental) 4 [H446 WT 4]


title: H446 (parental) 1 [H446 WT 1]


title: Irradiated cell 45 Bio Rep 3

tag: time point


title: H446 (parental) 2 [H446 WT 2]


title: H446  (MTI-101 resistant) 4 [H446 R4]

source_name: MTI-101-resistant H446


title: H446  (MTI-101 resistant) 3 [H446 R3]


title: H446  (MTI-101 resistant) 2 [H446 R2]


title: Irradiated cell 45 Bio Rep 1

tag: experiment type


title: Irradiated cell 44 Bio Rep 2


title: H446  (MTI-101 resistant) 1 [H446 R1]


title: Irradiated cell 44 Bio Rep 3


title: Irradiated cell 71 Bio Rep 2


title: PC-9 (parental) 4 [PC-9-WT 4]

description: processed data file: RPKM_PC9_for_GEO.txt

value: Lung adenocarcinoma


title: Irradiated cell 43 Bio Rep 3


title: PC-9 (parental) 3 [PC-9-WT 3]


title: Irradiated cell 43 Bio Rep 1


title: PC-9 (parental) 1 [PC-9-WT 1]


title: PC-9 (parental) 2 [PC-9-WT 2]


title: Irradiated cell 42 Bio Rep 3


title: PC-9R (MTI-101 resistant), removed from drug (5M) [PC-9R-RFD-5M]

source_name: MTI-101-resistant PC-9

value: Removed from MTI-101 drug pressure for 5 months


title: PC-9R (MTI-101 resistant), removed from drug (6M) [PC-9R-RFD-6M]

value: Removed from MTI-101 drug pressure for 6 months


title: Irradiated cell 42 Bio Rep 1


title: PC-9 (MTI-101 resistant) 3 [PC-9-R3]


title: PC-9R (MTI-101 resistant), removed from drug (4M) [PC-9R-RFD-4M]

value: Removed from MTI-101 drug pressure for 4 months


title: PC-9 (MTI-101 resistant) 4 [PC-9-R4]


title: Irradiated cell 42 Bio Rep 2


title: Irradiated cell 41 Bio Rep 3


title: Irradiated cell 41 Bio Rep 2


title: Irradiated cell 40 Bio Rep 2


title: Irradiated cell 40 Bio Rep 3


title: Irradiated cell 44 Bio Rep 1


title: Irradiated cell 43 Bio Rep 2


title: PC-9 (MTI-101 resistant) 2 [PC-9-R2]


title: Irradiated cell 41 Bio Rep 1


title: Irradiated cell 40 Bio Rep 1


title: Irradiated cell 38 Bio Rep 3


title: Irradiated cell 39 Bio Rep 3


title: Irradiated cell 39 Bio Rep 1


title: Irradiated cell 38 Bio Rep 1


title: Irradiated cell 38 Bio Rep 2


title: PC-9 (MTI-101 resistant) 1 [PC-9-R1]


title: Irradiated cell 39 Bio Rep 2


title: Mouse WT, pBAD, R1318_4

city: Bellinzona

first: Fabio

last: Grassi

address: Via Francesco Chiesa 5

country: Switzerland

institute: Institute for Research in Biomedicine

description: Gene expression data from small intestinal epithelium from GF mice colonized with E. colipApyr or E. colipBAD28.

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: GeneChip arrays were scanned using an Affymetrix GeneChip® Scanner 3000 7G using default parameters.

data_processing: Data was analyzed using Partek Genomics Suite version 6.6 using the RMA algorithm with RMA background correction, Quantile Normalization and Median Polish summarization.

organism: Mus

source_name: Germ free (GF) C57BL/6 and Igh-J-/- (B6.129P2-Igh-Jtm1Cgn/J) mice

label_protocol: Biotin-labelled cDNA targets were synthesized starting from 150 ng of total RNA as suggested by Affymetrix, starting from 5.5 µg of ssDNA.

growth_protocol: Intestinal epithelial cells (IECs) were isolated from small intestine of C57BL/6 and Igh-J-/- germ-free mice monocolonized with E.colipBAD28 and E.colipApyr.

extract_protocol: Total RNA was extracted from IECs through Trizol precipitation (Thermo Fisher) and then digested with Dnase I at 37 °C for 15 min to remove any contaminating DNA.

treatment_protocol: IECs were isolated as follow: the small intestine was flushed with PBS, fat and Peyer’s patches were removed. The small intestine was divided longitudinally, cut into 2-mm sections and washed twice, in calcium and magnesium free HBSS containing 2% fetal calf serum (FCS) (at 4 °C) to remove faces. The tissue was placed in 50 ml tubes, washed three times in HBSS containing 2% FCS at 4 °C, transferred to 25 cm tissue culture flasks and incubated at 37 °C in HBSS containing 10% FCS, 0.2 mmol/L EDTA, 1 mmol/L DTT. After 20 min incubation, the flasks were shaken vigorously for 30 s, and the supernatant containing IELs was separated from the tissue fragments using a 40-μm nylon filter. The supernatant containing the IEC was collected washed, suspended in RPMI 1640 at 4 °C and filtered.

value: small intestine lamina propria

tag: vector

value: pBAD

value: WT


title: Irradiated cell 37 Bio Rep 2

value: colon adenocarcinoma cells (MC38)

value: 15 Gy, single dose irradiation

value: 48 h after treatment


title: Irradiated cell 37 Bio Rep 1

value: single cell

value: FACS sorted tumor endothelial cells


title: Irradiated cell 37 Bio Rep 3


title: Mouse WT, pBAD, R1318_5


title: Irradiated cell 36 Bio Rep 2


title: Mouse Jh, R1285_25

value: Jh


title: Mouse WT, pBAD, R1318_3


title: Mouse WT, pBAD, R1318_2


title: Mouse WT, pBAD, R1318_1


title: Mouse Jh, R1285_24


title: Irradiated cell 36 Bio Rep 1


title: Irradiated cell 35 Bio Rep 3


title: Mouse Jh, R1285_23


title: Mouse Jh, R1285_22


title: Irradiated cell 35 Bio Rep 1


title: Mouse Jh, R1285_21


title: N4

city: Wuxi City

first: Ziyun

last: Zhou

state: Jiangsu Province

address: No. 299, Qingyang Road, Liangxi District

institute: The Affiliated Wuxi Children’s Hospital of Nanjing Medical University, Wuxi, China.

description: Peripheral blood

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Peripheral blood

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: whole blood

tag: group

value: TD

tag: gender

value: male


title: Irradiated cell 34 Bio Rep 3


title: Mouse WT, pHND10, R1285_20

tag: tissue


title: Irradiated cell 36 Bio Rep 3


title: Irradiated cell 33 Bio Rep 3


title: Irradiated cell 34 Bio Rep 2


title: Irradiated cell 34 Bio Rep 1


title: Mouse WT, pHND10, R1285_18


title: Mouse Jh, pBAD, R1285_15


title: Mouse Jh, pBAD, R1285_13


title: Irradiated cell 33 Bio Rep 1


title: Mouse Jh, pBAD, R1285_12


title: T4

description: Peripheral blood

value: ASD

tag: age


title: Irradiated cell 35 Bio Rep 2


title: Mouse WT, pHND10, R1285_16


title: Irradiated cell 32 Bio Rep 3


title: Irradiated cell 32 Bio Rep 2


title: T2

description: Peripheral blood

value: female


title: Mouse WT, pHND10, R1285_19


title: N1

description: Peripheral blood


title: T5

description: Peripheral blood


title: N3

description: Peripheral blood


title: Mouse Jh, pBAD, R1285_14


title: Irradiated cell 31 Bio Rep 3


title: Mouse Jh, pBAD, R1285_11


title: Mouse WT, pBAD, R1285_8


title: N2

description: Peripheral blood


title: Mouse WT, not treated, R1285_3


title: Mouse WT, not treated, R1285_4


title: Irradiated cell 30 Bio Rep 1


title: Irradiated cell 31 Bio Rep 1


title: Irradiated cell 31 Bio Rep 2


title: Mouse WT, not treated, R1285_1


title: T1

description: Peripheral blood


title: Irradiated cell 29 Bio Rep 3


title: Irradiated cell 30 Bio Rep 2


title: Irradiated cell 29 Bio Rep 2


title: Irradiated cell 27 Bio Rep 3


title: Irradiated cell 29 Bio Rep 1


title: Irradiated cell 30 Bio Rep 3


title: Irradiated cell 28 Bio Rep 3


title: Irradiated cell 28 Bio Rep 1


title: Irradiated cell 27 Bio Rep 2


title: Irradiated cell 26 Bio Rep 3


title: Liver_Non-Conpression_No.7

city: Kawasaki

first: kousuke

last: shimada

state: Kanagawa

address: 3-25-13 Tonomachi

department: Group for Food Functionality Assessment

institute: Kanagawa Institute of Industrial Science and Technology

description: Male, C57BL6N, Liver

hyb_protocol: Following fragmentation and terminal labeling, 2.3 micro g of ss-cDNA were hybridized for 16 hr at 45C on Clariom S, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CEL files were quantified with the qFarms, using the statistical language R (R-3.4.4) and Bioconductor 3.5.

source_name: Non-compression-loaded mouse liver

label_protocol: Biotinylated sense-strand cDNA (ss-cDNA) were prepared according to the standard manufacture's protocol from 200 ng total RNA (GeneChip WT PLUS Reagent Kit Manual Target Prepaeration for GeneChip Whole Transcript (WT) Expression Arrays, MAN0018137, Revision A.0, Thermo Fisher Scientific). Whole Transcript (WT) Expression Arrays, MAN0018137, Revision A.0, Thermo Fisher Scientific).

growth_protocol: We made the adjustable compression clothes for mice and, ten-weeks-C57BL/6N male mice were attached to adjustable compression clothes, and were divided into two groups (compression group or non-compression group which only wore the clothes). 8hr after compression load to trunk to compression group, we performed transcriptome analysis in liver tissue to investigate the functional mechanism of compression loading.

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

treatment_protocol: Mice were anesthetized using isoflurane, and the liver samples were collected. Liver sections were immediately frozen after excision using liquid nitrogen.

value: liver


title: Liver_Non-Conpression_No.5

description: Male, C57BL6N, Liver


title: Liver_Conpression_No.6

description: Male, C57BL6N, Liver

source_name: Compression-loaded mouse liver


title: Liver_Non-Conpression_No.1

description: Male, C57BL6N, Liver


title: Liver_Non-Conpression_No.3

description: Male, C57BL6N, Liver


title: Liver_Non-Conpression_No.4

description: Male, C57BL6N, Liver


title: Irradiated cell 26 Bio Rep 1


title: Irradiated cell 28 Bio Rep 2


title: Irradiated cell 27 Bio Rep 1


title: Irradiated cell 25 Bio Rep 3


title: Liver_Non-Conpression_No.2

description: Male, C57BL6N, Liver


title: Liver_Non-Conpression_No.6

description: Male, C57BL6N, Liver


title: Irradiated cell 25 Bio Rep 1


title: Irradiated cell 24 Bio Rep 3


title: Irradiated cell 24 Bio Rep 2


title: Liver_Conpression_No.5

description: Male, C57BL6N, Liver


title: Irradiated cell 26 Bio Rep 2


title: Irradiated cell 25 Bio Rep 2


title: Irradiated cell 23 Bio Rep 2


title: 11_MC38 APCKO_2 Dox

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

description: Tumors established with ishTDO2 APC-KO MC38 cells plus Dox replicate 2

hyb_protocol: Biotinylated cRNA was fragmented and hybridized to Mouse Genome 430 2.0 Array following the standard protocols

scan_protocol: Slides were scanned by GeneChip® Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

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

growth_protocol: The CRC cell lines MC38 (RRID:CVCL_B288) and its isogenic cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% Tet System Approved FBS (Clontech) and 100 U/ml ampicillin/penicillin. All cells were confirmed to be mycoplasma-free and maintained at 37 °C and 5% CO2.

extract_protocol: RNAs were isolated using Trizol (Invitrogen, Cat# 15596-026) and further purified with the RNeasy Mini Kit.

treatment_protocol: Inducible shTDO2 MC38 cell lines were injected to the C57BL/6 mouse cecum orthotopically and treated with Doxycycline water to induce TDO2 knockdown.

value: APC-KO

value: Dox


title: Irradiated cell 23 Bio Rep 1


title: Irradiated cell 22 Bio Rep 3


title: Irradiated cell 22 Bio Rep 2


title: 10_MC38 APCKO_1 Dox

description: Tumors established with ishTDO2 APC-KO MC38 cells plus Dox replicate 1


title: Irradiated cell 22 Bio Rep 1


title: 09_MC38 APCKO_3

description: Tumors established with ishTDO2 APC-KO MC38 cells no Dox replicate 3

value: no Dox


title: Liver_Conpression_No.4

description: Male, C57BL6N, Liver


title: Liver_Conpression_No.2

description: Male, C57BL6N, Liver


title: 08_MC38 APCKO_2

description: Tumors established with ishTDO2 APC-KO MC38 cells no Dox replicate 2


title: Liver_Conpression_No.3

description: Male, C57BL6N, Liver


title: Irradiated cell 24 Bio Rep 1


title: Liver_Conpression_No.1

description: Male, C57BL6N, Liver


title: Irradiated cell 23 Bio Rep 3


title: 06_MC38_3 Dox

description: Tumors established with ishTDO2 APC-WT MC38 cells plus Dox replicate 3

value: APC-WT


title: 03_MC38_3

description: Tumors established with ishTDO2 APC-WT MC38 cells no Dox replicate 3


title: 07_MC38 APCKO_1

description: Tumors established with ishTDO2 APC-KO MC38 cells no Dox replicate 1


title: Irradiated cell 21 Bio Rep 2


title: Irradiated cell 21 Bio Rep 1


title: Irradiated cell 21 Bio Rep 3


title: 05_MC38_2 Dox

description: Tumors established with ishTDO2 APC-WT MC38 cells plus Dox replicate 2


title: 04_MC38_1 Dox

description: Tumors established with ishTDO2 APC-WT MC38 cells plus Dox replicate 1


title: 01_MC38_1

description: Tumors established with ishTDO2 APC-WT MC38 cells no Dox replicate 1


title: Irradiated cell 20 Bio Rep 3


title: Irradiated cell 20 Bio Rep 2


title: Irradiated cell 20 Bio Rep 1


title: Irradiated cell 19 Bio Rep 3


title: Irradiated cell 19 Bio Rep 1


title: Mac4_GSK_d14

city: London

first: Ilaria

last: Malanchi

address: 1 Midland Rd,

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.2.29) and Bowtie2 were used to aling reads to the mouse mm10 transcriptome, taken from known Gene reference table available at UCSC
The “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default
Differential expression analysis was performed with the DESeq2 package (version 1.12.4) within the R programming (version 3.3.1)
Assembly: Mouse Ensembl GRCh38 - release89
Supplementary files format and content: Tab delimited text files containing TMM normalised data. Rows represent Ensembl mouse genes and columns represent individual samples.

source_name: Cancer infiltrating macrophages in tumour 14 days after fat pat injection of GSKi  pretreated 4T1 cells

extract_protocol: For macrophage isolation, F4/80+ cells were obtained by using the Anti-F4/80 MicroBeads UltraPure kit (Milteny, 130-110-443) following the manufacturer’s instructions. Approximately 2x107 single-cells from the tumour were stained with a mix of 180μl MACS buffer and 20 μl of Anti-F4/80 MicroBeads for 15 minutes at 4°C in the dark. During this incubation, an LS column was placed onto a MidiMACS separator where magnetic field was applied, and the column was rinsed with 3ml of MACS buffer. Cells were washed twice with 4ml of MACS buffer and resuspended in 1ml prior to proceeding to magnetic separation by applying the cell suspension onto the column. Columns were washed thrice with 3ml of MACS buffer before being carefully removed from the separator and placed on a FACS tube. 4.5ml of MACS buffer was added onto the LS column and the plunger was firmly pushed to elute the F4/80+ cell fraction which had been retained within the column due to the F4/80+ positive selection. To increase the purity of the cells, the eluted fraction was applied to a second round of separation with a new LS column.

treatment_protocol: Tumour enstablished from DMSO or GSKi pre-treated 4T1 cells: 5 μM of GSK269962A (Axon, 1167) for five days

value: Macrophage


title: Mac3_GSK_d14


title: Mac2_GSK_d8

source_name: Cancer infiltrating macrophages in tumour 8 days after fat pat injection of GSKi  pretreated 4T1 cells


title: Mac3_DMSO_d14

source_name: Cancer infiltrating macrophages in tumour 14 days after fat pat injection of DMSO  pretreated 4T1 cells


title: Mac1_GSK_d14


title: Mac3_GSK_d8


title: Irradiated cell 18 Bio Rep 3

city: Ljubljana

first: Bostjan

last: Markelc

address: Zaloska cesta 2

institute: Institute of Oncology Ljubljana

data_processing:
tophat v2.1.0
cufflinks-2.2.1
htseq  0.9.1
Genome_build: GRCm38 release 88
Supplementary_files_format_and_content: txt

extract_protocol:
Dissected tumors were finely chopped with scalpels and the obtained fragments digested in HBSS (with Calcium and Magnesium; GIBCO) containing a mix of Collagenases 1 and 3 (Worthington; 3 mg ml−1), dispase II (Roche; 7 mg ml−1), DNase I (Invitrogen; 2 U ml−1) and left at 37 °C with gentle agitation for 20 minutes. A total of 25x106 cells were stained in a final volume of 100 μl of antibody mix for 15-20 minutes, in ice, protected from light. Cells were subsequently washed with 2 ml PBS-5% FBS, centrifuged at 500g for 5 minutes and resuspended in 500 μl PBS-5% FBS. 7-AAD was added right before the sample acquisition. Sorting was performed by using a Fusion cell sorter (BD Biosciences). The dissociated cells were centrifuged at 500g for 5 minutes, resuspended in PBS-5% FBS and filtered through 50 μm cell strainers before being counted and used for flow cytometry. 100 cells per population were sorted in 4 μl of lysis mix (0.4% Triton X + RNAse Inhibitor (1:20), dNTPS (10 mM), Oligo dT (10 μM) - according to the original Smart-seq2 protocol49) for bulk RNAseq, and 1 cell per well of a 96 well plate for single cell RNAseq, and immediately processed for RNA-sequencing or stored at -80 °C.
A 5.7 μl of retro-transcription mix (see reference for details) was added to each sample. Retro-transcription was carried out according to the original Smart-seq2 protocol and cDNA was then pre-amplified for 15 cycles. After PCR pre-amplification, cDNA was purified using Ampure XP magnetic beads according to the manufacturer's instructions, in a ratio of 0.8 to 1 with cDNA, resuspended in 17.5 μl of buffer EB (Qiagen) and stored at –20 °C. Quality and concentration of the cDNA generated were assessed using High-Sensitivity Bioanalyzer kit (Agilent). 1 ng of pre-amplified cDNA was tagmented and indexed with Nextera XT DNA Sample Preparation kit (Illumina) according to the manufacturer's instructions. The product was purified with AMPure XP beads (1:1 ratio) and eluted in 17.5 μl of EB buffer (Qiagen). Samples were loaded on a High-Sensitivity DNA chip (Agilent Technologies) to check for library size and quality and concentration measured with Qubit High-Sensitivity DNA kit (Invitrogen). Libraries were pooled to a final concentration ranging between 2 nM and 10 nM and sequenced with Illumina Hiseq 4000 (25 bp single-end read) at the Wellcome Trust Centre for Human Genetics in Oxford.

treatment_protocol: Once tumors reached 80-100 mm3 mice were randomly assigned to experimental groups. Mice were anesthetized under inhalation with isoflurane and led shielded with only the tumors exposed to radiation. Tumors received  15 Gy X-ray radiation treatment (300 kV, dose rate of 2.25 Gy per minute) delivered to tumors using a Gulmay RS320 irradiation system (Gulmay Medical Ltd).

value: colon adenocarcinoma cells (MC38)


title: Mac2_GSK_d14


title: 02_MC38_2

description: Tumors established with ishTDO2 APC-WT MC38 cells no Dox replicate 2


title: Liver_Conpression_No.7

description: Male, C57BL6N, Liver


title: Mac1_DMSO_d14


title: Irradiated cell 33 Bio Rep 2

value: 15 Gy, single dose irradiation


title: Mac3_DMSO_d8

source_name: Cancer infiltrating macrophages in tumour 8 days after fat pat injection of  DMSO pretreated 4T1 cells


title: Mac2_DMSO_d8


title: Irradiated cell 17 Bio Rep 2

value: 48 h after treatment


title: Irradiated cell 17 Bio Rep 3

value: single cell


title: Irradiated cell 19 Bio Rep 2

value: FACS sorted tumor endothelial cells


title: Mac2_DMSO_d14


title: Mac4_DMSO_d14


title: Irradiated cell 16 Bio Rep 3


title: Irradiated cell 17 Bio Rep 1


title: Mac1_DMSO_d8


title: Fibro1_GSK

source_name: Cancer infiltrating fibroblasts from tumour esnstablished by GASKi pretreated 4T1 cells

extract_protocol: For fibroblast isolation, cells were isolated from Balb/cAnN mice orthotopically transplanted with 4T1 tumours pre-treated with DMSO or GSK. Single-cell suspensions were incubated with mouse FcR Blocking Reagent and subsequently with the following APC labelled antibodies – CD45, CD31, CD326 and hCD2. Cells were washed and incubated with magnetic anti-APC MicroBeads (Miltenyi, 130-090-855). Magnetically labelled immune, endothelial, epithelial and cancer cells were isolated using LD columns, washed thrice with 3ml of MACS and the unlabelled flow-through cell fraction was the mesenchymal cells that we will refer to as fibroblasts hereafter. To increase the purity of the cells, the eluted fraction was applied to a second round of separation with a new LD column.

value: Fibroblast

value: GSK


title: Fibro2_GSK


title: Fibro2_DMSO

source_name: Cancer infiltrating fibroblasts from tumour esnstablished by DMSO pretreated 4T1 cells

value: DMSO


title: Irradiated cell 16 Bio Rep 2


title: Fibro1_DMSO


title: Irradiated cell 16 Bio Rep 1


title: Mac1_GSK_d8


title: Irradiated cell 15 Bio Rep 2


title: Irradiated cell 14 Bio Rep 3


title: Irradiated cell 15 Bio Rep 3


title: Irradiated cell 14 Bio Rep 2


title: Irradiated cell 15 Bio Rep 1


title: Irradiated cell 13 Bio Rep 3


title: Irradiated cell 14 Bio Rep 1


title: 81 WT

city: New Haven

first: Pramod

last: Mistry

address: 300 Cedar St

institute: Yale University

library_source: transcriptomic single cell

data_processing:
The pre-processed digital gene expression matrices as obtained from cellranger. These matrices were processed using Seurat (Satija et al., 2015). The clusters were determined using Louvain algorithm for community detection (Vincent D Blondel, 2008). Differential gene expression between the clusters was carried out using the MAST method (Finak et al., 2015). The visualizations and analysis were carried out in R (R Core Team). The data is visualized as tSNE (Hinton, 2002). From 14day pups we sequenced total of 4895 CD45+ cells. For GZ161 treatment experiments we sequenced total of 40763 CD45+ cells that consists of 4 groups of mice with 3 mice/ each group.
Assembly: mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix

source_name: Brain CD45+ cells

extract_protocol:
Brain was harevested and cells were isolated by enzymatic digestion followed by gradient centrifugation. Isolated cells were then flow sorted using anti-CD45 antibody.
10X Genomics V3 3’ Gene Expression kit and sequenced on NovaSeq flow cells to achieve high read depth

value: Brain

value: Gbawt/wt K14 Cre (wild type)

value: day 14


title: 61 HET

value: Gbalnl/wt K14 Cre (hetrozygote)


title: 50 Neo

data_processing:
mRNA sequence data were uploaded to a high-performance computing system by PartekFlow software (v7.0, Partek, St. Louis, MO), adapter trimmed and remapped to mouse genome, mm10 using STAR v2.5.3a aligner with default setting (Phred:20) for read mapping. Statistical analysis was carried out using false discovery rate (FDR) correction through the Benjamin-Hochberg method.
Assembly: mm10
Supplementary files format and content: read count text file

source_name: Microglia

extract_protocol:
Brain was harevested and cells were isolated by enzymatic digestion followed by gradient centrifugation. Isolated cells were then flow sorted using anti-CD45 antibody.
RNAseq libraries were constructed using the Affymetrix miRNA Galaxy Arrays.

value: Gbalnl/lnl K14 Cre (Knock out)


title: Irradiated cell 13 Bio Rep 2

source_name: Tumor endothelial cells


title: 48 WT


title: 59 KO


title: 45 Neo


title: 43 WT


title: Irradiated cell 13 Bio Rep 1


title: Irradiated cell 32 Bio Rep 1


title: Irradiated cell 12 Bio Rep 2


title: Irradiated cell 12 Bio Rep 1


title: TCF4_MC38 APC KO

description: binding peaks for TCF4 on the promoters of TDO2 gene in APC-KO MC38 cells.

data_processing:
Base-calling was performed with NextSeq RTA version 2.4.11.0; bcl2fastq version 2.20.0 was used to convert the bcl files into fastq files
ChIP-seq reads were aligned to the mm9/hg19 genome assembly using Bowtie version 1.2.2 with the following criteria: --best --chunkmbs 320
Peak-calling was performed using MACS version 1.4.2
Bigwig files were generated using deepTools version 2.7.15 by scaling the bam files to reads per kilobase per million (RPKM) using the following criteria: bamCoverage –b–normalizeUsing RPKM–smoothLength 300–binSize 30–extendReads 200 –o
Differential peaks were called using MACS2 with the following criteria: bdgdiff –g 60 –l 120
Assembly: mm9
Supplementary files format and content: bigwig

source_name: MC38 with APC knockout

extract_protocol:
Chromatin from PFA fixed cells were cross-linked with 1% PFA and then reactions were quenched using 0.125 M glycine. Cells were lysed with ChIP lysis buffer [10 mM Tris-HCl (pH 8.0), 140 mM NaCl, 1 mM EDTA (pH 8.0), 1% Triton X-100, 0.2% SDS and 0.1% deoxycholic acid] for 30 min on ice. Chromatin fragmentation was performed using a Diagenode BioruptorPico sonicator (30 s on and 30 s off, 45 cycles) and incubated with the appropriate mixture of antibody and Dynabeads (ThermoFisher Scientific, Cat# 10003D) overnight. Immune complexes were washed with RIPA buffer (three times), once with RIPA-500 (RIPA with 500 mM NaCl), and once with LiCl wash buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 250 mM LiCl, 0.5% NP-40 and 0.5% deoxycholic acid]. Elution and reverse-crosslinking were performed in direct elution buffer [10 mM Tris-Cl (pH 8.0), 5 mM EDTA, 300 mM NaCl, 0.5% SDS] containing proteinase K (20 mg/ml) at 65°C overnight.
Eluted DNA was purified using AMPure beads (Beckman-Coulter, Cat# 754 A63880), and then used to generate libraries using NEBNext Ultra DNA Library kit (New 755 England BioLabs Inc., Cat# E7370)

tag: antibody


title: IgG_MC38

description: control peaks on the promoters of TDO2 gene in APC-WT MC38 cells.

value: IgG


title: Irradiated cell 11 Bio Rep 2


title: Irradiated cell 12 Bio Rep 3


title: IgG_MC38 APC KO

description: control peaks on the promoters of TDO2 gene in APC-KO MC38 cells.


title: 12_MC38 APCKO_3 Dox

description: Tumors established with ishTDO2 APC-KO MC38 cells plus Dox replicate 3

tag: cell line

value: APC-KO

value: Dox


title: 49 Neo


title: Irradiated cell 11 Bio Rep 3

tag: cell type


title: TCF4_MC38

description: binding peaks for TCF4 on the promoters of TDO2 gene in APC-WT MC38 cells.


title: mock_2

city: CAMBRIDGE

first: Shawn

last: Liu

address: 455 MAIN STREET

institute: Whitehead Institute for Biomedical Research

data_processing:
The first 40 bp of the reads were mapped to mouse genome (mm10) using STAR, which was indexed with Ensembl GRCm38.91 gene annotation. The read counts were obtained using featureCounts function from Subread package with unstranded option.
Assembly: mm10
Supplementary files format and content: tab delimited text file with raw gene counts for every gene

growth_protocol: Five-week old male mice labeled with ChR2-YFP transgene1 after conditioning were euthanized by isoflurane. Mouse brains were rapidly extracted, and the hippocampal regions were isolated by microdissection.

extract_protocol:
Clontech's SMARTerUltra-lowPOLYA-V4: Up to 10 ng of sample was prepared using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines. Briefly, RNA underwent reverse transcription via template switching and amplification, resulting in double stranded cDNA. The amount of cDNA between 100-3000 bp was calculated by Fragment Analyzer and Qubit. 150pg of the sample in range was then added to Illumina’s Nextera XT and processed according to manufacturer’s guidelines. Briefly, the cDNA underwent tagmentation, using Nextera XT’s transposase, and unique dual indexes were added by PCR amplification. Final libraries went through QC with the Fragment Analyzer and qPCR on a Roche Light Cycler 480 II. All libraries were then pooled and sequenced at single-end 40 base-pair using the Illumina HiSeq 2500.   Clontech’s SMART-seq v4 Ultra Low Input RNA Kit: Sequencing libraries were prepared using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines, followed by Illumina NexteraXT. Briefly, RNA underwent reverse transcription via template switching and amplification, resulting in double stranded cDNA. cDNA quality and quantity was assessed by Agilent TapeStation 2200 and Qubit. cDNA was converted to sequencing libraries by Illumina Nextera XT. Briefly, the cDNA underwent tagmentation, using Nextera XT’s transposase, and dual indexes were added by PCR amplification. Final libraries went through QC with the TapeStation and Qubit. All libraries were then pooled and sequenced at paired-end 100bp using the Illumina NovaSeq 6000.
Clontech's SMARTerUltra-lowPOLYA-V4 was used except neutral samples, which were prepared with Clontech’s SMART-seq v4 Ultra Low Input RNA Kit

treatment_protocol: Eight mice were pooled by each experimental condition. Single cell suspension was prepared according to the guideline of Adult Brain Dissociation Kit (Miltenyi Botec, Cat No: 13-107-677). Briefly, the hippocampal samples were incubated with digestion enzymes in the C Tube placed on the gentleMACS Octo Dissociator with Heaters with gentleMACS Program: 37C_ABDK_01. After termination of the program, the samples were applied through a MACS SmartStrainer (70 μm). Then a debris removal step and a red blood cell removal step were applied to obtain single cell suspension. The single cell suspension was subject to a BD FACSAria cell sorter according to the manufacturer’s protocol to isolate EYFP-single cell population.

value: male mice in the home cage

value: brain


title: mock_3

source_name: Five-week old male mice labeled with ChR2-YFP transgene1 after conditioning were euthanized by isoflurane


title: Irradiated cell 10 Bio Rep 3

value: colon adenocarcinoma cells (MC38)

value: 15 Gy, single dose irradiation


title: Irradiated cell 9 Bio Rep 3

value: 48 h after treatment

value: single cell


title: Irradiated cell 10 Bio Rep 1

value: FACS sorted tumor endothelial cells


title: Irradiated cell 11 Bio Rep 1


title: Irradiated cell 8 Bio Rep 3


title: HG+PC-NVs

city: Shinheung- Dong, Jung-Gu Incheon

first: GUO NAN

last: YIN

address: 7-206, 3rd ST B dong, 3 floor room 307-2

department: Urology

institute: Inha university hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: mouse corpus cavernous tissue

growth_protocol: Growth in complement medium 199 (M199) contained with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin, 0.5 mg/ml heparin

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

treatment_protocol: Treatment with glucose for 5 days

value: mouse cavernous endothelial cells

value: HG+PC-NVs (high glucose+PC-NVs)


title: neg_3

value: male mice were subjected to four 2 second 1.5mA foot shocks


title: pos_2

value: the mice were subjected to female exposure for 1 hour in a clean homecage


title: WT_plusIAA_R3

city: Würzburg

first: Elmar

last: Wolf

address: Am Hubland

institute: University of Würzburg

data_processing:
For 4sU-seq, reads were mapped to hg19 with Bowtie2, reads mapping to rRNA, exons and blacklist regions were removed and then normalized based on read depth. Differential expression was analysed on genes with more than a sum of 90 counts over all conditions and logCPM > 2
Assembly: hg19
Supplementary files format and content: read-depth normalized reads and logFC
Library strategy: 4sU-Seq

growth_protocol: U2OS N-AID-RBM8A and U2OS WT cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
U2OS cell lysates were spiked with 4sU-treated mouse T-cell lysates. Total RNA was isolated using QIAzol, purified with the miRNeasy mini kit, precipitated to reduce volume and biotinylated. This was followed by 4sU-RNA pulldown using MyOne streptavidin beads, followed by purification with the RNeasy MinElute cleanup kit
4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 11 PCR cycles. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform.

treatment_protocol: 500 mM auxin (6 h) + 15 min 2 mM 4sU labelling at the end of the 6h

value: human bone osteosarcoma epithelial cells

value: 6h auxin; last 15 min 4sU


title: Irradiated cell 8 Bio Rep 1


title: WT_plusIAA_R1


title: neg_1


title: Kl22_plusIAA_R3


title: WT_plusIAA_R2


title: Irradiated cell 7 Bio Rep 1


title: Kl22_minusIAA_R3

value: 6h H2O; last 15 min 4sU


title: Irradiated cell 8 Bio Rep 2


title: Irradiated cell 6 Bio Rep 1


title: mock_1


title: Irradiated cell 6 Bio Rep 2


title: HG+HBS

value: HG+HBS (high glucose+HBS)


title: pos_1


title: Irradiated cell 9 Bio Rep 2


title: Irradiated cell 9 Bio Rep 1


title: Kl22_plusIAA_R2


title: Irradiated cell 7 Bio Rep 3


title: Irradiated cell 10 Bio Rep 2


title: VSX2-Adult human ChIP-Seq Input, Rep2

city: Pittsburgh

first: Shuchang

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

data_processing:
Low-quality reads and adapter sequences trimming by Trimmomatic (version 0.38)
Read alignment to mouse reference genome mm10 by BWA (version 0.7.17)
Aligned reads filtering by Samtools (version 1.9)
Mark duplicate by Picard tool (version 2.18.12)
Peak calling by MACS2 (version 2.1.1.20160309)
Genome_build: hg38
Supplementary_files_format_and_content: WIG

source_name: Adult human retina

extract_protocol:
Retinae were fixed, lysed and sheared to an average length of 300-500 bp. After incubation with antibody, beads were washed and DNA was extracted with phenol chroloform and precipitated with ethanol.
Libraries were prepared according to Illumina's instructions

treatment_protocol: untreated

tag: developmental stage

value: Adult

value: retina

tag: apparent sex

value: Male

tag: apparent race

value: White

tag: postmortem interval

value: <6 hours

tag: chip antibody

value: untreated


title: VSX2-Adult human ChIP-Seq Treatment, Rep2

value: VSX2 (Exalpha, Cat No. X1180P, Lot No 14166)

tag: treatment


title: Irradiated cell 4 Bio Rep 3

tag: strain

tag: tumor model

value: colon adenocarcinoma cells (MC38)

value: 15 Gy, single dose irradiation

value: 48 h after treatment

value: single cell


title: U87MG_ID4_3

city: Seoul

first: Sang-Hun

last: Choi

address: Anamro 145

department: Biotechnology

institute: Korea University

data_processing:
Data were processed using Complete Genomics sequencing instrument.
Briefly, raw reads were filtered through several steps; removing reads with adaptors, removing reads when unknown bases are more than 10%, and have low quality. After filtering, the remaining reads are stored as FASTQ format.
Reads mapping were processed by using Bowtie2 and BWA softwares.
Gene expression was calculated by FPKM method to eliminate the influence of different gene length and sequencing discrepancy.
Finally, a probability value (PA) was calculated to screen differentially expressed genes.
Genome_build: hg19 (UCSC)
Supplementary_files_format_and_content: Tab-delimited text file which includes: 1) FPKMs, 2) read counts

source_name: Glioblastoma cells

growth_protocol: U87MG cells were grown in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin, 1% L-glutamine, and gentamicin sulfate (50µg/ml).

extract_protocol:
Total RNA was isolated from U87MG cells using TRIzol reagent (3 prime) according to the manufacturer's instructions.
Libraries were prepared for QuantSeq3' mRNA by using hg19(UCSC) platform. All procedures were proceeded by ebiogen coporation.
Lexogen (Quant-Seq library prep kit)

value: Brain

value: Malignant glioma-derived cells

value: ID4 lentivirus for 24 hours

tag: genotype

value: ID4 overexpression


title: Irradiated cell 7 Bio Rep 2

tag: time point

tag: experiment type

value: FACS sorted tumor endothelial cells


title: Kl22_plusIAA_R1

value: human bone osteosarcoma epithelial cells

value: 6h auxin; last 15 min 4sU


title: Irradiated cell 18 Bio Rep 1


title: Irradiated cell 4 Bio Rep 2


title: Irradiated cell 4 Bio Rep 1


title: Irradiated cell 3 Bio Rep 3


title: Irradiated cell 6 Bio Rep 3


title: Kl22_minusIAA_R1

value: 6h H2O; last 15 min 4sU


title: Irradiated cell 5 Bio Rep 3


title: Irradiated cell 3 Bio Rep 2


title: Kl22_minusIAA_R2


title: Irradiated cell 5 Bio Rep 1


title: VSX2-Adult human ChIP-Seq Treatment, Rep1

value: Adult

value: retina

value: Female

value: 1.4 hours


title: U87MG_ID3_2

value: ID3 lentivirus for 24 hours

value: ID3 overexpression


title: U87MG_ID3_3


title: U87MG_ID2_3

value: ID2 lentivirus for 24 hours

value: ID2 overexpression


title: Irradiated cell 5 Bio Rep 2

value: colon adenocarcinoma cells (MC38)

value: 15 Gy, single dose irradiation

value: 48 h after treatment

value: single cell


title: Irradiated cell 2 Bio Rep 1


title: Irradiated cell 2 Bio Rep 2


title: U87MG_ID4_2

value: Brain

value: Malignant glioma-derived cells

value: ID4 lentivirus for 24 hours

value: ID4 overexpression


title: Irradiated cell 18 Bio Rep 2

value: FACS sorted tumor endothelial cells


title: U87MG_ID4_1


title: U87MG_ID2_2


title: Irradiated cell 2 Bio Rep 3


title: Irradiated cell 3 Bio Rep 1


title: U87MG_ID3_1